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2017
Global phylogenetic analysis of contemporary aleutian mink disease viruses (AMDVs)
Ryt-Hansen P, Hagberg EE, Chriél M, Struve T, Pedersen AG, Larsen LE, Hjulsager CK
Virol J., 2017 |
PubMed
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Evolutionary analysis of whole-genome sequences confirms inter-farm transmission of Aleutian mink disease virus
Hagberg EE, Pedersen AG, Larsen LE, Krarup A
J Gen Virol, 2017 |
PubMed
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Sequencing and de novo assembly of 150 genomes from Denmark as a population reference
Maretty L, Jensen JM, Petersen B, Sibbesen JA, Liu S, Villesen P, Skov L, Belling K, Have CT, Izarzugaza JMG, Grosjean M, Bork-Jensen J, Grove J, Als TD, Huang S, Chang Y, Xu R, Ye W, Rao J, Guo X, Sun J, Cao H, Ye C, van Beusekom J, Espeseth T, Flindt E, Friborg RM, Halager AE, Le Hellard S, Hultman CM, Lescai F, Li S, Lund O, Løngren P, Mailund T, Matey-Hernandez ML, Mors O, Pedersen CNS, Sicheritz-Pontén T, Sullivan P, Syed A, Westergaard D, Yadav R, Li N, Xu X, Hansen T, Krogh A, Bolund L, Sørensen TIA, Pedersen O, Gupta R, Rasmussen S, Besenbacher S, Børglum AD, Wang J, Eiberg H, Kristiansen K, Brunak S, Schierup MH
Nature, 2017 |
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Cross-recognition of a pit viper (Crotalinae) polyspecific antivenom explored through high-density peptide microarray epitope mapping
Engmark M, Lomonte B, Gutiérrez JM, Laustsen AH, De Masi F, Andersen MR, Lund O
PLoS, 2017 |
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Contamination of the Arctic reflected in microbial metagenomes from the Greenland ice sheet
Hauptmann AL, Sicheritz-Pontén T, Cameron KA, Bælum J, Plichta DR, Dalgaard M, Stibal M
Environmental Research Letters, 2017 |
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Comparative performance of the BGISEQ-500 versus Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing
Tze Mak SS, Gopalakrishnan S, Carøe C, Geng C, Liu S, Sinding MHS, Kuderna LFK, Zhang W, Fu S, Vieira FG, Germonpré M, Bocherens H, Fedorov S, Petersen B, Sicheritz-Pontén T, Marques-Bonet T, Zhang G, Jiang H, Gilbert MTP
Gigascience, 2017 |
Relevant URL
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The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics
Gopalakrishnan S, Castruita JAS, Sinding MHS, Kuderna LFK, Räikkönen J, Petersen B, Sicheritz-Ponten T, Larson G, Orlando L, Marques-Bonet T, Hansen AJ, Dalén L, Gilbert MTP
BMC Genomics, 2017 |
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Diversity, prevalence and longitudinal occurrence of type II toxin-antitoxin systems of Pseudomonas aeruginosa infecting cystic fibrosis lungs
Andersen SB, Ghoul M, Griffin AS, Petersen B, Johansen HK, Molin S,
Frontiers in Microbiology, 2017 |
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Outbreak tracking of Aleutian mink disease virus (AMDV) using partial NS1 gene sequencing,
Ryt-Hansen P, Hjulsager CK, Hagberg EE, Chriél M, Struve T, Pedersen AG, Larsen LE
Virology Journal, 2017 |
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Prediction and in vitro verification of potential CTL epitopes conserved among PRRSV-2 strains.
Welner S, Nielsen M, Rasmussen M, Buus S, Jungersen G, Larsen LE
Immunogenetics, 2017 |
PubMed
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Protein-altering and regulatory genetic variants near GATA4 implicated in bicuspid aortic valve
Yang B, Zhou W, Jiao J, Nielsen JB, Mathis MR, Heydarpour M, Lettre G, Folkersen L, Prakash S, Schurmann C, Fritsche L, Farnum GA, Lin M, Othman M, Hornsby W, Driscoll A, Levasseur A, Thomas M, Farhat L, Dubé MP, Isselbacher EM, Franco-Cereceda A, Guo DC, Bottinger EP, Deeb GM, Booher A, Kheterpal S, Chen YE, Kang HM, Kitzman J, Cordell HJ, Keavney BD, Goodship JA, Ganesh SK, Abecasis G, Eagle KA, Boyle AP, Loos RJF, Eriksson P, Tardif JC, Brummett CM, Milewicz DM, Body SC, Willer CJ
Nat Commun, 2017 |
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High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology
Nag S, Dalgaard MD, Kofoed PE, Ursing J, Crespo M, Andersen LO, Aarestrup FM, Lund O, Alifrangis M
Sci Rep, 2017 |
PubMed
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Transcriptome analysis of root-knot nematode (Meloidogyne incognita)-infected tomato (Solanum lycopersicum) roots reveals complex gene expression profiles and metabolic networks of both host and nematode during susceptible and resistance responses.
Shukla N, Yadav R, Kaur P, Rasmussen S, Goel S, Agarwal M, Jagannath A, Gupta
Mol Plant Pathol, 2017 |
PubMed
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Obesity is associated with depot-specific alterations in adipocyte DNA methylation and gene expression
Sonne SB, Yadav R, Yin G, Dalgaard MD, Myrmel LS, *Gupta R, Wang J, Madsen L, Kajimura S, *Kristiansen K
Adipocyte, 2017 |
PubMed
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Gene expression plasticity across hosts of an invasive scale insect species
Christodoulides N, Van Dam AR, Peterson DA, Frandsen RJN, Mortensen UH, Petersen B, Rasmussen S, Normark BB, Hardy NB
PLoS ONE, 2017 |
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BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes
Jespersen MC, Peters B, Nielsen M, Marcatili P
Nucleic Acids Res, 2017 |
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Positive diversifying selection is a pervasive adaptive force throughout the Drosophila radiation
Cicconardia F, Marcatili P, Arthofera W, Schlick-Steinera BC, Steinera FM
sciencedirect.com, 2017 |
Relevant URL
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Identifying low density lipoprotein cholesterol associated variants in the Annexin A2 (ANXA2) gene
Fairoozy RH, Cooper J, White J, Giambartolomei C, Folkersen L, Wannamethee SG, Jefferis BJ, Whincup P, Ben-Shlomo Y, Kumari M, Kivimaki M, Wong A, Hardy R, Kuh D, Gaunt TR, Casas JP, McLachlan S, Price JF, Hingorani A, Franco-Cereceda A, Grewal T, Kalea AZ, Humphries SE; UCLEB consortium
Atherosclerosis, 2017 |
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MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads.
Petersen TN, Lukjancenko O, Thomsen MCF, Maddalena Sperotto M, Lund O, Møller Aarestrup F, Sicheritz-Pontén T
PLoS ONE, 2017 |
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MuPeXI: Prediction of neo-epitopes from tumor sequencing data
Bjerregaard AM, Nielsen M, Hadrup SR, Szallasi Z, Eklund AC
Cancer Immunol Immunother, 2017 |
PubMed
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Transcriptional changes induced by bevacizumab combination therapy in responding and non-responding recurrent glioblastoma patients
Urup T, Staunstrup LM, Michaelsen SR, Vitting-Seerup K, Bennedbæk M, Toft A, Olsen LR, Jønson L, Issazadeh-Navikas S, Broholm H, Hamerlik P, Poulsen HS, Lassen U
BMC Cancer, 2017 |
Relevant URL
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MHC-I ligand discovery using targeted database searches of mass spectrometry data: Implications for T cell immunotherapies.
Murphy JP, Konda P, Schuster H, Kowalewski D, Clements D, Cohen A, Sharif T, Kim Y, Nielsen M, Stevanovic S, Lee PWK, Gujar S
J Proteome Res., 2017 |
PubMed
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GibbsCluster: unsupervised clustering and alignment of peptide sequences.
Andreatta M, Alvarez B, Nielsen M
Nucleic Acids Res., 2017 |
PubMed
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NNAlign: a platform to construct and evaluate artificial neural network models of receptor-ligand interactions.
Nielsen M, Andreatta M
Nucleic Acids Res, 2017 |
PubMed
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Mapping of 79 loci for 83 plasma protein biomarkers in cardiovascular disease.
Folkersen L, Fauman E, Sabater-Lleal M, Strawbridge RJ, Frånberg M, Sennblad B, Baldassarre D, Veglia F, Humphries SE, Rauramaa R, de Faire U, Smit AJ, Giral P, Kurl S, Mannarino E, Enroth S, Johansson Å, Enroth SB, Gustafsson S, Lind L, Lindgren C, Morris AP, Giedraitis V, Silveira A, Franco-Cereceda A, Tremoli E; IMPROVE study group, Gyllensten U, Ingelsson E, Brunak S, Eriksson P, Ziemek D, Hamsten A, Mälarstig A
PLoS Genet, 2017 |
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TANTIGEN: a comprehensive database of tumor T cell antigens.
Olsen LR, Tongchusak S, Lin H, Reinherz EL, Brusic V, Zhang GL
Cancer Immunol Immunother, 2017 |
PubMed
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Chromosome-wise Protein Interaction Patterns and Their Impact on Functional Implications of Large-Scale Genomic Aberrations.
Kirk IK, Weinhold N, Belling K, Skakkebæk NE, Jensen TS, Leffers H, Juul A, Brunak S
Cell Systems, 2017 |
PubMed
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Genome Sequence of Talaromyces atroroseus, Which Produces Red Colorants for the Food Industry
Thrane U, Rasmussen KB, Petersen B, Rasmussen S, Sicheritz-Pontén T, Mortensen UH
Genome Announc., 2017 |
PubMed
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Functional analysis of the coronary heart disease risk locus on chromosome 21q22
Beaney K, Smith AJP, Folkersen L, Palmen J, Wannamethee SG, Jefferis BJMH, Whincup PH, Gaunt TR, Casas JP, Ben-Shlomo Y, Price JF, Kumari M, Wong A, Ong KK, Hardy RJ, Kuh DJL, Wareham NJ, Kivimäki M, Eriksson P, Humphries SE
Disease Markers, 2017 |
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Complete mitochondrial genome of the Oriental Hornet, Vespa orientalis F. (Hymenoptera: Vespidae)
Haddad NJ, Al-Nakeeb K, Petersen B, Dalén L, Blom N, Sicheritz-Pontén T
Mitochondrial DNA, 2017 |
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CD49a Expression Defines Tissue-Resident CD8+ T Cells Poised for Cytotoxic Function in Human Skin.
Cheuk S, Schlums H, Gallais Sérézal I, Martini E, Chiang SC, Marquardt N, Gibbs A, Detlofsson E, Introini A, Forkel M, Höög C, Tjernlund A, Michaëlsson J, Folkersen L, Mjösberg J, Blomqvist L, Ehrström M, Ståhle M, Bryceson YT, Eidsmo L
Cell Immunity, 2017 |
PubMed
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EBI3 regulates the NK cell response to mouse cytomegalovirus infection.
Jensen H, Chen SY, Folkersen L, Nolan GP, Lanier LL
Proc Natl Acad Sci U S A, 2017 |
PubMed
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Discovery of new candidate genes for rheumatoid arthritis through integration of genetic association data with expression pathway analysis.
Shchetynsky K, Diaz-Gallo LM, Folkersen L, Hensvold AH, Catrina AI, Berg L, Klareskog L, Padyukov L
Arthritis Res Ther, 2017 |
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Therapeutic Vaccine Against Primate Papillomavirus Infections of the Cervix.
Ragonnaud E, Andersson AC, Mariya S, Pedersen AG, Burk RD, Folgori A, Colloca S, Cortese R, Nicosia A, Pamungkas J, Iskandriati D, Holst PJ
J Immunother, 2017 |
PubMed
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Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut
Pipek O, Ribli D, Molnár J, Póti Á, Krzystanek M, Bodor A, Tusnády GE, Szallasi Z, Csabai I, Szüts D
BMC Bioinformatics, 2017 |
Relevant URL
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Breadth of T cell responses after immunization with adenovirus vectors encoding ancestral antigens or polyvalent papillomavirus antigens.
Ragonnaud E, Pedersen AG, Holst PJ
Scand J Immuno, 2017 |
PubMed
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Early differences in islets from prediabetic NOD mice: combined microarray and proteomic analysis
Crèvecoeur I, Gudmundsdottir V, Vig S, Sodré FMC, D’Hertog W, Fierro AC, Van Lommel L, Gysemans C, Marchal K, Waelkens E, Schuit F, Brunak S, Overbergh L, Mathieu C
Diabetologia, 2017 |
PubMed
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ArrayPitope: Automated Analysis of Amino Acid Substitutions for Peptide Microarray-Based Antibody Epitope Mapping
Hansen CS, Østerbye T, Marcatili P, Lund O, Buus S, Nielsen M
PLoS One, 2017 |
PubMed
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Perturbed CD8+ T cell TIGIT/CD226/PVR axis despite early initiation of antiretroviral treatment in HIV infected individuals
Tauriainen J, Scharf L, Frederiksen J, Naji A, Ljunggren HG, Sönnerborg A, Lund O, Reyes-Terán G, Hecht FM, Deeks SG, Betts MR, Buggert M, Karlsson AC
Scientific Reports, 2017 |
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Cutavirus in cutaneous malignant melanoma.
Mollerup S, Fridholm H, Vinner L, Kjartansdóttir KR, Friis-Nielsen J, Asplund M, Herrera JAR, Steiniche T, Mourier T, Brunak S, Willerslev E, Izarzugaza JMG, Hansen AJ, Nielsen LP
Emerg Infect Dis, 2017 |
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Norwegian patients and retail chicken meat share cephalosporin-resistant Escherichia coli and IncK/blaCMY-2 resistance plasmids
Berg ES, Wester AL, Ahrenfeldt J, Mo SS, Slettemeås JS, Steinbakk M, Samuelsen Ø, Grude N, Simonsen GS, Løhr IH, Jørgensen SB, Tofteland S, Lund O, Dahle UR, Sunde M
Clinical Microbiology and Infection 201, 2017 |
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Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods
Ahrenfeldt J, Skaarup C, Hasman H, Pedersen AG, Aarestrup FM, Lund O
BMC Genomics. 18(1):19, 2017 |
PubMed
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2016
Fish Oil-Derived Fatty Acids in Pregnancy and Wheeze and Asthma in Offspring.
Bisgaard H, Stokholm J, Chawes BL, Vissing NH, Bjarnadóttir E, Schoos AM, Wolsk HM, Pedersen TM, Vinding RK, Thorsteinsdóttir S, Følsgaard NV, Fink NR, Thorsen J, Pedersen AG, Waage J, Rasmussen MA, Stark KD, Olsen SF, Bønnelykke K
New England Journal of Medicine, 2016 |
PubMed
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New Genome-Wide Algorithm Identifies Novel In-Vivo Expressed Mycobacterium Tuberculosis Antigens Inducing Human T-Cell Responses with Classical and Unconventional Cytokine Profiles
Coppola M, van Meijgaarden KE, Franken KLMC, Commandeur S, Dolganov G, Kramnik I, Schoolnik GK, Comas I, Lund O, Prins C, van den Eeden SJF, Korsvold GE, Oftung F, Geluk A, Ottenhoff THM
Sci. Rep, 2016 |
PubMed
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Automated Clustering Analysis of Immunoglobulin Sequences in Chronic Lymphocytic Leukemia Based on 3D Structural Descriptors
Marcatili, P, Mochament, K, Agathangelidis, A, Moschonas, P, Sutton, L, Yan, X, Bikos, V, Vardi, A, Chailyan, A, Stavroyianni, N, Kjærgaard Jensen, K, Anagnostopoulos, A, Chiorazzi, N, Belessi, C, Rosenquist, R, Ghia, P, Stamatopoulos, K, Hadzidimitriou, A, Tzovaras &, D
Blood, 2016 |
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A novel approach to probe host-pathogen interactions of bovine digital dermatitis, a model of a complex polymicrobial infection
Marcatili P, Nielsen MW, Sicheritz-Pontén T, Jensen TK, Schafer-Nielsen C, Boye M, Nielsen M, Klitgaard K
BMC Genomics, 2016 |
PubMed
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A scored human protein-protein interaction network to catalyze genomic interpretation.
Li T, Wernersson R, Hansen RB, Horn H, Mercer J, Slodkowicz G, Workman CT, Rigina O, Rapacki K, Stærfeldt HH, Brunak S, Jensen TS, Lage K
Nature Methods, 2016 |
Relevant URL
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High-throughput immuno-profiling of mamba (Dendroaspis) venom toxin epitopes using high-density peptide microarrays
Engmark M, Andersen MR, Laustsen AH, Patel J, Sullivan E, de Masi F, Hansen CS, Kringelum JV, Lomonte B, Gutiérrez JM, Lund O
Scientific Reports, 2016 |
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Ranking factors involved in diabetes remission after bariatric surgery using machine-learning integrating clinical and genomic biomarkers
Krogh Pedersen H, Gudmundsdottir V, Krogh Pedersen M, Brorsson C, Brunak S, Gupta R
npj Genomic Medicine, 2016 |
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MetaPhinder—Identifying Bacteriophage Sequences in Metagenomic Data Sets
Jurtz VI, Villarroel J, Lund O, Larsen MV, Nielsen M
PLoS One, 2016 |
PubMed
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Asparaginase-associated pancreatitis: a study on phenotype and genotype in the NOPHO ALL2008 protocol.
Wolthers BO, Frandsen TL, Abrahamsson J, Albertsen BK, Helt LR, Heyman M, Jónsson ÓG, Kõrgvee LT, Lund B, Raja RA, Rasmussen KK, Taskinen M, Tulstrup M, Vaitkevi?ien? GE, Yadav R, Gupta R, Schmiegelow K
Leukemia, 2016 |
PubMed
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Nutritional stress induced by tryptophan-degrading enzymes results in ATF4-dependent reprogramming of the amino acid transporter profile in tumor cells.
Timosenko E, Ghadbane H, Silk JD, Shepherd D, Gileadi U, Howson LJ, Laynes R, Zhao Q, Strausberg RL, Olsen LR, Taylor S, Buffa FM, Boyd R, Cerundolo V
American Association for Cancer Research, 2016 |
PubMed
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Whole Genome Sequencing as a Tool for Species Identification of Clinical Strains of Mitis Group Streptococci.
Rasmussen LH, Dargis R, Højholt K, Christensen JJ, Skovgaard O, Justesen US, Rosenvinge FS, Moser C, Lukjancenko O, Rasmussen S, Nielsen XC
European Journal of Clinical Microbiology & Infectious Diseases, 2016 |
PubMed
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A Genomic History of Aboriginal Australia.
Malaspinas A-S#, Westaway MC#, Muller C#, Sousa VC#, Lao O#, Alves I#, Bergstro?m A#, Athanasiadis G^, Cheng JY^, Crawford JE^, Heupink TH^, Machold E^, Peischl S^, Rasmussen S^, Schiffels S^, Subramanian S^, Wright JL^, Albrechtsen A, Barbieri C, Dupanloup I, Eriksson A, Margaryan A, Moltke I, Pugach I, Korneliussen TS, Levkivsky IP, Moreno-Mayar JV, Ni S, Racimo F, Sikora M, Xue Y, Aghakhanian FA, Brucato N, Brunak S, Campos PF, Clark W, Ellingva?g S, Fourmile G, Gerbault P, Injie D, Koki G, Leavesley M, Logan B, Lynch A, Matisoo-Smith EA, McAllister PJ, Mentzer AJ, Metspalu M, Migliano AB, Murgha L, Phipps ME, Pomat W, Reynolds D, Ricaut FX, Siba P, Thomas MG, Wales T, Wall C, Oppenheimer SJ, Tyler-Smith C, Durbin R, Dortch J, Manica A, Schierup MH, Foley RA, Lahr MM, Bowern C, Wall JD, Mailund T, Stoneking M, Nielsen R, Sandhu MS, Excoffier L, Lambert DM, Willerslev E
Nature, 2016 |
PubMed
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Alpha proteobacterial ancestry of the [Fe-Fe]-hydrogenases in anaerobic eukaryotes.
Esposti DM, Cortez D, Lozano L, Rasmussen S, Nielsen HB, Romero EM
Biology Direct, 2016 |
PubMed
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The genetics of blood pressure regulation and its target organs from association studies in 342,415 individuals.
Ehret GB, Ferreira T, Chasman DI, Jackson AU, Schmidt EM, Johnson T, Thorleifsson G, Luan J, Donnelly LA, Kanoni S, Petersen AK, Pihur V, Strawbridge RJ, Shungin D, Hughes MF, Meirelles O, Kaakinen M, Bouatia-Naji N, Kristiansson K, Shah S, Kleber ME, Guo X, Lyytikäinen LP, Fava C, Eriksson N, Nolte IM, Magnusson PK, Salfati EL, Rallidis LS, Theusch E, Smith AJ, Folkersen L, Witkowska K, Pers TH, Joehanes R, Kim SK, Lataniotis L, Jansen R, Johnson AD, Warren H, Kim YJ, Zhao W, Wu Y, Tayo BO, Bochud M; CHARGE-EchoGen Consortium; CHARGE-HF Consortium; Wellcome Trust Case Control Consortium, Absher D, Adair LS, Amin N, Arking DE, Axelsson T, Baldassarre D, Balkau B, Bandinelli S, Barnes MR, Barroso I, Bevan S, Bis JC, Bjornsdottir G, Boehnke M, Boerwinkle E, Bonnycastle LL, Boomsma DI, Bornstein SR, Brown MJ, Burnier M, Cabrera CP, Chambers JC, Chang IS, Cheng CY, Chines PS, Chung RH, Collins FS, Connell JM, Döring A, Dallongeville J, Danesh J, de Faire U, Delgado G, Dominiczak AF, Doney AS, Drenos F, Edkins S, Eicher JD, Elosua R, Enroth S, Erdmann J, Eriksson P, Esko T, Evangelou E, Evans A, Fall T, Farrall M, Felix JF, Ferrières J, Ferrucci L, Fornage M, Forrester T, Franceschini N, Franco OH, Franco-Cereceda A, Fraser RM, Ganesh SK, Gao H, Gertow K, Gianfagna F, Gigante B, Giulianini F, Goel A, Goodall AH, Goodarzi MO, Gorski M, Gräßler J, Groves CJ, Gudnason V, Gyllensten U, Hallmans G, Hartikainen AL, Hassinen M, Havulinna AS, Hayward C, Hercberg S, Herzig KH, Hicks AA, Hingorani AD, Hirschhorn JN, Hofman A, Holmen J, Holmen OL, Hottenga JJ, Howard P, Hsiung CA, Hunt SC, Ikram MA, Illig T, Iribarren C, Jensen RA, Kähönen M, Kang HM, Kathiresan S, Keating BJ, Khaw KT, Kim YK, Kim E, Kivimaki M, Klopp N, Kolovou G, Komulainen P, Kooner JS, Kosova G, Krauss RM, Kuh D, Kutalik Z, Kuusisto J, Kvaløy K, Lakka TA, Lee NR, Lee IT, Lee WJ, Levy D, Li X, Liang KW, Lin H, Lin L, Lindström J, Lobbens S, Männistö S, Müller G, Müller-Nurasyid M, Mach F, Markus HS, Marouli E, M
Nature Genetics, 2016 |
PubMed
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Upstream freshwater and terrestrial sources are differentially reflected in the bacterial community structure along a small Arctic river and its estuary
Hauptmann AL, Markussen TN, Stibal M, Olsen N, Elberling B, Bælum J, Sicheritz-Pontén T, Jacobsen CS
Front. Microbiol, 2016 |
Relevant URL
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Large-scale detection of antigen-specific T cells using peptide-MHC-I multimers labeled with DNA barcodes
Bentzen AK, Marquard AM, Lyngaa R, Saini SK, Ramskov S, Donia M, Such L, Furness AJS, McGranahan N, Rosenthal R, Straten PT, Szallasi Z, Svane IM, Swanton C, Quezada SA, Jakobsen SN, Eklund AC, Hadrup SR
Nat Biotechnol, 2016 |
PubMed
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”Structure-based Discovery of Novel US28 Small Molecule Ligands with Different Modes of Action”
Lückmann M, Amarandi RM, Papargyri N, Jakobsen MH, Christiansen E, Jensen LJ, Pui A, Schwartz TW, Rosenkilde MM, Frimurer TM
Chem Biol Drug Des, 2016 |
PubMed
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The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota
Lagkouvardos I, Pukall R, Abt B, Foesel BU, Meier-Kolthoff JP, Kumar N, Bresciani A, Martínez I, Just S, Ziegler C, Brugiroux S, Garzetti D, Wenning M, Bui TPN, Wang J, Hugenholtz F, Plugge CM, Peterson DA, Hornef MW, Baines JF, Smidt H, Walter J, Kristiansen K, Nielsen HB, Haller D, Overmann J, Stecher B, Clavel T
Nature Microbiology, 2016 |
Relevant URL
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GLP-1 Induces Barrier Protective Expression in Brunner\'s Glands and Regulates Colonic Inflammation.
Bang-Berthelsen CH, Holm TL, Pyke C, Simonsen L, Søkilde R, Pociot F, Heller RS, Folkersen L, Kvist PH, Jackerott M, Fleckner J, Vilién M, Knudsen LB, Heding A, Frederiksen KS
Inflamm Bowel Dis, 2016 |
PubMed
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Linear epitope mapping of peanut allergens demonstrates individualized and persistent antibody-binding patterns.
Hansen CS, Dufva M, Bøgh KL, Sullivan E, Patel J, Eiwegger T, Szépfalusi Z, Nielsen M, Christiansen A
J Allergy Clin Immunol, 2016 |
PubMed
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The hunt for fatal myocardial infarction biomarkers: predictive circulating microRNAs
Francesco Russo, Milena Rizzo, Kirstine Belling, Søren Brunak, Lasse Folkersen
Annals of Translational Medicine, 2016 |
Relevant URL
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Loss of BRCA1 or BRCA2 markedly increases the rate of base substitution mutagenesis and has distinct effects on genomic deletions
Zámborszky J, Szikriszt B, Gervai JZ, Pipek O, Póti Á, Krzystanek M, Ribli D, Szalai-Gindl JM, Csabai I, Szallasi Z, Swanton C, Richardson AL, Szüts D
Oncogene, 2016 |
PubMed
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Pan-Specific Prediction of Peptide-MHC Class I Complex Stability, a Correlate of T Cell Immunogenicity
Rasmussen M, Fenoy E, Harndahl M, Kristensen AB, Nielsen IK, Nielsen M, Buus S
J Immunol, 2016 |
PubMed
Relevant URL
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Integration of known DNA, RNA and protein biomarkers provides prediction of anti-TNF response in rheumatoid arthritis: results from the COMBINE study
Folkersen L, Brynedal B, Marcela Diaz-Gallo L, Ramsköld D, Shchetynsky K, Westerlind H, Sundström Y, Schepis D, Hensvold A, Vivar N, Eloranta M, Rönnblom L, Brunak S, Malmström V, Catrina A, Moerch UGW, Klareskog L, Padyukov L, Berg L
Molecular Medicine, 2016 |
PubMed
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Enhanced base excision repair capacity in carotid atherosclerosis may protect nuclear DNA but not mitochondrial DNA
Skarpengland T, Dahl TB, Skjelland M, Scheffler K, Sousa MM, Gregersen I, Ku?nierczyk A, Sharma A, Slupphaug G, Eide L, Segers FM, Skagen KR, Dahl CP, Russell D, Folkersen L, Krohg-Sørensen K, Holm S, Bjørås M, Aukrust P, Halvorsen B
Free Radic Biol Med, 2016 |
PubMed
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USP2 as a potential link between miR-125b and psoriasis.
Wei T, Folkersen L, Biskup E, Xu N, Manfe V, Niazi O, Gniadecki R
British Journal of Dermatology, 2016 |
PubMed
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Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut
Roager HM, Hansen LBS, Bahl MI, Frandsen HL, Carvalho V, Gøbel RJ, Dalgaard MD, Sparholt M, Vestergaard H, Hansen T, Sicheritz-Ponten T, Nielsen HB, Pedersen O, Lauritzen L, Kristensen M, Gupta R, Licht TR
Nature Microbiology, 2016 |
Relevant URL
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Plasmodium falciparum var genes expressed in children with severe malaria encode CIDRa1 domains
Jespersen JS, Wang CW, Mkumbaye SI, Minja DT, Petersen B, Turner L, Petersen JE, Lusingu JP, Theander TG, Lavstsen T
EMBO Molecular Medicine, 2016 |
PubMed
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KinMutRF: a random forest classifier of sequence variants in the human protein kinase superfamily
Pons T, Vazquez M, Matey-Hernandez ML, Brunak S, Valencia A, Izarzugaza JMG
BMC Genomics, 2016 |
Relevant URL
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A Drosophila Genome-Wide Screen Identifies Regulators of Steroid Hormone Production and Developmental Timing
Danielsen ET, Moeller ME, Yamanaka N, Ou Q, Laursen JM, Soenderholm C, Zhuo R, Phelps B, Tang K, Zeng J, Kondo S, Nielsen CH, Harvald EB, Faergeman NJ, Haley MJ, O\'Connor KA, King-Jones K, O\'Connor MB, Rewitz KF
Developmental Cell, 2016 |
PubMed
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A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and Surveillance
Thomsen MCF, Ahrenfeldt J, Cisneros JLB, Jurtz V, Larsen MV, Hasman H, Aarestrup FM, Lund O
PLoS ONE, 2016 |
PubMed
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The stepwise evolution of the exome during acquisition of docetaxel resistance in breast cancer cells
Hansen SN, Ehlers NS, Zhu S, Thomsen MB, Nielsen RL, Liu D, Wang G, Hou Y, Zhang X, Xu X, Bolund L, Yang H, Wang J, Moreira J, Ditzel HJ, Brünner N, Schrohl AS, Stenvang J, Gupta R
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Angiotensinogen and HLA class II predict bevacizumab response in recurrent glioblastoma patients
Urup T, Michaelsen SR, Olsen LR, Toft A, Christensen IJ, Grunnet K, Winther O, Broholm H, Kosteljanetz M, Issazadeh-Navikas S, Poulsen HS, Lassen U
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MicroRNA 486-3P as a stability marker in acute coronary syndrome
Wei T, Folkersen L, Ehrenborg E, Gabrielsen A
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PubMed
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NLRP3 Inflammasome Expression and Activation in Human Atherosclerosis
Paramel Varghese G, Folkersen L, Strawbridge RJ, Halvorsen B, Yndestad A, Ranheim T, Krohg-Sørensen K, Skjelland M, Espevik T, Aukrust P, Lengquist M, Hedin U, Jansson JH, Fransén K, Hansson GK, Eriksson P, Sirsjö A
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HostPhinder: A Phage Host Prediction Tool
Villarroel J, Kleinheinz KA, Jurtz V, Zschach H, Lund O, Nielsen M, Larsen MV
Viruses, 2016 |
PubMed
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Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp.
Palomo A, Jane Fowler S, Gülay A, Rasmussen S, Sicheritz-Ponten T, Smets BF
ISME Journal, 2016 |
PubMed
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A comprehensive survey of the mutagenic impact of common cancer cytotoxics
Szikriszt B, Póti Á, Pipek O, Krzystanek M, Kanu N, Molnár J, Ribli D, Szeltner Z, Tusnády GE, Csabai I, Szallasi Z, Swanton C, Szüts D
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Pharmacogenomics in diabetes mellitus: insights into drug action and drug discovery
Zhou K, Pedersen HK, Dawed AY, Pearson ER
Nature Reviews Endocrinology, 2016 |
PubMed
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A fast and robust method for whole genome sequencing of the Aleutian Mink Disease Virus (AMDV) genome
Hagberg EE, Krarup A, Fahnøe U, Larsen LE, Dam-Tuxen R, Pedersen AG
J Virol Methods, 2016 |
PubMed
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Using expected sequence features to improve basecalling accuracy of amplicon pyrosequencing data
Rask TS, Petersen B, Chen DS, Day KP, Pedersen AG
BMC Bioinformatics, 2016 |
PubMed
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Dental calculus and the evolution of the human oral microbiome
Warinner C
California Dental Association Journal, in press, 2016 |
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A comprehensive profile of recurrent glioblastoma
Campos B, Olsen LR, Urup T, Poulsen HS
Oncogene, doi:10.1038/onc.2016.85, 2016 |
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NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets
Nielsen M, Andreatta M
Genome Medicine, 8:33, 2016 |
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How compelling are the data for Epstein-Barr virus being a trigger for systemic lupus and other autoimmune diseases?
Draborg A, Izarzugaza JM, Houen G
Current Opinion in Rheumatology, doi: 10.1097/BOR.0000000000000289, 2016 |
PubMed
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Picornavirus-Induced Airway Mucosa Immune Profile in Asymptomatic Neonates
Wolsk HM, Følsgaard NV, Birch S, Brix S, Hansel TT, Johnston SL, Kebadze T, Chawes BL, Bønnelykke K, Bisgaard H
J Infect Dis. 213(8):1262-70. doi: 10.1093/infdis/jiv594, 2016 |
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Siblings Promote a Type 1/Type 17-oriented immune response in the airways of asymptomatic neonates
Wolsk HM, Chawes BL, Følsgaard NV, Rasmussen MA, Brix S, Bisgaard H
Allergy, doi: 10.1111/all.12847, 2016 |
PubMed
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Effect of High-dose Vitamin D3 Supplementation during Pregnancy on Risk of Persistent Wheeze in the Offspring
Chawes BL, Bønnelykke K, Stokholm J, Vissing NH, Bjarnadóttir E, Schoos A-MM, Wolsk HM, Pedersen TM, Vinding R, Thorsteinsdóttir S, Arianto L, Hallas H, Heickendorff L, Brix S, Rasmussen MA, Bisgaard H
JAMA, 315(4):353-361, 2016 |
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Model studies of lipid flip-flop in membranes
Parisio G, Ferrarini A, Sperotto MM
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T cell recognition is shaped by epitope sequence conservation in the host proteome and microbiome
Bresciani A, Paul S, Schommer N, Dillon MB, Bancroft T, Greenbaum J, Sette A, Nielsen M, Peters B
Immunology. doi: 10.1111/imm.12585, 2016 |
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The Length Distribution of Class I-Restricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC Allele-Specific Binding Preference
Trolle T, McMurtrey CP, Sidney J, Bardet W, Osborn SC, Kaever T, Sette A, Hildebrand WH, Nielsen M, Peters B
J Immunol. pii: 1501721, 2016 |
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MECP2 Is a Frequently Amplified Oncogene with a Novel Epigenetic Mechanism That Mimics the Role of Activated RAS in Malignancy
Neupane M, Clark AP, Landini S, Birkbak NJ, Eklund AC, Lim E, Culhane AC, Barry WT, Schumacher SE, Beroukhim R, Szallasi Z, Vidal M, Hill DE, Silver DP
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A robust prognostic gene expression signature for early stage lung adenocarcinoma.
Krzystanek M, Moldvay J, Szüts D, Szallasi Z, Eklund AC
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Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers
Friis-Nielsen J, Kjartansdóttir KR, Mollerup S, Asplund M, Mourier T, Jensen RH, Hansen TA, Rey-Iglesia A, Richter SR, Nielsen IB, Alquezar-Planas DE, Olsen PV, Vinner L, Fridholm H, Nielsen LP, Willerslev E, Sicheritz-Pontén T, Lund O, Hansen AJ, Izarzugaza JM, Brunak S
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MDPI
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Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove
McMurtrey C, Trolle T, Sansom T, Remesh SG, Kaever T, Bardet W, Jackson K, Nielsen M, McLeod R, Zajonc DM, Blader IJ, Peters B, Sette A, Hildebrand W
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Propionibacterium acnes - disease causing agent or common contaminant? Detection in diverse patient samples by next generation sequencing
Mollerup S, Friis-Nielsen J, Vinner L, Hansen TA, Richter SR, Fridholm H, Herrera JA, Lund O, Brunak S, Izarzugaza JM, Mourier T, Nielsen LP, Hansen AJ
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wKinMut-2: Identification and Interpretation of Pathogenic Variants in Human Protein Kinases
Vazquez M, Pons T, Brunak S, Valencia A, Izarzugaza JM
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Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale
Schierup M, Villsen P, Wang J, Xu X, Li N, Kristiansen K, Krogh A, Sørensen TIA, Hansen T, Pedersen O, Brunak S, Gupta R, Rasmussen S, Lund O, Bolund L, Børglum AD, Eiberg H, Flindt EN, Xu R, Sun J, Liu H, Jiang H, Wang O, Cheng X, Demontis D, Besenbacher S, Mailund T, Friborg RM, Pedersen CNS, Liu S, Huang S, Rao J, Ye W, Chang Y, Li S, Guo X, Cao H, Ye C, Maretty L, Sibbesen JA, Albrechtsen A, Bork-Jensen J, Have CT, Izarzugaza JMG, Belling K, Yadav R, Grove J, Als TD, Lescal F
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Inflammatory Mediator Profiling of n-butanol Exposed Upper Airways in Individuals with Multiple Chemical Sensitivity
Dantoft TM, Skovbjerg S, Andersson L, Claeson AS, Lind N, Nordin S, Brix S
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The elusive endogenous adipogenic PPARy agonists: Lining up the suspects
Hallenborg P, Petersen RK, Kouskoumvekaki I, Newman JW, Madsen L, Kristiansen K
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LOX1 inhibition with small molecules
Gousiadou C, Kouskoumvekaki I
J Mol Graph Model. 2015 Dec 11;63:99-109. doi: 10.1016/j.jmgm.2015.12.001, 2015 |
PubMed
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Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota
Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Pedersen HK, Arumugam M, Kristiansen K, Voigt AY, Vestergaard H, Hercog R, Costea PI, Kultima JR, Li J, Jørgensen T, Levenez F, Dore J, MetaHIT consortium, Nielsen HB, Brunak S, Raes J, Hansen T, Wang J, Ehrlich SD, Bork P, Pedersen O
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Quantification of oxidative stress phenotypes based on high-throughput growth profiling of protein kinase and phosphatase knockouts
Altintas A, Martini J, Mortensen UH, Workman CT
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Obesity and Bariatric Surgery Drive Epigenetic Variation of Spermatozoa in Humans
Donkin I, Versteyhe S, Ingerslev LR, Qian K, Mechta M, Nordkap L, Mortensen B, Appel EVR, Jørgensen N, Kristiansen VB, Hansen T, Workman CT, Zierath JR, Barres R
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Reads2Type: a web application for rapid microbial taxonomy identification
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Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments
Librado P, Der Sarkissian C, Ermini L, Schubert M, Jónsson H, Albrechtsen A, Fumagalli M, Yang MA, Gamba C, Seguin-Orlando A, Mortensen CD, Petersen B, Hoover CA, Lorente-Galdos B, Nedoluzhko A, Boulygina E, Tsygankova S, Neuditschko M, Jagannathan V, Thèves C, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Sicheritz-Ponten T, Popov R, Grigoriev S, Alekseev AN, Rubin EM, McCue M, Rieder S, Leeb T, Tikhonov A, Crubézy E, Slatkin M, Marques-Bonet T, Nielsen R, Willerslev E, Kantanen J, Prokhortchouk E, Orlando L
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A combined prediction strategy increases identification of peptides bound with high affinity and stability to porcine MHC class I molecules SLA-1*04:01, SLA-2*04:01, and SLA-3*04:01
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Tools and data services registry: a community effort to document bioinformatics resources
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Season of birth shapes neonatal immune function
Thysen AH, Rasmussen MA, Kreiner-Møller E, Larsen JM, Følsgaard NV, Bønnelykke K, Stokholm J, Bisgaard H, Brix S
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Distinct inflammatory and cytopathic characteristics of Escherichia coli isolates from inflammatory bowel disease patients
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Divergent Response Profile in Activated Cord Blood T cells from First-born Child Implies Birth-order-associated in Utero Immune Programming
Kragh M, Larsen JM, Thysen AH, Rasmussen MA, Wolsk HM, Bisgaard H, Brix S
Allergy, 2015 |
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Maternal fatty acid desaturase genotype correlates with infant immune responses at 6 months
Muc M, Kreiner-Møller E, Larsen JM, Birch S, Brix S, Bisgaard H, Lauritzen L
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Prelabor cesarean section bypasses natural immune cell maturation
Thysen AH, Larsen JM, Rasmussen MA, Stokholm J, Bønnelykke K, Bisgaard H, Brix S
J Allergy Clin Immunol, 2015 |
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The effect of maternal Inflammation on foetal programming of metabolic disease
Ingvorsen C, Brix S, Ozanne SE, Hellgren LI
Acta Physiol, 2015 |
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A modern approach for epitope prediction: identification of foot-and-mouth disease virus peptides binding bovine leukocyte antigen (BoLA) class I molecules
Pandya M, Rasmussen M, Hansen A, Nielsen M, Buus S, Golde W, Barlow J
Immunogenetics, 2015 |
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Creation of Functional Viruses from Non-Functional cDNA Clones Obtained from an RNA Virus Population by the Use of Ancestral Reconstruction
Fahnøe U, Pedersen AG, Dräger C, Orton RJ, Blome S, Höper D, Beer M, Rasmussen TB
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Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago
Rasmussen S, Allentoft ME, Nielsen K, Orlando L, Sikora M, Sjögren KG, Pedersen AG, Schubert M, Van Dam A, Kapel CMO, Nielsen HB, Brunak S, Avetisyan P, Epimakhov A, Khalyapin MV, Gnuni A, Kriiska A, Lasak I, Metspalu M, Moiseyev V, Gromov A, Pokutta D, Saag L, Varul L, Yepiskoposyan L, Sicheritz-Pontén T, Foley RA, Lahr MM, Nielsen R, Kristiansen K, Willerslev E
Cell, 2015 |
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Definition of the HLA class I-associated viral antigen repertoire from HIV-1-infected cells
Ternette N, Yang H, Partridge T, Llano A, Cedeño S, Fischer R, Charles PD, Dudek NL, Mothe B, Crespo M, Fischer WM, Korber BT, Nielsen M, Borrow P, Purcell AW, Brander C, Dorrell L, Kessler BM, Hanke T
European Journal of Immunology, 2015 |
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Within-host microevolution of Pseudomonas aeruginosa in Italian cystic fibrosis patients
Marvig RL, Dolce D, Sommer LM, Petersen B, Ciofu O, Campana S, Molin S, Taccetti G, Johansen HK
BMC Microbiology, 2015 |
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Biomedcentral
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Structural Characterization of Peptide Antibodies
Chailyan A, Marcatili P
Peptide Antibodies: Methods and Protocols, 2015 |
PubMed
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Prediction of Antibody Epitopes
Nielsen M, Marcatili P
Peptide Antibodies: Methods and Protocols, 2015 |
PubMed
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Exploiting homology information in non-template based prediction of protein structures
Iacoangeli A, Marcatili P, Tranmontano A
Journal of Chemical Theory and Computation, 2015 |
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Marquard AM, Birkbak NJ, Thomas CE, Favero F, Krzystanek M, Lefebvre C, Ferté C, Jamal-Hanjani M, Wilson GA, Shafi S, Swanton C, André F, Szallasi Z, Eklund AC
BMC Medical Genomics, 2015 |
Biomedcentral
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A catalog of the mouse gut metagenome
Xiao L, Feng Q, Licht TR, Dworzynski P, Nielsen HB, Arumugam M, Wang J, Madsen L, Kristiansen K
Nature Biotechnology, 2015 |
PubMed
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Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification
Andreatta M, Karosiene E, Rasmussen M, Stryhn A, Buus S, Nielsen M
Immunogenetics, Sep 29, 2015 |
PubMed
Immunogenetics
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Germ Cell Cancer and Multiple Relapses: Toxicity and Survival
Lauritsen J, Kier MG, Mortensen MS, Bandak M, Gupta R, Holm NV, Agerbaek M, Daugaard G
J Clin Oncol, 2015 |
PubMed
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Kinome-wide Decoding of Network-Attacking Mutations Rewiring Cancer Signaling
Creixell P, Schoof EM, Simpson CD, Longden J, Miller CJ, Lou HJ, Perryman L, Cox TR, Zivanovic N, Palmeri A, Wesolowska-Andersen A, Helmer-Citterich M, Ferkinghoff-Borg J, Itamochi H, Bodenmiller B, Erler JT, Turk BE, Linding R
Cell, 2015 |
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Unmasking Determinants of Specificity in the Human Kinome
Creixell P, Palmeri A, Miller CJ, Lou HJ, Santini CC, Nielsen M, Turk BE, Linding R
Cell, Sep 16, 2015 |
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Evolutionary Genomics and Conservation of the Endangered Przewalski’s Horse
Sarkissian CD, Ermini L, Schubert M, Yang MA, Librado P, Fumagalli M, Jónsson H, Bar-Gal GK, Albrechtsen A, Vieira FG, Petersen B, Ginolhac A, Seguin-Orlando A, Magnussen K, Fages A, Gamba C, Lorente-Galdos B, Polani S, Steiner C, Neuditschko M, Jagannathan V, Feh C, Greenblatt CL, Ludwig A, Abramson NI, Zimmermann W, Schafberg R, Tikhonov A, Sicheritz-Ponten T, Willerslev E, Marques-Bonet T, Ryder OA, McCue M, Rieder S, Leeb T, Slatkin M, Orlando L
Current Biology 24 Sep, 2015 |
Cell
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Functional Analysis of a Carotid Intima-Media Thickness Locus Implicates
Boardman-Pretty F, Smith AJ, Cooper J, Palmen J, Folkersen L, Hamsten A, Catapano AL, Melander O, Price JF, Kumari M, Deanfield JE, Kivimäki M, Gertow K, Baragetti A, Norata GD, Humphries SE
Circ Cardiovasc Genet, 2015 |
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Genomic Evidence for the Pleistocene and recent population history of Native Americans
Raghavan M, Steinrücken M, Harris K, Schiffels S, Rasmussen S, DeGiorgio M, Albrechtsen A, Valdiosera C, Ávila-Arcos MC, Malaspinas AS, Eriksson A, Moltke I, Metspalu M, Homburger JR, Wall J, Cornejo OE, Moreno-Mayar JV, Korneliussen TS, Pierre T, Rasmussen M, Campos PF, Damgaard Pde B, Allentoft ME, Lindo J, Metspalu E, Rodríguez-Varela R, Mansilla J, Henrickson C, Seguin-Orlando A, Malmström H, Stafford T Jr, Shringarpure SS, Moreno-Estrada A, Karmin M, Tambets K, Bergström A, Xue Y, Warmuth V, Friend AD, Singarayer J, Valdes P, Balloux F, Leboreiro I, Vera JL, Rangel-Villalobos H, Pettener D, Luiselli D, Davis LG, Heyer E, Zollikofer CP, Ponce de León MS, Smith CI, Grimes V, Pike KA, Deal M, Fuller BT, Arriaza B, Standen V, Luz MF, Ricaut F, Guidon N, Osipova L, Voevoda MI, Posukh OL, Balanovsky O, Lavryashina M, Bogunov Y, Khusnutdinova E, Gubina M, Balanovska E, Fedorova S, Litvinov S, Malyarchuk B, Derenko M, Mosher MJ, Archer D, Cybulski J, Petzelt B, Mitchell J, Worl R, Norman PJ, Parham P, Kemp BM, Kivisild T, Tyler-Smith C, Sandhu MS, Crawford M, Villems R, Smith DG, Waters MR, Goebel T, Johnson JR, Malhi RS, Jakobsson M, Meltzer DJ, Manica A, Durbin R, Bustamante CD, Song YS, Nielsen R, Willerslev E
Science, 2015 |
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Population genomics of Bronze Age Eurasia
Allentoft ME, Sikora M, Sjögren KG, Rasmussen S, Rasmussen M, Stenderup J, Damgaard PB, Schroeder H, Ahlström T, Vinner L, Malaspinas AS, Margaryan A, Higham T, Chivall D, Lynnerup N, Harvig L, Baron J, Della Casa P, D?browski P, Duffy PR, Ebel AV, Epimakhov A, Frei K, Furmanek M, Gralak T, Gromov A, Gronkiewicz S, Grupe G, Hajdu T, Jarysz R, Khartanovich V, Khokhlov A, Kiss V, Kolá? J, Kriiska A, Lasak I, Longhi C, McGlynn G, Merkevicius A, Merkyte I, Metspalu M, Mkrtchyan R, Moiseyev V, Paja L, Pálfi G, Pokutta D, Pospieszny ?, Price TD, Saag L, Sablin M, Shishlina N, Smr?ka V, Soenov VI, Szeverényi V, Tóth G, Trifanova SV, Varul L, Vicze M, Yepiskoposyan L, Zhitenev V, Orlando L, Sicheritz-Pontén T, Brunak S, Nielsen R, Kristiansen K, Willerslev E
Nature, 2015 |
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Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance
Nordahl Petersen T, Rasmussen S, Hasman H, Carøe C, Bælum J, Charlotte Schultz A, Bergmark L, Svendsen CA, Lund O, Sicheritz-Pontén T, Aarestrup FM
Nature Scientific Reports 5, 2015 |
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Functional Analysis of a Carotid Intima-Media Thickness Locus Implicates BCAR1 and Suggests a Causal Variant
Boardman-Pretty F, Smith AJ, Cooper J, Palmen J, Folkersen L, Hamsten A, Catapano AL, Melander O, Price JF, Kumari M, Deanfield JE, Kivimäki M, Gertow K, Baragetti A, Norata GD, Humphries SE
Circ Cardiovasc Genet, 2015 |
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Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing
Vinner L, Mourier T, Friis-Nielsen J, Gniadecki R, Dybkaer K, Rosenberg J, Langhoff JL, Santa Cruz DF, Fonager J, Izarzugaza JM, Gupta R, Sicheritz-Ponten T, Brunak S, Willerslev E, Nielsen LP, Hansen AJ
Nature Scientific Reports 5, 2015 |
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High-throughput sequencing enhanced phage display enables the identification of patient-specific epitope motifs in serum
Christiansen A, Kringelum JV, Hansen CS, Bøgh KL, Sullivan E, Patel J, Rigby NM, Eiwegger T, De Masi F, Nielsen M, Lund O, Dufva M
Nature, 2015 |
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The Danish Elixir Node
Brunak S, Ison J, Rapacki K, Sperotto MM
BioZoom, 2015 |
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Convolutional LSTM Networks for Subcellular Localization of Proteins
Sønderby SK, Sønderby CK, Nielsen H, Winther O
Algorithms for Computational Biology, 2015 |
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Ebolavirus comparative genomics
Jun SR, Leuze MR, Nookaew I, Uberbacher EC, Land M, Zhang Q, Wanchai V, Chai J, Nielsen M, Trolle T, Lund O, Buzard GS, Pedersen TD, Wassenaar TM, Ussery DW
FEMS Microbiol Rev, 2015 |
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Global gene expression profiling of brown to white adipose tissue transformation in sheep reveals novel transcriptional components linked to adipose remodeling
Basse AL, Dixen K, Yadav R, Tygesen MP, Qvortrup K, Kristiansen K, Quistorff B, Gupta R, Wang J, Hansen JB
BMC Genomics, 2015 |
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Eukaryotic glycosylation: online methods for site prediction on protein sequences
Joshi HJ, Gupta R
Methods in Molecular Biology, 2015 |
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Inherited coding variants at the CDKN2A locus influence susceptibility to acute lymphoblastic leukaemia in children
Xu H, Zhang H, Yang W, Yadav R, Morrison AC, Qian, Devidas M, Liu Y, Perez-Andreu V, Zhao X, Gastier-Foster JM, Lupo P, Neale G, Raetz E, Larsen E, Bowman WP, Carroll WL, Winick N, Williams R, Hansen T, Holm JC, Mardis E, Fulton R, Pui CH, Zhang J, Mullighan CG, Evans WE, Hunger SP, Gupta R, Schmiegelow K, Loh ML, Relling MV, Yang JJ
Nature Communications, 2015 |
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The potential role of Alu Y in the development of resistance to SN38 (Irinotecan) or oxaliplatin in colorectal cancer
Lin X, Stenvang J, Rasmussen MH, Zhu S, Jensen NF, Tarpgaard LS, Yang G, Belling KC, Andersen CL, Li J, Bolund L, Brunner N
BMC Genomics 16:404 doi: 10.1186/s12864-015-1552-y, 2015 |
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AllelicImbalance: A bioconductor package for detecting, managing, and visualizing allele expression imbalance data from RNA sequencing
Gådin JR, Hooft FMV, Eriksson P, Folkersen L
BMC Bioinformatics, 2015 |
BMC Bioinformatics
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Applying Genetics in Inflammatory Disease Drug Discovery
Folkersen L, Biswas S, Frederiksen KS, Keller P, Fox B, Fleckner J
Drug Discovery Today, 2015 |
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LYRA, a webserver for lymphocyte receptor structural modeling
Klausen MS, Anderson MV, Jespersen MC, Nielsen M, Marcatili P
Nucleic Acids Research, 2015 |
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Somatic Cell Fusions Reveal Extensive Heterogeneity in Basal-like Breast Cancer
Su Y, Subedee A, Bloushtain-Qimron N, Savova V, Krzystanek M, Li L, Marusyk A, Tabassum DP, Zak A, Flacker MJ, Li M, Lin JJ, Sukumar S, Suzuki H, Long H, Szallasi Z, Gimelbrant A, Maruyama R, Polyak K
Cell Reports, 2015 |
PubMed
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Towards high-throughput immunomics for infectious diseases: use of next-generation peptide microarrays for rapid discovery and mapping of antigenic determinants
Carmona SJ, Nielsen M, Schafer-Nielsen C, Mucci J, Altcheh J, Balouz V, Tekiel V, Frasch AC, Campetella O, Buscaglia CA, Agüero F
Molecular & Cellular Proteomics, 2015 |
PubMed
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Pan-cancer analysis of genomic scar signatures associated with homologous recombination deficiency suggests novel indications for existing cancer drugs
Marquard AM, Eklund AC, Joshi T, Krzystanek M, Favero F, Wang ZC, Richardson AL, Silver DP, Szallasi Z, Birkbak NJ
Biomarker Research, 2015 |
Biomarker Research
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Thrombocytosis of Liver Metastasis from Colorectal Cancer as Predictive Factor
Jósa V, Krzystanek M, Vass T, Lang T, Juhász V, Szilágyi K, Tihanyi B, Harsányi L, Szállási Z, Salamon F, Baranyai Z
Pathol Oncol Res., 2015 |
PubMed
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Relationship of postoperative thrombocytosis and survival of patients with colorectal cancer
Josa V, Krzystanek M, Eklund AC, Salamon F, Zarand A, Szallasi Z, Baranyai Z
International journal of surgery, 2015 |
PubMed
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Individualization of treatments with drugs metabolized by CES1: combining genetics and metabolomics.
Rasmussen HB, Bjerre D, Linnet K, Jürgens G, Dalhoff K, Stefansson H, Hankemeier T, Kaddurah-Daouk R, Taboureau O, Brunak S, Houmann T, Jeppesen P, Pagsberg AK, Plessen K, Dyrborg J, Hansen PR, Hansen PE, Hughes T, Werge T
Pharmacogenomics, 2015 |
PubMed
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A proteomic study of the regulatory role for STAT-1 in cytokine-induced beta-cell death
Rondas D, Gudmundsdottir V, D\'Hertog W, Crèvecoeur I, Waelkens E, Brunak S, Mathieu C, Overbergh L
Proteomics. Clinical Applications, 2015 |
PubMed
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Transcriptome and genome size analysis of the venus flytrap
Jensen MK, Vogt JK, Bressendorff S, Seguin-Orlando A, Petersen M, Sicheritz-Pontén T, Mundy J
PLoS One, 2015 |
PubMed
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FluKB: A Knowledge-Based System for Influenza Vaccine Target Discovery and Analysis of the Immunological Properties of Influenza Viruses
Simon C, Kudahl UJ, Jing Sun, Olsen LR, Zhang GL, Reinherz EL, Brusic V
Journal of Immunology Research, 2015 |
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Automated benchmarking of peptide-MHC class I binding predictions
Trolle T, Metushi IG, Greenbaum JA, Kim Y, Sidney J, Lund O, Sette A, Peters B, Nielsen M
Bioinformatics, 2015 |
PubMed
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miR-18b overexpression identifies mantle cell lymphoma patients with poor outcome and improves the MIPI-B prognosticator
Husby S, Ralfkiaer U, Garde C, Zandi R, Ek S, Kolstad A, Jerkeman M, Laurell A, Räty R, Pedersen LB, Pedersen A, Ehinger M, Sundström C, Karjalainen-Lindsberg ML, Delabie J, Clasen-Linde E, Brown P, Cowland J, Workman CT, Geisler CH, Grønbæk K
Blood, 2015 |
PubMed
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Establishment and characterization of models of chemotherapy resistance in colorectal cancer: towards a predictive signature of chemoresistance
Jensen NF, Stenvang J, Beck MK, Hana?kova?c B, Belling KC, Do KN, Viuff B, Nygaard SB, Gupta R, Rasmussen MH, Tarpgaard LS, Hansen TP, Budinská E, Pfeiffer P, Bosman F, Tejpar S, Rothi A, Delorenzi M, Andersen CL, Rømer MU, Brünner N, Moreira JMA
Molecular Oncology 9 doi: 10.1016/j.molonc.2015.02.008, 2015 |
PubMed
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Developing a molecular roadmap of drug-food interactions
Jensen K, Ni Y, Panagiotou G, Kouskoumvekaki I
PLoS Computational Biology, 2015 |
PubMed
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Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses.
Zepeda Mendoza ML, Sicheritz-Pontén T, Gilbert MT
Briefings in Bioinformatics, 2015 |
PubMed
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Traces of ATCV-1 associated with laboratory component contamination
Kjartansdóttir KR, Friis-Nielsen J, Asplund M, Mollerup S, Mourier T, Jensen RH, Hansen TA, Rey-Iglesia A, Richter SR, Alquezar-Planas DE, Olsen PV, Vinner L, Fridholm H, Sicheritz-Pontén T, Nielsen LP, Brunak S, Willerslev E, Izarzugaza JM, Hansen AJ
Proceedings of the National Academy of Sciences, 2015 |
PubMed
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PLA2G10 Gene Variants, sPLA2 Activity and Coronary Heart Disease Risk
Guardiola M, Exeter HJ, Perret C, Folkersen L, Van\'t Hooft F, Eriksson P, Franco-Cereceda A, Paulsson-Berne G, Palmen J, Li KW, Cooper JA, Khaw KT, Mallat Z, Ninio E, Karabina SA, Humphries SE, Boekholdt SM, Holmes MV, Talmud PJ
Circ Cardiovasc Genet, 2015 |
PubMed
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Metagenomic heterogeneity explains dual immune effects of endotoxins
Brix S, Eriksen C, Larsen JM, Bisgaard H
J Allergy Clin Immunol., 2015 |
PubMed
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Chronic obstructive pulmonary disease and asthma-associated Proteobacteria, but not commensal Prevotella spp., promote Toll-like receptor 2-independent lung inflammation and pathology.
Larsen JM, Musavian HS, Butt TM, Ingvorsen C, Thysen AH, Brix S
Immunology, 2015 |
PubMed
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Neonates with reduced neonatal lung function have systemic low-grade inflammation.
Chawes BL, Stokholm J, Bønnelykke K, Brix S, Bisgaard H
J Allergy Clin Immunol., 2015 |
PubMed
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Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios
Besenbacher S, Liu S, Izarzugaza JM, Grove J, Belling KC, Bork-Jensen J, Huang S, Als TD, Li S, Yadav R, Rubio-García A, Lescai F, Demontis D, Rao J, Ye W, Mailund T, Friborg RM, Pedersen CN, Xu R, Sun J, Liu H, Wang O, Cheng X, Flores D, Rydza E, Rapacki K, Damm Sørensen J, Chmura P, Westergaard D, Dworzynski P, Sørensen TI, Lund O, Hansen T, Xu X, Li N, Bolund L, Pedersen O, Eiberg H, Krogh A, Børglum AD, Brunak S, Kristiansen K, Schierup MH, Wang J, Gupta R, Villesen P, Rasmussen S
Nature Communications, 2015 |
PubMed
Relevant URL
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Acquisition of docetaxel resistance in breast cancer cells reveals upregulation of ABCB1 expression as a key mediator of resistance accompanied by discrete upregulation of other specific genes and pathways
Hansen SN, Westergaard D, Thomsen MB, Vistesen M, Do KN, Fogh L, Belling KC, Wang J, Yang H, Gupta R, Ditzel HJ, Moreira J, Brünner N, Stenvang J, Schrohl AS
Tumour Biology 36 doi: 10.1007/s13277-015-3072-4, 2015 |
PubMed
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Gene expression analysis identifies global gene dosage sensitivity in cancer
Fehrmann RS, Karjalainen JM, Krajewska M, Westra HJ, Maloney D, Simeonov A, Pers TH, Hirschhorn JN, Jansen RC, Schultes EA, van Haagen HH, de Vries EG, Te Meerman GJ, Wijmenga C, van Vugt MA, Franke L
Nature Genetics, 2015 |
PubMed
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Structural Conservation Despite Huge Sequence Diversity Allows EPCR Binding by the PfEMP1 Family Implicated in Severe Childhood Malaria
Lau CK, Turner L, Jespersen JS, Lowe ED, Petersen B, Wang CW, Petersen JE, Lusingu J, Theander TG, Lavstsen T, Higgins MK
Cell Host & Microbe, 2015 |
PubMed
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2014
Thrombocytosis portends adverse prognostic significance in patients with stage II colorectal carcinoma
Guo T, Krzystanek M, Szallasi Z, Szallasi A
F1000 Research, 2014 |
PubMed
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Cofactory: sequence-based prediction of cofactor specificity of Rossmann folds
Geertz-Hansen HM, Blom N, Feist AM, Brunak S, Petersen TN
Proteins, 2014 |
PubMed
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Annotation of loci from genome-wide association studies using tissue-specific quantitative interaction proteomics
Lundby A, Rossin EJ, Steffensen AB, Acha MR, Newton-Cheh C, Pfeufer A, Lynch SN; QT Interval International GWAS Consortium (QT-IGC), Olesen SP, Brunak S, Ellinor PT, Jukema JW, Trompet S, Ford I, Macfarlane PW, Krijthe BP, Hofman A, Uitterlinden AG, Stricker BH, Nathoe HM, Spiering W, Daly MJ, Asselbergs FW, van der Harst P, Milan DJ, de Bakker PI, Lage K, Olsen JV
Nature Methods, 2014 |
PubMed
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Patient stratification and identification of adverse event correlations in the space of 1190 drug related adverse events
Roitmann E, Eriksson R, Brunak S
Frontiers in Physiology, 2014 |
PubMed
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Discrepancies in listed adverse drug reactions in pharmaceutical product information supplied by the regulatory authorities in Denmark and the USA
Eriksson R, Aagaard L, Jensen LJ, Borisova L, Hørlück D, Brunak S, Hansen EH
Pharmacology Research & Perspectives, 2014 |
PubMed
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Modules, networks and systems medicine for understanding disease and aiding diagnosis
Gustafsson M, Nestor CE, Zhang H, Barabási AL, Baranzini S, Brunak S, Chung KF, Federoff HJ, Gavin AC, Meehan RR, Picotti P, Pujana MÀ, Rajewsky N, Smith KG, Sterk PJ, Villoslada P, Benson M
Genome Medicine, 2014 |
PubMed
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Lineage-specific interface proteins match up the cell cycle and differentiation in embryo stem cells
Re A, Workman CT, Waldron L, Quattrone A, Brunak S
Stem Cell Research, 2014 |
PubMed
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A random set scoring model for prioritization of disease candidate genes using protein complexes and data-mining of GeneRIF, OMIM and PubMed records
Jiang L, Edwards SM, Thomsen B, Workman CT, Guldbrandtsen B, Sørensen P
BMC Bioinformatics, 2014 |
PubMed
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Natural genetic variation impacts expression levels of coding, non-coding, and antisense transcripts in fission yeast
Clément-Ziza M, Marsellach FX, Codlin S, Papadakis MA, Reinhardt S, Rodríguez-López M, Martin S, Marguerat S, Schmidt A, Lee E, Workman CT, Bähler J, Beyer A
Molecular Systems Biology, 2014 |
PubMed
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Transcriptome profiling of brown adipose tissue during cold exposure reveals extensive regulation of glucose metabolism.
Hao Q, Yadav R, Basse AL, Petersen S, Sonne SB, Rasmussen S, Zhu Q, Lu Z, Wang J, Audouze K, Gupta R, Madsen L, Kristiansen K, Hansen JB
The American Journal of Physiology - Endocrinology and Metabolism, 2014 |
PubMed
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Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products
Almeida M, Hébert A, Abraham AL, Rasmussen S, Monnet C, Pons N, Delbès C, Loux V, Batto JM, Leonard P, Kennedy S, Ehrlich SD, Pop M, Montel MC, Irlinger F, Renault P
BMC genomics, 2014 |
PubMed
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Airway Mucosal Immune-Suppression in Neonates of Mothers Receiving A(H1N1)pnd09 Vaccination During Pregnancy.
Bischoff AL, Følsgaard NV, Vissing NH, Birch S, Brix S, Bisgaard H
Pediatr Infect Dis J, 2014 |
PubMed
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Reduced ex vivo stimulated IL-6 response in infants randomized to fish oil from 9 to 18 months, especially among PPARG2 and COX2 wild types
Harsløf LB, Damsgaard CT, Andersen AD, Aakjær DL, Michaelsen KF, Hellgren LI, Frøkiær H, Vogel U, Lauritzen L
Prostaglandins Leukot Essent Fatty Acids, 2014 |
PubMed
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Whole-genome analyses resolve early branches in the tree of life of modern birds
Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY7, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MP, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli KP, O\'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G
Science, 2014 |
PubMed
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The transcriptome of corona radiata cells from individual MII oocytes that after ICSI developed to embryos selected for transfer: PCOS women compared to healthy women
Wissing M, Sonne S, Westergaard D, Nguyen K, Belling KC, Høst T, Mikkelsen A
Journal of Ovarian Research 7:110 doi:10.1186/s13048-014-0110-6, 2014 |
PubMed
Relevant URL
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Hand eczema and stratum corneum ceramides
Jungersted JM, Høgh JK, Hellgren LI, Wilkinson S, Jemec GB, Agner T
Clinical and Experimental Dermatology, 2014 |
PubMed
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Prehistoric genomes reveal the genetic foundation and cost of horse domestication.
Schubert M, Jónsson H, Chang D, Der Sarkissian C, Ermini L, Ginolhac A, Albrechtsen A, Dupanloup I, Foucal A, Petersen B, Fumagalli M, Raghavan M, Seguin-Orlando A, Korneliussen TS, Velazquez AM, Stenderup J, Hoover CA, Rubin CJ, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, MacHugh DE, Kalbfleisch T, MacLeod JN, Rubin EM, Sicheritz-Ponten T, Andersson L, Hofreiter M, Marques-Bonet T, Gilbert MT, Nielsen R, Excoffier L, Willerslev E, Shapiro B, Orlando L
Proceedings of the National Academy of Sciences of the United States of America, 2014 |
PubMed
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Different binding motifs of the celiac disease-associated HLA molecules DQ2.5, DQ2.2, and DQ7.5 revealed by relative quantitative proteomics of endogenous peptide repertoires
Bergseng E, Dørum S, Arntzen MO, Nielsen M, Nygård S, Buus S, de Souza GA, Sollid LM
Immunogenetics, 2014 |
PubMed
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Speciation with gene flow in equids despite extensive chromosomal plasticity
Jónsson H, Schubert M, Seguin-Orlando A, Ginolhac A, Petersen L, Fumagalli M Albrechtsen A, Petersen B, Korneliussen TS, Vilstrup JT, Lear T, Myka JL, Lundquist J, Miller DC, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Stagegaard J, Strauss G, Bertelsen MF, Sicheritz-Ponten T, Antczak DF, Bailey E, Nielsen R, Willerslev E, Orlando L
Proceedings of the National Academy of Sciences, 2014 |
PubMed
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The microbiome of New World vultures
Roggenbuck M, Bærholm Schnell I, Blom N, Bælum J, Bertelsen MF, Pontén TS, Sørensen SJ, Gilbert MT, Graves GR, Hansen LH
Nature Communications, 2014 |
PubMed
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Defining the role of common variation in the genomic and biological architecture of adult human height
Wood AR, Esko T, Yang J, Vedantam S, Pers TH, Gustafsson S, Chu AY, Estrada K, Luan J, Kutalik Z, Amin N, Buchkovich ML, Croteau-Chonka DC, Day FR, Duan Y, Fall T, Fehrmann R, Ferreira T, Jackson AU, Karjalainen J, Lo KS, Locke AE, Mägi R, Mihailov E, Porcu E, Randall JC, Scherag A, Vinkhuyzen AA, Westra HJ, Winkler TW, Workalemahu T, Zhao JH, Absher D, Albrecht E, Anderson D, Baron J, Beekman M, Demirkan A, Ehret GB, Feenstra B, Feitosa MF, Fischer K, Fraser RM, Goel A, Gong J, Justice AE, Kanoni S, Kleber ME, Kristiansson K, Lim U, Lotay V, Lui JC, Mangino M, Mateo Leach I, Medina-Gomez C, Nalls MA, Nyholt DR, Palmer CD, Pasko D, Pechlivanis S, Prokopenko I, Ried JS, Ripke S, Shungin D, Stancáková A, Strawbridge RJ, Sung YJ, Tanaka T, Teumer A, Trompet S, van der Laan SW, van Setten J, Van Vliet-Ostaptchouk JV, Wang Z, Yengo L, Zhang W, Afzal U, Arnlöv J, Arscott GM, Bandinelli S, Barrett A, Bellis C, Bennett AJ, Berne C, Blüher M, Bolton JL, Böttcher Y, Boyd HA, Bruinenberg M, Buckley BM77, Buyske S, Caspersen IH, Chines PS, Clarke R, Claudi-Boehm S, Cooper M, Daw EW, De Jong PA, Deelen J, Delgado G, Denny JC, Dhonukshe-Rutten R, Dimitriou M, Doney AS, Dörr M, Eklund N, Eury E, Folkersen L, Garcia ME, Geller F, Giedraitis V, Go AS, Grallert H, Grammer TB, Gräßler J, Grönberg H, de Groot LC, Groves CJ, Haessler J, Hall P, Haller T, Hallmans G, Hannemann A, Hartman CA, Hassinen M, Hayward C, Heard-Costa NL, Helmer Q, Hemani G, Henders AK, Hillege HL, Hlatky MA, Hoffmann W, Hoffmann P1, Holmen O, Houwing-Duistermaat JJ, Illig T, Isaacs A, James AL, Jeff J, Johansen B, Johansson A, Jolley J, Juliusdottir T, Junttila J, Kho AN, Kinnunen L, Klopp N, Kocher T, et al
Nature Genetics, 2014 |
PubMed
Nature Genetics
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SNPsnap: a Web-based tool for identification and annotation of matched SNPs.
Pers TH, Timshel P, Hirschhorn JN
Bioinformatics, 2014 |
PubMed
Bioinformatics
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A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations
Clemente FJ, Cardona A, Inchley CE, Peter BM, Jacobs G, Pagani L, Lawson DJ, Antão T, Vicente M, Mitt M, DeGiorgio M, Faltyskova Z, Xue Y, Ayub Q, Szpak M, Mägi R, Eriksson A, Manica A, Raghavan M, Rasmussen M, Rasmussen S, Willerslev E, Vidal-Puig A, Tyler-Smith C, Villems R, Nielsen R, Metspalu M, Malyarchuk B, Derenko M, Kivisild T
American Journal of Human Genetics, 2014 |
PubMed
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Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil
Malaspinas AS, Lao O, Schroeder H, Rasmussen M, Raghavan M, Moltke I, Campos PF, Sagredo FS, Rasmussen S, Gonçalves VF, Albrechtsen A, Allentoft ME, Johnson PL, Li M, Reis S, Bernardo DV, DeGiorgio M, Duggan AT, Bastos M, Wang Y, Stenderup J, Moreno-Mayar JV, Brunak S, Sicheritz-Ponten T, Hodges E, Hannon GJ, Orlando L, Price TD, Jensen JD, Nielsen R, Heinemeier J, Olsen J, Rodrigues-Carvalho C, Lahr MM, Neves WA, Kayser M, Higham T, Stoneking M, Pena SD, Willerslev E
Current Biology, 2014 |
PubMed
Relevant URL
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Genome-wide Ancestry Patterns in Rapanui Suggest Pre-European Admixture with Native Americans
Moreno-Mayar JV, Rasmussen S, Seguin-Orlando A, Rasmussen M, Liang M, Flåm ST, Lie BA, Gilfillan GD, Nielsen R, Thorsby E, Willerslev E, Malaspinas AS
Current Biology, 2014 |
PubMed
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Uncovering the Peptide-Binding Specificities of HLA-C: A General Strategy To Determine the Specificity of Any MHC Class I Molecule
Rasmussen M, Harndahl M, Stryhn A, Boucherma R, Nielsen LL, Lemonnier FA, Nielsen M, Buus S
Journal of Immunology, 2014 |
PubMed
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Spatial and temporal diversity in genomic instability processes defines lung cancer evolution
de Bruin EC, McGranahan N, Mitter R, Salm M, Wedge DC, Yates L, Jamal-Hanjani M, Shafi S, Murugaesu N, Rowan AJ, Grönroos E, Muhammad MA, Horswell S, Gerlinger M, Varela I, Jones D, Marshall J, Voet T, Van Loo P, Rassl DM, Rintoul RC, Janes SM, Lee SM, Forster M, Ahmad T, Lawrence D, Falzon M, Capitanio A, Harkins TT, Lee CC, Tom W, Teefe E, Chen SC, Begum S, Rabinowitz A, Phillimore B, Spencer-Dene B, Stamp G, Szallasi Z, Matthews N, Stewart A, Campbell P, Swanton C
Science, 2014 |
PubMed
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Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data
Favero F, Joshi T, Marquard AM, Birkbak NJ, Krzystanek M, Li Q, Szallasi Z, Eklund AC
Annals of Oncology, 2014 |
PubMed
Annals of Oncology
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Whey-reduced weight gain is associated with a temporary growth reduction in young mice fed a high-fat diet
Tranberg B, Madsen AN, Hansen AK, Hellgren LI
Journal of Nutritional Biochemistry, 2014 |
PubMed
Relevant URL
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Hybridization Capture Using Short PCR Products Enriches Small Genomes by Capturing Flanking Sequences (CapFlank)
Tsangaras K, Wales N, Sicheritz-Pontén T, Rasmussen S, Michaux J, Ishida Y, Morand S, Kampmann ML, Gilbert MT, Greenwood AD
PLoS One, 2014 |
PubMed
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M. tuberculosis promotes Th17 expansion via regulation of human dendritic cells towards a high CD14 and low IL-12p70 phenotype that reprograms upon exogenous IFN-γ
Søndergaard JN, Laursen JM, Rosholm LB, Brix S
Int Immunol, 2014 |
PubMed
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Airway Mucosal Immune-Suppression in Neonates of Mothers Receiving A(H1N1)pnd09 Vaccination During Pregnancy
Bischoff AL, Følsgaard NV, Vissing NH, Birch S, Brix S, Bisgaard H
The Pediatric Infectious Disease Journal, 2014 |
PubMed
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Rescue of the highly virulent classical swine fever virus strain
Fahnøe U, Pedersen AG, Risager PC, Nielsen J, Belsham GJ, Höper D, Beer M, Rasmussen TB
Virology, 2014 |
PubMed
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Characterizing the human hematopoietic CDome
Barnkob MS, Simon C, Olsen LR
Frontiers in Genetics, 2014 |
PubMed
Relevant URL
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The Genome of the Chicken DT40 Bursal Lymphoma Cell Line
Molnár J, Póti A, Pipek O, Krzystanek M, Kanu N, Swanton C, Tusnády GE, Szállási Z, Csabai I, Szüts D
G3 (Bethesda), 2014 |
PubMed
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Interpretation of Appearance: The Effect of Facial Features on First Impressions and Personality
Wolffhechel K, Fagertun J, Jacobsen UP, Majewski W, Hemmingsen AS, Larsen CL, Lorentzen SK, Jarmer H
PLoS One, 2014 |
PubMed
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Acid Hydrolysis of Wheat Gluten Induces Formation of New Epitopes but Does Not Enhance Sensitizing Capacity by the Oral Route: A Study in “Gluten Free” Brown Norway Rats
Kroghsbo S, Andersen NB, Rasmussen TF, Jacobsen S, Madsen CB
PLoS One. 2014 Sep 10, 2014 |
PubMed
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Characterization of binding specificities of bovine leucocyte class I molecules: impacts for rational epitope discovery
Hansen AM, Rasmussen M, Svitek N, Harndahl M, Golde WT, Barlow J, Nene V, Buus S, Nielsen M
Immunogenetics, 2014 Sep 4, 2014 |
PubMed
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COPD and asthma-associated Proteobacteria, but not commensal Prevotella spp.,promote TLR2-independent lung inflammation and pathology
Larsen JM, Musavian HS, Butt TM, Ingvorsen C, Thysen AH, Brix S
Immunology. 2014 Sep 1, 2014 |
PubMed
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The genetic prehistory of the New World Arctic.
Raghavan M, DeGiorgio M, Albrechtsen A, Moltke I, Skoglund P, Korneliussen TS, Grønnow B, Appelt M, Gulløv HC, Friesen TM, Fitzhugh W, Malmström H, Rasmussen S, Olsen J, Melchior L, Fuller BT, Fahrni SM, Stafford T Jr, Grimes V, Renouf MA, Cybulski J, Lynnerup N, Lahr MM, Britton K, Knecht R, Arneborg J, Metspalu M, Cornejo OE, Malaspinas AS, Wang Y, Rasmussen M, Raghavan V, Hansen TV, Khusnutdinova E, Pierre T, Dneprovsky K, Andreasen C, Lange H, Hayes MG, Coltrain J, Spitsyn VA, Götherström A, Orlando L, Kivisild T, Villems R, Crawford MH, Nielsen FC, Dissing J, Heinemeier J, Meldgaard M, Bustamante C, O\'Rourke DH, Jakobsson M, Gilbert MT, Nielsen R, Willerslev E
Science. 2014 Aug 29;345(6200):1255832, 2014 |
PubMed
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Development of synchronous VHL syndrome tumors reveals contingencies and constraints to tumor evolution
Fisher R, Horswell S, Rowan A, Salm MP, de Bruin EC, Gulati S, McGranahan N, Stares M, Gerlinger M, Varela I, Crockford A, Favero F, Quidville V, André F, Navas C, Grönroos E, Nicol D, Hazell S, Hrouda D, Brien TO, Matthews N, Phillimore B, Begum S, Rabinowitz A, Biggs J, Bates PA, McDonald NQ, Stamp G, Spencer-Dene B, Hsieh JJ, Xu J, Pickering L, Gore M, Larkin J, Swanton C
Genome Biology 2014 Aug 27;15(8):433., 2014 |
PubMed
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Solid-phase synthesis and biological evaluation of N-dipeptido L-homoserine lactones as quorum sensing activators.
Hansen MR, Le Quement ST, Jakobsen TH, Skovstrup S, Taboureau O, Tolker-Nielsen T, Givskov M, Nielsen TE
Chembiochem. 2014 Feb 10;15(3):460-5. doi: 10.1002/cbic.201300533., 2014 |
PubMed
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Proteome reference maps of the Lotus japonicus nodule and root.
Dam S, Dyrlund TF, Ussatjuk A, Jochimsen B, Nielsen K, Goffard N, Ventosa M, Lorentzen A, Gupta V, Andersen SU, Enghild JJ, Ronson CW, Roepstorff P, Stougaard J
Proteomics. 2014 Feb;14(2-3):230-40., 2014 |
PubMed
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Oxidative stress response pathways: Fission yeast as archetype.
Papadakis MA, Workman CT
Critical Reviews in Microbiology. 2014 Feb 27, 2014 |
PubMed
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RNA-protein interactions: an overview
Re A, Joshi T, Kulberkyte E, Morris Q, Workman CT
Methods in Molecular Biology 2014;1097:491-521., 2014 |
PubMed
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Colony morphology and transcriptome profiling of Pseudomonas putida KT2440 and its mutants deficient in alginate or all EPS synthesis under controlled matric potentials.
Gulez G, Altintas A, Fazli M, Dechesne A, Workman CT, Tolker-Nielsen T, Smets BF
Microbiologyopen. 2014 Jun 10., 2014 |
PubMed
|
Synthetic promoter library for modulation of actinorhodin production in Streptomyces coelicolor A3(2).
Sohoni SV, Fazio A, Workman CT, Mijakovic I, Lantz AE
PLoS One. 2014 Jun 25;9(6):e99701, 2014 |
PubMed
|
Lysine deacetylase inhibition prevents diabetes by chromatin-independent immunoregulation and β-cell protection.
Christensen DP, Gysemans C, Lundh M, Dahllöf MS, Noesgaard D, Schmidt SF, Mandrup S, Birkbak N, Workman CT, Piemonti L, Blaabjerg L, Monzani V, Fossati G, Mascagni P, Paraskevas S, Aikin RA, Billestrup N, Grunnet LG, Dinarello CA, Mathieu C, Mandrup-Poulsen T
PNAS, Proceedings of the National Academy of Sciences 2014 Jan 21;111(3):1055-9., 2014 |
PubMed
|
STAT3 induction of miR-146b forms a feedback loop to inhibit the NF-κB to IL-6 signaling axis and STAT3-driven cancer phenotypes
Xiang M, Birkbak NJ, Vafaizadeh V, Walker SR, Yeh JE, Liu S, Kroll Y, Boldin M, Taganov K, Groner B, Richardson AL, Frank DA
Science Signaling. 2014 Jan 28;7(310):ra11, 2014 |
PubMed
|
An elevated pro-inflammatory cytokine profile in multiple chemical sensitivity.
Dantoft TM, Elberling J, Brix S, Szecsi PB, Vesterhauge S, Skovbjerg S
Psychoneuroendocrinology. 2014 Feb;40:140-50., 2014 |
PubMed
|
Multiparametric bioinformatics distinguish the CD4/CD8 ratio as a suitable laboratory predictor of combined T cell pathogenesis in HIV infection.
Buggert M, Frederiksen J, Noyan K, Svärd J, Barqasho B, Sönnerborg A, Lund O, Nowak P, Karlsson AC
Journal of Immunology 2014 Mar 1;192(5):2099-108., 2014 |
PubMed
|
Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica.
Leekitcharoenphon P, Nielsen EM, Kaas RS, Lund O, Aarestrup FM
PLoS One. 2014 Feb 4;9(2):e87991., 2014 |
PubMed
|
Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli.
Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, Aarestrup FM
Journal of Clinical Microbiology. 2014 May;52(5):1501-10, 2014 |
PubMed
|
In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing
Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O, Villa L, Møller Aarestrup F, Hasman H
Antimicrobial Agents and Chemotherapy. 2014 Jul;58(7):3895-903., 2014 |
PubMed
|
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.
Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto JM, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Doré J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Léonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sørensen S, Tap J, Tims S, Ussery DW, Yamada T, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD, MetaHIT Consortium
Nature Biotechnology. 2014 Jul 6., 2014 |
PubMed
|
T-bet and Eomes Are Differentially Linked to the Exhausted Phenotype of CD8+ T Cells in HIV Infection
Buggert M, Tauriainen J, Yamamoto T, Frederiksen J, Ivarsson MA, Michaëlsson J, Lund O, Hejdeman B, Jansson M, Sönnerborg A, Koup RA, Betts MR, Karlsson AC
PLoS Pathogens 2014 Jul 17;10(7):e1004251, 2014 |
PubMed
|
NetFCM: A semi-automated web-based method for flow cytometry data analysis
Frederiksen J, Buggert M, Karlsson AC, Lund O
Cytometry A. 2014 Jul 18., 2014 |
PubMed
|
Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms.
Kaas RS, Leekitcharoenphon P, Aarestrup FM, Lund O
PLoS One. 2014 Aug 11;9(8):e104984, 2014 |
PubMed
|
Acute and perinatal-programming effects of a fat-rich diet on rat muscle mitochondrial function and hepatic lipid accumulation.
Hellgren LI, Jensen RI, Waterstradt MS, Quistorff B, Lauritzen L
Acta Obstetricia et Gynecologica Scandinavica . 2014 Jul 22., 2014 |
PubMed
|
Natural mannosylation of HIV-1 gp120 imposes no immunoregulatory effects in primary human plasmacytoid dendritic cells
Søndergaard JN, Vinner L, Brix S
Molecular Immunology 2014 Jun;59(2):180-7., 2014 |
PubMed
|
NetMHCstab - predicting stability of peptide-MHC-I complexes; impacts for cytotoxic T lymphocyte epitope discovery
Jørgensen KW, Rasmussen M, Buus S, Nielsen M
Immunology. 2014 Jan;141(1):18-26., 2014 |
PubMed
|
Temporal disease trajectories condensed from population-wide registry data covering 6.2 million patients
Jensen AB1, Moseley PL2, Oprea TI3, Ellesøe SG4, Eriksson R1, Schmock H5, Jensen PB4, Jensen LJ4, Brunak S1
Nature Communication. 2014 Jun 24;5:4022., 2014 |
PubMed
|
An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.
Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, Dechene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D Jr, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, de Bakker PI, Duzkale H, Dworzy Ski P, Fairbrother W, Francioli L, Funke BH, Giovanni MA, Handsaker RE, Lage K, Lebo MS, Lek M, Leshchiner I, Macarthur DG, McLaughlin HM, Murray MF, Pers TH, Polak PP, Raychaudhuri S, Rehm HL, Soemedi R, Stitziel NO, Vestecka S, Supper J, Gugenmus C, Klocke B, Hahn A, Schubach M, Menzel M, Biskup S, Freisinger P, Deng M, Braun M, Perner S, Smith RJ, Andorf JL, Huang J, Ryckman K, Sheffield VC, Stone EM, Bair T, Black-Ziegelbein EA, Braun TA, Darbro B, Deluca AP, Kolbe DL, Scheetz TE, Shearer AE, Sompallae R, Wang K, Bassuk AG, Edens E, Mathews K, Moore SA, Shchelochkov OA, Trapane P, Bossler A, Campbell CA, Heusel JW, Kwitek A, Maga T, Panzer K, Wassink T, Van Daele D, Azaiez H, Booth K, Meyer N, Segal MM, Williams MS, Tromp G, White P, Corsmeier D, Fitzgerald-Butt S, Herman G, Lamb-Thrush D, McBride KL, Newsom D, Pierson CR, Rakowsky AT, Maver A, Lovre IL, Palanda IA, Peterlin B, Torkamani A, Wedell A, Huss M, Alexeyenko A, Lindvall JM, Magnusson M, Nilsson D, Stranneheim H, Taylan F, Gilissen C, Hoischen A, van Bon B, Yntema H, Nelen M, Zhang W, Sager J, Zhang L, Blair K, Kural D, Cariaso M, Lennon GG, Javed A, Agrawal S, Ng PC, Sandhu KS, Krishna S, Veeramachaneni V, Isakov O, Halperin E, Friedman E, Shomron N, Glusman G, Roach JC, Caballero J, Cox HC, Mauldin D, Ament SA, Rowen L, Richards DR, Lucas FA, Gonzalez-Garay ML, Caskey CT, Bai Y, Huang Y, Fang F, Zhang Y, Wang Z, Barrera J, Garcia-Lobo JM, González-Lamuño D, Llorca J, Rodriguez MC, Varela I, Reese MG, De La Vega FM, Kiruluta E, Cargill M, Hart RK, Sorenson JM, Lyon GJ, Stevenson DA, Bray BE, Moore BM, Eilbeck K, Yandell M, Zhao H, Hou L, Chen X, Yan X, Chen M, Li C, Yang C, Gunel M, Li
Genome Biology. 2014 Mar 25;15(3):R53, 2014 |
PubMed
|
Biological insights from 108 schizophrenia-associated genetic loci.
Ripke S, Neale BM, Corvin A, Walters JT, Farh KH, Holmans PA, Lee P, Bulik-Sullivan B, Collier DA, Huang H, Pers TH, Agartz I, Agerbo E, Albus M, Alexander M, Amin F, Bacanu SA, Begemann M, Belliveau RA Jr, Bene J, Bergen SE, Bevilacqua E, Bigdeli TB, Black DW, Bruggeman R, Buccola NG, Buckner RL, Byerley W, Cahn W, Cai G, Campion D, Cantor RM, Carr VJ, Carrera N, Catts SV, Chambert KD, Chan RC, Chen RY, Chen EY, Cheng W, Cheung EF, Chong SA, Cloninger CR, Cohen D, Cohen N, Cormican P, Craddock N, Crowley JJ, Curtis D, Davidson M, Davis KL, Degenhardt F, Del Favero J, Demontis D, Dikeos D, Dinan T, Djurovic S, Donohoe G, Drapeau E, Duan J, Dudbridge F, Durmishi N, Eichhammer P, Eriksson J, Escott-Price V, Essioux L, Fanous AH, Farrell MS, Frank J, Franke L, Freedman R, Freimer NB, Friedl M, Friedman JI, Fromer M, Genovese G, Georgieva L, Giegling I, Giusti-Rodríguez P, Godard S, Goldstein JI, Golimbet V, Gopal S, Gratten J, de Haan L, Hammer C, Hamshere ML, Hansen M, Hansen T, Haroutunian V, Hartmann AM, Henskens FA, Herms S, Hirschhorn JN, Hoffmann P, Hofman A, Hollegaard MV, Hougaard DM, Ikeda M, Joa I, Julià A, Kahn RS, Kalaydjieva L, Karachanak-Yankova S, Karjalainen J, Kavanagh D, Keller MC, Kennedy JL, Khrunin A, Kim Y, Klovins J, Knowles JA, Konte B, Kucinskas V, Ausrele Kucinskiene Z, Kuzelova-Ptackova H, Kähler AK, Laurent C, Keong JL, Lee SH, Legge SE, Lerer B, Li M, Li T, Liang KY, Lieberman J, Limborska S, Loughland CM, Lubinski J, Lönnqvist J, Macek M Jr, Magnusson PK, Maher BS, Maier W, Mallet J, Marsal S, Mattheisen M, Mattingsdal M, McCarley RW, McDonald C, McIntosh AM, Meier S, Meijer CJ, Melegh B, Melle I, Mesholam-Gately RI, Metspalu A, Michie PT, Milani L, Milanova V, Mokrab Y, Morris DW, Mors O, Murphy KC, Murray RM, Myin-Germeys I, Müller-Myhsok B, Nelis M, Nenadic I, Nertney DA, Nestadt G, Nicodemus KK, Nikitina-Zake L, Nisenbaum L, Nordin A, O\'Callaghan E, O\'Dushlaine C, O\'Neill FA, Oh SY, Olincy A, Olsen L, Van Os J, Pantelis C, Papadimit
Nature. 2014 Jul 24;511(7510):421-7., 2014 |
PubMed
|
Genome-wide association analyses identify variants in developmental genes associated with hypospadias.
Geller F, Feenstra B, Carstensen L, Pers TH, van Rooij IA, Körberg IB, Choudhry S, Karjalainen JM, Schnack TH, Hollegaard MV, Feitz WF, Roeleveld N, Hougaard DM, Hirschhorn JN, Franke L, Baskin LS, Nordenskjöld A, van der Zanden LF, Melbye M
Nature Genetics. 2014 Aug 10., 2014 |
PubMed
|
Tracking Genomic Cancer Evolution for Precision Medicine: The Lung TRACERx Study.
Jamal-Hanjani M, Hackshaw A, Ngai Y, Shaw J, Dive C, Quezada S, Middleton G, de Bruin E, Le Quesne J, Shafi S, Falzon M, Horswell S, Blackhall F, Khan I, Janes S, Nicolson M, Lawrence D, Forster M, Fennell D, Lee SM, Lester J, Kerr K, Muller S, Iles N, Smith S, Murugaesu N, Mitter R, Salm M, Stuart A, Matthews N, Adams H, Ahmad T, Attanoos R, Bennett J, Birkbak NJ, Booton R, Brady G, Buchan K, Capitano A, Chetty M, Cobbold M, Crosbie P, Davies H, Denison A, Djearman M, Goldman J, Haswell T, Joseph L, Kornaszewska M, Krebs M, Langman G, MacKenzie M, Millar J, Morgan B, Naidu B, Nonaka D, Peggs K, Pritchard C, Remmen H, Rowan A, Shah R, Smith E, Summers Y, Taylor M, Veeriah S, Waller D, Wilcox B, Wilcox M, Woolhouse I, McGranahan N, Swanton C
PLoS Biology. 2014 Jul 8;12(7):e1001906, 2014 |
PubMed
|
Enhancing Reproducibility in Cancer Drug Screening: How Do We Move Forward?
Hatzis C, Bedard PL, Birkbak NJ, Beck AH, Aerts HJ, Stern DF, Shi L, Clarke R, Quackenbush J, Haibe-Kains B
Cancer Research. 2014 Aug 1;74(15):4016-4023, 2014 |
PubMed
|
Systematic Evaluation of the Prognostic Impact and Intratumour Heterogeneity of Clear Cell Renal Cell Carcinoma Biomarkers.
Gulati S, Martinez P, Joshi T, Birkbak NJ, Santos CR, Rowan AJ, Pickering L, Gore M, Larkin J, Szallasi Z, Bates PA, Swanton C, Gerlinger M
European Urology. 2014 Jul 18. pii: S0302-2838(14)00627-7., 2014 |
PubMed
|
Genomic profiling of thousands of candidate polymorphisms predicts risk of relapse in 778 Danish and German childhood acute lymphoblastic leukemia patients.
Wesolowska A, Borst L, Dalgaard MD, Yadav R, Rasmussen KK, Wehner PS, Rasmussen M, Orntoft TF, Nordentoft I, Koehler R, Bartram CR, Schrappe M, Sicheritz-Ponten T, Gautier L, Marquart H, Madsen HO, Brunak S, Stanulla M, Gupta R, Schmiegelow K
Leukemia. 2014 Jul 3., 2014 |
PubMed
|
Discovery of biomarkers for glycaemic deterioration before and after the onset of type 2 diabetes: rationale and design of the epidemiological studies within the IMI DIRECT Consortium.
Koivula RW, Heggie A, Barnett A, Cederberg H, Hansen TH, Koopman AD, Ridderstråle M, Rutters F, Vestergaard H, Gupta R, Herrgård S, Heymans MW, Perry MH, Rauh S, Siloaho M, Teare HJ, Thorand B, Bell J, Brunak S, Frost G, Jablonka B, Mari A, McDonald TJ, Dekker JM, Hansen T, Hattersley A, Laakso M, Pedersen O, Koivisto V, Ruetten H, Walker M, Pearson E, Franks PW; DIRECT Consortium
Diabetologia. 2014 Jun;57(6):1132-42., 2014 |
PubMed
|
Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis.
Wesolowska A, Bahl MI, Carvalho V, Kristiansen K, Sicheritz-Pontén T, Gupta R, Licht TR
Microbiome. 2014 Jun 5;2:19, 2014 |
PubMed
|
NutriChem: a systems chemical biology resource to explore the medicinal value of plant-based foods
Jensen K, Panagiotou G, Kouskoumvekaki I
Nucleic Acids Research, Database issue, 2014 |
Nucleic Acids Research
|
MR1-restricted MAIT cells display ligand discrimination and pathogen selectivity through distinct T cell receptor usage
Gold MC, McLaren JE, Reistetter JA, Smyk-Pearson S, Ladell K, Swarbrick GM, Yu YY, Hansen TH, Lund O, Nielsen M, Gerritsen B, Kesmir C, Miles JJ, Lewinsohn DA, Price DA, Lewinsohn DM
Journal of Experimental Medicine. 2014 Jul 28;211(8):1601-10., 2014 |
PubMed
|
An integrated catalog of reference genes in the human gut microbiome
Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T, Juncker AS, Manichanh C, Chen B, Zhang W, Levenez F, Wang J, Xu X, Xiao L, Liang S, Zhang D, Zhang Z, Chen W, Zhao H, Al-Aama JY, Edris S, Yang H, Wang J, Hansen T, Nielsen HB, Brunak S, Kristiansen K, Guarner F, Pedersen O, Doré J, Ehrlich SD, Bork P, Wang J
Nature Biotechnology. 2014 Jul 6, 2014 |
PubMed
|
Improving Biotech Education through Gamified Laboritory Simulations.
Bonde M, Makransky G, Wandall J, Larsen MV, Morsing M, Jarmer H & Sommer M
Nature Biotechnology. 2014 Jul 8;32(7):694-7., 2014 |
PubMed
|
Exploring Mechanisms of Diet-Colon Cancer Associations through Candidate Molecular Interaction Networks.
Westergaard D, Li J, Jensen K, Kouskoumvekaki I, Panagiotou G
BMC Genomics. 2014 May 17;15:380, 2014 |
PubMed
|
NetTepi: an integrated method for the prediction of T cell epitopes
Trolle T, Nielsen M
Immunogenetics. 2014 Aug;66(7-8):449-56., 2014 |
PubMed
|
LocTree3 prediction of localization.
Goldberg T, Hecht M, Hamp T, Karl T, Yachdav G, Ahmed N, Altermann U, Angerer P, Ansorge S, Balasz K, Bernhofer M, Betz A, Cizmadija L, Do KT, Gerke J, Greil R, Joerdens V, Hastreiter M, Hembach K, Herzog M, Kalemanov M, Kluge M, Meier A, Nasir H, Neumaier U, Prade V, Reeb J, Sorokoumov A, Troshani I, Vorberg S, Waldraff S, Zierer J, Nielsen H, Rost B
Nucleic Acids Research. 2014 Jul;42(Web Server issue):W350-5., 2014 |
PubMed
|
A DNA binding-site landscape and regulatory network analysis for the family of NAC stress response transcription factors in Arabidopsis thaliana.
Lindemose S, Jensen KM, Van de Velde Jan, O’Shea C, Heyndrickx KS, Workman CT, Vandepoele Klaas, Skriver K, De Masi F
Nucleic Acids Research. 2014 Aug 1;42(12):7681-93., 2014 |
PubMed
|
KinomeXplorer: an integrated platform for kinome biology studies
Horn H, Schoof EM, Kim J, Robin X, Miller ML, Diella F, Palma A, Cesareni G, Jensen LJ, Linding R
Nature Methods. 2014 Jun;11(6):603-4., 2014 |
PubMed
|
Software-supported USER cloning strategies for site-directed mutagenesis and DNA assembly
Genee HJ, Bonde MT, Bagger FO, Jespersen JB, Sommer MOA, Wernersson R, Olsen LR
ACS Synthetic Biology . 2014 May 9., 2014 |
PubMed
|
Use of \"one-pot, mix-and-read\" peptide-MHC class I tetramers and predictive algorithms to improve detection of cytotoxic T lymphocyte responses in cattle.
Svitek N, Hansen AM, Steinaa L, Saya R, Awino E, Nielsen M, Buus S, Nene V
Veterinary Research. 2014 Apr 28;45:50., 2014 |
PubMed
|
Identification and HLA-Tetramer-Validation of Human CD4+ and CD8+ T Cell Responses against HCMV Proteins IE1 and IE2.
Braendstrup P, Mortensen BK, Justesen S, Osterby T, Rasmussen M, Hansen AM, Christiansen CB, Hansen MB, Nielsen M, Vindeløv L, Buus S, Stryhn A
PLoS One. 2014 Apr 23;9(4):e94892., 2014 |
PubMed
|
Identification of odorant-receptor interactions by global mapping of the human odorome.
Audouze K, Tromelin A, Le Bon AM, Belloir C, Petersen RK, Kristiansen K, Brunak S, Taboureau O
PLoS One. 2014 Apr 2;9(4):e93037., 2014 |
PubMed
|
Towards in vivo regulon kinetics: PurR activation by PRPP during purine depletion in Lactococcus lactis
Jendresen CB, Dimitrov P, Gautier L, Lui M, Martinussen J, Kilstrup M
Microbiology. 2014 Jul;160(Pt 7):1321-31, 2014 |
PubMed
|
Children with asthma by school age display aberrant immune responses to pathogenic airway bacteria as infants.
Larsen JM, Brix S, Thysen AH, Birch S, Rasmussen MA, Bisgaard H
Journal of Allergy and Clinical Immunology. 2014 Apr;133(4):1008-13, 2014 |
PubMed
|
Lactate dehydrogenase as a selection criterion for ipilimumab treatment in metastatic melanoma
Kelderman S, Heemskerk B, van Tinteren H, van den Brom RR, Hospers GA, van den Eertwegh AJ, Kapiteijn EW, de Groot JW, Soetekouw P, Jansen RL, Fiets E, Furness AJ, Renn A, Krzystanek M, Szallasi Z, Lorigan P, Gore ME, Schumacher TN, Haanen JB, Larkin JM, Blank CU
Cancer Immunology, Immunotherapy . 2014 May;63(5):449-58., 2014 |
PubMed
|
Polychlorinated dibenzo-p-dioxins, furans, and biphenyls (PCDDs/PCDFs and PCBs) in breast milk and early childhood growth and IGF1.
Wohlfahrt-Veje C, Audouze K, Brunak S, Antignac JP, le Bizec B, Juul A, Skakkebæk NE, Main KM
Reproduction. 2014 Mar 2;147(4):391-9., 2014 |
PubMed
|
Benchmarking of Methods for Genomic Taxonomy.
Larsen MV, Cosentino S, Lukjancenko O, Saputra D, Rasmussen S, Hasman H, Sicheritz-Pontén T, Aarestrup FM, Ussery DW, Lund O
Journal of Clinical Microbiology. 2014 May;52(5):1529-39., 2014 |
PubMed
|
Applying the ResFinder and VirulenceFinder web-services for easy identification of acquired antibiotic resistance and E. coli virulence genes in bacteriophage and prophage nucleotide sequences.
Kleinheinz KA, Joensen KG, Larsen MV
Bacteriophage. 2014 Jan 1;4(1):e27943., 2014 |
PubMed
|
Applicability of computational systems biology in toxicology.
Kongsbak K, Hadrup N, Audouze K, Vinggaard AM
Basic & Clinical Pharmacology & Toxicology . 2014 Jul;115(1):45-9., 2014 |
PubMed
|
Host genome variations and risk of infections during induction treatment for childhood acute lymphoblastic leukaemia.
Lund B, Wesolowska A, Lausen B, Borst L, Rasmussen KK, Müller K, Klungland H, Gupta R, Schmiegelow K
European Journal of Haematology. 2014 Apr;92(4):321-30., 2014 |
PubMed
|
Archival Bone Marrow Samples: Suitable for Multiple Biomarker Analysis?
Lund B, Wesolowska A, Lausen B, Borst L, Rasmussen KK, Müller K, Klungland H, Gupta R, Schmiegelow K
Diagnostic Molecular Pathology . 2014 Jan 30., 2014 |
PubMed
|
The genome of a Late Pleistocene human from a Clovis burial site in western Montana.
Rasmussen M, Anzick SL, Waters MR, Skoglund P, DeGiorgio M, Stafford TW Jr, Rasmussen S, Moltke I, Albrechtsen A, Doyle SM, Poznik GD, Gudmundsdottir V, Yadav R, Malaspinas AS, White SS 5th, Allentoft ME, Cornejo OE, Tambets K, Eriksson A, Heintzman PD, Karmin M, Korneliussen TS, Meltzer DJ, Pierre TL, Stenderup J, Saag L, Warmuth VM, Lopes MC, Malhi RS, Brunak S, Sicheritz-Ponten T, Barnes I, Collins M, Orlando L, Balloux F, Manica A, Gupta R, Metspalu M, Bustamante CD, Jakobsson M, Nielsen R, Willerslev E
Nature. 2014 Feb 13;506(7487):225-9., 2014 |
PubMed
|
Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European.
Olalde I, Allentoft ME, Sánchez-Quinto F, Santpere G, Chiang CW, DeGiorgio M, Prado-Martinez J, Rodríguez JA, Rasmussen S, Quilez J, Ramírez O, Marigorta UM, Fernández-Callejo M, Prada ME, Encinas JM, Nielsen R, Netea MG, Novembre J, Sturm RA, Sabeti P, Marquès-Bonet T, Navarro A, Willerslev E, Lalueza-Fox C
Nature. 2014 Mar 13;507(7491):225-8, 2014 |
PubMed
|
Improved pan-specific MHC class I peptide-binding predictions using a novel representation of the MHC-binding cleft environment.
Carrasco Pro S, Zimic M, Nielsen M
Tissue Antigens. 2014 Feb;83(2):94-100., 2014 |
PubMed
|
Tolerance of Whole-Genome Doubling Propagates Chromosomal Instability and Accelerates Cancer Genome Evolution
Dewhurst SM, McGranahan N, Burrell RA, Rowan AJ, Grönroos E, Endesfelder D, Joshi T, Mouradov D, Gibbs P, Ward RL, Hawkins NJ, Szallasi Z, Sieber OM, Swanton C
Cancer Discovery. 2014 Feb;4(2):175-85., 2014 |
PubMed
|
Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions.
Kim Y, Sidney J, Buus S, Sette A, Nielsen M, Peters B
BMC Bioinformatics, 2014 |
PubMed
|
Bacterial diversity in snow on North Pole ice floes.
Hauptmann AL, Stibal M, Bælum J, Sicheritz-Pontén T, Brunak S, Bowman JS, Hansen LH, Jacobsen CS, Blom N
Extremophiles. 2014 Jun 21, 2014 |
PubMed
Springer Link
|
Prenatal undernutrition and postnatal overnutrition are associated with permanent changes in hepatic metabolism markers and fatty acid composition in sheep.
Hou L, Hellgren LI, Kongsted AH, Vaag A, Nielsen MO
Acta Physiologica, 2014 |
PubMed
|
Effects of pregnancy on obesity-induced inflammation in a mouse model of fetal programming.
Ingvorsen C, Thysen AH, Fernandez-Twinn DS, Nordby P, Nielsen KF, Ozanne SE, Brix S, Hellgren LI
Nature - International Journal of Obesity, 2014 |
PubMed
|
Effects on metabolic markers are modified by PPARG2 and COX2 polymorphisms in infants randomized to fish oil.
Harslof LB, Damsgaard CT, Hellgren LI, Andersen AD, Vogel U, Lauritzen L
Genes & Nutrition 9(3):396 doi:10.1007/s12263-014-0396-4, 2014 |
PubMed
|
Large-scale analysis of B-cell epitopes on influenza virus hemagglutinin – implications for cross-reactivity of neutralizing antibodies
Sun J, Kudahl UJ, Simon C, Cao Z, Reinherz EL, Brusic V
Frontiers In Immunology, 2014 |
PubMed
|
Integrated Text Mining and Chemoinformatics Analysis Associates Diet to Health Benefit at Molecular Level
Jensen K, Panagiotou G, Kouskoumvekaki I
PLOS Computational Biology, 2014 |
Relevant URL
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A genome-wide association study identifies CDHR3 as a susceptibility locus for early childhood asthma with severe exacerbations.
Bønnelykke K, Sleiman P, Nielsen K, Kreiner-Møller E, Mercader JM, Belgrave D, den Dekker HT, Husby A, Sevelsted A, Faura-Tellez G, Mortensen LJ, Paternoster L, Flaaten R, Mølgaard A, Smart DE, Thomsen PF, Rasmussen MA, Bonàs-Guarch S, Holst C, Nohr EA, Yadav R, March ME, Blicher T, Lackie PM, Jaddoe VW, Simpson A, Holloway JW, Duijts L, Custovic A, Davies DE, Torrents D, Gupta R, Hollegaard MV, Hougaard DM, Hakonarson H, Bisgaard H
Nature Genetics. 46(1):51-5 doi:10.1038/ng.2830, 2014 |
PubMed
|
2013
Detection of serological biomarkers by proximity extension assay for detection of colorectal neoplasias in symptomatic individuals
Thorsen SB, Lundberg M, Villablanca A, Christensen SL, Belling KC, Nielsen BS, Knowles M, Gee N, Nielsen HJ, Brünner N, Christensen IJ, Fredriksson S, Stenvang J, Assarsson E
Journal of Translational Medicine 11:253 doi:10.1186/1479-5876-11-253, 2013 |
PubMed
Relevant URL
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Evaluation of thrombocytosis as predictive factor in colorectal cancer
Baranyai Z, Jósa V, Krzystanek M, Eklund AC, Szász AM, Szállási Z
Magyar Sebészet (Hungarian Journal of Surgery), 2013 |
PubMed
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Personalized network-based treatments in oncology.
Robin X, Creixell P, Radetskaya O, Santini CC, Longden J, Linding R
Nature Clinical Pharmacology & Therapeutics . 2013 Dec;94(6):646-50., 2013 |
PubMed
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The SH2 domain interaction landscape.
Tinti M, Kiemer L, Costa S, Miller ML, Sacco F, Olsen JV, Carducci M, Paoluzi S, Langone F, Workman CT, Blom N, Machida K, Thompson CM, Schutkowski M, Brunak S, Mann M, Mayer BJ, Castagnoli L, Cesareni G
Cell Reports. 2013 Apr 25;3(4):1293-305., 2013 |
PubMed
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Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing.
Zankari E, Hasman H, Kaas RS, Seyfarth AM, Agersø Y, Lund O, Larsen MV, Aarestrup FM
Journal of Antimicrobial Chemotherapy. 2013 Apr;68(4):771-7., 2013 |
PubMed
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PathogenFinder--distinguishing friend from foe using bacterial whole genome sequence data
Cosentino S, Voldby Larsen M, Møller Aarestrup F, Lund O
PLoS One. 2013 Oct 28;8(10):e77302., 2013 |
PubMed
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Low-bandwidth and non-compute intensive remote identification of microbes from raw sequencing reads.
Gautier L, Lund O
PLoS One. 2013 Dec 31;8(12):e83784, 2013 |
PubMed
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DNA secondary structures are associated with recombination in major Plasmodium falciparum variable surface antigen gene families
Sander AF, Lavstsen T, Rask TS, Lisby M, Salanti A, Fordyce SL, Jespersen JS, Carter R, Deitsch KW, Theander TG, Pedersen AG, Arnot DE
Nucleic Acids Research, 2013 |
PubMed
Relevant URL
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BlockLogo: Visualization of peptide and sequence motif conservation
Olsen LR, Kudahl UJ, Simon C, Sun J, Schönbach C, Reinherz EL, Zhang GL, Brusic V
Journal of Immunological Methods :37-44 doi:10.1016/j.jim.2013.08.014, 2013 |
PubMed
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Targeting of conserved gag-epitopes in early HIV infection is associated with lower plasma viral load and slower CD4(+) T cell depletion.
Perez CL, Milush JM, Buggert M, Eriksson EM, Larsen MV, Liegler T, Hartogensis W, Bacchetti P, Lund O, Hecht FM, Nixon DF, Karlsson AC
AIDS Research and Human Retroviruses 29(3):602-12 doi:10.1089/AID.2012.0171, 2013 |
PubMed
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Rapid whole genome sequencing for the detection and characterization of microorganisms directly from clinical samples.
Hasman H, Saputra D, Sicheritz-Ponten T, Lund O, Svendsen CA, Frimodt-Møller N, Aarestrup FM
Journal of Clinical Microbiology. 52(1):139-46 doi:10.1128/JCM.02452-13, 2013 |
PubMed
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Adipose tissue trans-fatty acids and changes in body weight and waist circumference.
Hansen CP, Berentzen TL, Ostergaard JN, Dahm CC, Hellgren LI, Schmidt EB, Tjønneland A, Sørensen TI, Overvad K, Jakobsen MU
British Journal of Nutrition 111(7):1283-91 doi:10.1017/S0007114513003747, 2013 |
PubMed
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Epithelial entry rather than the ensuing systemic immune response determines the pathogenicity of two Salmonella enterica serovar Typhimurium strains in a mouse model.
Brandt R, Petersen A, Brix S, Licht TR, Frøkiær H
Microbes and Infection 15(13):911-9 doi:10.1016/j.micinf.2013.08.004, 2013 |
PubMed
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Complete genes may pass from food to human blood
Spisák S, Solymosi N, Ittzés P, Bodor A, Kondor D, Vattay G, Barták BK, Sipos F, Galamb O, Tulassay Z, Szallasi Z, Rasmussen S, Sicheritz-Ponten T, Brunak S, Molnar B, Csabai I
PLoS ONE 8(7):e69805 doi:10.1371/journal.pone.0069805, 2013 |
PubMed
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wKinMut: An integrated tool for the analysis and interpretation of mutations in human protein kinases
Izarzugaza JMG, Vazquez M, Pozo A, Valencia A
BMC Bioinformatics 2013, 14:345, 2013 |
BMC Bioinformatics - biomedcentral
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Deep phenotyping of the unselected COPSAC2010 birth cohort study.
Bisgaard H, Vissing NH, Carson CG, Bischoff AL, Følsgaard NV, Kreiner-Møller E, Chawes BL, Stokholm J, Pedersen L, Bjarnadóttir E, Thysen AH, Nilsson E, Mortensen LJ, Olsen SF, Schjørring S, Krogfelt KA, Lauritzen L, Brix S, Bønnelykke K
Clinical & Experimental Allergy 43(12):1384-94 doi:10.1111/cea.12213, 2013 |
PubMed
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The comparison of thrombocytosis and platelet-lymphocyte ratio as potential prognostic markers in colorectal cancer
Baranyai Z, Krzystanek M, Jósa V, Dede K, Ágoston E, Szász AM, Sinkó D, Szarvas V, Salamon F, Eklund AC, Szallasi Z, Jakab F
Thrombosis and Haemostasis, 2013 |
Schattauer
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Computational optimisation of targeted DNA sequencing for cancer detection
Martinez P, McGranahan N, Birkbak NJ, Gerlinger M, Swanton C
Scientific Reports 3:3309 doi:10.1038/srep03309, 2013 |
PubMed
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Inconsistency in large pharmacogenomic studies
Haibe-Kains B, El-Hachem N, Birkbak NJ, Jin AC, Beck AH, Aerts HJWL, Quackenbush J
Nature (2013/11/27 ) doi:10.1038/nature12831, 2013 |
Nature
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Whole-Exome Sequencing of 2,000 Danish Individuals and the Role of Rare Coding Variants in Type 2 Diabetes
Lohmueller KE, Sparsø T, Li Q, Andersson E, Korneliussen T, Albrechtsen A, Banasik K, Grarup N, Hallgrimsdottir I, Kiil K, Kilpeläinen TO, Krarup NT, Pers TH, Sanchez G, Hu Y, DeGiorgio M, Jørgensen T, Sandbæk A, Lauritzen T, Brunak S, Kristiansen K, Li Y, Hansen T, Wang J, Nielsen R, Pedersen O
AJHG, The American Journal of Human Genetics - Cell, 2013 |
PubMed
AJHG
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Bacterial natural transformation by highly fragmented and damaged DNA
Overballe-Petersen S, Harms K, Orlando LA, Mayar JV, Rasmussen S, Dahl TW, Rosing MT, Poole AM, Sicheritz-Ponten T, Brunak S, Inselmann S, de Vries J, Wackernagel W, Pybus OG, Nielsen R, Johnsen PJ, Nielsen KM, Willerslev E
PNAS, Proceedings of the National Academy of Sciences U.S.A. 110(49):19860-5 doi:10.1073/pnas.1315278110, 2013 |
PubMed
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Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans
Raghavan M, Skoglund P, Graf KE, Metspalu M, Albrechtsen A, Moltke I, Rasmussen S, Stafford Jr TW, Orlando L, Metspalu E, Karmin M, Tambets K, Rootsi S, Magi R, Campos PF, Balanovska E, Balanovsky O, Khusnutdinova E, Litvinov S, Osipova LP, Fedorova SA, Voevoda MI, DeGiorgio M, Sicheritz-Ponten T, Brunak S, Demeshchenko S, Kivisild T, Villems R, Nielsen R, Jakobsson M, Willerslev E
Nature, 2013/11/20/online, 10.1038/nature12736, 2013 |
Nature
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HELQ promotes RAD51 paralogue-dependent repair to avert germ cell loss and tumorigenesis.
Adelman CA, Lolo RL, Birkbak NJ, Murina O, Matsuzaki K, Horejsi Z, Parmar K, Borel V, Skehel JM, Stamp G, D\\\'Andrea A, Sartori AA, Swanton C, Boulton SJ
Nature 502(7471):381-4 doi:10.1038/nature12565, 2013 |
PubMed
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Tumor Mutation Burden Forecasts Outcome in Ovarian Cancer with BRCA1 or BRCA2 Mutations
Birkbak NJ, Kochupurakkal B, Izarzugaza JMG, Eklund AC, Li Y, Liu J, Szallasi Z, Matulonis UA, Richardson AL, Iglehart JD, Wang ZC
Research Article | published 12 Nov 2013 | PLOS ONE 10.1371/journal.pone.0080023, 2013 |
PLOS ONE
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Metagenomic species profiling using universal phylogenetic marker genes.
Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Doré J, Ehrlich SD, Stamatakis A, Bork P
Nature Methods 10(12):1196-9 doi:10.1038/nmeth.2693, 2013 |
PubMed
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Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes.
Barah P, Jayavelu ND, Rasmussen S, Nielsen HB, Mundy J, Bones AM
BMC Genomics 14:722 doi:10.1186/1471-2164-14-722, 2013 |
PubMed
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Mapping Condition Dependent Regulation of Lipid Metabolism in Saccharomyces cerevisiae.
Jewett MC, Workman CT, Nookaew I, Pizarro FA, Agosin E, Hellgren LI, Nielsen J
G3 (Bethesda) 3(11):1979-95 doi:10.1534/g3.113.006601, 2013 |
PubMed
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A nondegenerate code of deleterious variants in mendelian Loci contributes to complex disease risk.
Blair DR, Lyttle CS, Mortensen JM, Bearden CF, Jensen AB, Khiabanian H, Melamed R, Rabadan R, Bernstam EV, Brunak S, Jensen LJ, Nicolae D, Shah NH, Grossman RL, Cox NJ, White KP, Rzhetsky A
Cell 155(1):70-80 doi:10.1016/j.cell.2013.08.030, 2013 |
PubMed
Relevant URL
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Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics
Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümü? ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M
Science, 2013 |
Relevant URL
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Evaluation of peptide selection approaches for epitope-based vaccine design
Schubert B, Lund O, Nielsen M
Tissue Antigens, 82: 243–251. doi: 10.1111/tan.12199, 2013 |
Relevant URL
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A computational approach to mechanistic and predictive toxicology of pesticides
Kongsbak K, Vinggaard AM, Hadrup N, Audouze K
ALTEX 31(1):11-22 doi:10.14573/altex.1304241, 2013 |
PubMed
Relevant URL
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A computational approach to chemical etiologies of diabetes
Audouze K, Brunak S, Grandjean P
Scientific Reports 2013, 2013 |
Relevant URL
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The effect of network biology on drug toxicology
Gautier L, Taboureau O, Audouze K
Expert Opinion on Drug Metabolism & Toxicology 9(11):1409-18 doi:10.1517/17425255.2013.820704, 2013 |
PubMed
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Prediction of Disease Causing Non-Synonymous SNPs by the Artificial Neural Network Predictor NetDiseaseSNP
Johansen MB, Izarzugaza JM, Brunak S, Petersen TN, Gupta R
PLoS ONE 8(7):e68370 doi:10.1371/journal.pone.0068370, 2013 |
PubMed
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Richness of human gut microbiome correlates with metabolic markers.
Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jørgensen T, Brandslund I, Nielsen HB, Juncker AS, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Clément K, Doré J, Kleerebezem M, Kristiansen K, Renault P, Sicheritz-Ponten T, de Vos WM, Zucker JD, Raes J, Hansen T; MetaHIT consortium, Bork P, Wang J, Ehrlich SD, Pedersen O, Guedon E, Delorme C, Layec S, Khaci G, van de Guchte M, Vandemeulebrouck G, Jamet A, Dervyn R, Sanchez N, Maguin E, Haimet F, Winogradski Y, Cultrone A, Leclerc M, Juste C, Blottière H, Pelletier E, LePaslier D, Artiguenave F, Bruls T, Weissenbach J, Turner K, Parkhill J, Antolin M, Manichanh C, Casellas F, Boruel N, Varela E, Torrejon A, Guarner F, Denariaz G, Derrien M, van Hylckama Vlieg JE, Veiga P, Oozeer R, Knol J, Rescigno M, Brechot C, M\\\'Rini C, Mérieux A, Yamada T
Nature 500(7464):541-6 doi:10.1038/nature12506, 2013 |
PubMed
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ATAF1 transcription factor directly regulates abscisic acid biosynthetic gene NCED3 in Arabidopsis thaliana.
Jensen MK, Lindemose S, Masi Fd, Reimer JJ, Nielsen M, Perera V, Workman CT, Turck F, Grant MR, Mundy J, Petersen M, Skriver K
FEBS Open Bio 3:321-7 doi:10.1016/j.fob.2013.07.006, 2013 |
PubMed
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Effects of butter from mountain-pasture grazing cows on risk markers of the metabolic syndrome compared with conventional Danish butter: a randomized controlled study.
Werner LB, Hellgren LI, Raff M, Jensen SK, Petersen RA, Drachmann T, Tholstrup T
Lipids in Health and Disease 12:99 doi:10.1186/1476-511X-12-99, 2013 |
PubMed
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Whey protein reduces early life weight gain in mice fed a high-fat diet.
Tranberg B, Hellgren LI, Lykkesfeldt J, Sejrsen K, Jeamet A, Rune I, Ellekilde M, Nielsen DS, Hansen AK
PLoS ONE 8(8):e71439 doi:10.1371/journal.pone.0071439, 2013 |
PubMed
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Computational approaches to identify functional genetic variants in cancer genomes.
International Cancer Genome Consortium Mutation Pathways, Consequences Subgroup of the Bioinformatics Analyses Working Group, Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N
Nature Methods 10(8):723-9 doi:10.1038/nmeth.2562, 2013 |
PubMed
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Global characterization of signalling networks associated with tamoxifen resistance in breast cancer.
Browne BC, Hochgräfe F, Wu J, Millar EK, Barraclough J, Stone A, McCloy RA, Lee CS, Roberts C, Ali NA, Boulghourjian A, Schmich F, Linding R, Farrow L, Gee JM, Nicholson RI, O\\\'Toole SA, Sutherland RL, Musgrove EA, Butt AJ, Daly RJ
FEBS Journal . 280(21):5237-57 doi:10.1111/febs.12441, 2013 |
PubMed
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TIMP1 overexpression mediates resistance of MCF-7 human breast cancer cells to fulvestrant and down-regulates progesterone receptor expression.
Bjerre C, Vinther L, Belling KC, Würtz SO, Yadav R, Lademann U, Rigina O, Do KN, Ditzel HJ, Lykkesfeldt AE, Wang J, Nielsen HB, Brünner N, Gupta R, Schrohl AS, Stenvang J
Tumour Biology. 34(6):3839-51 doi:10.1007/s13277-013-0969-7, 2013 |
PubMed
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TIMP-1 increases expression and phosphorylation of proteins associated with drug resistance in breast cancer cells.
Hekmat O, Munk S, Fogh L, Yadav R, Francavilla C, Horn H, Wurtz SO, Schrohl AS, Damsgaard B, Romer MU, Belling KC, Jensen NF, Gromova I, Bekker-Jensen DB, Moreira JM, Jensen LJ, Gupta R, Lademann U, Brunner N, Olsen JV, Stenvang J
Journal of Proteome Research. 12(9):4136-51 doi:10.1021/pr400457u, 2013 |
PubMed
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Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics.
Kouskoumvekaki I, Shublaq N, Brunak S
Briefings in Bioinformatics, 2013 |
PubMed
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Concordance of gene expression in human protein complexes reveals tissue specificity and pathology
Börnigen D, Pers TH, Thorrez L, Huttenhower C, Moreau Y, Brunak S
Nucleic Acids Research. 41(18):e171 doi:10.1093/nar/gkt661, 2013 |
PubMed
Relevant URL
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NetMHCIIpan-3.0, a common pan-specific MHC class II prediction method including all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ
Karosiene E, Rasmussen M, Blicher T, Lund O, Buus S, Nielsen M
Immunogenetics 65(10):711-24 doi:10.1007/s00251-013-0720-y, 2013 |
PubMed
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MicroRNA profiling in ocular adnexal lymphoma: A role for MYC and NFKB1 mediated dysregulation of microRNA expression in aggressive disease.
Hother C, Rasmussen P, Joshi T, Reker D, Ralfkiaer U, Workman C, Heegaard S, Ralfkiaer E, Grønbæk K
Investigative Ophthalmology & Visual Science. 54(8):5169-75 doi:10.1167/iovs.13-12272, 2013 |
PubMed
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Meta-analysis of genome-wide association studies identifies ten loci influencing allergic sensitization
Bønnelykke K, Matheson MC, Pers TH, Granell R, Strachan DP, Alves AC, Linneberg A, Curtin JA, Warrington NM, Standl M, Kerkhof M, Jonsdottir I, Bukvic BK, Kaakinen M, Sleimann P, Thorleifsson G, Thorsteinsdottir U, Schramm K, Baltic S, Kreiner-Møller E, Simpson A, St Pourcain B, Coin L, Hui J, Walters EH, Gupta R, et al
Nature Genetics (2013), 2013 |
Relevant URL
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The piRNAs forge an immune system for the genome.
Muller S, Raman Pandey R, Pillai RS
International Journal of Medical Sciences (Paris) 29(5):487-94 doi:10.1051/medsci/2013295011, 2013 |
PubMed
Relevant URL
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Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.
Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert M, Cappellini E, Petersen B, Moltke I, Johnson PL, Fumagalli M, Vilstrup JT, Raghavan M, Korneliussen T, Malaspinas AS, Vogt J, Szklarczyk D, Kelstrup CD, Vinther J, Dolocan A, Stenderup J, Velazquez AM, Cahill J, Rasmussen M, Wang X, Min J, Zazula GD, Seguin-Orlando A, Mortensen C, Magnussen K, Thompson JF, Weinstock J, Gregersen K, Røed KH, Eisenmann V, Rubin CJ, Miller DC, Antczak DF, Bertelsen MF, Brunak S, Al-Rasheid KA, Ryder O, Andersson L, Mundy J, Krogh A, Gilbert MT, Kjær K, Sicheritz-Ponten T, Jensen LJ, Olsen JV, Hofreiter M, Nielsen R, Shapiro B, Wang J, Willerslev E
Nature 499(7456):74-8 doi:10.1038/nature12323, 2013 |
PubMed
Relevant URL
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MHCcluster, a method for functional clustering of MHC molecules
Thomsen MCF, Lundegaard C, Buus S, Lund O, Nielsen M
Immunogenetics 65(9):655-65 doi:10.1007/s00251-013-0714-9, 2013 |
PubMed
Relevant URL
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SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments
Jessen L, Hoof I, Lund O, Nielsen M
Nucleic Acids Research 2013; doi: 10.1093/nar/gkt497, 2013 |
Relevant URL
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Pre- and early-postnatal nutrition modify gene and protein expressions of muscle energy metabolism markers and phospholipid Fatty Acid composition in a muscle type specific manner in sheep.
Hou L, Kongsted AH, Ghoreishi SM, Takhtsabzy TK, Friedrichsen M, Hellgren LI, Kadarmideen HN, Vaag A, Nielsen MO
PLoS ONE 8(6):e65452 doi:10.1371/journal.pone.0065452, 2013 |
PubMed
Relevant URL
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Parallel evolution of tumor subclones mimics diversity between tumors.
Martinez P, Birkbak NJ, Gerlinger M, McGranahan N, Burrell R, Rowan A, Joshi T, Fisher R, Larkin J, Szallasi Z, Swanton C
The Journal of Pathology. 230(4):356-64 doi:10.1002/path.4214, 2013 |
PubMed
Relevant URL
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Transcriptome profiling of mice testes following low dose irradiation
Belling KC, Tanaka M, Dalgaard MD, Nielsen JE, Nielsen HB, Brunak S, Almstrup K, Leffers H
Reproductive Biology and Endocrinology 11:50 doi:10.1186/1477-7827-11-50, 2013 |
Relevant URL
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MISTIC: mutual information server to infer coevolution
Simonetti FL, Teppa E, Chernomoretz A, Nielsen M, Buslje CM
Nucleic Acids Research. (2013), 2013 |
Relevant URL
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MetaRanker 2.0: a web server for prioritization of genetic variation data
Pers TH, Dworzynski P, Thomas C, Lage K, Brunak S
Nucleic Acids Research, 2013 |
Relevant URL
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Mutations in FGF17, IL17RD, DUSP6, SPRY4, and FLRT3 Are Identified in Individuals with Congenital Hypogonadotropic Hypogonadism.
Miraoui H, Dwyer A, Sykiotis GP, Plummer L, Chung W, Feng B, Beenken A, Clarke J, Pers TH, Dworzynski P, Keefe K, Niedziela M, Raivio T, Crowley Jr WF, Seminara SB, Quinton R, Hughes VA, Kumanov P, Young J, Yialamas MA, Hall JE, Van Vliet G, Chanoine JP, Rubenstein J, Mohammadi M, Tsai PS, Sidis Y, Lage K, Pitteloud N
AJHG, The American Journal of Human Genetics - Cell. 92(5):725-43 doi:10.1016/j.ajhg.2013.04.008, 2013 |
PubMed
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The CIN4 chromosomal instability qPCR classifier defines tumor aneuploidy and stratifies outcome in grade 2 breast cancer.
Szász AM, Li Q, Eklund AC, Sztupinszki Z, Rowan A, Tõkés AM, Székely B, Kiss A, Szendrõi M, Gyõrffy B, Szállási Z, Swanton C, Kulka J
PLoS ONE 8(2):e56707 doi:10.1371/journal.pone.0056707, 2013 |
PubMed
Relevant URL
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Deconvoluting complex tissues for expression quantitative trait locus-based analyses.
Seo JH, Li Q, Fatima A, Eklund A, Szallasi Z, Polyak K, Richardson AL, Freedman ML
Philosophical Transactions of the Royal Society B: Biological Sciences. 368(1620):20120363 doi:10.1098/rstb.2012.0363, 2013 |
PubMed
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Regulatory coordination between two major intracellular homeostatic systems: heat shock response and autophagy
Dokladny K, Zuhl MN, Mandell M, Bhattacharya D, Schneider S, Deretic V, Moseley PL
The Journal of Biological Chemistry. 288(21):14959-72 doi:10.1074/jbc.M113.462408, 2013 |
PubMed
Relevant URL
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FADS genotype and diet are important determinants of DHA status: a cross-sectional study in Danish infants.
Harsløf LB, Larsen LH, Ritz C, Hellgren LI, Michaelsen KF, Vogel U, Lauritzen L
The American Journal of Clinical Nutrition. 97(6):1403-10 doi:10.3945/ajcn.113.058685, 2013 |
PubMed
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Transcriptome responses to combinations of stresses in Arabidopsis.
Rasmussen S, Barah P, Suarez-Rodriguez MC, Bressendorff S, Friis P, Costantino P, Bones AM, Nielsen HB, Mundy J
Plant Physiology 161(4):1783-94 doi:10.1104/pp.112.210773, 2013 |
PubMed
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Targeted metabolic engineering guided by computational analysis of single-nucleotide polymorphisms (SNPs).
Udatha DB, Rasmussen S, Sicheritz-Pontén T, Panagiotou G
Methods in Molecular Biology . 985:409-28 doi:10.1007/978-1-62703-299-5_20, 2013 |
PubMed
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Prognostic and Predictive Markers in Metastatic Renal Cell Carcinoma
Khattak MA, Bakr F, Krzystanek M, Szallasi Z, Gerlinger M, Santos C, Swanton C, Pickering LM, Gore ME, Larkin JM
Journal of Clinical Oncology. 31(7):971-2 doi:10.1200/JCO.2012.46.9353, 2013 |
PubMed
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Biasogram: Visualization of Confounding Technical Bias in Gene Expression Data
Krzystanek M, Szallasi Z, Eklund AC
PLOS ONE, April 16 2013, 2013 |
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Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology
Steentoft C, Vakhrushev SY, Joshi HJ, Kong Y, Vester-Christensen MB, Schjoldager KT, Lavrsen K, Dabelsteen S, Pedersen NB, Marcos-Silva L, Gupta R, Paul Bennett E, Mandel U, Brunak S, Wandall HH, Levery SB, Clausen H
The EMBO Journal . 32(10):1478-88 doi:10.1038/emboj.2013.79, 2013 |
PubMed
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Predictions of Phase Separation in Three-Component Lipid Membranes by the MARTINI Force Field.
Davis RS, Kumar PBS, Sperotto MM, Laradji M
The Journal of Physical Chemistry B, 117, 4072.4080 (2013), 2013 |
Relevant URL
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HExpoChem: a systems biology resource to explore human exposure to chemicals.
Taboureau O, Jacobsen UP, Kalhauge C, Edsgärd D, Rigina O, Gupta R, Audouze K
Bioinformatics 29(9):1231-2 doi:10.1093/bioinformatics/btt112, 2013 |
PubMed
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Pathogenic bacteria colonizing the airways in asymptomatic neonates stimulates topical inflammatory mediator release.
Følsgaard NV, Schjørring S, Chawes BL, Rasmussen MA, Krogfelt KA, Brix S, Bisgaard H
American Journal of Respiratory and Critical Care Medicine . 187(6):589-95 doi:10.1164/rccm.201207-1297OC, 2013 |
PubMed
Relevant URL
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Phytanic acid stimulates glucose uptake in a model of skeletal muscles, the primary porcine myotubes.
Che BN, Oksbjerg N, Hellgren LI, Nielsen JH, Young JF
Lipids in Health and Disease 12:14 doi:10.1186/1476-511X-12-14, 2013 |
PubMed
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Content and distribution of phytanic acid diastereomers in organic milk as affected by feed composition
Che BN, Kristensen T, Nebel C, Dalsgaard TK, Hellgren LI, Young JF, Larsen MK
Journal of Agricultural and Food Chemistry . 61(1):225-30 doi:10.1021/jf304079r, 2013 |
PubMed
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CMG-biotools, a free workbench for basic Comparative Microbial Genomics
Vesth T, Lagesen K, Acar O, Ussery D
PLoS ONE, in the press, 2013 |
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Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes
Alsmark C, Foster PG, Sicheritz-Ponten T, Nakjang S, Embley TM, Hirt RP
Genome Biology. 14(2):R19, 2013 |
PubMed
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Discovery of a Novel Selective PPAR Ligand with Partial Agonist Binding Properties by Integrated in Silico in Vitro Work Flow
Kouskoumvekaki I, Petersen RK, Fratev F, Taboureau O, Nielsen TE, Oprea TI, Sonne S, Flindt E, Jónsdóttir SO, Kristiansen K
Journal of Chemical Information and Modeling 53(4):923-37 doi:10.1021/ci3006148, 2013 |
PubMed
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In Vivo SILAC-Based Proteomics Reveals Phosphoproteome Changes during Mouse Skin Carcinogenesis
Zanivan S, Meves A, Behrendt K, Schoof EM, Neilson LJ, Cox J, Tang HR, Kalna G, van Ree JH, van Deursen JM, Trempus CS, Machesky LM, Linding R, Wickström SA, Fässler R, Mann M
Cell Reports 3(2):552-66 doi:10.1016/j.celrep.2013.01.003, 2013 |
PubMed
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In silico peptide-binding predictions of passerine MHC class I reveal similarities across distantly related species, suggesting convergence on the level of protein function
Follin E, Karlsson M, Lundegaard C, Nielsen M, Wallin S, Paulsson K, Westerdahl H
Immunogenetics 65(4):299-311 doi:10.1007/s00251-012-0676-3, 2013 |
PubMed
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Bioinformatics Identification of Antigenic Peptide: Predicting the Specificity of Major MHC Class I and II Pathway Players
Lund O, Karosiene E, Lundegaard C, Larsen MV, Nielsen M
Methods in Molecular Biology . 960:247-60 doi:10.1007/978-1-62703-218-6_19, 2013 |
PubMed
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Accurate prediction of secondary metabolite gene clusters in filamentous fungi
Andersen MR, Nielsen JB, Klitgaard A, Petersen LM, Zachariasen M, Hansen TJ, Blicher LH, Gotfredsen CH, Larsen TO, Nielsen KF, Mortensen UH
PNAS, Proceedings of the National Academy of Sciences U.S.A. 110(1):E99-107 doi:10.1073/pnas.1205532110, 2013 |
PubMed
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2012
Divergent pro-inflammatory profile of human dendritic cells in response to commensal and pathogenic bacteria associated with the airway microbiota
Larsen JM, Steen-Jensen DB, Laursen JM, Søndergaard JN, Musavian HS, Butt TM, Brix S
Plos ONE, 2012 |
PubMed
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Differential protein pathways in 1,25-dihydroxyvitamin d(3) and dexamethasone modulated tolerogenic human dendritic cells.
Ferreira GB, Kleijwegt FS, Waelkens E, Lage K, Nikolic T, Hansen DA, Workman CT, Roep BO, Overbergh L, Mathieu C
Journal of Proteome Research. 2012 Feb 3;11(2):941-71, 2012 |
PubMed
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Transcriptome dynamics of Pseudomonas putida KT2440 under water stress.
Gülez G, Dechesne A, Workman CT, Smets BF
Applied and Environmental Microbiology. 2012 Feb;78(3):676-83, 2012 |
PubMed
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Gene prioritization for livestock diseases by data integration.
Jiang L, Sørensen P, Thomsen B, Edwards SM, Skarman A, Røntved CM, Lund MS, Workman CT
Physiological Genomics. 2012 Mar 1;44(5):305-17, 2012 |
PubMed
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Multilocus sequence typing of total-genome-sequenced bacteria.
Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Sicheritz-Pontén T, Ussery DW, Aarestrup FM, Lund O
Journal of Clinical Microbiology 2012 Apr;50(4):1355-61., 2012 |
PubMed
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Identification of a novel UTY-encoded minor histocompatibility antigen.
Mortensen BK, Rasmussen AH, Larsen ME, Larsen MV, Lund O, Braendstrup P, Harndahl M, Rasmussen M, Buus S, Stryhn A, Vindeløv L
Scandinavian Journal of Immunology . 2012 Aug;76(2):141-50., 2012 |
PubMed
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Structural analysis of B-cell epitopes in antibody:protein complexes.
Kringelum JV, Nielsen M, Padkjær SB, Lund O
Molecular Immunology 2013 Jan;53(1-2):24-34, 2012 |
PubMed
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Characterization of HIV-specific CD4+ T cell responses against peptides selected with broad population and pathogen coverage.
Buggert M, Norström MM, Czarnecki C, Tupin E, Luo M, Gyllensten K, Sönnerborg A, Lundegaard C, Lund O, Nielsen M, Karlsson AC
PLoS One. 2012;7(7):e39874, 2012 |
PubMed
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The cancer exome generated by alternative mRNA splicing dilutes predicted HLA class I epitope density.
Stranzl T, Larsen MV, Lund O, Nielsen M, Brunak S
PLoS One. 2012;7(9):e38670, 2012 |
PubMed
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Integrating genome-based informatics to modernize global disease monitoring, information sharing, and response.
Aarestrup FM, Brown EW, Detter C, Gerner-Smidt P, Gilmour MW, Harmsen D, Hendriksen RS, Hewson R, Heymann DL, Johansson K, Ijaz K, Keim PS, Koopmans M, Kroneman A, Lo Fo Wong D, Lund O, Palm D, Sawanpanyalert P, Sobel J, Schlundt J
Emerging Infectious Diseases. 2012 Nov;18(11):e1., 2012 |
PubMed
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Reliable B cell epitope predictions: impacts of method development and improved benchmarking.
Kringelum JV, Lundegaard C, Lund O, Nielsen M
PLoS Comput Biol. 2012 Dec;8(12):e1002829., 2012 |
PubMed
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Mycobacterium leprae virulence-associated peptides are indicators of exposure to M. leprae in Brazil, Ethiopia and Nepal.
Bobosha K, Tang ST, van der Ploeg-van Schip JJ, Bekele Y, Martins MV, Lund O, Franken KL, Khadge S, Pontes MA, Gonçalves Hde S, Hussien J, Thapa P, Kunwar CB, Hagge DA, Aseffa A, Pessolani MC, Pereira GM, Ottenhoff TH, Geluk A
Mem. Inst. Oswaldo Cruz:112-23 pii:S0074-02762012000900018, 2012 |
PubMed
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Identification of acquired antimicrobial resistance genes
Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, Aarestrup FM, Larsen MV
Journal of Antimicrobial Chemotherapy. 67(11):2640-4 doi:10.1093/jac/dks261, 2012 |
PubMed
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snpTree-a web-server to identify and construct SNP trees from whole genome sequence data
Leekitcharoenphon P, Kaas RS, Thomsen MCF, Friis C, Rasmussen S, Aarestrup FM
BMC Genomics:S6 doi:10.1186/1471-2164-13-S7-S6, 2012 |
PubMed
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Polyclonality of concurrent natural populations of Alteromonas macleodii.
Gonzaga A, Martin-Cuadrado AB, López-Pérez M, Megumi Mizuno C, García-Heredia I, Kimes NE, Lopez-García P, Moreira D, Ussery D, Zaballos M, Ghai R, Rodriguez-Valera F
Genome Biology and Evolution 4(12):1360-74 doi:10.1093/gbe/evs112, 2012 |
PubMed
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Polyclonality of concurrent natural populations of Alteromonas macleodii.
Gonzaga A, Martin-Cuadrado AB, López-Pérez M, Megumi Mizuno C, García-Heredia I, Kimes NE, Lopez-García P, Moreira D, Ussery D, Zaballos M, Ghai R, Rodriguez-Valera F
Genome Biology and Evolution 4(12):1360-74 doi:10.1093/gbe/evs112, 2012 |
PubMed
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PROTEINCHALLENGE: Crowd sourcing in proteomics analysis and software development
Martin SF, Falkenberg H, Dyrlund TF, Khoudoli GA, Mageean CJ, Linding R
Journal of Proteomics 88:41-6 doi:10.1016/j.jprot.2012.11.014, 2012 |
PubMed
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A comparative analysis of the intestinal metagenomes present in guinea pigs
Hildebrand F, Ebersbach T, Nielsen HB, Li X, Sonne SB, Bertalan M, Dimitrov P, Madsen L, Qin J, Wang J, Raes J, Kristiansen K, Licht TR
BMC Genomics 13:514 doi:10.1186/1471-2164-13-514, 2012 |
PubMed
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Association between chemical pattern in breast milk and congenital cryptorchidism: modelling of complex human exposures
Krysiak-Baltyn K, Toppari J, Skakkebaek NE, Jensen TS, Virtanen HE, Schramm KW, Shen H, Vartiainen T, Kiviranta H, Taboureau O, Audouze K, Brunak S, Main KM
International Journal of Andrology . 35(3):294-302 doi:10.1111/j.1365-2605.2012.01268.x, 2012 |
PubMed
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ChemProt-2.0: visual navigation in a disease chemical biology database
Kim Kjærulff S, Wich L, Kringelum J, Jacobsen UP, Kouskoumvekaki I, Audouze K, Lund O, Brunak S, Oprea TI, Taboureau O
Nucleic Acids Research. 41:D464-9 doi:10.1093/nar/gks1166, 2012 |
PubMed
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Polyclonality of concurrent natural populations of Alteromonas macleodii
Gonzaga A, Martin-Cuadrado AB, López-Pérez M, Mizuno CM, García-Heredia I, Kimes NE, Lopez-García P, Moreira D, Ussery D, Zaballos M, Ghai R, Rodriguez-Valera F
Genome Biology and Evolution 4(12):1360-74 doi:10.1093/gbe/evs112, 2012 |
PubMed
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The chemical interactome space between the human host and the genetically defined gut metabotypes
Jacobsen UP, Nielsen HB, Hildebrand F, Raes J, Sicheritz-Ponten T, Kouskoumvekaki I, Panagiotou G
The ISME Journal advance online publication, 22 November 2012; doi:10.1038/ismej.2012.141, 2012 |
Relevant URL
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Is the pan-genome also a pan-selectome?
Rodriguez-Valera F, Ussery DW
F1000 Research, 1:16 (doi: 10.3410/f1000research.1-16.v1), 2012 |
Relevant URL
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Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach
Andreatta M, Lund O, Nielsen M
Bioinformatics 29(1):8-14 doi:10.1093/bioinformatics/bts621, 2012 |
PubMed
Relevant URL
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From essential to persistent genes: A functional approach to construct synthetic life
Acevedo-Rocha CG, Fang G, Schmidt M, Ussery DW, Danchin A
Trends in Genetics, in the press (2012), 2012 |
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Isolation of IL-12p70-competent human monocyte-derived dendritic cells
Søndergaard JN, Brix S
Journal of Immunological Methods 386:112-6 doi:10.1016/j.jim.2012.09.005, 2012 |
PubMed
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A domain sequence approach to pangenomics: applications to Escherichia coli
Snipen LG, Ussery DW
F1000 Research, 1:19 (doi: 10.3410/f1000research.1-19.v1), 2012 |
Relevant URL
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Hyperactivity of the Ero1á oxidase elicits endoplasmic reticulum stress but no broad antioxidant response
Hansen HG, Schmidt JD, Soeltoft CL, Ramming T, Geertz-Hansen HM, Christensen B, Sorensen ES, Juncker AS, Appenzeller-Herzog C, Ellgaard L
The Journal of Biological Chemistry. 287(47):39513-23 doi:10.1074/jbc.M112.405050, 2012 |
PubMed
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Telomeric allelic imbalance indicates defective DNA repair and sensitivity to DNA-damaging agents
Birkbak NJ, Wang ZC, Kim JY, Eklund AC, Li Q, Tian R, Bowman-Colin C, Li Y, Greene-Colozzi A, Iglehart JD, Tung N, Ryan PD, Garber JE, Silver DP, Szallasi Z, Richardson AL
Cancer Discovery 2(4):366-75 doi:10.1158/2159-8290.CD-11-0206, 2012 |
PubMed
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Profiles of genomic instability in high-grade serous ovarian cancer predict treatment outcome
Wang ZC, Birkbak NJ, Culhane AC, Drapkin R, Fatima A, Tian R, Schwede M, Alsop K, Daniels KE, Piao H, Liu J, Etemadmoghadam D, Miron A, Salvesen HB, Mitchell G, Defazio A, Quackenbush J, Berkowitz RS, Iglehart JD, Bowtell DD; for the Australian Ovarian Cancer Study Group, Matulonis UA
Clin. Cancer Res. 18(20):5806-15 doi:10.1158/1078-0432.CCR-12-0857, 2012 |
PubMed
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Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction
Teppa E, Wilkins AD, Nielsen M, Marino Buslje C
BMC Bioinformatics 13:235 doi:10.1186/1471-2105-13-235, 2012 |
PubMed
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Identification of peptides from foot-and-mouth disease virus structural proteins bound by class I swine leukocyte antigen (SLA) alleles, SLA-1*0401 and SLA-2*0401
Pedersen LE, Harndahl M, Nielsen M, Patch JR, Jungersen G, Buus S, Golde WT
Anim. Genet. 44(3):251-8 doi:10.1111/j.1365-2052.2012.02400.x, 2012 |
PubMed
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Cholera in Haiti: Lack of evidence for a contribution of non-O1 Vibro cholera
Mekalanos JJ, Robins W, Ussery DW, Davis BM, Schadt E, Waldor MK
PNAS, in the press, September, 2012, 2012 |
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Navigating cancer network attractors for tumor-specific therapy
Creixell P, Schoof EM, Erler JT, Linding R
Nature Biotechnology 30(9):842-8 doi:10.1038/nbt.2345, 2012 |
PubMed
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Novel Microcephalic Primordial Dwarfism Disorder Associated with Variants in the Centrosomal Protein Ninein
Dauber A, LaFranchi SH, Maliga Z, Lui JC, Moon JE, McDeed C, Henke K, Zonana J, Kingman GA, Pers TH, Baron J, Rosenfeld RG, Hirschhorn JN, Harris MP, Hwa V
The Journal of Clinical Endocrinology & Metabolism August 29, 2012 jc.2012-2150, 2012 |
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Interpretation of the consequences of mutations in protein kinases: combined use of bioinformatics and text mining
Izarzugaza JM, Krallinger M, Valencia A
Front. Physio. 3:323. doi: 10.3389/fphys.2012.00323, 2012 |
Relevant URL
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Computational genomics, proteomics, and phylogeny analysis of twenty one mycobacterial genomes (Tuberculosis & non Tuberculosis strains)
Zakham F, Aouane O, Ussery D, Benjouad A, Ennaji MM
The Journal of Microbial Informatics and Experimintaion, in the press (August, 2012), 2012 |
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Campylobacter fetus subspecies: Comparative genomics and prediction of potential virulence targets
Ali A, Soares SC, Santos AR, Guimarães LC, Barbosa E, Almeida SS, Abreu VA, Carneiro AR, Ramos RT, Bakhtiar SM, Hassan SS, Ussery DW, On S, Silva A, Schneider MP, Lage AP, Miyoshi A, Azevedo V
Gene 508(2):145-56 doi:10.1016/j.gene.2012.07.070, 2012 |
PubMed
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Analysis of Co-evolving Genes in Campylobacter jejuni and and C. coli
Snipen L, Wassenaar T, Altermann E, Olson J, Kathariou S, Lagesen K, Takamiya M, Knoechel S, Ussery DW, Meinersmann RJ
Microbial Informatics and Experimentation, 2012 |
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Bayesian prediction of bacterial growth temperature range based on genome sequences
Jensen DB, Vest TC, Hallin PF, Pedersen AG, Ussery D
BMC Genomics, 2012 |
PubMed
Relevant URL
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Mutational properties of amino acid residues: implications for evolvability of phosphorylatable residues
Creixell P, Schoof EM, Tan CS, Linding R
Philosophical Transactions of the Royal Society B: Biological Sciences. 367(1602):2584-93 doi:10.1098/rstb.2012.0076, 2012 |
PubMed
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Two novel methods for using genome sequences to infer taxonomy
Ussery DW, Gordon SV
Microbiology (Reading, Engl.) 158:1414 doi:10.1099/mic.0.059816-0, 2012 |
PubMed
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LeuO is a global regulator of gene expression in Salmonella enterica serovar Typhimurium
Dillon SC, Espinosa E, Hokamp K, Ussery DW, Casadesús J, Dorman CJ
Mol. Microbiol. 85(6):1072-89 doi:10.1111/j.1365-2958.2012.08162.x, 2012 |
PubMed
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Cells, shared memory and breaking the PTM code
Creixell P, Linding R
Mol. Syst. Biol. 8:598 doi:10.1038/msb.2012.33, 2012 |
PubMed
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Flip-Flop of Steroids in Phospholipid Bilayers: Effects of the Chemical Structure on Transbilayer Diffusion
Parisio G, Sperotto MM, Ferrarini A
J. Am. Chem. Soc. 134(29):12198-208 doi:10.1021/ja304007t, 2012 |
PubMed
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A Steered Molecular Dynamics Study of Binding and Translocation Processes in the GABA Transporter.
Skovstrup S, David L, Taboureau O, Jørgensen FS
PLoS ONE 7(6):e39360 doi:10.1371/journal.pone.0039360, 2012 |
PubMed
Relevant URL
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MicroRNA expression profiling of carcinoma in situ cells of the testis
Novotny GW, Belling KC, Bramsen JB, Nielsen JE, Bork-Jensen J, Almstrup K, Sonne SB, Kjems J, Rajpert-De Meyts E, Leffers H
Endocr. Relat. Cancer 19(3):365-79 doi:10.1530/ERC-11-0271, 2012 |
PubMed
Relevant URL
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Docosahexaenoic acid status at 9 months is inversely associated with communicative skills in 3-year-old girls
Engel S, Tronhjem KM, Hellgren L, Michaelsen KF, Lauritzen L
PubMed, 2012 |
Relevant URL
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Immune epitope database analysis resource
Kim Y, Ponomarenko J, Zhu Z, Tamang D, Wang P, Greenbaum J, Lundegaard C, Sette A, Lund O, Bourne PE, Nielsen M, Peters B
PubMed, 2012 |
Relevant URL
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Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion
Thomsen MCF, Nielsen M
Oxford Journals, 2012 |
Relevant URL
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Peptide-MHC class I stability is a better predictor than peptide affinity of CTL immunogenicity
Harndahl M, Rasmussen M, Roder G, Pedersen ID, Sørensen M, Nielsen M, Buus S
Wiley, 2012 |
Relevant URL
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Designing bovine T cell vaccines via reverse immunology
Nene V, Svitek N, Toye P, Golde WT, Barlow J, Harndahl M, Buus S, Nielsen M
Science Direct, 2012 |
Relevant URL
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Network Medicine Strikes a Blow against Breast Cancer
Erler JT, Linding R
Cell, volume 149, issue 4, 2012 |
Relevant URL
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Neonatal cytokine profile in the airway mucosal lining fluid is skewed by maternal atopy
Følsgaard NV, Chawes BL, Rasmussen MA, Bischoff AL, Carson CG, Stokholm J, Pedersen L, Hansel TT, Bønnelykke K, Brix S, Bisgaard H
Am J Respir Crit Care Med, 2012 |
Relevant URL
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Ceramide profile in hypohidrotic ectodermal dysplasia.
Jungersted JM, Høgh JK, Hellgren LI, Agner T, Jemec GB
Clin Exp Dermatol, 2012 |
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Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.
Nicolas P, Mäder U, Dervyn E, Rochat T, Leduc A, Pigeonneau N, Bidnenko E, Marchadier E, Hoebeke M, Aymerich S, Becher D, Bisicchia P, Botella E, Delumeau O, Doherty G, Denham EL, Fogg MJ, Fromion V, Goelzer A, Hansen A, Härtig E, Harwood CR, Homuth G, Jarmer H, Jules M, Klipp E, Le Chat L, Lecointe F, Lewis P, Liebermeister W, March A, Mars RA, Nannapaneni P, Noone D, Pohl S, Rinn B, Rügheimer F, Sappa PK, Samson F, Schaffer M, Schwikowski B, Steil L, Stülke J, Wiegert T, Devine KM, Wilkinson AJ, van Dijl JM, Hecker M, Völker U, Bessières P, Noirot P
Science 335(6072):1103-6 doi:10.1126/science.1206848, 2012 |
PubMed
Relevant URL
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LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs
Will S, Joshi T, Hofacker IL, Stadler PF, Backofen R
RNA, 2012 |
Relevant URL
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Mapping the Genome of Plasmodium falciparum on the Druglike Chemical Space Reveals Novel Anti-malarial Targets and Potential Drug Leads
Jensen K, Plichta D, Panagiotou G, Kouskoumvekaki I
Mol. BioSyst., 2012 |
DOI: 10.1039/C2MB00008C
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How well do the substrates KISS the enzyme? Molecular docking program selection for feruloyl esterases
Udatha G, Sugaya N, Olsson L, Panagiotou G
Nature, Scientific Reports 2, Article number: 323. 20 March, 2012 |
Relevant URL
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TLR2 Controls Intestinal Carcinogen Detoxication by CYP1A1
Do KN, Fink LN, Jensen TE, Gautier L, Parlesak A
PLoS ONE 7(3): e32309. doi:10.1371/journal.pone.0032309, 2012 |
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Multilocus Sequence Typing of Total Genome Sequenced Bacteria
Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H et al
Journal of Clinical Microbiology. 2012. 50(4): 1355-1361., 2012 |
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Global Network Reorganization During Dynamic Adaptations of Bacillus subtilis Metabolism
Buescher JM, Liebermeister W, Jules M, Uhr M, Muntel J, Botella E, Hessling B, Kleijn RJ, Chat LL, Lecointe F, Mäder U, Nicolas P, Piersma S, Rügheimer F, Becher D, Bessieres P, Bidnenko E, Denham EL, Dervyn E, Devine KM, Doherty G, Drulhe S, Felicori L, Fogg MJ, Goelzer A, Hansen A, Harwood CR, Hecker M, Hubner S, Hultschig C, Jarmer H, Klipp E, Leduc A, Lewis P, Molina F, Noirot P, Peres S, Pigeonneau N, Pohl S, Rasmussen S, Rinn D, Schaffer M, Schnidder J, Schwikowski B, Van Dijl JM, Veiga P, Walsh S, Wilkinson AJ, Stelling J, Aymerich S, Sauer U
Science, 2 March, 2012 |
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Global transcriptional mapping, RNA polymerase distribution and the unique sRNA complement of the model pathogen Salmonella enterica serovar Typhimurium
Kröger C, Dillon SC, Cameron ADS, Papenfort K, Sivasankaran SK, Hokamp K, Chao Y, Sittka A, Hébrard M, Händler K, Colgan A, Leekitcharoenphon P, Langridge GC, Lohan AJ, Loftus B, Lucchini S, Thompson A, Ussery DW, Sharma CM, Dorman CJ, Thomson N, Vogel J, Hinton JCD
Proceedings of the National Academy of Science USA , 2012 (in press), 2012 |
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Genomic variation in Salmonella enterica core genes for epidemiological typing
Leekitcharoenphon P, Lukjancenko O, Friis C, Aarestrup FM, Ussery DW
BMC Genomics 2012, 13:88, 2012 |
pubmed link
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Genome-wide analysis of cytogenetic aberrations in ETV6/RUNX1-positive childhood acute lymphoblastic leukaemia
Borst L, Wesolowska A, Joshi T, Borup R, Nielsen FC, Andersen MK, Jonsson OG, Wehner PS, Wesenberg F, Frost B-M, Gupta R, Schmiegelow K
British Journal of Haematology 2012 Mar;, 2012 |
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Characterizing the binding motifs of 11 common human HLA-DP and HLA-DQ molecules using NNAlign
Andreatta M, Nielsen M
Immunology (publication ahead of print), 2012 |
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The impact of network biology in pharmacology and toxicology
Panagiotou G, Taboureau O
SAR QSAR Environ Res., 2012 |
Relevant URL
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Toxicogenomics investigation under eTOX project
Taboureau O, Hersey A, Audouze K, Gautier K, Jacobsen UP, Akhtar R, Atkinson F, Overington JP, Brunak S
. Pharmacogenom. Pharmacoproteomics, 2012 |
Relevant URL
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Intratumor heterogeneity and branched evolution revealed by multiregion sequencing
Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E, Martinez P, Matthews N, Stewart A, Tarpey P, Varela I, Phillimore B, Begum S, McDonald NQ, Butler A, Jones D, Raine K, Latimer C, Santos CR, Nohadani M, Eklund AC, Spencer-Dene B, Clark G, Pickering L, Stamp G, Gore M, Szallasi Z, Downward J, Futreal PA, Swanton C
N Engl J Med., 2012 |
Relevant URL
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Predictions versus high- throughput experiments in T-cell epitope discovery: competition or synergy?
Lundegaard C, Lund O, Nielsen M
Expert Rev. Vaccines 11(1), 43–54 (2012), 2012 |
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Prediction of drug efficacy for cancer treatment based on comparative analysis of chemosensitivity and gene expression data
Wan P, Li Q, Larsen JE, Eklund AC, Parlesak A, Rigina O, Nielsen SJ, Björkling F, Jónsdóttir SÓ
Bioorg. Med. Chem. 20(1):167-76 doi:10.1016/j.bmc.2011.11.019, 2012 |
PubMed
Relevant URL
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A genome-wide association study of men with symptoms of testicular dysgenesis syndrome and its network biology interpretation.
Dalgaard MD, Weinhold N, Edsgärd D, Silver JD, Pers TH, Nielsen JE, Jørgensen N, Juul A, Gerds TA, Giwercman A, Giwercman YL, Cohn-Cedermark G, Virtanen HE, Toppari J, Daugaard G, Jensen TS, Brunak S, Rajpert-De Meyts E, Skakkebæk NE, Leffers H, Gupta R
Journal of Medical Genetics, 2012 |
Relevant URL
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Androgen receptor signalling in peritubular myoid cells is essential for normal differentiation and function of adult Leydig cells
Welsh M, Moffat L, Belling KC, de France LR, Segatelli TM, Saunders PTK
Int. J. Androl. 35(1):25-40 doi:10.1111/j.1365-2605.2011.01150.x,, 2012 |
PubMed
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2011
Ex vivo intestinal adhesion of Escherichia coli LF82 in Crohn\'s disease
Jensen SR, Fink LN, Nielsen OH, Brynskov J, Brix S
Microb Pathog, 2011 |
PubMed
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Immune system simulation online.
Rapin N, Lund O, Castiglione F
Bioinformatics. 2011 Jul 15;27(14):2013-4., 2011 |
PubMed
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Human leukocyte antigen (HLA) class I restricted epitope discovery in yellow fever and dengue viruses: importance of HLA binding strength
Lund O, Nascimento EJ, Maciel M Jr, Nielsen M, Larsen MV, Lundegaard C, Harndahl M, Lamberth K, Buus S, Salmon J, August TJ, Marques ET Jr
PLoS One. 2011;6(10):e26494, 2011 |
PubMed
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Chromosomal instability confers intrinsic multidrug resistance
Lee AJ, Endesfelder D, Rowan AJ, Walther A, Birkbak NJ, Futreal PA, Downward J, Szallasi Z, Tomlinson IP, Howell M, Kschischo M, Swanton C
Cancer Res. 71(5):1858-70 doi:10.1158/0008-5472.CAN-10-3604, 2011 |
PubMed
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A breast cancer meta-analysis of two expression measures of chromosomal instability reveals a relationship with younger age at diagnosis and high risk histopathological variables
Endesfelder D, McGranahan N, Birkbak NJ, Szallasi Z, Kschischo M, Graham TA, Swanton C
Oncotarget 2(7):529-37, 2011 |
PubMed
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CERT depletion predicts chemotherapy benefit and mediates cytotoxic and polyploid-specific cancer cell death through autophagy induction
Lee AJ, Roylance R, Sander J, Gorman P, Endesfelder D, Kschischo M, Jones NP, East P, Nicke B, Spassieva S, Obeid LM, Birkbak NJ, Szallasi Z, McKnight NC, Rowan AJ, Speirs V, Hanby AM, Downward J, Tooze SA, Swanton C
The Journal of Pathology. 226(3):482-94 doi:10.1002/path.2998, 2011 |
PubMed
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MicroRNA-130a-mediated down-regulation of Smad4 contributes to reduced sensitivity to TGF-β1 stimulation in granulocytic precursors
Häger M, Pedersen CC, Larsen MT, Andersen MK, Hother C, Grønbæk K, Jarmer H, Borregaard N, Cowland JB
Blood, 118, 6649-59, 2011, 2011 |
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Evolution and diversification of Pseudomonas aeruginosa in the paranasal sinuses of cystic fibrosis children have implications for chronic lung infection
Hansen SK, Rau MH, Johansen HK, Ciofu O, Jelsbak L, Yang L, Folkesson A, Jarmer HØ, Aanæs K, von Buchwald C, Høiby N, Molin S
ISME J., 6, 31-45, 2011, 2011 |
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The impact of ultraviolet therapy on stratum corneum ceramides and barrier function.
Jungersted JM, Høgh JK, Hellgren LI, Jemec GB, Agner T
Photodermatol Photoimmunol Photomed, 2011 |
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PSICQUIC and PSISCORE - Accessing and Scoring Molecular Interactions
Aranda B, Rigina O, et al
Nature Methods, 2011 |
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Identification of MHC class II restricted T-cell-mediated reactivity against MHC class I binding Mycobacterium tuberculosis peptides
Wang M, Tang ST, Stryhn A, Justesen S, Larsen MV et al
Immunology. 2011. 132(4):482-91, 2011 |
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A systems biology approach to identify potential health risk from chemical exposure
Audouze K
Miljø og Sundhed, 17, 2011(1) p.19-25, 2011 |
Relevant URL
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Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts.
Roque FS, Jensen PB, Schmock H, Dalgaard M, Andreatta M, et al
PLoS Comput Biol 7(8): e1002141, 2011 |
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Induction of foot-and-mouth disease virus (FMDV) specific cytotoxic T cell killing by vaccination.
Patch JR, Pedersen LE, Toka FN, Moreas M, Grubman MJ, Nielsen M, Jungersen G, Buus S, Golde WT
Clin Vaccine Immunol.; 18(2):280-8., 2011 |
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Porcine major histocompatibility complex (MHC) class I molecules and analysis of their peptide-binding specificities.
Pedersen LE, Golde WT, Lund O, Nielsen M, Buus S
Immunogenetics, 2011 |
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Machine learning competition in immunology - Prediction of HLA class I binding peptides
Zhang GL6, Ansari HR, Bradley P, Cawley GC, Hertz T, Hu X, Jojic N, Kim Y, Kohlbacher O, Lund O, Lundegaard C, Magaret CA, Nielsen M, Papadopoulos H, Raghava GP, Tal VS, Xue LC, Yanover C, Zhu S, Rock MT, Crowe JE Jr, Panayiotou C, Polycarpou MM, Duch W, Brusic V
J Immunol Methods., 2011 |
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Human Leukocyte Antigen (HLA) Class I Restricted Epitope Discovery in Yellow Fewer and Dengue Viruses: Importance of HLA Binding Strength.
Lund O4, Nascimento EJM, Maciel M Jr, Nielsen M, Larsen MV, Lundegaard C, Harndahl M, Lamberth K, Buus S, Salmon J, August TJ, Marques Jr ETA
PLoS ONE 6(10): e26494. doi:10.1371/journal.pone.0026494, 2011 |
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NNAlign: A Web-Based Prediction Method Allowing Non-Expert End-User Discovery of Sequence Motifs in Quantitative Peptide Data
Andreatta M, Schafer-Nielsen C, Lund O, Buus S, Nielsen M
PLoS ONE 6(11): e26781. doi:10.1371/journal.pone.0026781, 2011 |
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Designing bovine T-cell vaccines via reverse immunology
Nene T, Svitek N, Toye P, Golde WT, Barlow J, Buus S, Nielsen M
In presss Ticks and Tick-Borne Diseases,, 2011 |
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Jetset: selecting the optimal microarray probe set to represent a gene
Li Q, Birkbak NJ, Gyorffy B, Szallasi Z, Eklund AC
BMC Bioinformatics 12:474 doi:10.1186/1471-2105-12-474, 2011 |
PubMed
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SignalP 4.0: discriminating signal peptides from transmembrane regions
Petersen TN, Brunak S, von Heijne G, Nielsen H
Nature Methods 8(10):785-6 doi:10.1038/nmeth.1701, 2011 |
PubMed
Relevant URL
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Associating Drugs, Targets and Clinical Outcomes into an Integrated Network Affords a New Platform for Computer- Aided Drug Repurposing
Oprea TI, Nielsen SK, Ursu O, Yang JJ, Taboureau O, Mathias SL, Kouskoumvekaki I, Sklar LA, Bologa C
Molecular Informatics, 2011 |
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The strength of intron donor splice sites in human genes displays a bell-shaped pattern
Wang K, Wernersson R, Brunak S
Bioinformatics. 2011 Nov 15;27(22):3079-84. Epub 2011 Oct 12., 2011 |
Relevant URL
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Linking genotype and phenotype of Saccharomyces cerevisiae strains reveals metabolic engineering targets and leads to triterpene hyper-producers.
Madsen KM, Udatha GD, Semba S, Otero JM, Koetter P, Nielsen J, Ebizuka Y, Kushiro T, Panagiotou G
PubMed, 2011 |
Relevant URL
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An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia
Rasmussen M, Guo X, Wang Y, Lohmueller KE, Rasmussen S, Albrechtsen A, Skotte L, Lindgren S, Metspalu M, Jombart T, Kivisild T, Zhai W, Eriksson A, Manica A, Orlando L, De La Vega F, Tridico S, Metspalu E, Nielsen K, Ávila-Arcos MA, Moreno-Mayar JV, Muller C, Dortch J, Gilbert MTP, Lund O, Wesolowska A, Karmin M, Weinert LA, Wang B, Li J, Tai S, Xiao F, Hanihara T, van Driem G, Jha AR, Ricaut FX, de Knijf P, Migliano AB, Gallego-Romero I, Kristiansen K, Lambert DM, Brunak S, Forster P, Brinkmann B, Nehlich O, Bunce M, Richards M, Gupta R, Bustamante CD, Krogh A, Foley RA, Lahr MM, Balloux F, Sichertitz-Pontén T, Villems R, Nielsen R, Jun W, Willerslev E
Science 334(6052):94-8 doi:10.1126/science.1211177, 2011 |
PubMed
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A distinct adipose tissue gene expression response to caloric restriction predicts 6-mo weight maintenance in obese subjects
Mutch DM, Pers TH, Temanni MR, Pelloux V, Marquez-Quiñones A, Holst C, Martinez JA, Babalis D, van Baak MA, Hanjieva-Darlenska T, Walker CG, Astrup A, Saris WHM, Langin D, Viguerie N, Zucker JD, Clément K, on behalf of the DiOGenes Project
American Journal of Clinical Nutrition, 2011 |
Relevant URL
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NetMHCcons: a consensus method for the major histocompatibility complex class I predictions
Karosiene E, Lundegaard C, Lund O, Nielsen M
Immunogenetics, 2011 |
Relevant URL
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Protein Interaction-Based Genome-Wide Analysis of Incident Coronary Heart Disease
Jensen MK, Pers TH, Dworzynski P, Girman CJ, Brunak S, Rimm EB
Circ Cardiovasc Genet 4(5):549-56 doi:10.1161/CIRCGENETICS.111.960393, 2011 |
PubMed
Relevant URL
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Application of Computational Systems Biology to Explore Environmental Toxicity Hazards
Audouze K, Grandjean P
Environ. Health Perspect. 119(12):1754-9 doi:10.1289/ehp.1103533, 2011 |
PubMed
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BDDCS Applied to Over 900 Drugs
Benet LZ, Broccatelli F, Oprea TI
AAPS J 13(4):519-47 doi:10.1208/s12248-011-9290-9, 2011 |
PubMed
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International Dairy Journal
Bonomi F, Sørensen RB, Favalli S, Ferranti P, Fierro O, Frøkier H, Ragg E, Lametti S
Elsevier, April 26, 2011 |
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Defining the Pseudomonas Genus: Where Do We Draw the Line with Azotobacter?
Özen AI, Ussery DW
Springer, July 13, 2011 |
Relevant URL
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Effect of industrially produced trans fat on markers of endothelial dysfunction and systemic inflammation: evidence from a randomized trial in overweight women
Bendsen NT, Stender S, Szecsi PB, Pedersen SB, Basu S, Hellgren LI, Newman JW, Larsen TM, Haugaard SB, Astrup A
J. Lipid Res. 52(10):1821-8 doi:10.1194/jlr.M014738, 2011 |
PubMed
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The Effect of Dietary Fish Oil in addition to Lifestyle Counselling on Lipid Oxidation and Body Composition in Slightly Overweight Teenage Boys
Pedersen MH, Mølgaard C, Hellgren LI, Matthiessen J, Holst JJ, Lauritzen L
J Nutr Metab 2011:348368 doi:10.1155/2011/348368, 2011 |
PubMed
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Relationship of Extreme Chromosomal Instability with Long-term Survival in a Retrospective Analysis of Primary Breast Cancer
Roylance R, Endesfelder D, Gorman P, Burrell RA, Sander J, Tomlinson I, Hanby AM, Speirs V, Richardson AL, Birkbak NJ, Eklund AC, Downward J, Szallasi Z, Kschischo M, Swanton C
Cancer Epidemiol. Biomarkers Prev. 20(10):2183-94 doi:10.1158/1055-9965.EPI-11-0343, 2011 |
PubMed
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Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response
Li Q, Eklund AC, Birkbak NJ, Desmedt C, Haibe-Kains B, Sotiriou C, Symmans WF, Pusztai L, Brunak S, Richardson AL, Szallasi Z
BMC Bioinformatics 12:310 doi:10.1186/1471-2105-12-310, 2011 |
PubMed
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OpenFreezer: a reagent information management software system
Olhovsky M, Williton K, Dai AY, Pasculescu A, Lee JP, Goudreault M, Wells CD, Park JG, Gingras A, Linding R, Pawson T, Colwill K
Nature Methods, 2011 |
Relevant URL
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Cost-effective multiplexing before capture allows screening of 25 000 clinically relevant SNPs in childhood acute lymphoblastic leukemia
Wesolowska A, Dalgaard MD, Borst L, Gautier L, Bak M, Weinhold N, Nielsen BF, Helt LR, Audouze K, Nersting J, Tommerup N, Brunak S, Sicheritz-Ponten T, Leffers H, Schmiegelow K, Gupta R
Leukemia 25(6):1001-6 doi:10.1038/leu.2011.32, 2011 |
PubMed
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Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene
Bowman JS, Rasmussen S, Blom N, Deming JW, Rysgaard S, Sicheritz-Ponten T
ISME J 6(1):11-20 doi:10.1038/ismej.2011.76, 2011 |
PubMed
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Cancer stem cell overexpression of nicotinamide N-methyltransferase enhances
D’Andrea FP, Safwat A, Kassem M, Gautier L, Overgaard J
Radiotherapy and Oncology, May 13, 2011 |
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Muscle ceramide content is similar after 3 weeks\\\' consumption of fat or carbohydrate diet in a crossover design in patients with type 2 diabetes
Helge JW, Tobin L, Drachmann T, Hellgren LI, Dela F, Galbo H
Eur. J. Appl. Physiol. 112(3):911-8 doi:10.1007/s00421-011-2041-x, 2011 |
PubMed
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A Randomized Controlled Intervention with Fish Oil versus Sunflower Oil from 9 to 18 Months of Age - Exploring Changes in Growth and Skinfold Thicknesses
Andersen AD, Michaelsen KF, Hellgren LI, Trolle E, Lauritzen L
Pediatr. Res. 70(4):368-74 doi:10.1038/pr.2011.593, 2011 |
PubMed
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FARO server: Meta-analysis of gene expression by matching gene expression signatures to a compendium of public gene expression data
Manijak MP, Nielsen HB
BMC Res Notes 4:181 doi:10.1186/1756-0500-4-181, 2011 |
PubMed
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Effect of dairy fat on plasma phytanic acid in healthy volunteers - A randomized controlled study
Werner LB, Hellgren LI, Raff M, Jensen SK, Petersen RA, Drachmann T, Tholstrup T
Lipids in Health and Disease 10:95 doi:10.1186/1476-511X-10-95, 2011 |
PubMed
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Probiotika
Nielsen OH, Brix S, Kjeldsen HC, Johannessen T, Løge I
Sundhed.dk, March, 2011 |
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Diversion of flux toward sesquiterpene production in Saccharomyces cerevisiae by fusion of host and heterologous enzymes
Albertsen L, Chen Y, Bach LS, Rattleff S, Maury J, Brix S, Nielsen J, Mortensen UH
Appl. Environ. Microbiol. 77(3):1033-40 doi:10.1128/AEM.01361-10, 2011 |
PubMed
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Quantification of specific E. coli in gut mucosa from Crohn\'s disease patients
Jensen SR, Fink LN, Struve C, Sternberg C, Andersen JB, Brynskov J, Nielsen OH, Brix S
J. Microbiol. Methods 86(1):111-4 doi:10.1016/j.mimet.2011.04.002, 2011 |
PubMed
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Are NOD2 polymorphisms linked to a specific disease endophenotype of Crohn’s Disease?
Jensen SR, Nielsen OH, Brix S
Inflamm. Bowel Dis. 17(11):2392-401 doi:10.1002/ibd.21656, 2011 |
PubMed
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Fish oil combined with short chain fatty acids synergistically prevent tissue accumulation of free fatty acids during weight loss in obese mice
Pedersen MH, Lauritzen L, Hellgren LI
British Journal of Nutrition, June 3, 2011 |
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Response to Comment on “Positive Selection of Tyrosine Loss in Metazoan Evolution”
Tan CSH, Schoof EM, Creixell P, Pasculescu A, Wendell A Lim, Pawson T, Bader GD, Linding R
Science, May 20, 2011 |
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Fish intake, erythrocyte n-3 fatty acid status and metabolic health in Danish
Lauritzen L, Harsløf LBS, Hellgren L, Pedersen MH, Mølgaard C
British Journal of Nutrition, June 3, 2011 |
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Effects of topical corticosteroid and tacrolimus on ceramides and irritancy to sodium lauryl sulphate in healthy skin
Jungersted JM, Høgh JK, Hellegren LI, Jemec GB, Agner T
Acta Derm. Venereol. 91(3):290-4 doi:10.2340/00015555-1064, 2011 |
PubMed
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The Genomic Standards Consortium
Field D, Amaral-Zettler, L, Cochrane G, Cole JR, Dawyndt P, Garrity G, Gilbert J, Glöckner F, Hirschman L, Karsch-Mizrachi I, Klenk H, Knight R, Kottmann R, Kyrpides N, Meyer F, San Gil I, Sansone S, Schriml L, Sterk P, Tatusova T, Ussery D, White O, Wooley J
PLoS Biology, 2011 |
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The Salmonella enterica Pan-genome
Jacobsen A, Hendriksen RS, Aaresturp FM, Ussery DW, Friis C
Microb. Ecol. 62(3):487-504 doi:10.1007/s00248-011-9880-1, 2011 |
PubMed
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PINTA: a web server for network-based gene prioritization from expression data
Nitsch D, Tranchevent LC, Gonçalves JP, Vogt JK, Madeira SC, Moreau Y
Nucleic Acids Research. 39:W334-8 doi:10.1093/nar/gkr289, 2011 |
PubMed
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Associating Drugs, Targets and Clinical Outcomes into an Integrated Network Affords a New Platform for Computer-Aided Drug Repurposing
Tudor I Oprea, Sonny Kim Nielsen, Oleg Ursu, Jeremy J Yang, Olivier Taboureau, Stephen L Mathias, Irene Kouskoumvekaki, Larry A Sklar, Cristian G Bologa
Molecular Informatics), March 17, 2011 |
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Mycobacterial species as case-study of comparative genome analysis
Zakham F, Belayachi L, Ussery D, Akrim M, Benjouad A, El Aouad R, Ennaji MM
Cell. Mol. Biol. (Noisy-le-grand):OL1462-9, 2011 |
PubMed
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Revealing the beneficial effect of protease supplementation to high gravity beer fermentations using \"-omics\" techniques
Piddocke MP, Fazio A, Vongsangnak W, Wong ML, Heldt-Hansen HP, Workman C, Nielsen J, Olsson L
Microb. Cell Fact. 10:27 doi:10.1186/1475-2859-10-27, 2011 |
PubMed
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In silico Predictions of hERG Channel Blockers in Drug Discovery: From Ligand-Based and Target-Based Approaches to Systems Chemical Biology
Taboureau O, Jørgensen FS
Comb. Chem. High Throughput Screen. 14(5):375-87, 2011 |
PubMed
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Evolutionary dynamics of bacteria in a human host environment
Yang L, Jelsbak L, Marvig RL, Damkiær S, Workman CT, Rau MH, Hansen SK, Folkesson A, Johansen HK, Ciofu O, Høiby N, Sommer MO, Molin S
Proceedings of the National Academy of Sciences U.S.A. 108(18):7481-6 doi:10.1073/pnas.1018249108, 2011 |
PubMed
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Genome Sequence of the Campylobacter jejuni strain 327, a turkey strain isolated from a slaughterhouse
Takamiya M, Ozen A, Rasmussen M, Alter T, Gilbert T, Ussery D, Knøchel S
Standards in Genomic Sciences, May 12, 2011 |
Relevant URL
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Enterotypes of the human gut microbiome
Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J; MetaHIT Consortium, Antolín M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Mérieux A, Melo Minardi R, M\'rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, Bork P
Nature 473(7346):174-80 doi:10.1038/nature09944, 2011 |
PubMed
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Correlation of sCD23 release and immunoglobulin (E, A, G, M) synthesis by peripheral blood lymphocytes of atopic patients
Bujanowski-Weber J, Knöller I, Pfeil T, Luther H, Altmeyer P, König W
International Archives of Allergy and Immunology . 92(2):113-8, 2011 |
PubMed
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Meta-analysis of heterogeneous data sources for genome-scale identification of risk genes in complex phenotypes
Pers TH, Hansen NT, Lage K, Koefoed P, Dworzynski P, Miller ML, Flint TJ, Mellerup E, Dam H, Andreassen OA, Djurovic S, Melle I, Børglum AD, Werge T, Purcell S, Ferreira MA, Kouskoumvekaki I, Workman CT, Hansen T, Mors O, Brunak S
Genet. Epidemiol. 35(5):318-32 doi:10.1002/gepi.20580, 2011 |
PubMed
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Back to the Roots: Prediction of Biologically Active Natural Products from Ayurveda Traditional Medicine
Polur H, Joshi T, Workman CT, Lavekar G, Kouskoumvekaki I
Molecular Informatics, February 10, 2011 |
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Paradoxical relationship between chromosomal instability and survival outcome in cancer
Birkbak NJ, Eklund AC, Li Q, McClelland SE, Endesfelder D, Tan P, Tan IB, Richardson AL, Szallasi Z, Swanton C
Cancer Res. 71(10):3447-52 doi:10.1158/0008-5472.CAN-10-3667, 2011 |
PubMed
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Using a structural and logics systems approach to infer bHLH DNA binding specificity determinants
De Masi F, Grove CA, Vedenko A, Alibés A, Gisselbrecht SS, Serrano L, Bulyk ML, Walhout AJ
Nucleic Acids Research. 39(11):4553-63 doi:10.1093/nar/gkr070, 2011 |
PubMed
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Functional analysis of frequently expressed Chinese rhesus macaque MHC class I molecules Mamu-A1*02601 and Mamu-B*08301 reveals HLA-A2 and HLA-A3 supertypic specificities
Southwood S, Solomon C, Hoof I, Rudersdorf R, Sidney J, Peters B, Wahl A, Hawkins O, Hildebrand W, Mothé BR, Sette A
Immunogenetics 63(5):275-90 doi:10.1007/s00251-010-0502-8, 2011 |
PubMed
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Genome-Based In Silico Identification of New Mycobacterium tuberculosis Antigens Activating Polyfunctional CD8+ T Cells in Human Tuberculosis
Tang ST, van Meijgaarden KE, Caccamo N, Guggino G, Klein MR, van Weeren P, Kazi F, Stryhn A, Zaigler A, Sahin U, Buus S, Dieli F, Lund O, Ottenhoff TH
The Journal of Immunology. 186(2):1068-80 doi:10.4049/jimmunol.1002212, 2011 |
PubMed
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Bistability in autoimmune diseases
Rapin N, Mosekilde E, Lund O
Autoimmunity 44(4):256-60 doi:10.3109/08916934.2010.523233, 2011 |
PubMed
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A Closer Look at Bacteroides: Phylogenetic Relationship and Genomic Implications of a Life in the Human Gut
Karlsson FH, Ussery DW, Nielsen J, Nookaew I
Microb. Ecol. 61(3):473-85 doi:10.1007/s00248-010-9796-1, 2011 |
PubMed
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Comparative analysis of a large panel of non-starch polysaccharides reveals structures with selective regulatory properties in dendritic cells
Wismar R, Brix S, Lærke HN, Frøkiær H
Mol Nutr Food Res 55(3):443-54 doi:10.1002/mnfr.201000230, 2011 |
PubMed
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2010
Early adaptive developments of Pseudomonas aeruginosa after the transition from life in the environment to persistent colonization in the airways of human cystic fibrosis hosts.
Rau MH, Hansen SK, Johansen HK, Thomsen LE, Workman CT, Nielsen KF, Jelsbak L, Høiby N, Yang L, Molin S
Environmental Microbiology . 2010 Jun;12(6):1643-58., 2010 |
PubMed
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Lazarus1, a DUF300 protein, contributes to programmed cell death associated with Arabidopsis acd11 and the hypersensitive response
Malinovsky FG, Brodersen P, Fiil BK, McKinney LV, Thorgrimsen S, Beck M, Nielsen HB, Pietra S, Zipfel C, Robatzek S, Petersen M, Hofius D, Mundy J
PLoS ONE 5(9):e12586 doi:10.1371/journal.pone.0012586, 2010 |
PubMed
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Yeast biological networks unfold the interplay of antioxidants, genome and phenotype, and reveal a novel regulator of the oxidative stress response.
Otero JM, Papadakis MA, Udatha DB, Nielsen J, Panagiotou G
PubMed, 2010 |
Relevant URL
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ImmunoGrid: towards agent-based simulations of the human immune system at a natural scale
Halling-Brown M, Pappalardo F, Rapin N, Zhang P, Alemani D, Emerson A, Castiglione F, Duroux P, Pennisi M, Miotto O, Churchill D, Rossi E, Moss DS, Sansom CE, Bernaschi M, Lefranc MP, Brunak S, Lund O, Motta S, Lollini PL, Murgo A, Palladini A, Basford KE, Brusic V, Shepherd AJ
Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences 368(1920):2799-815 doi:10.1098/rsta.2010.0067, 2010 |
PubMed
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HLA class I binding 9mer peptides from influenza A virus induce CD4 T cell responses
Wang M, Larsen MV, Nielsen M, Harndahl M, Justesen S, Dziegiel MH, Buus S, Tang ST, Lund O, Claesson MH
PLoS ONE 5(5):e10533 doi:10.1371/journal.pone.0010533, 2010 |
PubMed
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Plasmodium falciparum population dynamics in a cohort of pregnant women in Senegal
Guitard J, Andersen P, Ermont C, Gnidehou S, Fievet N, Lund O, Deloron P, Ndam NT
Malar. J. 9:165 doi:10.1186/1475-2875-9-165, 2010 |
PubMed
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Identification of CD8+ T cell epitopes in the West Nile virus polyprotein by reverse-immunology using NetCTL
Larsen MV, Lelic A, Parsons R, Nielsen M, Hoof I, Lamberth K, Loeb MB, Buus S, Bramson J, Lund O
PLoS ONE 5(9):e12697 doi:10.1371/journal.pone.0012697, 2010 |
PubMed
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MULTIPRED2: a computational system for large-scale identification of peptides predicted to bind to HLA supertypes and alleles
Zhang GL, Deluca DS, Keskin DB, Chitkushev L, Zlateva T, Lund O, Reinherz EL, Brusic V
Journal of Immunological Methods 374:53-61 doi:10.1016/j.jim.2010.11.009, 2010 |
PubMed
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Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains
Canelas AB, Harrison N, Fazio A, Zhang J, Pitkänen JP, van den Brink J, Bakker BM, Bogner L, Bouwman J, Castrillo JI, Cankorur A, Chumnanpuen P, Daran-Lapujade P, Dikicioglu D, van Eunen K, Ewald JC, Heijnen JJ, Kirdar B, Mattila I, Mensonides FI, Niebel A, Penttilä M, Pronk JT, Reuss M, Salusjärvi L, Sauer U, Sherman D, Siemann-Herzberg M, Westerhoff H, de Winde J, Petranovic D, Oliver SG, Workman CT, Zamboni N, Nielsen J
Nature Communication 1:145 doi:10.1038/ncomms1150, 2010 |
PubMed
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An Inordinate Fondness of Bacteria - a review of Signature in the Cell by Stephen Meyer
Ussery DW
NCSE Reports, 2010 |
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One Small Step for Bacteria, or One Giant Leap for Mankind?
Ussery DW
Journal of Cosmology, 2010 |
Read article
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Structural Properties of MHC Class II Ligands, Implications for the Prediction of MHC Class II Epitopes
Jørgensen KW, Buus S, Nielsen M
PLoS One, 2010 |
Read article
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Induction of foot-and-mouth disease virus (FMDV) specific cytotoxic T cell killing by vaccination
Patch JR, Pedersen LE, Toka FN, Moreas M, Grubman MJ, Nielsen M, Jungersen G, Buus S, Golde WT
Clin. Vaccine Immunol. 18(2):280-8 doi:10.1128/CVI.00417-10, 2010 |
PubMed
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Proteome analysis of pod and seed development in the model legume Lotus japonicus
Nautrup-Pedersen G, Dam S, Laursen BS, Siegumfeldt AL, Nielsen K, Goffard N, Stærfeldt HH, Friis C, Sato S, Tabata S, Lorentzen A, Roepstorff P, Stougaard J
Rev Esp Enferm Dig 78(4):205-9, 2010 |
PubMed
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An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators
Gautier L
BMC Bioinformatics, 2010 |
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Strain M4-5 Isolated From Human Colonic Flora Attenuates Intestinal Inflammation
Avram-Hananel L, Stock J, Parlesak A, Bode C, Schwartz B, Durans E
Dis. Colon Rectum 53(12):1676-86 doi:10.1007/DCR.0b013e3181f4b148, 2010 |
PubMed
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Minimising Immunohistochemical False Negative ER Classification Using a Complementary 23 Gene Expression Signature of ER Status
Li Q, Eklund AC, Juul N, Haibe-Kains B, Workman CT, Richardson AL, Szallasi Z, Swanton C
PLoS ONE 5(12):e15031 doi:10.1371/journal.pone.0015031, 2010 |
PubMed
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In Silico Prediction of Human Pathogenicity in the γ-Proteobacteria
Andreatta M, Nielsen M, Møller Aarestrup F, Lund O
PLoS ONE 5(10):e13680 doi:10.1371/journal.pone.0013680, 2010 |
PubMed
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Pharmacophore-driven identification of PPARã agonists from natural sources
Petersen RK, Christensen KB, Assimopoulou AN, Fretté X, Papageorgiou VP, Kristiansen K, Kouskoumvekaki I
J. Comput. Aided Mol. Des. 25(2):107-16 doi:10.1007/s10822-010-9398-5, 2010 |
PubMed
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Peptide binding predictions for HLA DR, DP and DQ molecules
Wang P, Sidney J, Kim Y, Sette A, Lund O, Nielsen M, Peters B
BMC Bioinformatics 11:568 doi:10.1186/1471-2105-11-568, 2010 |
PubMed
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NetTurnP - Neural Network Prediction of Beta-turns by Use of Evolutionary Information and Predicted Protein Sequence Features
Petersen B, Lundegaard C, Petersen TN
PLoS ONE 5(11):e15079 doi:10.1371/journal.pone.0015079, 2010 |
PubMed
NetTurnP
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HLArestrictor-a tool for patient-specific predictions of HLA restriction elements and optimal epitopes within peptides
Erup Larsen M, Kloverpris H, Stryhn A, Koofhethile CK, Sims S, Ndung\'u T, Goulder P, Buus S, Nielsen M
Immunogenetics 63(1):43-55 doi:10.1007/s00251-010-0493-5, 2010 |
PubMed
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Ethicity and Stratum Corneum Ceramides
Jungersted JM, Høgh J, Hellgren LI, Jemec G & Agner T
Br. J. Dermatol. 163(6):1169-73 doi:10.1111/j.1365-2133.2010.10080.x, 2010 |
PubMed
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Transcriptome differentiation along the dorso-ventral axis in laser-captured microdissected rat hippocampal granular cell layer
Christensen T, Bisgaard CF, Nielsen HB, Wiborg O
Neuroscience 170(3):731-41 doi:10.1016/j.neuroscience.2010.07.016, 2010 |
PubMed
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Many Putative Endocrine Disruptors Inhibit Prostaglandin Synthesis
Kristensen DM, Skalkam ML, Audouze K, Lesné L, Desdoits-Lethimonier C, Frederiksen H, Brunak S, Skakkebaek NE, Jégou B, Hansen JB, Junker S, Leffers H
Environ. Health Perspect. 119(4):534-41 doi:10.1289/ehp.1002635, 2010 |
PubMed
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NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure
Nielsen M, Justesen S, Lund O, Lundegaard C, Buus S
Immunome Res 6:9 doi:10.1186/1745-7580-6-9, 2010 |
PubMed
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Prediction of epitopes using neural network based methods
Lundegaard C, Lund O, Nielsen M
Journal of Immunological Methods 374:26-34 doi:10.1016/j.jim.2010.10.011, 2010 |
PubMed
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State of the art and challenges in sequence based T-cell epitope prediction
Lundegaard C, Hoof I, Lund O, Nielsen M
Immunome Res:S3 doi:10.1186/1745-7580-6-S2-S3, 2010 |
PubMed
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Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic Residue Identification
Buslje CM, Teppa E, Doménico TD, Delfino JM, Nielsen M
PLoS Comput. Biol. 6(11):e1000978 doi:10.1371/journal.pcbi.1000978, 2010 |
PubMed
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Novel insights into the global proteome responses of insulin-producing INS-1E cells to different degrees of endoplasmic reticulum stress
D\\\'Hertog W, Maris M, Ferreira GB, Verdrengh E, Lage K, Hansen DA, Cardozo AK, Workman CT, Moreau Y, Eizirik DL, Waelkens E, Overbergh L, Mathieu C
Journal of Proteome Research. 9(10):5142-52 doi:10.1021/pr1004086, 2010 |
PubMed
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BioXSD: the common data-exchange format for everyday bioinformatics web services
Kalas M, Puntervoll P, Joseph A, Bartaseviciute E (Karosiene published as Bartaseviciute), Töpfer A, Venkataraman P, Pettifer S, Bryne JC, Ison J, Blanchet C, Rapacki K, Jonassen I
Bioinformatics 26(18):i540-6 doi:10.1093/bioinformatics/btq391, 2010 |
PubMed
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ChemProt: a disease chemical biology database
Taboureau O, Nielsen SK, Audouze K, Weinhold N, Edsgärd D, Roque FS, Kouskoumvekaki I, Bora A, Curpan R, Jensen TS, Brunak S, Oprea TI
Nucleic Acids Research. 39:D367-72 doi:10.1093/nar/gkq906, 2010 |
PubMed
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PGC-1{alpha}, A Potential Therapeutic Target for Early Intervention in Parkinson\\\\\\\'s Disease
Zheng B, Liao Z, Locascio JJ, Lesniak KA, Roderick SS, Watt ML, Eklund AC, Zhang-James Y, Kim PD, Hauser MA, Grünblatt E, Moran LB, Mandel SA, Riederer P, Miller RM, Federoff HJ, Wüllner U, Papapetropoulos S, Youdim MB, Cantuti-Castelvetri I, Young AB, Vance JM, Davis RL, Hedreen JC, Adler CH, Beach TG, Graeber MB, Middleton FA, Rochet JC, Scherzer CR
Science Translational Medicine 2(52):52ra73 doi:10.1126/scitranslmed.3001059, 2010 |
PubMed
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Autoimmunity in Arabidopsis acd11 Is Mediated by Epigenetic Regulation of an Immune Receptor
Palma K, Thorgrimsen S, Malinovsky FG, Fiil BK, Nielsen HB, Brodersen P, Hofius D, Petersen M, Mundy J
PLoS Pathog. 6(10):e1001137 doi:10.1371/journal.ppat.1001137, 2010 |
PubMed
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Equitoxic Doses of 5-Azacytidine and 5-Aza-2ŒDeoxycytidine Induce Diverse Immediate and Overlapping Heritable Changes in the Transcriptome
Qiu X, Hother C, Ralfkiær UM, Søgaard A, Lu Q, Workman CT, Liang G, Jones PA, Grønbæk K
PLoS ONE 5(9) doi:10.1371/journal.pone.0012994, 2010 |
PubMed
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Insight into Antigenic Diversity of VAR2CSA-DBL5å Domain from Multiple Plasmodium falciparum Placental Isolates
Gnidehou S, Jessen L, Gangnard S, Ermont C, Triqui C, Quiviger M, Guitard J, Lund O, Deloron P, Ndam NT
PLoS ONE 5(10) doi:10.1371/journal.pone.0013105, 2010 |
PubMed
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Ultrastructural and molecular distinctions between the porcine inner cell mass and epiblast reveal unique pluripotent cell states
Hall VJ, Jacobsen JV, Rasmussen MA, Hyttel P
Dev. Dyn. 239(11):2911-20 doi:10.1002/dvdy.22424, 2010 |
PubMed
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The interplay of descriptor-based computational analysis with pharmacophore modeling builds the basis for a novel classification scheme for feruloyl esterases
Udatha DB, Kouskoumvekaki I, Olsson L, Panagiotou G
Biotechnol. Adv. 29(1):94-110 doi:10.1016/j.biotechadv.2010.09.003, 2010 |
PubMed
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Navigating the human metabolome for biomarker identification and design of pharmaceutical molecules
Kouskoumvekaki I, Panagiotou G
Journal of Biomedicine and Biotechnology, 2010 |
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Design of an Enterobacteriaceae Pan-genome Microarray Chip
Lukjancenko O, Ussery DW
CSBio 2010 Proceedings, 115: 174-189, 2010 |
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The Genome Atlas Resource
Qureshi M, Rotenberg E, Staerfeldt HH, Hansson L, Ussery DW
CSBio 2010 Proceedings, 115: 149-158, 2010 |
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Combining substrate specificity analysis with support vector classifiers reveals feruloyl esterase as a phylogenetically informative protein group
Olivares R, Sunner H, Frisvad JC, Olsson L, Nielsen J, Panagiotou G
PLoS ONE 5(9):e12781 doi:10.1371/journal.pone.0012781, 2010 |
PubMed
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Antioxidant properties of modified rutin esters by DPPH, reducing power, iron chelation and human low density lipoprotein assays
Lue BM, Nielsen NS, Jacobsen C, Hellgren LI, Guo Z, Xu XB
Food Chemistry, 123:221-230, 2010 |
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Changes in skin barrier during treatment with systemic alitretinoin: focus on skin susceptibility and stratum corneum ceramides
Jungersted JM, Hogh JK, Hellgren LI, Jemec GB, Agner T
Arch. Dermatol. Res. 302(9):653-6 doi:10.1007/s00403-010-1057-0, 2010 |
PubMed
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Improved glucose tolerance after intensive life style intervention occurs without changes in muscle ceramide or triacylglycerol in morbidly obese subjects
Helge JW, Stallknecht B, Drachmann T, Hellgren LI, Jimenez-Jimenez R, Andersen JL, Richelsen B, Bruun JM
Acta Physiologica 201(3):357-64 doi:10.1111/j.1748-1716.2010.02180.x, 2010 |
PubMed
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Skin barrier response to occlusion of healthy and irritated skin: Differences in trans-epidermal water loss, erythema and stratum corneum lipids
Jungersted JM, Hogh JK, Hellgren LI, Jemec GB, Agner T
Contact Derm. 63(6):313-9 doi:10.1111/j.1600-0536.2010.01773.x, 2010 |
PubMed
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Twenty-eight divergent polysaccharide loci specifying within and amongst strain capsule diversity in three strains of Bacteroides fragilis
Patrick S, Blakely GW, Houston S, Moore J, Abratt VR, Bertalan M, Cerdeño-Tárraga AM, Quail MA, Corton N, Corton C, Bignell A, Barron A, Clark L, Bentley SD, Parkhill J
Microbiology (Reading, Engl.) 156:3255-69 doi:10.1099/mic.0.042978-0, 2010 |
PubMed
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Plasmodium falciparum Erythrocyte Membrane Protein 1 Diversity in Seven Genomes – Divide and Conquer
Rask TS, Hansen DA, Theander TG, Pedersen AG, Lavstsen T
PLoS Comput. Biol. 6(9) doi:10.1371/journal.pcbi.1000933, 2010 |
PubMed
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Country-specific chemical signatures of persistent environmental compounds in breast milk
Krysiak-Baltyn K, Toppari J, Skakkebaek NE, Jensen TS, Virtanen HE, Schramm KW, Shen H, Vartiainen T, Kiviranta H, Taboureau O, Brunak S, Main KM
International Journal of Andrology . 33(2):270-8 doi:10.1111/j.1365-2605.2009.00996.x, 2010 |
PubMed
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The EMBRACE web service collection
Pettifer S, Ison J, Kalas M, Thorne D, McDermott P, Jonassen I, Liaquat A, Fernández JM, Rodriguez JM; INB-Partners, Pisano DG, Blanchet C, Uludag M, Rice P, Bartaseviciute E (Karosiene published as Bartaseviciute), Rapacki K, Hekkelman M, Sand O, Stockinger H, Clegg AB, Bongcam-Rudloff E, Salzemann J, Breton V, Attwood TK, Cameron G, Vriend G
Nucleic Acids Research. 38:W683-8 doi:10.1093/nar/gkq297, 2010 |
PubMed
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Genomic comparisons of Brucella spp. and closely related bacteria using base compositional and proteome based methods
Bohlin J, Snipen L, Cloeckaert A, Lagesen K, Ussery D, Kristoffersen AB, Godfroid J
BMC Evol. Biol. 10:249 doi:10.1186/1471-2148-10-249, 2010 |
PubMed
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Predictive biomarker discovery through the parallel integration of clinical trial and functional genomics datasets
Swanton C, Larkin JM, Gerlinger M, Eklund AC, Howell M, Stamp G, Downward J, Gore M, Futreal PA, Escudier B, Andre F, Albiges L, Beuselinck B, Oudard S, Hoffmann J, Gyorffy B, Torrance C, Boehme KA, Volkmer H, Toschi L, Nicke B, Beck M, Szallasi Z
Genome Med 2(8):53 doi:10.1186/gm174, 2010 |
PubMed
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Targeting chromosomal instability and tumour heterogeneity in HER2 positive breast cancer
Burrell RA, Juul N, Johnston SR, Reis-Filho J, Szallasi Z, Swanton C
J. Cell. Biochem. 111(4):782-90 doi:10.1002/jcb.22781, 2010 |
PubMed
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Genomic Characterization of Campylobacter jejuni strain M1
Friis C, Wassenaar T, Javed M, Snipen L, Lagesen K, Hallin P, Newell D, Toszeghy M, RIdley A, Manning G, Ussery D
PLoS ONE 5(8):e12253 doi:10.1371/journal.pone.0012253, 2010 |
PubMed
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Analysis of intra-genomic GC content homogeneity within prokaryotes
Bohlin J, Snipen L, Hardy SP, Kristoffersen AB, Lagesen K, Donsvik T, Skjerve E, Ussery DW
BMC Genomics 11:464 doi:10.1186/1471-2164-11-464, 2010 |
PubMed
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Lykke i absurditetens tidsalder
Schou T
Dagbladet Information, 3. juni 2010, 2010 |
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Mice, men and MHC supertypes
Lundegaard C
Expert Rev Vaccines 9(7):713-8 doi:10.1586/erv.10.76, 2010 |
PubMed
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Bioinformatics Training: A Review of Challenges, Actions and Support Requirements
Schneider MV, Watson J, Attwood T, Rother K, Budd A, McDowall J, Via A, Fernandes P, Nyronen T, Blicher T, Jones P, Blatter MC, De Las Rivas J, Phillip Judge D, van der Gool W, Brooksbank C
Briefings in Bioinformatics 11(6):544-51 doi:10.1093/bib/bbq021, 2010 |
PubMed
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Using protein design algorithms to understand the molecular basis of disease caused by protein-DNA interactions: the Pax6 example
Alibes A, Nadra A, De Masi F, Bulyk M, Serrano L, Stricher F
Nucleic Acids Research. 38(21):7422-31 doi:10.1093/nar/gkq683, 2010 |
PubMed
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Transcriptomes of the desiccation- tolerant resurrection plant Craterostigma plantagineum
Rodriguez MC, Edsgärd D, Hussain SS, Alquezar D, Rasmussen M, Gilbert T, Nielsen HB, Bartels D, Mundy J
Plant J. 63(2):212-28 doi:10.1111/j.1365-313X.2010.04243.x, 2010 |
PubMed
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Comparison of 61 Sequenced Escherichia coli Genomes Microbial Ecology
Lukjancenko O, Wassenaar TM, Ussery DW
Microb. Ecol. 60(4):708-20 doi:10.1007/s00248-010-9717-3, 2010 |
PubMed
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Dissecting spatio-temporal protein networks driving human heart development and related disorders
Lage K, Møllgård K, Greenway S, Wakimoto H, Gorham JM, Workman CT, Bendsen E, Hansen NT, Rigina O, Roque FS, Wiese C, Christoffels VM, Roberts AE, Smoot LB, Pu WT, Donahoe PK, Tommerup N, Brunak S, Seidman CE, Seidman JG, Larsen LA
Mol. Syst. Biol. 6:381 doi:10.1038/msb.2010.36, 2010 |
PubMed
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CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles
Nielsen M, Lundegaard C, Lund O, Petersen TN
Nucleic Acids Research. 38:W576-81 doi:10.1093/nar/gkq535, 2010 |
PubMed
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Lactobacillus acidophilus induces virus immune defence genes in murine dendritic cells by a Toll-like receptor-2-dependent mechanism
Weiss G, Rasmussen S, Zeuthen LH, Nielsen BN, Jarmer H, Jespersen L, Frøkiær H
Immunology 131(2):268-81 doi:10.1111/j.1365-2567.2010.03301.x, 2010 |
PubMed
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Bifidobacterium bifidum Actively Changes the Gene Expression Profile Induced by Lactobacillus acidophilus in Murine Dendritic Cells
Weiss G, Rasmussen S, Nielsen Fink L, Jarmer H, Nøhr Nielsen B, Frøkiær H
PLoS ONE 5(6):e11065 doi:10.1371/journal.pone.0011065, 2010 |
PubMed
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Major histocompatibility complex class I binding predictions as a tool in epitope discovery
Lundegaard C, Lund O, Buus S, Nielsen M
Immunology 130(3):309-18 doi:10.1111/j.1365-2567.2010.03300.x, 2010 |
PubMed
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Effects of Fish Oil Supplementation on Markers of the Metabolic Syndrome
Pedersen MH, Mølgaard C, Hellgren LI, Lauritzen L
J. Pediatr. 157(3):395-400, 400.e1 doi:10.1016/j.jpeds.2010.04.001, 2010 |
PubMed
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Homology Modelling of the GABA Transporter and Analysis of Tiagabine Binding.
Skovstrup S, Taboureau O, Bräuner-Osborne H, Jørgensen FS
ChemMedChem 5(7):986-1000 doi:10.1002/cmdc.201000100, 2010 |
PubMed
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Differential sensitivity of melanoma cell lines with BRAFV600E mutation to the specific raf inhibitor PLX4032
Søndergaard JN, Nazarian R, Wang Q, Guo D, Hsueh T, Mok S, Sazegar H, MacConaill LE, Barretina JG, Kehoe SM, Attar N, von Euw E, Zuckerman JE, Chmielowski B, Comin-Anduix B, Koya RC, Mischel PS, Lo RS, Ribas A
J Transl Med 8:39 doi:10.1186/1479-5876-8-39, 2010 |
PubMed
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Deciphering Diseases and Biological Targets for Environmental Chemicals using Toxicogenomics Networks
Audouze K, Juncker AS, Roque F, Krysiak-Baltyn K, Weinhold N, Taboureau O, Jensen TS, Brunak S
PLoS Comput. Biol. 6(5):e1000788 doi:10.1371/journal.pcbi.1000788, 2010 |
PubMed
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MHC Class II epitope predictive algorithms
Nielsen M, Lund O, Buus S, Lundegaard C
Immunology 130(3):319-28 doi:10.1111/j.1365-2567.2010.03268.x, 2010 |
PubMed
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Computational Immunology Meets Bioinformatics: The Use of Prediction Tools for Molecular Binding in the Simulation of the Immune System
Rapin N, Lund O, Bernaschi M, Castiglione F
PLoS ONE 5(4):e9862 doi:10.1371/journal.pone.0009862, 2010 |
PubMed
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Parallel Genetic and Phenotypic Evolution of DNA Superhelicity in Experimental Populations of Escherichia coli
Crozat E, Winkworth C, Gaffé J, Hallin PF, Riley MA, Lenski RE, Schneider D
Mol. Biol. Evol. 27(9):2113-28 doi:10.1093/molbev/msq099, 2010 |
PubMed
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Prediction of Glycosylation Sites in Proteins
Julenius K, Johansen M, Zhang Y, Brunak S, Gupta R
Bioinformatics for Glycobiology and Glycomics, 2010 |
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Protein annotation in the era of personal genomics
Blicher T, Gupta R, Wesolowska A, Jensen LJ, Brunak S
Curr. Opin. Struct. Biol. 20(3):335-41 doi:10.1016/j.sbi.2010.03.008, 2010 |
PubMed
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Metabolic network topology reveals transcriptional regulatory signatures of type 2 diabetes
Zelezniak A, Pers TH, Soares S, Patti ME, Patil KR
PLoS Comput. Biol. 6(4):e1000729 doi:10.1371/journal.pcbi.1000729, 2010 |
PubMed
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Malaria vaccine design - Identification of epitopes and characterization of antigenic variation in the PfEMP1 family
Rask TS
Ph.D. thesis, 2010 |
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Ceramides and barrier function in healthy skin
Jungerstedt J, Hellgren LI, Drachmann T, Hoegh JG, Jemec GBE, Agner T
Acta Derm. Venereol. 90(4):350-3 doi:10.2340/00015555-0894, 2010 |
PubMed
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NetCTLpan: pan-specific MHC class I pathway epitope predictions
Stranzl T, Larsen MV, Lundegaard C, Nielsen M
Immunogenetics 62(6):357-68 doi:10.1007/s00251-010-0441-4, 2010 |
PubMed
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The Degree of Predicted Minor Histocompatibility Antigen Mismatch Correlates with Poorer Clinical Outcome of Non-myeloablative Allogeneic Hematopoietic Cell Transplantation
Larsen ME, Kornblit B, Larsen MV, Masmas TN, Nielsen M, Thiim M, Garred P, Stryhn A, Lund O, Buus S, Vindelov L
Biol. Blood Marrow Transplant. 16(10):1370-81 doi:10.1016/j.bbmt.2010.03.022, 2010 |
PubMed
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Interdisciplinary Analysis of HIV-Specific CD8+ T Cell Responses against Variant Epitopes Reveals Restricted TCR Promiscuity
Hoof I, Pérez CL, Buggert M, Gustafsson RK, Nielsen M, Lund O, Karlsson AC
The Journal of Immunology. 184(9):5383-91 doi:10.4049/jimmunol.0903516, 2010 |
PubMed
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Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis
Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M
Science Signaling 3(104):ra3 doi:10.1126/scisignal.2000475, 2010 |
PubMed
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Acupuncture Induces a Pro-Inflammatory Immune Response Intensified by a Conditioning-Expectation Effect
Karst M, Schneidewind D, Scheinichen D, Juettner B, Bernateck M, Molsberger A, Parlesak A, Passie T, Hoy L, Fink M
Forsch Komplementmed 17(1):21-7 doi:10.1159/000264657, 2010 |
PubMed
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The Type 1 Diabetes - HLA Susceptibility Interactome - Identification of HLA Genotype-Specific Disease Genes for Type 1 Diabetes
Brorsson C, Hansen NT, Bergholdt R, Brunak S, Pociot F
PLoS ONE 5(3):e9576 doi:10.1371/journal.pone.0009576, 2010 |
PubMed
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Chemoinformatics-assisted development of new anti-biofilm compounds
Dürig A, Kouskoumvekaki I, Vejborg RM, Klemm P
Appl. Microbiol. Biotechnol. 87(1):309-17 doi:10.1007/s00253-010-2471-0, 2010 |
PubMed
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Standard operating procedure for computing pangenome trees
Snipen L, Ussery DW
Standards in Genomic Sciences, 2010 |
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A human gut microbial gene catalogue established by metagenomic sequencing
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, MetaHIT Consortium, Bork P, Ehrlich DS & Wang J
Nature 464(7285):59-65 doi:10.1038/nature08821, 2010 |
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Nature frontpage
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Assessment of an RNA interference screen-derived mitotic and ceramide pathway metagene as a predictor of response to neoadjuvant paclitaxel for primary triple-negative breast cancer: a retrospective analysis of five clinical trials
Juul N, Szallasi Z, Eklund AC, Li Q, Burrell RA, Gerlinger M, Valero V, Andreopoulou E, Esteva FJ, Symmans WF, Desmedt C, Haibe-Kains B, Sotiriou C, Pusztai L, Swanton C
Lancet Oncol. 11(4):358-65 doi:10.1016/S1470-2045(10)70018-8, 2010 |
PubMed
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The phosphorylation specificity of B-RAF(WT), B-RAF(D594V), B-RAF(V600E) and B-RAF(K601E) kinases: An in silico study
Fratev F, Jónsdóttir SO
J. Mol. Graph. Model. 28(7):598-603 doi:10.1016/j.jmgm.2009.12.005, 2010 |
PubMed
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Limitations of Ab Initio Predictions of Peptide Binding to MHC Class II Molecules
Zhang H, Wang P, Papangelopoulos N, Xu Y, Sette A, Bourne PE, Lund O, Ponomarenko J, Nielsen M, Peters B
PLoS ONE 5(2):e9272 doi:10.1371/journal.pone.0009272, 2010 |
PubMed
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Stratum corneum lipids, skin barrier function and filaggrin mutations in patients with atopic eczema
Jungersted JM, Scheer H, Mempel M, Baurecht H, Cifuentes L, Høgh JK, Hellgren LI, Jemec GBE, Agner T & Weidinger S
Allergy 65(7):911-8 doi:10.1111/j.1398-9995.2010.02326.x, 2010 |
PubMed
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OCT4 and downstream factors are expressed in human somatic urogenital epithelia and in culture of epididymal spheres
Kristensen DM, Nielsen JE, Kalisz M, Dalgaard MD, Audouze K, Larsen ME, Jacobsen GK, Horn T, Brunak S, Skakkebaek NE, Leffers H
Mol. Hum. Reprod. 16(11):835-45 doi:10.1093/molehr/gaq008, 2010 |
PubMed
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Trichomonas vaginalis vast BspA-like gene family: evidence for functional diversity from structural organisation and transcriptomics
Noel CJ, Diaz N, Sicheritz-Ponten T, Safarikova L, Tachezy J, Tang P, Fiori PL, Hirt RP
BMC Genomics 11:99 doi:10.1186/1471-2164-11-99, 2010 |
PubMed
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The MHC motif viewer: a visualization tool for MHC binding motifs
Rapin N, Hoof I, Lund O, Nielsen M
Curr Protoc Immunol:Unit 18.17 doi:10.1002/0471142735.im1817s88, 2010 |
PubMed
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Ancient Human Genome Sequence of an Extinct Palaeo-Eskimo
Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, Metspalu M, Metspalu E, Kivisild T, Gupta R, Bertalan M, Nielsen K, Gilbert MTP, Wang Y, Raghavan M, Campos PF, Kamp HM, Wilson AS, Gledhill A, Tridico S, Bunce M, Lorenzen ED, Binladen J, Guo X, Zhao J, Zhang X, Zhang H, Li Z, Chen M, Orlando L, Kristiansen K, Bak M, Tommerup N, Bendixen C, Pierre TL, Grønnow B, Meldgaard M, Andreasen C, Fedorova SA, Osipova LP, Higham TFG, Ramsey CB, Hansen TV, Nielsen FC, Crawford MH, Brunak S, Sicheritz-Ponten T, Villems R, Nielsen R, Krogh A, Wang J, Willerslev E
Nature 463(7282):757-62 doi:10.1038/nature08835, 2010 |
PubMed
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CD4+ T cell activation is differentially modulated by bacteria-primed dendritic cells, but generally downregulated by n-3 polyunsaturated fatty acids
Brix S, Lund P, Kjaer TMR, Straarup EM, Hellgren LI, Frøkiær H
Immunology 129(3):338-50 doi:10.1111/j.1365-2567.2009.03163.x, 2010 |
PubMed
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Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results
Gauthier NP, Jensen LJ, Wernersson R, Brunak S, Jensen TS
Nucleic Acids Research. 38:D699-702 doi:10.1093/nar/gkp1044, 2010 |
PubMed
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Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis
Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M
Science Signaling 3(104):ra3 doi:10.1126/scisignal.2000475, 2010 |
PubMed
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Amplification of LAPTM4B and YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer
Li Y, Zou L, Li Q, Haibe-Kains B, Tian R, Li Y, Desmedt C, Sotiriou C, Szallasi Z, Iglehart JD, Richardson AL, Wang ZC
Nature Medicine. 16(2):214-8 doi:10.1038/nm.2090, 2010 |
PubMed
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Efficacy of Neoadjuvant Cisplatin in Triple-Negative Breast Cancer
Silver DP, Richardson AL, Eklund AC, Wang ZC, Szallasi Z, Li Q, Juul N, Leong CO, Calogrias D, Buraimoh A, Fatima A, Gelman RS, Ryan PD, Tung NM, De Nicolo A, Ganesan S, Miron A, Colin C, Sgroi DC, Ellisen LW, Winer EP, Garber JE
Journal of Clinical Oncology. 28(7):1145-53 doi:10.1200/JCO.2009.22.4725, 2010 |
PubMed
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The Thousandth Genome – A Cautionary Tale
Lagesen K, Ussery DW, Wassenaar TM
Microbiology 156:603-609, 2010 |
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Lactobacillus acidophilus induces a slow but more sustained chemokine and cytokine response in naive foetal enterocytes compared to commensal Escherichia coli
Zeuthen LH, Fink LN, Metzdorff SB, Kristensen MB, Licht TR, Nellemann C, Frokiaer H
BMC Immunol. 11:2 doi:10.1186/1471-2172-11-2, 2010 |
PubMed
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Genomic Analysis of Two-Component Signal Transduction Proteins in Basidiomycetes
Lavín JL, Ramírez L, Ussery DW, Pisabarro AG, Oguiza JA
J. Mol. Microbiol. Biotechnol. 18(2):63-73 doi:10.1159/000277654, 2010 |
PubMed
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Differences in two-component signal transduction proteins among the genus Brucella: implications for host preference and pathogenesis
Lavín JL, Binnewies TT, Pisabarro AG, Ussery DW, García-Lobo JM, Oguiza JA
Veterinary Microbiology, in the press, 2010 |
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Phytanic acid: An overlooked bioactive fatty acid in dairy products?
Lars I Hellgren
Annals of the New York Academy of Sciences. 1190:42-9 doi:10.1111/j.1749-6632.2009.05254.x, 2010 |
PubMed
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Validation of Cyanoacrylate Method for Collection of Stratum Corneum in Human Skin for Lipid Analysis
Jungersted JM, Hellgren LI, Drachmann T, Jemec GBE, Agner T
Skin Pharmacol Physiol 23(2):62-7 doi:10.1159/000265676, 2010 |
PubMed
Read abstract
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Comparative Genomics of Green Sulfur Bacteria
Davenport C, Ussery DW, Tümmler B
Photosyn. Res. 104:137-52 doi:10.1007/s11120-009-9515-2, 2010 |
PubMed
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Lipid assymetry in plant plasma membranes: phosphate deficiency-induced phospholipid replacement is restricted to the cytosolic leaflet
Tjällström H, Hellgren LI, Wieslander Å & Sandelius AS
FASEB J. 24(4):1128-38 doi:10.1096/fj.09-139410, 2010 |
PubMed
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Mutational mapping and modeling of the binding site for (S)-citalopram in the human serotonin transporter
Andersen J, Olsen L, Hansen KB, Taboureau O, Jorgensen FS, Jorgensen AM, Bang-Andersen B, Egebjerg J, Stromgaard K, Kristensen AS
The Journal of Biological Chemistry, 2010 |
PubMed
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On the Origins of a Vibrio species
Vesth T, Wassenaar TM, Hallin PF, Snipen L, Lagesen K, , Ussery DW
Microbial Ecology, 59:1-13, 2010 |
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2009
Predicting functionality of protein-DNA interactions by integrating diverse evidence.
Ucar D, Beyer A, Parthasarathy S, Workman CT
Bioinformatics. 2009 Jun 15;25(12):i137-44., 2009 |
PubMed
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IL-1 receptor antagonism and muscle gene expression in patients with type 2 diabetes.
Berchtold LA, Larsen CM, Vaag A, Faulenbach M, Workman CT, Kruhøffer M, Donath M, Mandrup-Poulsen T
European Cytokine Network . 2009 Jun;20(2):81-7., 2009 |
PubMed
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Specificity and Promiscuity in Functional Divergence of C. elegans bHLH Transcription Factors
Grove C, De Masi F, Newburger D, Barrasa I, Bulyk ML, Walhout AC
Cell, 2009 |
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High-Resolution DNA Binding Specificity Analysis of Yeast Transcription Factors
Zhu C, Byers K, McCord RP, Shi Z, Berger MF, Newburger D, Saulrieta K, Smith Z, Shah M, Radhakrishnan M, Phillipakis AA, Hu Y, De Masi F, Pacek M, Rolfs A, Murthy TVS, LaBaer J, Bulyk ML
Genome Res. 19(4):556-66 doi:10.1101/gr.090233.108, 2009 |
PubMed
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Genome - and HLA-Wide Scanning and Validation of Cytotoxic CD8+ T Cell Responses in Bacterial and Viral Pathogens
Tuyet Tang S
Ph.D. thesis, 2009 |
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Bioinformatics and simulation of the immune system
Rapin N
Ph.D. thesis, 2009 |
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Integrative analyses of complex phenotypes
Hansen NT
Ph.D. thesis, 2009 |
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Prediction and analysis of MHC class I binding specificities beyond humans
Hoof I
Ph.D. thesis, 2009 |
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Degenerate Peptide Specificity of MHC Molecules and T cell Receptors in Immunodominance and Tolerance
Frankild S
Ph.D. thesis, 2009 |
|
Systems biology analysis of pre-mRNA splicing and alternative splicing, and its role in cancers
Wang K
Ph.D.thesis, 2009 |
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Bioinformatics Analysis of Peptide:Protein Binding
Zhang H
Ph.D. thesis, 2009 |
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Computational tools and Interoperability in Comparative Genomics
Hallin PF
Ph.D. thesis, 2009 |
|
Analysis of gene expression profiles of microdissected cell populations indicates that testicular carcinoma in situ is an arrested gonocyte
Sonne SB, Almstrup K, Dalgaard M, Juncker AS, Edsgard D, Ruban L, Harrison NJ, Schwager C, Abdollahi A, Huber PE, Brunak S, Gjerdrum LM, Moore HD, Andrews PW, Skakkebaek NE, Rajpert-De Meyts E, Leffers H
Cancer Res. 15;69(12):5241-50., 2009 |
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Studies on Monitoring and Tracking Genetic Resources
Garrity GM, Thompson LM, Ussery DW, Paskin N, Baker D, Desmeth P, Schindel DE, Ong PS
Convention on Biological Diversity (21 January, 2009)[UNEP/CBD/ABS/GTLE/2/INF/4], 2009 |
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Dietary fibers as immunoregulatory compounds in health and disease
Wismar R, Brix S, Frøkiær H, Lærke HN
Annals of the New York Academy of Sciences, 2009 |
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Pseudomonas aeruginosa quorum-sensing signal molecules interfere with dendritic cell-induced T-cell proliferation
Skindersoe ME, Zeuthen LH, Brix S, Fink LN, Lazenby J, Whittall C, Williams P, Diggle SP, Froekiaer H, Cooley M, Givskov M
FEMS Immunol. Med. Microbiol. 55(3):335-45 doi:10.1111/j.1574-695X.2008.00533.x, 2009 |
PubMed
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Probiotic yogurt in the elderly with intestinal bacterial overgrowth: endotoxaemia and innate immune functions
Schiffrin EJ, Parlesak A, Bode C, Bode JC, van\'t Hof MA, Grathwohl D, Guigoz Y
Br. J. Nutr. 101(7):961-6, 2009 |
PubMed
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Phosphatidylcholine reverses ethanol-induced increase in transepithelial endotoxin permeability and abolishes transepithelial leukocyte activation
Mitzscherling K, Volynets V, Parlesak A
Alcohol. Clin. Exp. Res. 33(3):557-62 doi:10.1111/j.1530-0277.2008.00869.x, 2009 |
PubMed
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The type 2 diabetes associated minor allele of rs2237895 KCNQ1 associates with reduced insulin release following an oral glucose load
Holmkvist J, Banasik K, Andersen G, Unoki H, Jensen TS, Pisinger C, Borch-Johnsen K, Sandbaek A, Lauritzen T, Brunak S, Maeda S, Hansen T, Pedersen O
PLoS One. 11;4(6):e5872, 2009 |
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An online survival analysis tool to rapidly assess the effect of 22,277 genes on breast cancer prognosis using microarray data of 1,809 patients
Györffy B, Lanczky A, Eklund AC, Denkert C, Budczies J, Li Q, Szallasi Z
Breast Cancer Res. Treat. 123(3):725-31 doi:10.1007/s10549-009-0674-9, 2009 |
PubMed
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The 2008 update of the Aspergillus nidulans genome annotation: a community effort
Wortman JR, Gilsenan JM, Joardar V, Deegan J, Clutterbuck J, Andersen MR, Archer D, Bencina M, Braus G, Coutinho P, von Döhren H, Doonan J, Driessen AJ, Durek P, Espeso E, Fekete E, Flipphi M, Estrada CG, Geysens S, Goldman G, de Groot PW, Hansen K, Harris SD, Heinekamp T, Helmstaedt K, Henrissat B, Hofmann G, Homan T, Horio T, Horiuchi H, James S, Jones M, Karaffa L, Karányi Z, Kato M, Keller N, Kelly DE, Kiel JA, Kim JM, van der Klei IJ, Klis FM, Kovalchuk A, Krasevec N, Kubicek CP, Liu B, Maccabe A, Meyer V, Mirabito P, Miskei M, Mos M, Mullins J, Nelson DR, Nielsen J, Oakley BR, Osmani SA, Pakula T, Paszewski A, Paulsen I, Pilsyk S, Pócsi I, Punt PJ, Ram AF, Ren Q, Robellet X, Robson G, Seiboth B, van Solingen P, Specht T, Sun J, Taheri-Talesh N, Takeshita N, Ussery D, vanKuyk PA, Visser H, van de Vondervoort PJ, de Vries RP, Walton J, Xiang X, Xiong Y, Zeng AP, Brandt BW, Cornell MJ, van den Hondel CA, Visser J, Oliver SG, Turner G
Fungal Genetics and Biology, 45:S2-S13,, 2009 |
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Studies on Monitoring and Tracking Genetic Resources: An Executive Summary
Garrity GM, Thompson LM, Ussery DW, Paskin N, Baker D, Desmeth P, Schindel DE, Ong PS
Standards in Genomic Sciences, 1:78-86, 2009 |
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The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding
Zhang H, Lund O, Nielsen M
Bioinformatics 25(10):1293-9 doi:10.1093/bioinformatics/btp137, 2009 |
PubMed
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Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information
Buslje CM, Santos J, Delfino JM, Nielsen M
Bioinformatics 25(9):1125-31 doi:10.1093/bioinformatics/btp135, 2009 |
PubMed
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Stretches of alternating pyrimidine/ purines and purines are respectively linked with pathogenicity and growth temperature in prokaryotes
Bohlin J, Hardy SP, Ussery DW
BMC Genomics 10:346 doi:10.1186/1471-2164-10-346, 2009 |
PubMed
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Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization
Aron C Eklund; Pia Friis; Rasmus Wernersson; Zoltan Szallasi
Nucleic Acids Research. 38(4):e27 doi:10.1093/nar/gkp1116, 2009 |
PubMed
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Transcriptomic variation in a coral reveals pathways of clonal organisation
Line K Bay, Bjørn Nielsen H, Hanne Jarmer, Francois Seneca, Madeleine J H van Oppe
Marine Genomics, 2009 |
Read abstract
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Induction of regulatory T cells by probiotics: potential for treatment of allergy?
Fink LN
Clinical & Experimental Allergy, (40) 5–8., 10.1111/j.1365-2222.2009.03408.x, 2009 |
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Some putative prebiotics increase the severity of Salmonella enterica serovar Typhimurium infection in mice
Petersen A, Heegaard PMH, Pedersen AL, Andersen JB, Sørensen RB, Frøkiær H, Lahtinen SJ, Ouwehand AC, Poulsen M & Licht TR
BMC Microbiology, 2009 |
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The Immune Epitope Database 2.0
Vita R, Zarebski L, Greenbaum JA, Emami H, Hoof I, Salimi N, Damle R, Sette A, Peters B
Nucleic Acids Research. 2009 Nov 11, 2009 |
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Genomic taxonomy of vibrios
Thompson CC, Vicente AC, Souza RC, Vasconcelos AT, Vesth T, Alves N Jr, Ussery DW, Iida T, Thompson FL
BMC Evol. Biol. 9:258 doi:10.1186/1471-2148-9-258, 2009 |
PubMed
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Analysis of genomic signatures in prokaryotes using multinomial regression and hierarchical clustering
Bohlin J, Skjerve E, Ussery DW
BMC Genomics, 10:487, 2009 |
Read article
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Systematic Characterization of Cellular Localization and Expression Profiles of Proteins Containing MHC Ligands
Juncker AS, Larsen MV, Weinhold N, Nielsen M, Brunak S, Lund O
/PLoS ONE/ ; 4(10): e7448. doi:10.1371/journal.pone.0007448, 2009 |
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GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes
Hallin PF, Stærfeldt HH, Rotenberg E, Binnewies TT, Benham CJ, , Ussery DW
Standards in Genomic Sciences, 1:204-215, 2009 |
Relevant URL
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Higher variability in the number of sexual partners in males can contribute to a higher prevalence of sexually transmitted diseases in females
Gouveia-Oliveira R, Pedersen AG
J. Theor. Biol. 261(1):100-6 doi:10.1016/j.jtbi.2009.06.028, 2009 |
PubMed
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Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus PAL5
Bertalan M, Albano R, Padua V, Rouws L, Rojas C, Hemerly A, Teixeira K, Schwab S, Araujo J, Oliveira A, Franca L, Magalhaes V, Alqueres S, Cardoso A, Almeida W, Loureiro MM, Nogueira E, Cidade D, Oliveira D, Simao T, Macedo J, Valadao A, Dreschsel M, Freitas F, Vidal M, Guedes H, Rodrigues E, Meneses C, Brioso P, Pozzer L
BMC Genomics 10:450doi:10.1186/1471-2164-10-450, 2009 |
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An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction.
Nielsen M, Lund O
BMC bioinformatics, 2009 |
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Impaired uptake and/or utilisation of leucine is suppressed by the SPT15-300 allele of the TATA binding protein gene.
Baerends RJ, Qiu JL, Rasmussen S, Nielsen HB, Brandt A
Appl. Environ. Microbiol. 75(19):6055-61 doi:10.1128/AEM.00989-09, 2009 |
PubMed
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Transcriptional landscape estimation from tiling array data using a model of signal shift and drift.
Nicolas P, Leduc A, Robin S, Rasmussen S, Jarmer H, Bessières P
Bioinformatics 25(18):2341-7 doi:10.1093/bioinformatics/btp395, 2009 |
PubMed
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The transcriptionally active regions in the genome of Bacillus subtilis
Rasmussen S, Nielsen HB, Jarmer H
Mol. Microbiol. 73(6):1043-57 doi:10.1111/j.1365-2958.2009.06830.x, 2009 |
PubMed
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Microbial comparative pan-genomics using binomial mixture models
Snipen L, Almøy T, Ussery DW
BMC Genomics 10:385 doi:10.1186/1471-2164-10-385, 2009 |
PubMed
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An in silico study of the molecular basis of B-RAF activation and conformational stability
Fratev FF, Jónsdóttir SÓ
BMC Struct. Biol. 9:47 doi:10.1186/1472-6807-9-47, 2009 |
PubMed
Link to publication
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Expression profiling of human genetic and protein interaction networks in type 1 diabetes
Bergholdt R, Brorsson C, Lage K, Nielsen JH, Brunak S, Pociot F
PLoS ONE 4(7):e6250 doi:10.1371/journal.pone.0006250, 2009 |
PubMed
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Proteome analysis demonstrates profound alterations in human dendritic cell nature by TX527, an analogue of vitamin D
Ferreira GB, van Etten E, Lage K, Hansen DA, Moreau Y, Workman CT, Waer M, Verstuyf A, Waelkens E, Overbergh L, Mathieu C
Proteomics 9(14):3752-64 doi:10.1002/pmic.200800848, 2009 |
PubMed
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The validation and assessment of machine learning: a game of prediction from high-dimensional data
Pers TH, Albrechtsen A, Holst C, Sørensen TI, Gerds TA
PLoS ONE 4(8):e6287 doi:10.1371/journal.pone.0006287, 2009 |
PubMed
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A generic method for assignment of reliability scores applied to solvent accessibility predictions
Petersen B, Petersen TN, Andersen P, Nielsen M, Lundegaard C
BMC Struct. Biol. 9:51 doi:10.1186/1472-6807-9-51, 2009 |
PubMed
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InterMap3D: predicting and visualizing co-evolving protein residues
Gouveia-Oliveira R, Roque FS, Wernersson R, Sicheritz-Ponten T, Sackett PW, Mølgaard A, Pedersen AG
Bioinformatics 25(15):1963-5 doi:10.1093/bioinformatics/btp335, 2009 |
PubMed
PDF
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Evolution of the leukotoxin promoter in genus Mannheimia
Larsen J, Pedersen AG, Davies R, Kuhnert P, Frey J, Christensen H, Bisgaard M, Olsen J
BMC Evol. Biol. 9:121 doi:10.1186/1471-2148-9-121, 2009 |
PubMed
PDF
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Controlled indole-3-acetaldoxime production through ethanol-induced expression of CYP79B2
Mikkelsen MD, Fuller VL, Hansen BG, Nafisi M, Olsen CE, Nielsen HB, Halkier BA
Planta 229(6):1209-17 doi:10.1007/s00425-009-0907-5, 2009 |
PubMed
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Microarray analysis reveals transcriptional plasticity in the reef building coral Acropora millepora
Bay LK, Ulstrup KE, Nielsen HB, Jarmer H, Goffard N, Willis BL, Miller DJ, van Oppen MJH
Molecular Ecology; doi: 10.1111/j.1365-294X.2009.04257.x, 2009 |
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Genome-wide gene expression profiling of SCID mice with T-cell-mediated Colitis
Brudzewsky D, Pedersen AE, Claesson MH, Gad M, Kristensen NN, Lage K, Jensen T, Tommerup N, Larsen LA, Knudsen S, Tümer Z
Scand. J. Immunol. 69(5):437-46 doi:10.1111/j.1365-3083.2009.02243.x, 2009 |
PubMed
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Evaluation of microarray preprocessing algorithms based on concordance with rt-PCR in clinical samples
Gyorffy B, Molnar B, Lage H, Szallasi Z, Eklund AC
PLoS ONE 4(5):e5645 doi:10.1371/journal.pone.0005645, 2009 |
PubMed
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Chromosomal instability determines taxane response
Swanton C, Nicke B, Schuett M, Eklund AC, Ng C, Li Q, Hardcastle T, Lee A, Roy R, East P, Kschischo M, Endesfelder D, Wylie P, Kim SN, Chen JG, Howell M, Ried T, Habermann JK, Auer G, Brenton JD, Szallasi Z, Downward J
PNAS, Proceedings of the National Academy of Sciences U.S.A. 106(21):8671-6 doi:10.1073/pnas.0811835106, 2009 |
PubMed
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Macrophages and Adipocytes in Human Obesity: Adipose Tissue Gene Expression and Insulin Sensitivity during Calorie Restriction and Weight Stabilization
Capel F, Klimcáková E, Viguerie N, Roussel B, Vítková M, Kováciková M, Polák J, Kovácová Z, Galitzky J, Maoret JJ, Hanácek J, Pers TH, Bouloumié A, Stich V, Langin D
Diabetes 58(7):1558-67 doi:10.2337/db09-0033, 2009 |
PubMed
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ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization
Pappalardo F, Halling-Brown MD, Rapin N, Zhang P, Alemani D, Emerson A, Paci P, Duroux P, Pennisi M, Palladini A, Miotto O, Churchill D, Rossi E, Shepherd AJ, Moss DS, Castiglione F, Bernaschi M, Lefranc MP, Brunak S, Motta S, Lollini PL, Basford KE, Brusic V
Brief. Bioinformatics 10(3):330-40 doi:10.1093/bib/bbp014, 2009 |
PubMed
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Identification of T1D susceptibility genes within the MHC region by combining protein interaction networks and SNP genotyping data
Brorsson C, Hansen NT, Lage K, Bergholdt R, Brunak S, Pociot F; Diabetes Genetics Consortium
Diabetes Obes Metab:60-6 doi:10.1111/j.1463-1326.2008.01004.x, 2009 |
PubMed
|
Genetic Tools and Algorithms for Gene Discovery in Major Congenital Anomalies
Donahoe PK, Noonan KM, Lage K
Birth Defects Res. Part A Clin. Mol. Teratol. 85(1):6-12 doi:10.1002/bdra.20546, 2009 |
PubMed
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Expression analyses of human cleft palate tissue suggest a role for osteopontin and immune related factors in palatal development
Jakobsen LP, Borup R, Vestergaard J, Larsen LA, Lage K, Maroun LL, Kjaer I, Niemann CU, Andersen M, Knudsen MA, Møllgård K, Tommerup N
Exp. Mol. Med. 41(2):77-85, 2009 |
PubMed
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Kinase-specific prediction of protein phosphorylation sites.
Miller ML, Blom N
Methods in Molecular Biology . 527:299-310, x doi:10.1007/978-1-60327-834-8_22, 2009 |
PubMed
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High-affinity human leucocyte antigen class I binding variola-derived peptides induce CD4+ T cell responses more than 30 years post-vaccinia virus vaccination
Wang M, Tang ST, Lund O, Dziegiel MH, Buus S, Claesson MH
Clin. Exp. Immunol. 155(3):441-6 doi:10.1111/j.1365-2249.2008.03856.x, 2009 |
PubMed
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Transepithelial activation of human leukocytes by probiotics and commensal bacteria: role of Enterobacteriaceae-type endotoxin
Baeuerlein A, Ackermann S, Parlesak A
Microbiol. Immunol. 53(4):241-50, 2009 |
PubMed
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Analysis and prediction of gene splice sites in four Aspergillus genomes
Wang K, Ussery DW, Brunak S
Fungal Genet. Biol.:S14-8 doi:10.1016/j.fgb.2008.09.010, 2009 |
PubMed
|
Fatness-associated FTO gene variant increases mortality independent of fatness--in cohorts of Danish men
Zimmermann E, Kring SI, Berentzen TL, Holst C, Pers TH, Hansen T, Pedersen O, Sørensen TI, Jess T
PLoS ONE 4(2):e4428 doi:10.1371/journal.pone.0004428, 2009 |
PubMed
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Molecular basis of inactive B-RAF(WT) and B-RAF(V600E) ligand inhibition, selectivity and conformational stability: an in silico study.
Fratev F, Jónsdóttir SO, Mihaylova E, Pajeva I
Mol. Pharm. 6(1):144-57 doi:10.1021/mp8001107, 2009 |
PubMed
|
Classification of cytochrome P450 1A2 inhibitors and noninhibitors by machine learning techniques.
Vasanthanathan P, Taboureau O, Oostenbrink C, Vermeulen NP, Olsen L, Jørgensen FS
Drug Metab. Dispos. 37(3):658-64 doi:10.1124/dmd.108.023507, 2009 |
PubMed
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Virtual screening and prediction of site of metabolism for cytochrome P450 1A2 ligands.
Vasanthanathan P, Hritz J, Taboureau O, Olsen L, Jørgensen FS, Vermeulen NP, Oostenbrink C
Journal of Chemical Information and Modeling 49(1):43-52 doi:10.1021/ci800371f, 2009 |
PubMed
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Location of the antidepressant binding site in the serotonin transporter: Importance of SER438 in recognition of citalopram and tricyclic antidepressants.
Andersen J, Taboureau O, Hansen KB, Olsen L, Egebjerg J, Strømgaard K, Kristensen AS
The Journal of Biological Chemistry 284(15):10276-84 doi:10.1074/jbc.M806907200, 2009 |
PubMed
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The proteome of seed development in the model legume Lotus japonicus.
Dam S, Laursen BS, Ornfelt JH, Jochimsen B, Stærfeldt HH, Friis C, Nielsen K, Goffard N, Besenbacher S, Krusell L, Sato S, Tabata S, Thogersen IB, Enghild JJ, Stougaard J
Plant Physiology. 149(3):1325-40 doi:10.1104/pp.108.133405, 2009 |
PubMed
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Pan-specific MHC class I predictors: A benchmark of HLA class I pan-specific prediction methods
Zhang H, Lundegaard C, Nielsen M
Bioinformatics 25(1):83-9 doi:10.1093/bioinformatics/btn579, 2009 |
PubMed
|
NetMHCpan, a method for MHC class I binding prediction beyond humans.
Hoof I, Peters B, Sidney J, Pedersen LE, Sette A, Lund O, Buus S, Nielsen M
Immunogenetics 61(1):1-13 doi:10.1007/s00251-008-0341-z, 2009 |
PubMed
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2008
Contributions to the study of coevolution, at micro and macroscales
Gouveia-Oliveira R
Ph.D. thesis, 2008 |
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Linear motifs in phosphorylation-dependent signalling
Miller ML
Ph.D. thesis, 2008 |
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Bioinformatics and systems biology of human diseases
Lage K
Ph.D. thesis, 2008 |
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Concordance of exon array and real-time PCR assessment of gene expression following cancer cell cytotoxic drug exposure
Lee AJ, East P, Pepper S, Nicke B, Szallasi Z, Eklund AC, Downward J, Swanton C
Cell Cycle 7(24):3947-8, 2008 |
PubMed
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Acetone-water complexes at MRCI level using localized orbitals: n ->pi* and pi ->pi* electronic transitions
Hoyau S, Ben Amor N, Borini S, Evangelisti S, Maynau D
CHEMICAL PHYSICS LETTERS, Vol.: 451, Issue: 1-3, Pages: 141-146, Published: JAN 14 2008, 2008 |
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The effects of fish oil and high or low linoleic acid intake on fatty acid composition of human peripheral blood mononuclear cells
Damsgaard CT, Frokiaer H, Lauritzen L
BRITISH JOURNAL OF NUTRITION, Vol.: 99, Issue: 1, Pages: 147-154, Published: JAN 2008, 2008 |
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Fish oil in combination with high or low intakes of linoleic acid lowers plasma triacylglycerols but does not affect other cardiovascular risk markers in healthy men
Damsgaard CT, Frokiaer H, Andersen AD, Lauritzen L
JOURNAL OF NUTRITION, Vol.: 138, Issue: 6, Pages: 1061-1066, Published: JUN 2008, 2008 |
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Occurrence of multiple infections with different Borrelia burgdorferi genospecies in Danish Ixodes ricinus nymphs
Vennestrøm J, Egholm H, Jensen PM
Parasitology International . 57(1):32-7, 2008 |
PubMed
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Integration of clinical chemistry, expression, and metabolite data leads to better toxicological class separation
Spicker JS, Brunak S, Frederiksen KS, Toft H
Toxicol. Sci. 102(2):444-54 doi:10.1093/toxsci/kfn001, 2008 |
PubMed
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Protein abundance profiling of the Escherichia coli cytosol
Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D
BMC Genomics 9:102 doi:10.1186/1471-2164-9-102, 2008 |
PubMed
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The minimum information about a genome sequence (MIGS) specification
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A
Nature Biotechnology. 26(5):541-7 doi:10.1038/nbt1360, 2008 |
PubMed
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Identification of glycosaminoglycan binding regions in the Plasmodium falciparum encoded placental sequestration ligand, VAR2CSA
Resende M, Nielsen MA, Dahlbäck M, Ditlev SB, Andersen P, Sander AF, Ndam NT, Theander TG, Salanti A
Malar. J. 7:104 doi:10.1186/1475-2875-7-104, 2008 |
PubMed
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Whole-genome pyrosequencing of an epidemic multidrug-resistant Acinetobacter baumannii strain belonging to the European clone II group
Iacono M, Villa L, Fortini D, Bordoni R, Imperi F, Bonnal RJ, Sicheritz-Ponten T, De Bellis G, Visca P, Cassone A, Carattoli A
Antimicrob. Agents Chemother. 52(7):2616-25 doi:10.1128/AAC.01643-07, 2008 |
PubMed
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Dietary soya saponins increase gut permeability and play a key role in the onset of soyabean-induced enteritis in Atlantic salmon ( Salmo salar L.)
Knudsen D, Jutfelt F, Sundh H, Sundell K, Koppe W, Frøkiaer H
Br. J. Nutr. 100(1):120-9 doi:10.1017/S0007114507886338, 2008 |
PubMed
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Arabidopsis mitogen-activated protein kinase kinases MKK1 and MKK2 have overlapping functions in defense signaling mediated by MEKK1, MPK4, and MKS1
Qiu JL, Zhou L, Yun BW, Nielsen HB, Fiil BK, Petersen K, Mackinlay J, Loake GJ, Mundy J, Morris PC
Plant Physiology. 148(1):212-22 doi:10.1104/pp.108.120006, 2008 |
PubMed
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Functional genomic analysis of drug sensitivity pathways to guide adjuvant strategies in breast cancer
Swanton C, Szallasi Z, Brenton JD, Downward J
Breast Cancer Res. 10(5):214 doi:10.1186/bcr2159, 2008 |
PubMed
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A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes
Lage K, Hansen NT, Karlberg EO, Eklund AC, Roque F, Donahoe PK, Szallasi Z, Jensen TS, Brunak S
Proc. Natl. Acad. Sci. U.S.A. 105(52):20870-5 doi:10.1073/pnas.0810772105, 2008 |
PubMed
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NetPhosBac - A predictor for Ser/Thr phosphorylation sites in bacterial proteins.
Miller ML, Soufi B, Jers C, Blom N, Macek B, Mijakovic I
Proteomics 9(1):116-25 doi:10.1002/pmic.200800285, 2008 |
PubMed
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MHC-I-restricted epitopes conserved among variola and other related orthopoxviruses are recognized by T cells 30 years after vaccination
Tang ST, Wang M, Lamberth K, Harndahl M, Dziegiel MH, Claesson MH, Buus S, Lund O
Arch. Virol. 153(10):1833-44 doi:10.1007/s00705-008-0194-7, 2008 |
PubMed
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Circular reasoning rather than cyclic expression
Jensen LJ, de Lichtenberg U, Jensen TS, Brunak S, Bork P
Genome Biol. 9(6):403 doi:10.1186/gb-2008-9-6-403, 2008 |
PubMed
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Bioavailability of omega-3 long-chain polyunsaturated fatty acids from foods
Mu H
Supplement to AgroFood industry hi-tech, 19 (4), 24-26, 2008 |
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Butter blend containing fish oil does not affect cholesterol absorption in a single meal study in humans
Overgaard J, Porsgaard T, Guo Z, Lauritzen L, Mu H
Mol Nutr Food Res 52(10):1140-6 doi:10.1002/mnfr.200700484, 2008 |
PubMed
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Comparison of 3 ad libitum diets for weight-loss maintenance, risk of cardiovascular disease, and diabetes: A 6-mo randomized, controlled trial
Due A, Larsen TM, Mu H, Hermansen K, Stender S, Astrup A
The American Journal of Clinical Nutrition. 88(5):1232-41, 2008 |
PubMed
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Staphylokokkens ømme punkt.
Jarmer HO
Dynamo, November 2008, 2008 |
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Classification of Cytochrome P450 1A2 Inhibitors and Non-Inhibitors by Machine Learning Techniques
Vasanthanathan P, Taboureau O, Oostenbrink C, Vermeulen NPE, Olsen L, Jorgensen FS
Drug Metab. Dispos. 37(3):658-64 doi:10.1124/dmd.108.023507, 2008 |
PubMed
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Phospholipase C-catalyzed sphingomyelin hydrolysis in a membrane reactor for ceramide production
Zhang L, Liang S, Hellgren LI, Jonsson GE, Xu X
Journal of Membrane Science, 2008 |
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A pathway-specific microarray analysis highlights the complex and co-ordinated transcriptional networks of the developing grain of field-grown barley
Hansen M, Friis C, Bowra S, Holm PB, Vincze E
J. Exp. Bot. 60(1):153-67 doi:10.1093/jxb/ern270, 2008 |
PubMed
Relevant URL
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Linear motif atlas for phosphorylation-dependent signaling.
Miller ML, Jensen LJ, Diella F, Jørgensen C, Tinti M, Li L, Hsiung M, Parker SA, Bordeaux J, Sicheritz-Ponten T, Olhovsky M, Pasculescu A, Alexander J, Knapp S, Blom N, Bork P, Li S, Cesareni G, Pawson T, Turk BE, Yaffe MB, Brunak S, Linding R
Science Signaling 1(35):ra2 doi:10.1126/scisignal.1159433, 2008 |
PubMed
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Fedtsyrebalance påvirker livsstilssygdomme og allergi
Hellgren LI, Brix S
FoodDTU, nr. 44, maj (2008)., 2008 |
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Allergen specific responses in cord and adult blood are differentially modulated in the presence of endotoxins
Eiwegger T, Mayer E, Brix S, Schabussova I, Dehlink E, Bohle B, Barkholt V, Szépfalusi Z
Clin Exp Allergy, ePub Sep (2008) DOI: 10.1111/j.1365-2222.2008.03080.x, 2008 |
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The peptide-binding specificity of HLA-A*3001 demonstrates membership of the HLA-A3 supertype
Lamberth K, Røder G, Harndahl M, Nielsen M, Lundegaard C, Schafer- Nielsen C, Lund O, Buus S
Immunogenetics 60(11):633-43 doi:10.1007/s00251-008-0317-z, 2008 |
PubMed
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Adjuvant auricular electroacupuncture and autogenic training in rheumatoid arthritis: a randomized controlled trial. Auricular acupuncture and autogenic training in rheumatoid arthritis.
Bernateck M, Becker M, Schwake C, Hoy L, Passie T, Parlesak A, Fischer MJ, Fink M, Karst M
Forsch Komplementmed 15(4):187-93 doi:10.1159/000141929, 2008 |
PubMed
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Towards a richer description of our complete collection of genomes and metagenomes: the ’Minimum Information about a Genome Sequence’ (MIGS) specification
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuolii SV, Ashburner M, Axelrod N, Baldauf S, Boore SBJ, Cochrane G, Cole J, Dawyndt P, Vos PD, dePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister A, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Moxon R, Nelson K, Parkhill J, Proctor L, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery DW, Vaughan B, Ward N, Whetzel T, Wilson G, Wipat A
Nature Biotechnology. 26(5):541-7 doi:10.1038/nbt1360, 2008 |
PubMed
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Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes
Bohlin J, Skjerve E, Ussery DW
BMC Genomics 9:104 doi:10.1186/1471-2164-9-104, 2008 |
PubMed
BMC Genomics link
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Transcriptomics and adaptive genomics of the asymptomatic bacteria Escherichia coli strain 83972
Hancock V, Seshasayee AS, Ussery DW, Luscombe NM, Klemm P
Mol. Genet. Genomics 279(5):523-34 doi:10.1007/s00438-008-0330-9, 2008 |
PubMed
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Investigations of oligonucleotide usage variance within and between prokaryotes
Bohlin J, Skjerve E, Ussery D
PLoS Comput. Biol. 4(4):e1000057 doi:10.1371/journal.pcbi.1000057, 2008 |
PubMed
PLoS Computational Biology link
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Toward a Standards-Compliant Genomic and Metagenomic Publication Record
Garrity GM, Field D, Kyrpides N, Hirschman L, Sansone SA, Angiuoli S, Cole JR, Glöckner FO, Kolker E, Kowalchuk G, Moran MA, Ussery D, White O
OMICS 12(2):157-60 doi:10.1089/omi.2008.A2B2, 2008 |
PubMed
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Protein-induced changes during the maturation process of human dendritic cells: A 2-D DIGE approach
Ferreira GB, Overbergh L, Etten EV, Lage K, D’Hertog W, Hansen DA, Maris M, Moreau Y, Workman CT, Waelkens E, Mathieu C
Proteomics Clinical Applications, Volume 2 Issue 9, Pages 1349 - 1360, 2008 |
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MHC motif viewer
Rapin N, Hoof I, Lund O, Nielsen M
Immunogenetics 60(12):759-65 doi:10.1007/s00251-008-0330-2, 2008 |
PubMed
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Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq.
Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT, Hinton JC, Vogel J
PLoS Genet. 4(8):e1000163 doi:10.1371/journal.pgen.1000163, 2008 |
PubMed
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The complete genome sequence and analysis of the human pathogen Campylobacter lari
Miller WG, Wang G, Binnewies TT, Parker CT
Foodborne Pathog. Dis. 5(4):371-86 doi:10.1089/fpd.2008.0101, 2008 |
PubMed
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Molecular analysis of the emergence of pandemic Vibrio parahaemolyticus
Boyd EF, Cohen AL, Naughton LM, Ussery DW, Binnewies TT, Stine OC, Parent MA
BMC Microbiol. 8:110 doi:10.1186/1471-2180-8-110, 2008 |
PubMed
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The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571
Lee KB, De Backer P, Aono T, Liu CT, Suzuki S, Suzuki T, Kaneko T, Yamada M, Tabata S, Kupfer DM, Najar FZ, Wiley GB, Roe B, Binnewies TT, Ussery DW, D’Haeze WD, Herder JD, Gevers D, Vereecke D, Holsters M, Oyaizu H
BMC Genomics 9:271 doi:10.1186/1471-2164-9-271, 2008 |
PubMed
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Detection of anoxia-reponsive genes in cultured cells of the rainbow trout Oncorhynchus mykiss (Walbaum), using an optimized, genome-wide oligoarray
Olohan LA, Li W, Wulff T, Jarmer HO, Gracey AY, Cossins AR
Journal of Fish Biology. 2008. 72, 2170-2186, 2008 |
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Arabidopsis MAP Kinase Kinases MKK1 and MKK2 have overlapping functions in defense signalling mediated by MEKK1, MPK4 and MKS1.
Qiu J, Nielsen HB, Fiil BK, Petersen K, MacKinlay J, Loake G, Mundy J, Morris PC
Plant Physiology. 148(1):212-22 doi:10.1104/pp.108.120006, 2008 |
PubMed
Relevant URL
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Arabidopsis MAP Kinase 4 regulates gene expression via transcription factor release in the nucleus
Qiu J, Fiil BK, Petersen K, Nielsen HB, Botanga CJ, Thorgrimsen S, Lichota J, Brodersen P, Grasser KD, Mattsson O, Glazebrook J, Mundy J, Petersen M
The EMBO Journal . 27(16):2214-21 doi:10.1038/emboj.2008.147, 2008 |
PubMed
Relevant URL
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Influence of dietary fatty acids on endocannabinoid and N-acylethanolamine levels in rat brain, liver and small intestine
Artmann A, Petersen G, Hellgren LI, Boberg J, Skonberg C, Nellemann C, Hansen SH, Hansen HS
Biochim. Biophys. Acta 1781(4):200-12 doi:10.1016/j.bbalip.2008.01.006, 2008 |
PubMed
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Lipids and skin barrier function--a clinical perspective
Jungersted JM, Hellgren LI, Jemec GB, Agner T
Contact Derm. 58(5):255-62 doi:10.1111/j.1600-0536.2008.01320.x, 2008 |
PubMed
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Kinetic study of sphingomyelin hydrolysis for ceramide production.
Zhang L, Hellgren LI, Xu X
Journal of Molecular Catalysis B: Enzymatic 51: 93-99., 2008 |
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Prediction of fat oxidation capacity using 1H-NMR and LC-MS lipid metabolomic data
Pers TH, Martin FP, Verdich C, Holst C, Johansen JV, Astrup A, Polak J, Martinez JA, Rezzi S, Blaak EE, Saris WHM, Kochhar S, Macdonald IA, Sørensen TIA, Ramadan Z
Chemometrics and Intelligent Laboratory Systems 93, 34–42, 2008 |
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Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: a three factor design
Fazio A, Jewett MC, Daran-Lapujade P, Mustacchi R, Usaite R, Pronk JT, Workman CT, Nielsen J
BMC Genomics 2008, 9:341, 2008 |
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GLI1 is involved in cell cycle regulation and proliferation of NT2 embryonal carcinoma stem cells
Vestergaard J, Lind-Thomsen A, Pedersen MW, Jarmer HO, Bak M, Hasholt L, Tommerup N, Tümer Z, Larsen LA
DNA Cell Biol. 27(5):251-6 doi:10.1089/dna.2007.0625, 2008 |
PubMed
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Global features of the Alcanivorax borkumensis SK2 genome
Reva ON, Hallin PF, Willenbrock H, Sicheritz-Ponten T, Tummler B, Ussery DW
Environ. Microbiol. 10(3):614-25, 2008 |
PubMed
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The genome BLASTatlas-a GeneWiz extension for visualization ofwhole-genome homology
Hallin PF, Binnewies TT, Ussery DW
Mol Biosyst 4(5):363-71 doi:10.1039/b717118h, 2008 |
PubMed
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Dendritic Cells from Peyer\'s Patches and Mesenteric Lymph Nodes Differ from Spleen Dendritic Cells in their Response to Commensal Gut Bacteria
Fink LN, Frøkiær H
Scand. J. Immunol. 68(3):270-9 doi:10.1111/j.1365-3083.2008.02136.x, 2008 |
PubMed
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Toll-like receptor 2 and nucleotide-binding oligomerization domain-2 play divergent roles in the recognition of gut-derived lactobacilli and bifidobacteria in dendritic cells
Zeuthen LH, Fink LN, Frøkiær H
Immunology 124(4):489-502 doi:10.1111/j.1365-2567.2007.02800.x, 2008 |
PubMed
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Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan
Nielsen M, Lundegaard C, Blicher T, Peters B, Sette A, Justesen S, Buus S, Lund O
PLoS Comput. Biol. 4(7):e1000107 doi:10.1371/journal.pcbi.1000107, 2008 |
PubMed
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Immune epitope database analysis resource (IEDB-AR)
Zhang Q, Wang P, Kim Y, Haste-Andersen P, Beaver J, Bourne PE, Bui HH, Buus S, Frankild S, Greenbaum J, Lund O, Lundegaard C, Nielsen M, Ponomarenko J, Sette A, Zhu Z, Peters B
Nucleic Acids Res. 36:W513-8 doi:10.1093/nar/gkn254, 2008 |
PubMed
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NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11
Lundegaard C, Lamberth K, Harndahl M, Buus S, Lund O, Nielsen M
Nucleic Acids Res. 36:W509-12 doi:10.1093/nar/gkn202, 2008 |
PubMed
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Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers
Lundegaard C, Lund O, Nielsen M
Bioinformatics 24(11):1397-8 doi:10.1093/bioinformatics/btn128, 2008 |
PubMed
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Prediction of pH-dependent solubility of Histone Deacetylase (HDAC)inhibitors
Kouskoumvekaki I, Hansen NT, Björkling F, Vadlamudi SM, Jónsdóttir SÓ
SAR QSAR Environ Res 19:167-77 doi:10.1080/10629360701843367, 2008 |
PubMed
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Humans with chimpanzee-like major histocompatibility complex-specificities control HIV-1 infection
Hoof I, Kesmir C, Lund O, Nielsen M
AIDS 22(11):1299-303 doi:10.1097/QAD.0b013e328302f39f, 2008 |
PubMed
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Alternative splicing in colon, bladder, and prostate cancer identified by exon-array analysis
Thorsen K, Sørensen KD, Brems-Eskildsen AS, Modin C, Gaustadnes M, Hein AMK, Kruhøffer M, Laurberg S, Borre M, Wang K, Brunak S, Krainer AR, Tørring N, Dyrskjøt L, Andersen CL, Ørntoft TF
Mol. Cell Proteomics 7(7):1214-24 doi:10.1074/mcp.M700590-MCP200, 2008 |
PubMed
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Structural Insight into Epitopes in the Pregnancy-Associated Malaria Protein VAR2CSA
Andersen P, Nielsen MA, Resende M, Rask TS, Dahlbäck M, Theander T, Lund O, Salanti A
PLoS Pathog. 4(2):e42 doi:10.1371/journal.ppat.0040042, 2008 |
PubMed
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Amino acid similarity accounts for T cell cross-reactivity and for \\\'holes\\\' in the T cell repertoire
Frankild S, de Boer RJ, Lund O, Nielsen M, Kesmir C
PLoS ONE 3(3):e1831 doi:10.1371/journal.pone.0001831, 2008 |
PubMed
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Broadly Immunogenic HLA Class I Supertype-Restricted Elite CTL Epitopes Recognized in a Diverse Population Infected with Different HIV-1 Subtypes
Pérez CL, Larsen MV, Gustafsson R, Norström MM, Atlas A, Nixon DF, Nielsen M, Lund O, Karlsson AC
The Journal of Immunology. 180(7):5092-100, 2008 |
PubMed
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Obesity - a social and physical risk
Parlesak A, Krömker D
J Dtsch Dermatol Ges 6(6):442-9 doi:10.1111/j.1610-0387.2008.06572.x, 2008 |
PubMed
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Correction of technical bias in clinical microarray data improves concordance with known biological information
Eklund AC, Szallasi Z
Genome Biol. 9(2):R26 doi:10.1186/gb-2008-9-2-r26, 2008 |
PubMed
Web
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Phylogenetic relationships between Sarcocystis species from reindeer and other Sarcocystidae deduced from ssu rRNA gene sequences
Dahlgren SS, Gouveia-Oliveira R, Gjerde B
Vet. Parasitol. 151(1):27-35, 2008 |
PubMed
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hERG Classification Model Based on a Combination of Support Vector Machine Method and GRIND Descriptors
Li Q, Jørgensen FS, Oprea T, Brunak S, Taboureau O
Mol. Pharm. 5(1):117-27 doi:10.1021/mp700124e, 2008 |
PubMed
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Identification of biomarkers for genotyping Aspergilli using non-linear methods for clustering and classification
Kouskoumvekaki I, Yang Z, Jonsdottir SO, Olsson L, Panagiotou G
BMC Bioinformatics 9:59 doi:10.1186/1471-2105-9-59, 2008 |
PubMed
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Is nutrient intake a gender-specific cause for enhanced susceptibility to alcohol-induced liver disease in women?
Wagnerberger S, Schäfer C, Schwarz E, Bode C, Parlesak A
Alcohol Alcohol. 43(1):9-14, 2008 |
PubMed
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Effect of gender on lipid-induced insulin resistance in obese subjects
Vistisen B, Hellgren LI, Vadset T, Scheede-Bergdahl C, Helge JW, Dela F, Stallknecht B
Eur. J. Endocrinol. 158(1):61-8 doi:10.1530/EJE-07-0493, 2008 |
PubMed
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Epithelial cells prime the immune response to an array of gut-derived commensals towards a tolerogenic phenotype through distinct actions of thymic stromal lymphopoietin and transforming growth factor-beta
Zeuthen LH, Fink LN, Frokiaer H
Immunology 123(2):197-208, 2008 |
PubMed
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2007
DASS: efficient discovery and p-value calculation of substructures in unordered data.
Hollunder J, Friedel M, Beyer A, Workman CT, Wilhelm T
Bioinformatics. 2007 Jan 1;23(1):77-83., 2007 |
PubMed
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Integration of biological networks and gene expression data using Cytoscape.
Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD
Nature Protocols. 2007;2(10):2366-82., 2007 |
PubMed
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Prediction of T-cell Epitopes for Therapeutic and Prophylactic Vaccines
Larsen MV
Ph.D. thesis, 2007 |
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Prediction and identification of B-cell epitopes using protein structure information
Andersen PH
Ph.D. thesis, 2007 |
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Sequence conservation of subdominant HLA-A2-binding CTL epitopes in HIV-1 clinical isolates and CD8+ T-lymphocyte cross-recognition may explain the immune reaction in infected individuals
Thorn M, Tang ST, Therrien D, Kløverpris H, Vinner L, Kronborg G, Gerstoft J, Corbet S, Fomsgaard A
APMIS 115(6):757-68, 2007 |
PubMed
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Inhibition of type I and type III interferons by a secreted glycoprotein from Yaba-like disease virus
Huang J, Smirnov SV, Lewis-Antes A, Balan M, Li W, Tang ST, Silke GV, Pütz MM, Smith GL, Kotenko SV
Proc. Natl. Acad. Sci. U.S.A. 104(23):9822-7, 2007 |
PubMed
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Characterization of near full-length genomes of HIV type 1 strains in Denmark: basis for a universal therapeutic vaccine
Andresen BS, Vinner L, Tang ST, Bragstad K, Kronborg G, Gerstoft J, Corbet S, Fomsgaard A
AIDS Res. Hum. Retroviruses 23(11):1442-8 doi:10.1089/aid.2007.0111, 2007 |
PubMed
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Proteome-analysis of gut bacteria-matured dendritic cells
Brix S, Kragh M, Sondergaard JN, Bjerkan L, Jacobsen S, Frokiaer H
Annals of Nutrition and Metabolism, 51:383-383 Suppl. 1 (2007), 2007 |
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The potential of gut bacteria-matured DCs to activate CD4+T cells highly depends on the lipid composition of the T cell membrane.
Brix S, Lund P, Kjaer TMR, Straarup EM, Hellgren LI, Frokiaer H
Annals of Nutrition and Metabolism, 51:65-65 Suppl. 1 (2007), 2007 |
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Identification of putative noncoding RNA genes in the Burkholderia cenocepacia J2315 genome
Coenye T, Drevinek P, Mahenthiralingam E, Shah SA, Gill RT, Vandamme P, Ussery DW
FEMS Microbiol. Lett. 276(1):83-92, 2007 |
PubMed
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Comparative genomic analysis of two-component regulatory proteins in Pseudomonas syringae
Lavin JL, Kiil K, Resano O, Ussery DW, Oguiza JA
BMC Genomics 8:397, 2007 |
PubMed
Link to article
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Synthesis of structured phospholipids by immobilized phospholipase A2 catalyzed acidolysis
Vikbjerg A, Mu H, Xu X
J. Biotechnol. 128(3):545-54, 2007 |
PubMed
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Oxidative stability of liposomes composed of DHA-containing phospholipids
Vikbjerg A, Andersen TL, Jørgensen K, Mu H, Xu X
J. Am. Oil Chem. Soc. 84:631-637, 2007 |
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Increased lipids in non-lipogenic tissues are indicators of the severity of type 2 diabetes in mice
Campbell JA, Hansen HS, Mu H, Mølgaard P
Prostaglandins Leukot. Essent. Fatty Acids 76(1):9-18, 2007 |
PubMed
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Food matrices affect the bioavailability of (n-3) polyunsaturated fatty acids in a single meal study in humans
Schram LB, Nielsen CJ, Porsgaard T, Nielsen NS, Holm R, Mu H
Food Res. Inter. 40:1062-1068., 2007 |
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Butter blend containing fish oil improves the level of n-3 fatty acids in biological tissues of hamster
Porsgaard T, Overgaard J, Krogh AL, Jensen MB, Guo Z, Mu H
Journal of Agricultural and Food Chemistry . 55(18):7615-9, 2007 |
PubMed
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The Complete Genome Sequence and Analysis of the EpsilonproteobacteriumArcobacter butzleri
Miller WG, Parker CT, Rubenfield M, Mendz GL, Wosten MM, Ussery DW, Stolz JF, Binnewies TT, Hallin PF, Wang G, Malek JA, Rogosin A, Stanker LH, Mandrell RE
PLoS ONE 2(12):e1358, 2007 |
PubMed
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Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray
Willenbrock H, Hallin PF, Wassenaar TM, Ussery DW
Genome Biol. 8(12):R267, 2007 |
PubMed
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Antisense-mediated suppression of C-hordein biosynthesis in the barley grain results in correlated changes in the transcriptome, protein profile, and amino acid composition
Hansen M, Lange M, Friis C, Dionisio G, Holm PB, Vincze E
J. Exp. Bot. 58(14):3987-95, 2007 |
PubMed
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Modeling the adaptive immune system: predictions and simulations
Lundegaard C, Lund O, Kesmir C, Brunak S, Nielsen M
Bioinformatics 23(24):3265-75, 2007 |
PubMed
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Forsg med ny online eksamensform i \\
Wernersson R
DTU Avisen, 2007 |
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Computational Analysis and Modeling of Bacterial Pathogenesis
Binnewies TT
PhD thesis, 2007 |
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Kemoinformatik: Lær computeren at finde nye lægemidler
Kouskoumvekaki I, Hansen NT, Jónsdóttir SÓ
Dansk Kemi, 88(8),23-25, 2007 |
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Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction
Larsen MV, Lundegaard C, Lamberth K, Buus S, Lund O, Nielsen M
BMC Bioinformatics 8:424, 2007 |
PubMed
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Integrative analysis for finding genes and networks involved in diabetes and other complex diseases
Bergholdt R, Størling ZM, Lage K, Karlberg EO, Olason PI, Aalund M, Nerup J, Brunak S, Workman CT, Pociot F
Genome Biol. 8(11):R253, 2007 |
PubMed
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Proteomics analysis of cytokine-induced dysfunction and death in insulin-producing INS-1E cells: new insights into the pathways involved
Hertog W, Overbergh L, Lage K, Ferreira GB, Maris M, Gysemans C, Flamez D, Cardozo AK, Van den Bergh G, Schoofs L, Arckens L, Moreau Y, Hansen DA, Eizirik DL, Waelkens E, Mathieu C
Mol. Cell Proteomics 6(12):2180-99, 2007 |
PubMed
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Kamp med og mod bakterier
Jarmer H
DTU-avisen, 27 April, nr. 5, 2007 |
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Det er ikke bare et fedt
Hellgren LI
Dansk Kemi, 88:14-6, 2007 |
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Immobilization of phospholipase C for the production of ceramide from sphingomyelin hydrolysis
Zhang L, Hellgren LI, Xu XB
J American Oil Chem Soc, 84:237-47, 2007 |
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The source of dietary fatty acids alter the activity of secretory sphingomyelinase in the rat
Drachmann T, Mathiassen JH, Pedersen MH, Hellgren LI
European Journal of Lipid Science and Technology, 109:1003-9, 2007 |
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Locating proteins in the cell using TargetP, SignalP and related tools
Emanuelsson O, Brunak S, von Heijne G, Nielsen H
Nature Protoc. 2, 953-971, 2007 |
PubMed
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Identification of a new hTERT-derived HLA-A*0201 restricted, naturally processed CTL epitope
Thorn M, Wang M, Kloverpris H, Schmidt EG, Fomsgaard A, Wenandy L, Berntsen A, Brunak S, Buus S, Claesson MH
Cancer Immunol, 2007 |
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Evolution of cell cycle control: same molecular machines, different regulation
de Lichtenberg U, Jensen TS, Brunak S, Bork P, Jensen LJ
Cell Cycle 6(15):1819-25, 2007 |
PubMed
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Dynamics of Escherichia coli Chromosome Segregation during Multifork Replication
Nielsen HJ, Youngren B, Hansen FG, Austin S
J. Bacteriol. 189(23):8660-6, 2007 |
PubMed
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DNA and origin region segregation are not affected by the transition from rod to sphere after inhibition of Escherichia coli MreB by A22
Karczmarek A, Martínez-Arteaga R, Alexeeva S, Hansen FG, Vicente M, Nanninga N, den Blaauwen T
Mol. Microbiol. 65(1):51-63, 2007 |
PubMed
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Structure and Content of the Entamoeba histolytica Genome
Clark CG, Alsmark UCM, Tazreiter M, Saito Y, Nakano, Ali V, Marion S, Weber C, Mukherjee C, Bruchhaus I, Tannich E, Leippe M, Sicheritz-Ponten T, Foster PG, Samuelson J, Noël CJ, Hirt RP, Embley TM, Gilchrist CA, Mann BJ, Singh U, Ackers JP, Bhattacharya S, Bhattacharya S, Lohia A, Guillén N, Duchêne M, Nozaki T, Hall N
Adv. Parasitol. 65:51-190, 2007 |
PubMed
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Trichomonas vaginalis surface proteins: a view from the genome
Hirt RP, Noel CJ, Sicheritz-Ponten T, Tachezy J, Fiori PL
Trends Parasitol. 23(11):540-7, 2007 |
PubMed
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Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2
Miller ML, Hanke S, Hinsby AM, Friis C, Brunak S, Mann M, Blom N
Mol. Cell Proteomics 7(1):181-92, 2007 |
PubMed
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Conjugated primary bile salts reduce permeability of endotoxin through intestinal epithelial cells and synergize with phosphatidylcholine in suppression of inflammatory cytokine production
Parlesak A, Schaeckeler S, Moser L, Bode C
Crit. Care Med. 35(10):2367-74, 2007 |
PubMed
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Human antigen-presenting cells respond differently to gut-derived probiotic bacteria but mediate similar strain-dependent NK and T cell activation
Fink LN, Zeuthen LH, Ferlazzo G, Frøkiær H
FEMS Immunol. Med. Microbiol. 51(3):535-46, 2007 |
PubMed
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Distinct gut-derived lactic acid bacteria elicit divergent dendritic cell-mediated NK cell responses
Fink LN, Zeuthen LH, Christensen HR, Morandi B, Frøkiær H, Ferlazzo G
International Immunology. 19(12):1319-27, 2007 |
PubMed
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HLA Alleles Associated with Slow Progression to AIDS Truly Prefer to Present HIV-1 p24
Borghans JA, Molgaard A, de Boer RJ, Kesmir C
PLoS ONE 2(9):e920, 2007 |
PubMed
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Branchio-Oto-Renal Syndrome: Detection of EYA1 and SIX1 mutations in five out of six Danish families by combining linkage, sequencing and MLPA analyses
Sanggaard KM, Kjaer KW, Eiberg H, Rendtorff ND, Johnsen T, Gimsing S, Dyrmose J, Nielsen KO, Lage K, Tranebjærg L
Eur. J. Hum. Genet. 15(11):1121-31, 2007 |
PubMed
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Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina
Arvas MM, Kivioja T, Mitchell A, Saloheimo M, Ussery DW, Penttila M, Oliver S
BMC Genomics 8:325, 2007 |
PubMed
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Dice & DNA
Wernersson R
BioScience Education e-journal, (in press), 2007 |
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Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method
Nielsen M, Lundegaard C, Lund O
BMC Bioinformatics 8:238, 2007 |
PubMed
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Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis
Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, Wortman JR, Bidwell SL, Alsmark UC, Besteiro S, Sicheritz-Ponten T, Noel CJ, Dacks JB, Foster PG, Simillion C, Van de Peer Y, Miranda-Saavedra D, Barton GJ, Westrop GD, Müller S, Dessi D, Fiori PL, Ren Q, Paulsen I, Zhang H, Bastida-Corcuera FD, Simoes-Barbosa A, Brown MT, Hayes RD, Mukherjee M, Okumura CY, Schneider R, Smith AJ, Vanacova S, Villalvazo M, Haas BJ, Pertea M, Feldblyum TV, Utterback TR, Shu CL, Osoegawa K, de Jong PJ, Hrdy I, Horvathova L, Zubacova Z, Dolezal P, Malik SB, Logsdon JM Jr, Henze K, Gupta A, Wang CC, Dunne RL, Upcroft JA, Upcroft P, White O, Salzberg SL, Tang P, Chiu CH, Lee YS, Embley TM, Coombs GH, Mottram JC, Tachezy J, Fraser-Liggett CM, Johnson PJ
Science 315(5809):207-12, 2007 |
PubMed
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State-Wide Molecular and Epidemiological Study on the Nosocomial Transmission of HCV in Hemodialysis Patients in Brazil
Carneiro MAS, Teles SA, Lampe E, Espirito-Santo MP, Gouveia-Oliveira R, Reis NRS, Yoshida CFT, Martins MBR
J Med Virol. Sep;79(9):1325-33, 2007 |
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Finding Coevolving Amino acid Residues using Row and Column Weighing of Mutual Information and Multi-Dimensional Amino acid Representation
Gouveia-Oliveira R, Pedersen AG
Algorithms Mol Biol 2:12, 2007 |
PubMed
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NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence
Nielsen M, Lundegaard C, Blicher T, Lamberth K, Harndahl M, Justesen S, Roder G, Peters B, Sette A, Lund O, Buus S
PLoS ONE 2(8):e796, 2007 |
PubMed
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Structure-function analysis of the ER oxidoreductase TMX3 reveals inter-domain stabilization of the N-terminal redox-active domain
Haugstetter J, Maurer MA, Blicher T, Pagac M, Wider G, Ellgaard L
The Journal of Biological Chemistry. 282(46):33859-67, 2007 |
PubMed
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The essential YycFG two-component system controls cell wall metabolism in Bacillus subtilis
Bisicchia P,Noone D,Lioliou E,Howell A,Quigley S,Jensen T,Jarmer H,Devine KM
Mol. Microbiol. 65(1):180-200, 2007 |
PubMed
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CycleBase.org - a comprehensive multi-organism online database of cell-cycle experiments
Gauthier NP, Jensen TS, de Lichtenberg U, Wernersson R, Larsen ME, Brunak S
Nucleic Acids Res. (in press), 2007 |
Web
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Probe Selection for DNA Microarrays using OligoWiz
Wernersson R, Juncker AS, Nielsen HB
Nat Protoc 2(11):2677-91, 2007 |
PubMed
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SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation
Panitz F, Stengaard H, Hornshøj H, Gorodkin J, Hedegaard J, Cirera S, Thomsen B, Madsen LB, Høj A, Vingborg RK, Zahn B, Wang X, Wang X, Wernersson R, Jørgensen CB, Scheibye-Knudsen K, Arvin T, Lumholdt S, Sawera M, Green T, Nielsen BJ, Havgaard JH, Brunak S, Fredholm M, Bendixen C
Bioinformatics 23(13):i387-91, 2007 |
PubMed
Web
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Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags
Gorodkin J, Cirera S, Hedegaard J, Gilchrist MJ, Panitz F, Jørgensen C, Scheibye-Knudsen K, Arvin T, Lumholdt S, Sawera M, Green T, Nielsen BJ, Havgaard JH, Rosenkilde C, Wang J, Li H, Li R, Liu B, Hu S, Dong W, Li W, Yu J, Wang J, Staerfeldt HH, Wernersson R, Madsen LB, Thomsen B, Hornshøj H, Bujie Z, Wang X, Wang X, Bolund L, Brunak S, Yang H, Bendixen C, Fredholm M
Genome Biol. 8(4):R45, 2007 |
PubMed
Web
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MaxAlign: maximizing usable data in an alignment
Gouveia-Oliveira R, Sackett PW, Pedersen AG
BMC Bioinformatics 8:312, 2007 |
PubMed
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Functional Associations by Response Overlap (FARO), a functional genomics approach matching gene expression phenotypes
Nielsen HB, Mundy J, Willenbrock H
PLoS ONE 2(7):e676, 2007 |
PubMed
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Analysis of cell death inducing compounds
Spicker JS, Pedersen HT, Nielsen HB, Brunak S
Archives of Toxicology, DOI 10.1007/s00204-007-0207-4, 2007 |
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Evidence for Vertical Inheritance and Loss of the Leukotoxin Operon in Genus Mannheimia
Larsen J, Pedersen AG, Christensen H, Bisgaard M, Angen Ø, Ahrens P, Olsen JE
J. Mol. Evol. 64(4):423-37, 2007 |
PubMed
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Monitoring novel metabolic pathways using metabolomics and machine learning: induction of the phosphoketolase pathway in Aspergillus nidulans cultivations
Panagiotou G, Kouskoumvekaki I, Jónsdóttir SÓ, Olsson L
Metabolomics,3,503-516, 2007 |
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A high-quality catalog of the Drosophila melanogaster proteome
Brunner E, Ahrens CH, Mohanty S, Baetschmann H, Loevenich S, Potthast F, Deutsch EW, Panse C, de Lichtenberg U, Rinner O, Lee H, Pedrioli PG, Malmstrom J, Koehler K, Schrimpf S, Krijgsveld J, Kregenow F, Heck AJ, Hafen E, Schlapbach R, Aebersold R
Nat. Biotechnol. 25(5):576-83, 2007 |
PubMed
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The implications of alternative splicing in the ENCODE protein complement
Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PI, Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA, Lopez G, Sadowski MI, Watson JD, Fariselli P, Rossi I, Nagy A, Wang K, Storling Z, Orsini M, Assenov Y, Blankenburg H, Huthmacher C, Ramirez F, Schlicker A, Denoued F, Jones P, Kerrien S, Orchard S, Antonarakis SE, Reymond A, Birney E, Brunak S, Casadio R, Guigo R, Harrow J, Hermjakob H, Jones DT, Lengauer T, Orengo CA, Patthy L, Thornton JM, Tramontano A, Valencia A
Proc. Natl. Acad. Sci. U.S.A. 104(13):5495-500, 2007 |
PubMed
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Sequence Characteristics Required for Cooperative Binding and Efficient inVivo Titration of the Replication Initiator Protein DnaA in E. coli
Hansen FG, Christensen BB, Atlung T
J. Mol. Biol. 367(4):942-52, 2007 |
PubMed
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Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88
Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, Turner G, de Vries RP, Albang R, Albermann K, Andersen MR, Bendtsen JD, Benen JA, van den Berg M, Breestraat S, Caddick MX, Contreras R, Cornell M, Coutinho PM, Danchin EG, Debets AJ, Dekker P, van Dijck PW, van Dijk A, Dijkhuizen L, Driessen AJ, d\'Enfert C, Geysens S, Goosen C, Groot GS, de Groot PW, Guillemette T, Henrissat B, Herweijer M, van den Hombergh JP, van den Hondel CA, van der Heijden RT, van der Kaaij RM, Klis FM, Kools HJ, Kubicek CP, van Kuyk PA, Lauber J, Lu X, van der Maarel MJ, Meulenberg R, Menke H, Mortimer MA, Nielsen J, Oliver SG, Olsthoorn M, Pal K, van Peij NN, Ram AF, Rinas U, Roubos JA, Sagt CM, Schmoll M, Sun J, Ussery D, Varga J, Vervecken W, van de Vondervoort PJ, Wedler H, Wosten HA, Zeng AP, van Ooyen AJ, Visser J, Stam H
Nat. Biotechnol. 25(2):221-31, 2007 |
PubMed
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The importance of virulence prediction and gene networks in microbial risk assessment
Wassenaar GM, Gamieldien J, Shatkin JA, Luber P, Moyer N, Carpenter T, Ussery DW
Human and Ecological Risk Assessment, 13, 1-15, 2007 |
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RNAmmer: consistent and rapid annotation of ribosomal RNA genes
Lagesen K, Hallin P, Rødland EA, Stærfeldt HH, Rognes T, Ussery DW
Nucleic Acids Res. 35(9):3100-8, 2007 |
PubMed
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Genome-wide analysis of the Arabidopsis leaf transcriptome reveals interaction of phosphate and sugar metabolism
Muller R, Morant M, Jarmer H, Nilsson L, Nielsen TH
Plant Physiology. 143(1):156-71, 2007 |
PubMed
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Midbrain expression of Delta-like 1 homologue is regulated by GDNF and is associated with dopaminergic differentiation
Christophersen NS, Gronborg M, Petersen TN, Fjord-Larsen L, Jorgensen JR, Juliusson B, Blom N, Rosenblad C, Brundin P
Exp. Neurol. 204(2):791-801, 2007 |
PubMed
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Prediction of protein phosphorylation sites in yeast
Ingrell CR, Miller ML, Jensen ON, Blom N
Bioinformatics 23(7):895-7, 2007 |
PubMed
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Human pregnancy-associated malaria-specific B cells target polymorphic, conformational epitopes in VAR2CSA
Barfod L, Bernasconi NL, Dahlback M, Jarrossay D, Andersen PH, Salanti A, Ofori MF, Turner L, Resende M, Nielsen MA, Theander TG, Sallusto F, Lanzavecchia A, Hviid L
Mol. Microbiol. 63(2):335-47, 2007 |
PubMed
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Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools
Greenbaum JA, Andersen PH, Blythe M, Bui HH, Cachau RE, Crowe J, Davies M, Kolaskar AS, Lund O, Morrison S, Mumey B, Ofran Y, Pellequer JL, Pinilla C, Ponomarenko JV, Raghava GP, van Regenmortel MH, Roggen EL, Sette A, Schlessinger A, Sollner J, Zand M, Peters B
J. Mol. Recognit. 20(2):75-82, 2007 |
PubMed
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A human phenome-interactome network of protein complexes implicated in genetic disorders
Lage K, Karlberg EO, Storling ZM, Olason PI, Pedersen AG, Rigina O, Hinsby AM, Tumer Z, Pociot F, Tommerup N, Moreau Y, Brunak S
Nat. Biotechnol. 25(3):309-16, 2007 |
PubMed
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Identification of a novel Mannheimia granulomatis lineage from pathological lesions in roe deer (Capreolus capreolus)
Bojesen AM, Larsen J, Pedersen AG, Mörner T, Mattson R, Bisgaard M
J. Wildl. Dis. 43(3):345-52, 2007 |
PubMed
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Improving comparability between microarray probe signals by thermodynamic intensity correction
Bruun GM, Wernersson R, Juncker AS, Willenbrock H, Nielsen HB
Nucleic Acids Res. 35(7):e48, 2007 |
PubMed
Web
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Investigating Signs of Recent Evolution in the Pool of Pro-viral DNA during Years of Successful HAART
Mens H, Pedersen AG, Jørgensen LB, Hue S, Gerstoft J, Katzenstein TL
AIDS Res. Hum. Retroviruses 23(1):107-15, 2007 |
PubMed
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2006
A systems approach to mapping DNA damage response pathways.
Workman CT, Mak HC, McCuine S, Tagne JB, Agarwal M, Ozier O, Begley TJ, Samson LD, Ideker T
Science. 2006 May 19;312(5776):1054-9., 2006 |
PubMed
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Integrated assessment and prediction of transcription factor binding.
Beyer A, Workman C, Hollunder J, Radke D, Möller U, Wilhelm T, Ideker T
PLoS Computational Biology. 2006 Jun 16;2(6):e70., 2006 |
PubMed
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Barley genes in action: Transcriptome analysis of developing barley embryos
Nielsen ME
Ph.D. thesis, 2006 |
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DNA Microarrays in Comparative Genomics and Transcriptomics
Willenbrock H
Ph.D. thesis, 2006 |
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Dynamics of chromosome segregation in bacteria
Nielsen HJ
Ph.D. thesis, 2006 |
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Kan kosten påvirke vores risiko for at udvikle allergi?
Brix S, Frokiaer H
Miljø og Sundhed, Indenrigs- og Sundhedsministeriets Miljømedicinske Forskningscenter, 31: 5-9 (2006)., 2006 |
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A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers
Carter SL, Eklund AC, Kohane IS, Harris LN, Szallasi Z
Nat. Genet. 38(9):1043-8, 2006 |
PubMed
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Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae
Regenberg B, Grotkjr T, Winther O, Fausbll A, Akesson M, Bro C, Hansen LK, Brunak S, Nielsen J
Genome Biol. 7, R107, 2006 |
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The Escherichia coli chromosome is organized with the left and right chromosome arms in separate cell halves
Nielsen HJ, Ottesen JR, Youngren B, Austin SJ, Hansen FG
Mol. Microbiol. 62(2):331-8, 2006 |
PubMed
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Progressive segregation of the Escherichia coli chromosome
Nielsen HJ, Li Y, Youngren B, Hansen FG, Austin S
Mol. Microbiol. 61(2):383-93, 2006 |
PubMed
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Insights into the quality of DnaA boxes and their cooperativity
Hansen FG, Christensen BB, Nielsen CB, Atlung T
J. Mol. Biol. 355(1):85-95, 2006 |
PubMed
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Lactic acid bacteria inducing a weak interleukin-12 and tumor necrosis factor alpha response in human dendritic cells inhibit strongly stimulating lactic acid bacteria but act synergistically with gram-negative bacteria
Zeuthen LH, Christensen HR, Frøkiaer H
Clin. Vaccine Immunol. 13(3):365-75, 2006 |
PubMed
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Crystal structures of two peptide-HLA-B*1501 complexes; structural characterization of the HLA-B62 supertype
Roder G, Blicher T, Justesen S, Johannesen B, Kristensen O, Kastrup J, Buus S, Gajhede M
Acta Crystallogr D Biol Crystallogr. Nov;62(Pt 11):1300-10, 2006 |
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FeatureMap3D - a tool to map protein features and sequence conservation onto homologous structures in the PDB
Wernersson R, Rapacki K, Staerfeldt HH, Sackett PW, Mølgaard A
Nucleic Acids Res. 34:W84-8, 2006 |
PubMed
Web
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Virtual Ribosome - a comprehensive DNA translation tool with support for integration of sequence feature annotation
Wernersson R
Nucleic Acids Res. 34:W385-8, 2006 |
PubMed
Web
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Mesoscopic Simulations of Biological Membranes
Smit B, Kranenburg K, Sperotto MM, Venturoli M
Lect. Notes Phys. 704, 259-286, 2006 |
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Modelling of proteins in membranes
Sperotto MM, May S, Baumgaertner A
Chemistry and Physics of Lipids 141:2-29, 2006 |
PubMed
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Mesoscopic Models of Biological Membranes
Venturoli M, Sperotto MM, Kranenburg M, Smit B
Physics Reports, 437: 1-54, 2006 |
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TAP-Independent MHC Class I Presentation
Larsen MV, Nielsen M, Weinzierl A, Lund O
Curr Immunol Rev, 2, 233-245, 2006 |
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Opening the pan-genomics box
Read T, Ussery DW
Current Opinion in Microbiology, 9:496-498, 2006 |
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Design of a 7 Genomes Escherichia coli Microarray for Comparative Genomic Profiling
Willenbrock H, Petersen A, Sekse C, Kiil K, Wasteson Y, Ussery DW
J. Bacteriol. 188(22):7713-21, 2006 |
PubMed
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Leaner and Meaner Genomes in Escherichia coli
Ussery DW
Genome Biol. 7(10):237, 2006 |
PubMed
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An environmental signature for 323 microbial genomes based on codon adaptation indices
Willenbrock H, Friis C, Juncker AS, Ussery DW
Genome Biol. 7(12):R114, 2006 |
PubMed
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Metabolic network driven analysis of genome-wide transcription data from Aspergillus nidulans
David H, Hofmann G, Oliveira AP, Jarmer H, Nielsen J
Genome Biol. 7(11):R108, 2006 |
PubMed
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Modelling the human immune system by combining bioinformatics and systems biology approaches
Rapin N, Kesmir C, Frankild S et al
Journal of Biological Physics, 32 (3-4), 335-353, 2006 |
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A community resource benchmarking predictions of peptide binding to MHC-I molecules
Peters B, Bui HH, Frankild S, Nielson M, Lundegaard C, Kostem E, Basch D, Lamberth K, Harndahl M, Fleri W, Wilson SS, Sidney J, Lund O, Buus S, Sette A
PLoS Comput. Biol. 2(6):e65, 2006 |
PubMed
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The validity of predicted T-cell epitopes
Lundegaard C, Nielsen M, Lund O
Trends Biotechnol. 24(12):537-8, 2006 |
PubMed
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CTL epitopes for influenza A including the H5N1 bird flu; genome-, pathogen-, and HLA-wide screening
Wang M, Lamberth K, Harndahl M, Roder G, Stryhn A, Larsen MV, Nielsen M, Lundegaard C, Tang ST, Dziegiel MH, Rosenkvist J, Pedersen AE, Buus S, Claesson MH, Lund O
Vaccine 25(15):2823-31, 2006 |
PubMed
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Prediction of pH-Dependent Aqueous Solubility of Druglike Molecules
Hansen NT, Kouskoumvekaki I, Jørgensen FS, Brunak S, Jónsdóttir SÓ
J Chem Inf Model 46(6):2601-9, 2006 |
PubMed
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Co-evolution of transcriptional and post-translational cell-cycle regulation
Jensen LJ, Jensen TS, de Lichtenberg U, Brunak S, Bork P
Nature 443(7111):594-7, 2006 |
PubMed
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Prediction of residues in discontinuous B-cell epitopes using protein 3D structures
Andersen PH, Nielsen M, Lund O
Protein Sci. 15(11):2558-67, 2006 |
PubMed
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Analysis and prediction of mammalian protein glycation
Johansen MB, Kiemer L, Brunak S
Glycobiology 16(9):844-53, 2006 |
PubMed
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An overabundance of phase 0 introns immediately after the start codon in eukaryotic genes
Nielsen H, Wernersson R
BMC Genomics 7:256, 2006 |
PubMed
Web
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Arabidopsis MAP kinase 4 regulates salicylic acid- and jasmonic acid/ethylene-dependent responses via EDS1 and PAD4
Brodersen P, Petersen M, Nielsen HB, Zhu S, Newman MA, Shokat KM, Rietz S, Parker J, Mundy J
Plant J. 47(4):532-46, 2006 |
PubMed
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Transcription analysis using high-density micro-arrays of Aspergillus nidulans wild-type and creA mutant during growth on glucose or ethanol
Mogensen J, Nielsen HB, Hofmann G, Nielsen J
Fungal Genet. Biol. 43(8):593-603, 2006 |
PubMed
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Epitope mapping and topographic analysis of VAR2CSA DBL3X involved in P. falciparum placental sequestration
Dahlbäck M, Rask TS, Andersen PH, Nielsen MA, Ndam NT, Resende M, Turner L, Deloron P, Lund O, Pedersen AG, Hviid L, Theander TG, Salanti A
PLoS Pathog. 2(11):e124, 2006 |
PubMed
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Protein Evolution is Faster Outside the Cell
Julenius K, Pedersen AG
Mol. Biol. Evol. 23(11):2039-48, 2006 |
PubMed
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The genomic code: inferring Vibrionaceae niche specialization
Reen FJ, Almagro-Moreno S, Ussery D et al
Nat. Rev. Microbiol. 4(9):697-704, 2006 |
PubMed
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Distinct developmental defense activations in barley embryos identified by transcriptome profiling
Nielsen ME, Lok F, Nielsen HB
Plant Mol. Biol. 61:589-601, 2006 |
PubMed
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Identification of Tn5397-like and Tn916-like transposons and diversity of the tetracycline resistance gene tet(M) in enterococci from humans, pigs and poultry
Agersø Y, Pedersen AG, Aarestrup FM
Journal of Antimicrobial Chemotherapy. 57(5):832-9, 2006 |
PubMed
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Transcriptome analysis of FSH and FSH variant stimulation in granulosa cells from IVM patients reveals novel regulated genes
Perlman S, Bouquin T, van den Hazel B, Jensen TH, Schambye HT, Knudsen S, Okkels JS
Mol. Hum. Reprod. 12(3):135-44, 2006 |
PubMed
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The more the merrier: comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast
Marguerat S, Jensen TS, de Lichtenberg U, Wilhelm BT, Jensen LJ, Bahler J
Yeast 23(4):261-77, 2006 |
PubMed
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Improved method for predicting linear B-cell epitopes
Larsen JE, Lund O, Nielsen M
Immunome Res 2:2, 2006 |
PubMed
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A Wiring of the Human Nucleolus
Hinsby AM, Kiemer L, Karlberg EO, Lage K, Fausboll A, Juncker AS, Andersen JS, Mann M, Brunak S
Mol. Cell 22(2):285-95, 2006 |
PubMed
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Structural features of fungal genomes
Wanchanthuek P, Hallin PF, Gouveia-Oliveira R, Ussery DW
Topics in Current Genetics, 15, 47-77, 2006 |
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Ten years of bacterial genome sequencing: comparative-genomics-based discoveries
Binnewies TT, Motro Y, Hallin PF, Lund O, Dunn D, La T, Hampson DJ, Bellgard M, Wassenaar TM, Ussery DW
Functional and Integrative Genomics, 6, [Epub ahead of print], 2006 |
PubMed
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The TNFalpha receptor TNFRSF1A and genes encoding the amiloride-sensitive sodium channel ENaC as modulators in cystic fibrosis
Stanke F, Becker T, Cuppens H, Kumar V, Cassiman JJ, Jansen S, Radojkovic D, Siebert B, Yarden J, Ussery DW, Wienker TF, Tummler B
Hum. Genet. 119(3):331-43, 2006 |
PubMed
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Genome update: purine strand bias in 280 bacterial genomes
Champ PC, Binnewies TT, Nielsen N, Zinman G, Kiil K, Wu H, Bohlin J, Ussery DW
Microbiology (Reading, Engl.) 152:579-83, 2006 |
PubMed
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Identification of novel genes regulated in the developing human ventral mesencephalon
Jorgensen JR, Juliusson B, Henriksen KF, Hansen C, Knudsen S, Petersen TN, Blom N, Seiger A, Wahlberg LU
Exp. Neurol. 198(2):427-37, 2006 |
PubMed
|
Crosstalk
Mundy J, Nielsen HB, Brodersen P
Trends Plant Sci. 11(2):63-4, 2006 |
PubMed
|
Origin of Replication in Circular Prokaryotic Chromosomes
Worning P, Jensen LJ, Hallin PF, Stærfeldt HH, Ussery DW
Environ. Microbiol. 8(2):353-61, 2006 |
PubMed
|
2005
enoLOGOS: a versatile web tool for energy normalized sequence logos.
Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, Benos PV
Nucleic Acids Research. 2005 Jul 1;33(Web Server issue):W389-92., 2005 |
PubMed
|
Preprocessing High-density Oligonucleotide Arrays
Bolstad B, Irizarry R, Gautier L, Wu Z
Statistics for Biology and Health, Springer, 2005 |
Relevant URL
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Systematic discovery of new recognition peptides mediating protein interaction netoworks
Neduva V, Linding R, Su-Angrand I, Stark A, De Masi F, Gibson T, Lewis J, Serrano L, Russell R
PLoS Biol. 3(12):e405, 2005 |
PubMed
|
High throughput production of mouse monoclonal antibodies using antigen microarrays
De Masi F, Chiarella P, Wilhelm H, Massimi M, Bullard B, Ansorge W, Sawyer A
Proteomics 5(16):4070-81, 2005 |
PubMed
|
Integrating protein feature based predictions into S ystems Biology
Fausbøll A
Ph.D. thesis, 2005 |
|
Interactions between milk proteins and the immune system: modulation of nonspecific and antigen-specific immune responses
Brix S
ISBN: 87-991021-0-2, 2005 |
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Effect of prior dietary exposure to cow’s milk protein on antigen-specific and nonspecific cellular proliferation in mice
Brix S, Magyar OH, Barkholt V, Frøkiær H
J Dairy Res, 72:217-225 (2005), 2005 |
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Milk-derived GM3 and GD3 differentially inhibit dendritic cell maturation and effector functionalities
Brønnum H, Seested T, Hellgren LI, Brix S, Frøkiær H
Scand J Immunol, 61:551-557 (2005), 2005 |
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Effect of maternal dietary cow’s milk on the immune response to beta-lactoglobulin in the offspring: A four generation study in mice
Brix S, Christensen HR, Barkholt V, Frøkiær H
Int Arch Allergy Immunol, 136:250-259 (2005), 2005 |
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Maternal transfer of oral tolerance to ingested soy proteins
Christensen HR, Brix S, Frokiaer H
Immunology, 116:61-61 Suppl. 1 Dec (2005), 2005 |
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The 3\' region of human papillomavirus type 16 early mRNAs decrease expression
Vinther J, Rosenstierne MW, Kristiansen K, Norrild B
BMC Infect. Dis. 5:83, 2005 |
PubMed
|
Genome Update: Protein secretion systems in 225 bacterial genomes
Binnewies TT, Bendtsen JD, Hallin PF, Nielsen N, Wassenaar TM, Pedersen MB, Klemm P, Ussery DW
Microbiology (Reading, Engl.) 151:1013-6, 2005 |
PubMed
|
Simulation studies of protein-induced bilayer deformations, and lipid-induced protein tilting, on a mesoscopic model for lipid bilayers with embedded proteins
Venturoli M, Smit B, Sperotto MM
Biophys. J. 88(3):1778-98, 2005 |
PubMed
|
Selection of proteins for human MHC class II presentation
Jiang L, Lund O, Tan JQ
Cell. Mol. Immunol. 2(1):49-56, 2005 |
PubMed
|
Extracytoplasmic function sigma factors in Pseudomona syringae
Oguiza JA, Kiil K, Ussery DW
Trends Microbiol. 13(12):565-8, 2005 |
PubMed
|
Genome opdate: Protein secretion systems in 225 bacterial genomes
Bennewies TT, Bendtsen JD, Hallin PF, Nielsen N, Wassenaar TM, Pedersen MB, Klemm P, Ussery DW
Microbiology (Reading, Engl.) 151:1013-6, 2005 |
PubMed
|
Genome update: Prediction of secreted proteins in 225 bacterial proteomes
Bendtsen JD, Binnewies TT, Hallin PF, Sicheritz-Pontén T, Ussery DW
Microbiology (Reading, Engl.) 151:1725-7, 2005 |
PubMed
|
The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota
Chen LM, Brugger K, Skovgaard M, Redder P, She QX, Torarinsson E, Greve B, Awayez M, Zibat A, Klenk HP, Garrett RA
J. Bacteriol. 187(14):4992-9, 2005 |
PubMed
|
Genome update: Prediction of membrane proteins in prokaryotic genomes
Bendtsen JD, Binnewies TT, Hallin PF, Ussery DW
Microbiology (Reading, Engl.) 151:2119-21, 2005 |
PubMed
|
Alcohol-induced surface attachment of Listeria monocytogenes: Which mechanisms lie behind?
Knudsen B, Jarmer H, Knochel S, Gravesen A
Biotechnology, 118, 158-158, 2005 |
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Temporal interactome for the eukaryotic cell cycle by data integration
Brunak S
Biotechnology, 118, 7-8, 2005 |
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Genome update: Sigma factors in 240 bacterial genomes
Kiil K, Binnewies TT, Sicheritz-Pontén T, Willenbrock H, Hallin PF, Wassenaart TM, Ussery DW
Microbiology (Reading, Engl.) 151:3147-50, 2005 |
PubMed
|
Improvement of galactose uptake in Saccharomyces cerevisiae through overexpression of phosphoglucomutase: Example of transcript analysis as a tool in inverse metabolic engineering
Bro C, Knudsen S, Regenberg B, Olsson L, Nielsen J
Appl. Environ. Microbiol. 71(11):6465-72, 2005 |
PubMed
|
A comparison study: Applying segmentation to array CGH data for downstream analyses
Willenbrock H, Fridlyand J
Bioinformatics 21(22):4084-91, 2005 |
PubMed
|
Genome update: Distribution of two.component trensduction systems in 250 bacterial genomes
Kiil K, Ferchaud JB, David C, Binnewies T, Wu H, Sicheritz-Pontén T, Willenbrock H, Ussery DW
Microbiology (Reading, Engl.) 151:3447-52, 2005 |
PubMed
|
Genetic evolution of HIV in patients remaining on a stable HAART regimen despite insufficient viral suppression
Kristiansen TB, Pedersen AG, Eugen-Olsen J, Katzenstein TL, Lundgren JD
Scand. J. Infect. Dis. 37:890-901, 2005 |
PubMed
Publication download
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Presence of a functional but dispensable Nuclear Export Signal in the HTLV-2 Tax protein
Chevalier SA, Meertens L, Calattini S, Gessain A, Kiemer L, Mahieux R
Retrovirology 2:70, 2005 |
PubMed
|
Integrating protein annotation resources through the Distributed Annotation System
Olason PI
Nucleic Acids Res. 33:W468-70, 2005 |
PubMed
|
New weakly expressed cell cycle-regulated genes in yeast
Hansen B, Schmidt P, Fausboll A, de Lichtenberg U, Wernersson R, Skøt Jensen T, Nielsen HB, Knudsen S, Brunak S
Yeast 22(15):1191-201, 2005 |
PubMed
|
Non-classical protein secretion in bacteria
Bendtsen J, Kiemer L, Fausboll A, Brunak S
BMC Microbiol. 5:58, 2005 |
PubMed
|
Identification and analysis of 21 novel disease-causing amino acid substitutions in the conserved part of ATP7A
Moller LB, Bukrinsky JT, Molgaard A, Paulsen M, Lund C, Tumer Z, Larsen S, Horn N
Hum. Mutat. 26(2):84-93, 2005 |
PubMed
|
The design and implementation of the immune epitope database and analysis resource
Peters B, Sidney J, Bourne P, Bui HH, Buus S, Doh G, Fleri W, Kronenberg M, Kubo R, Lund O, Nemazee D, Ponomarenko JV, Sathiamurthy M, Schoenberger SP, Stewart S, Surko P, Way S, Wilson S, Sette A
Immunogenetics 57(5):326-36, 2005 |
PubMed
|
Crystal ball. Systems biology: in the broadest sense of the word
Ussery DW, de Lichtenberg U, Jensen LJ
Environ. Microbiol. 7(4):482-3, 2005 |
PubMed
|
A Systems Biology Investigation and Comparison of the Cell Cycle in Eukaryotic Cells
Jensen TS
Ph.D. thesis, 2005 |
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Systems Biology of the Eukaryotic Cell Cycle
de Lichtenberg U
Ph.D. thesis, 2005 |
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Prediction and Analysis of Protein Motifs
Kiemer L
Ph.D. thesis, 2005 |
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An integrative approach to CTL epitope prediction: A combined algorithm integrating MHC class I binding, TAP transport
Larsen MV, Lundegaard C, Lamberth K, Buus S, Brunak S, Lund O, Nielsen M
Eur. J. Immunol. 35(8):2295-303, 2005 |
PubMed
|
Limited Inter- and Intra-patient Sequence Diversity of the Genetic Lineage A human metapneumovirus fusion gene
Winther TN, Madsen CD, Pedersen AG, von Linstow ML, Eugen-Olsen J, Hogh B
Virus Genes 31(1):89-97, 2005 |
PubMed
Publication download
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Characterization of rotavirus strains in a Danish population: high frequency of mixed infections and diversity within the VP4 gene of P [8] strains
Fischer TK, Eugen-Olsen J, Pedersen AG, Molbak K, Bottiger B, Rostgaard K, Nielsen NM
Journal of Clinical Microbiology. 43(3):1099-104, 2005 |
PubMed
Publication download
|
OligoWiz 2.0 - Integrating sequence feature annotation into the design of microarray probes
Wernersson R, Nielsen HB
The EMBO Journal . 24(14):2579-89, 2005 |
PubMed
|
The MAP kinase substrate MKS1 is a regulator of plant defense responses
Andreasson E, Jenkins T, Brodersen P, Thorgrimsen S, Petersen NH, Zhu S, Qiu JL, Micheelsen P, Rocher A, Petersen M, Newman MA, Nielsen HB, Hirt H, Somssich I, Mattsson O, Mundy J
The EMBO Journal . 24(14):2579-89, 2005 |
PubMed
|
Prediction of twin-arginine signal peptides
Bendtsen JD, Nielsen H, Widdick D, Palmer T, Brunak S
BMC Bioinformatics 6:167, 2005 |
PubMed
|
FeatureExtract--extraction of sequence annotation made easy
Wernersson R
Nucleic Acids Res. 33:W567-9, 2005 |
PubMed
|
Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing
Wernersson R, Schierup MH, Jorgensen FG, Gorodkin J, Panitz F, Staerfeldt HH, Christensen OF, Mailund T, Hornshoj H, Klein A, Wang J, Liu B, Hu S, Dong W, Li W, Wong GK, Yu J, Wang J, Bendixen C, Fredholm M, Brunak S, Yang H, Bolund L
BMC Genomics 6:70, 2005 |
PubMed
|
Implementation of a gene expression index cal-culation method based on the PDNN model
Nielsen HB, Gautier L, Knudsen S
Bioinformatics 21(5):687-8, 2005 |
PubMed
|
Comparison of computational methods for the identification of cell cycle-regulated genes
de Lichtenberg U, Jensen LJ, Fausboll A, Jensen TS, Bork P, Brunak S
Bioinformatics 21(7):1164-71, 2005 |
PubMed
|
The genome of the protist parasite Entamoeba histolytica
Loftus B, Anderson I, Davies R, Alsmark UC, Samuelson J, Amedeo P, Roncaglia P, Berriman M, Hirt RP, Mann BJ, Nozaki T, Suh B, Pop M, Duchene M, Ackers J, Tannich E, Leippe M, Hofer M, Bruchhaus I, Willhoeft U, Bhattacharya A, Chillingworth T, Churcher C, Hance Z, Harris B, Harris D, Jagels K, Moule S, Mungall K, Ormond D, Squares R, Whitehead S, Quail MA, Rabbinowitsch E, Norbertczak H, Price C, Wang Z, Guillen N, Gilchrist C, Stroup SE, Bhattacharya S, Lohia A, Foster PG, Sicheritz-Pontén T, Weber C, Singh U, Mukherjee C, El-Sayed NM, Petri WA Jr, Clark CG, Embley TM, Barrell B, Fraser CM, Hall N
Nature 433(7028):865-8, 2005 |
PubMed
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The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage
Nielsen M, Lundegaard C, Lund O, Kesmir C
Immunogenetics 57:33-41, 2005 |
PubMed
|
The Immune Epitope Database and Analysis Resource: From Vision to Blueprint
Peters B, Sidney J, Bourne P, Bui HH, Buus S, Doh G, Fleri W, Kronenberg M, Kubo R, Lund O, Nemazee D, Ponomarenko JV, Sathiamurthy M, Schoenberger S, Stewart S, Surko P, Way S, Wilson S, Sette A
PLoS Biol. 3(3):e91, 2005 |
PubMed
|
Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates
Jonsdottir SO, Jorgensen FS, Brunak S
Bioinformatics 21(10):2145-60, 2005 |
PubMed
|
Genome Update: proteome comparisons
Binnewies TT, Hallin PF, Staerfeldt HH, Ussery DW
Microbiology (Reading, Engl.) 151:1-4, 2005 |
PubMed
|
Genome update: 2D clustering of bacterial genomes
Willenbrock H, Binnewies TT, Hallin PF, Ussery DW
Microbiology (Reading, Engl.) 151:333-6, 2005 |
PubMed
|
Genome update: base skews in 200+ bacterial chromosomes
Hallin PF, Nielsen N, Devine KM, Binnewies TT, Willenbrock H, Ussery DW
Microbiology (Reading, Engl.) 151:633-7, 2005 |
PubMed
|
Lid L11 of the glutamine amidotransferase domain of CTP synthase mediates allosteric GTP activation of glutaminase activity
Willemoës M, Mølgaard A, Johansson E, Martinussen J
FEBS Journal. 272(3):856-64, 2005 |
PubMed
|
Dynamic Complex Formation During the Yeast Cell Cycle
de Lichtenberg U, Jensen LJ, Brunak S, Bork P
Science 307(5710):724-7, 2005 |
PubMed
|
2004
Alternative mapping of probes to genes for affymetrix chips
Gautier L, Møller M, Friis-Hansen L, Knudsen L
BMC Bioinformatics 5:111, 2004 |
PubMed
Relevant URL
|
Det vi spiser påvirker vores immunforsvar – men hvordan?
Christensen HR, Kjaer TMR, Brix S, Frokiaer H
Dansk Kemi, 84:26-27 (2004), 2004 |
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Immune response in mice to ingested soya protein: antibody production, oral tolerance and maternal transfer
Christensen HR, Brix S, Frøkiær H
Br. J. Nutr. 91(5):725-32, 2004 |
PubMed
|
Lipopolysaccharide contamination of beta-lactoglobulin affects the immune response against intraperitoneally and orally administrated antigen
Brix S, Kjær TMR, Barkholt V, Frøkiær H
Int Arch Allergy Immunol, 135:216-220 (2004), 2004 |
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Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins
Diella F, Cameron S, Gemünd C, Linding R, Via A, Kuster B, Sicheritz-Pontén T, Blom N, Gibson TJ
BMC Bioinformatics 5:79, 2004 |
PubMed
|
DNA bendability and Nucleosome positioning in transcriptional regulation
Dlakic M, Brunak S, Ussery DW
DNA Conformation in Transcription, chapter 14, 2004 |
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Transcriptional profiling of extracellular amino acid in Saccharomyces cerevisiae and the role of St1p and Stp2p
Eckert-Boulet N, Nielsen PS, Friis C, dos Santos MM, Nielsen J, Kielland-Brandt MC, Regenberg B
Yeast 21(8):635-48, 2004 |
PubMed
|
Biological Sequence Analysis of Archeal Genomes
Skovgaard M
Ph.D. thesis, 2004 |
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Analysis and Prediction of Translocation Signals in Eukaryotes and Prokaryotes
Bendtsen JD
Ph.D. thesis, 2004 |
|
Integrative Approaches to the Analysis of Microarrays Expression Data: Application to High-density nucleotide Arrays
Gautier L
Ph.D. thesis, 2004 |
|
Distribution and characterization of staphylococcal interspersed repeat units (SIRUs) and potential use for strain differentiation
Hardy KJ, Ussery DW, Oppenheim BA, Hawkey PM
Microbiology (Reading, Engl.) 150:4045-52, 2004 |
PubMed
|
Structure-function analysis of the human sialyltransferase ST3Gal I: role of n-glycosylation and a novel conserved sialylmotif
Jeanneau C, Chazalet V, Auge C, Soumpasis DM, Harduin-Lepers A, Delannoy P, Imberty A, Breton C
The Journal of Biological Chemistry. 279(14):13461-8, 2004 |
PubMed
|
QSPR models for various physical properties of carbohydrates based on molecular mechanics and quantum chemical calculations
Dyekjaer JD, Jonsdottir SO
Carbohydr. Res. 339(2):269-80, 2004 |
PubMed
|
ShcA regulates neurite outgrowth stimulated by neural cell adhesion molecule but not by fibroblast growth factor 2: evidence for a distinct fibroblast growth factor receptor response to neural cell adhesion molecule activation
Hinsby AM, Lundfald L, Ditlevsen DK, Korshunova I, Juhl L, Meakin SO, Berezin V, Bock E
J. Neurochem. 91(3):694-703, 2004 |
PubMed
|
Definition of supertypes for HLA molecules using clustering of specificity matrices
Lund O, Nielsen M, Kesmir C, Pedersen AG, Lundegaard C, Worning P, Sylvester-Hvid C, Lamberth K, Roder G, Justesen S, Buus S, Brunak S
Immunogenetics 55(12):797-810, 2004 |
PubMed
|
Genome update: correlation of bacterial genomic properties
Hallin PF, Coenye T, Binnewies TT, Jarmer H, Staerfeldt HH, Ussery DW
Microbiology (Reading, Engl.) 150:3899-903, 2004 |
PubMed
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Identification of a core set of genes that signifies pathways underlying cardiac hypertrophy
Strøm CC, Kruhøffer M, Knudsen S, Stensgaard-Hansen F, Jonassen TE, Ørntoft TF, Haunsø S, Sheikh SP
Comp. Funct. Genomics 5:459-70 doi:10.1002/cfg.428, 2004 |
PubMed
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Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites
Julenius K, Mølgaard A, Gupta R, Brunak S
Glycobiology 15(2):153-64, 2004 |
PubMed
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Genome Update: DNA repeats in bacterial genomes
Ussery DW, Binnewies TT, Gouveia-Oliveira R, Jarmer H, Hallin PF
Microbiology (Reading, Engl.) 150:3519-21, 2004 |
PubMed
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Genome Update: alignment
Ussery DW, Jensen MS, Poulsen TR, Hallin PF
Microbiology (Reading, Engl.) 150:2491-3, 2004 |
PubMed
|
NetAcet: prediction of N-terminal acetylation sites
Kiemer L, Bendtsen JB, Blom N
Bioinformatics 21(7):1269-70, 2004 |
PubMed
|
Chromatin architecture and gene expression in Escherichia coli
Willenbrock H, Ussery DW
Genome Biol. 5(12):252, 2004 |
PubMed
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Genome update: chromosome atlases
Hallin PF, Binnewies TT, Ussery DW
Microbiology (Reading, Engl.) 150:3091-3, 2004 |
PubMed
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Complete DNA sequence of the linear mitochondrial genome of the pathogenic yeast Candida parapsilosis
Nosek J, Novotna M, Hlavatovicova Z, Ussery DW, Fajkus J, Tomaska L
Mol. Genet. Genomics 272(2):173-80, 2004 |
PubMed
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Genome update: promoter profiles
Ussery DW, Tindbaek N, Hallin PF
Microbiology (Reading, Engl.) 150:2791-3, 2004 |
PubMed
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Genome update: alignment of bacterial chromosomes
Ussery DW, Jensen MS, Poulsen TR, Hallin PF
Microbiology (Reading, Engl.) 150:2491-3, 2004 |
PubMed
|
Genome Update: annotation quality in sequenced microbial genomes
Ussery DW, Hallin PF
Microbiology (Reading, Engl.) 150:2015-7, 2004 |
PubMed
|
CBS genome atlas database: a dynamic storage for bioinformatic results and sequence data
Hallin PF, Ussery DW
Bioinformatics 20(18):3682-6, 2004 |
PubMed
|
MHC Class I Epitope Binding Prediction Trained on Small Data Sets
Lundegaard C, Nielsen M, Lamberth K, Worning P, Sylvester-Hvid C, Søren Buus, Brunak S, Lund O
Lecture Notes in Computer Science, vol 3239, proceeding of ICARIS 2004, 217-225, 2004 |
Abstract from Springer-Verlag
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Arabidopsis VARIEGATED 3encodes a chloroplasttargeted, zinc-finger protein required for chloroplast and palisade cell development
Næsted H, Holm A, Jenkins T, Bjørn Nielsen H, Harris CA, Beale MH, Andersen M, Mant A, Scheller H, Camara B, Mattsson O, Mundy J
J. Cell. Sci. 117:4807-18, 2004 |
PubMed
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Implementation of a gene expression index calculatation method based on the PDNN model
Bjørn Nielsen H, Gautier L, Knudsen S
Bioinformatics 21(5):687-8, 2004 |
PubMed
|
Analysis and prediction of leucine-rich nuclear export signals
La Cour T, Kiemer L, Mølgaard A, Gupta R, Skriver K, Brunak S
Protein Eng. Des. Sel. 17(6):527-36, 2004 |
PubMed
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Predicting protein structure classes from function predictions
Sommer I, Rahnenfuhrer J, Domingues FS, de Lichtenberg U, Lengauer T
Bioinformatics 20(5):770-6, 2004 |
PubMed
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Feature-based prediction of non-classical and leaderless protein secretion
Bendtsen JD, Jensen LJ, Blom N, Von Heijne G, Brunak S
Protein Eng. Des. Sel. 17(4):349-56, 2004 |
PubMed
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Coronavirus 3CLpro proteinase cleavage sites: possible relevance to SARS virus pathology
Kiemer L, Lund O, Brunak S, Blom N
BMC Bioinformatics 5:72, 2004 |
PubMed
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Improved prediction of signal peptides: SignalP 3,0
Bendtsen JD, Nielsen H, von Heijne G, Brunak S
J. Mol. Biol. 340(4):783-95, 2004 |
PubMed
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Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry
Hjerrild M, Stensballe A, Rasmussen TE, Kofoed CB, Blom N, Sicheritz-Ponten T, Larsen MR, Brunak S, Jensen ON, Gammeltoft S
Journal of Proteome Research. 3(3):426-33, 2004 |
PubMed
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Genome Update: tRNAs in sequenced microbial genomes
Ussery DW, Hallin PF, Lagesen K, Wassenaar TM
Microbiology (Reading, Engl.) 150:1603-6, 2004 |
PubMed
|
Genome update: rRNAs in sequenced microbial genomes
Ussery DW, Hallin PF, Lagesen K, Coenye T
Microbiology (Reading, Engl.) 150:1113-5, 2004 |
PubMed
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TXTGate: profiling gene groups with text-based information
Glenisson P, Coessens B, Van Vooren S, Mathys J, Moreau Y, De Moor B
Genome Biol. 5(6):R43, 2004 |
PubMed
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Comprehensive analysis of the base composition around the transcription start site in Metazoa
Aerts S, Thijs G, Dabrowski M, Moreau Y, De Moor B
BMC Genomics 5(1):34, 2004 |
PubMed
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Prediction of immunophenotype, treatment response, and relapse in childhood acute lymphoblastic leukemia using DNA microarrays
Willenbrock H, Juncker AS, Schmiegelow K, Knudsen S, Ryder LP
Leukemia 18(7):1270-7, 2004 |
PubMed
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The transcriptional activation program of human neutrophils in skin lesions supports their important role in wound healing
Theilgaard-Monch K, Knudsen S, Follin P, Borregaard N
J. Immunol. 172(12):7684-93, 2004 |
PubMed
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Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence
Blom N, Sicheritz-Ponten T, Gupta R, Gammeltoft S, Brunak S
Proteomics 4(6):1633-49, 2004 |
PubMed
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Blood cell gene expression profiling in rheumatoid arthritis; Discriminative genes and effect of rheumatoid factor
Bovin LF, Rieneck K, Workman C, Nielsen H, Sorensen SF, Skjodt H, Florescu A, Brunak S, Bendtzen K
Immunol. Lett. 93:217-26, 2004 |
PubMed
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Representation of protein sequence information by amino acid subalphabets
Andersen CAF, Brunak S
AI Magazine, 25, 97-104, 2004 |
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SARS CTL vaccine candidates; HLA supertype-, genome-wide scanning and biochemical validation
Sylvester-Hvid C, Nielsen M, Lamberth K, Roder G, Justesen S, Lundegaard C, Worning P, Thomadsen H, Lund O, Brunak S, Buus S
Tissue Antigens 63(5):395-400, 2004 |
PubMed
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Crystal packing in two pH-dependent crystal forms of rhamnogalacturonan acetylesterase
Mølgaard A, Larsen S
Acta Crystallogr. D Biol. Crystallogr. 60:472-8, 2004 |
PubMed
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Using literature and data to learn Bayesian networks as clinical models of ovarian tumors
Antal P, Fannes G, Timmerman D, Moreau Y, De Moor B
Artif Intell Med 30(3):257-81, 2004 |
PubMed
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A first glimpse into the pattern and scale of gene transfer in Apicomplexa
Huang J, Mullapudi N, Sicheritz-Ponten T, Kissinger JC
Parasitology International . 34(3):265-74, 2004 |
PubMed
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Genome Update: AT content in sequenced prokaryotic genomes
Ussery DW, Hallin PF
Microbiology (Reading, Engl.) 150:749-52, 2004 |
PubMed
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Development of in vitro transposon assisted signal sequence trapping and its use in screening Bacillus halodurans C125 and Sulfolobus solfataricus P2 gene libraries
Becker F, Schnorr K, Wilting R, Tolstrup N, Bendtsen JD, Olsen PB
J. Microbiol. Methods 57(1):123-33, 2004 |
PubMed
|
Structure-function analysis of the human sialyltransferase ST3Gal I
Jeanneau C, Chazalet V, Auge C, Soumpasis DM, Harduin-Lepers A, Delannoy P, Imberty A, Breton C
The Journal of Biological Chemistry. 279(14):13461-8, 2004 |
PubMed
|
Genome Update: length distributions of sequenced prokaryotic genomes
Ussery DW, Hallin PF
Microbiology (Reading, Engl.) 150:513-6, 2004 |
PubMed
|
Heterozygote advantage fails to explain the high degree of polymorphism of the MHC
De Boer RJ, Borghans JA, Van Boven M, Kesmir C, Weissing FJ
Immunogenetics 55(11):725-31, 2004 |
PubMed
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affy--analysis of Affymetrix GeneChip data at the probe level
Gautier L, Cope L, Bolstad BM, Irizarry RA
Bioinformatics 20(3):307-15, 2004 |
PubMed
|
Improved prediction of MHC class I and II epitopes using a novel Gibbs sampling approach
Nielsen M, Lundegaard C, Worning P, Sylvester-Hvid C, Lamberth K, Buus S, Brunak S, Lund O
Bioinformatics 20(9):1388-97, 2004 |
PubMed
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Analysis and recognition of 5' UTR intron splice sites in human pre-mRNA
Eden E, Brunak S
Nucleic Acids Res. 32(3):1131-42, 2004 |
PubMed
|
Genome Update: 161 prokaryotic genomes sequenced, and counting
Ussery DW
Microbiology (Reading, Engl.) 150:261-3, 2004 |
PubMed
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Prediction of proprotein convertase cleavage sites
Duckert P, Brunak S, Blom N
Protein Engineering, Design & Selection, 17, 107-112, 2004 |
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Global regulation of virulence and the stress response by CsrA in the highly adapted human gastric pathogen Helicobacter pylori
Barnard FM, Loughlin MF, Fainberg HP, Messenger MP, Ussery DW, Williams P, Jenks PJ
Mol. Microbiol. 51(1):15-32, 2004 |
PubMed
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2003
Immunostimulatory potential of beta-lactoglobulin preparations: effects caused by endotoxin contamination
Brix S, Bovetto L, Fritsché R, Barkholt V, Frøkiaer H
J Allergy Clin Immunol, 2003 |
PubMed
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An R Package for Analyses of Affymetrix Oligonucleotide Arrays
Irizarry R, Gautier L, Cope L
Springer, Statistics for Biology and Health, 2003 |
Relevant URL
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Pedersen SB, Bovetto L, Fritsche R, Barkholt V, Frøkiaer H
Immunostimulatory potential of beta-lactoglobulin preparations: Effects caused by endotoxin contamination
J Allergy Clin Immunol, 112:1216-1222 (2003), 2003 |
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Analysis of Gene Expression and Regulatory Networks
Friis C
Ph.D. thesis, 2003 |
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Microarray Data Analysis
Nielsen HB
Ph.D. thesis, 2003 |
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Characterization of incompletely typed rotavirus strains from Guinea-Bissau: identification of G8 and G9 types and a high frequency of mixed infections
Fischer TK, Page NA, Griffin DD, Eugen-Olsen J, Pedersen AG, Valentiner-Branth P, Mølbak K, Sommerfelt H, Nielsen NM
Virology 311(1):125-33, 2003 |
PubMed
Publication download
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Modeling of the phase equilibria of polystyrene in methylcyclohexane with semi-empirical quantum mechanical methods I
Wilczura-Wachnik H, Jonsdottir SO
J Mol Model 9(2):108-13, 2003 |
PubMed
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EasyGene - – a prokaryotic gene finder that ranks ORFs by statistical significance
Larsen TS, Krogh A
BMC Bioinformatics 4:21, 2003 |
PubMed
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Bioinformatic analysis of functional differences between the immunoproteasome and the constitutive proteasome
Kesmir C, van Noort V, de Boer RJ, Hogeweg P
Immunogenetics 55(7):437-49, 2003 |
PubMed
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MUTAGEN: Multi-User Tool for Annotating GENomes
Brugger K, Redder P, Skovgaard M
Bioinformatics 19(18):2480-1, 2003 |
PubMed
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The sigma54 regulon (sigmulon) of Pseudomonas putida
Cases I, Ussery DW, de Lorenzo V
Environ. Microbiol. 5(12):1281-93, 2003 |
PubMed
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Selecting Informative Data for Developing Peptide-MHC Binding Predictors Using a Query by Committee Approach
Christensen JK, Lamberth K, Nielsen M, Lundegaard C, Worning P, Lauemøller SL, Buus S, Brunak S, Lund O
Neural Comput 15(12):2931-42, 2003 |
PubMed
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The Plasmid Genome Database
Molbak L, Tett A, Ussery DW, Wall K, Turner S, Bailey M, Field D
Microbiology (Reading, Engl.) 149:3043-5, 2003 |
PubMed
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Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach
Buus S, Lauemoller SL, Worning P, Kesmir C, Frimurer T, Corbet S, Fomsgaard A, Hilden J, Holm A, Brunak S
Tissue Antigens 62(5):378-84, 2003 |
PubMed
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Functionality of System Components: Conservation of Protein Function in Protein Feature Space
Jensen LJ, Ussery DW, Brunak S
Genome Res. 13(11):2444-9, 2003 |
PubMed
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Genomic characteristics of the Campylobacter fetus sap island
Zheng-Chao Tu, Ussery DW, Pride DT, Blaser MJ
Genome Letters, 2, 34-40, 2003 |
Genome Letters website
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GenePublisher: Automated analysis of DNA microarray data
Knudsen S, Workman C, Sicheritz-Ponten T, Friis C
Nucleic Acids Res. 31(13):3471-6, 2003 |
PubMed
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Sequence analysis of three mitochondrial DNA molecules reveals interesting differences among Saccharomyces yeasts
Langkjær RB, Casaregola S, Ussery DW, Gaillardin C, Piskur J
Nucleic Acids Res. 31(12):3081-91, 2003 |
PubMed
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Strand misalignments lead to quasipalindrome correction
van Noort V, Worning P, Ussery DW, Rosche WA, Sinden RR
Trends Genet. 19(7):365-9, 2003 |
PubMed
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Optimization and immune recognition of multiple novel conserved HLA-A2, human immunodeficiency virus type 1-specific CTL epitopes
Corbet S, Nielsen HV, Vinner L, Lauemøller S, Therrien D, Tang ST, Kronborg G, Mathiesen L, Chaplin P, Brunak S, Buus S, Fomsgaard A
J. Gen. Virol. 84:2409-21, 2003 |
PubMed
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Prediction of lipoprotein signal peptides in Gram-negative bacteria
Juncker AS, Willenbrock H, Von Heijne G, Brunak S, Nielsen H, Krogh A
Protein Sci. 12(8):1652-62, 2003 |
PubMed
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Predicting proteasomal cleavage sites: a comparison of available methods
Saxova P, Buus S, Brunak S, Kesmir C
International Immunology. 15(7):781-7, 2003 |
PubMed
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Plasmodium falciparum merozoite surface protein 1
Hoessli DC, Poincelet M, Gupta R, Ilangumaran S, Nasir-ud-Din
Eur. J. Biochem. 270(2):366-75, 2003 |
PubMed
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RevTrans: multiple alignment of coding DNA from aligned amino acid sequences
Wernersson R, Pedersen AG
Nucleic Acids Res. 31(13):3537-9, 2003 |
PubMed
PDF
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Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays
Nielsen HB, Wernersson R, Knudsen S
Nucleic Acids Res. 31(13):3491-6, 2003 |
PubMed
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Classification of Dukes´ B and C colorectal cancers using expression arrays
Frederiksen CM, Knudsen S, Laurberg S, Ørntoft TF
J. Cancer Res. Clin. Oncol. 129(5):263-71, 2003 |
PubMed
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Protein feature based identification of cell cycle regulated proteins in yeast
de Lichtenberg U, Jensen TS, Jensen LJ, Brunak S
J. Mol. Biol. 329(4):663-74, 2003 |
PubMed
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RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box
Petersen L, Larsen TS, Ussery DW, On SL, Krogh A
J. Mol. Biol. 326(5):1361-72, 2003 |
PubMed
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Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome
Jensen LJ, Skovgaard M, Sicheritz-Ponten T, Jørgensen MK, Lundegaard C, Pedersen CC, Petersen N, Ussery D
BMC Genomics 4(1):12, 2003 |
PubMed
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Reliable prediction of T-cell epitopes using neural networks with novel sequence representations
Nielsen M, Lundegaard C, Worning P, Lauemøller SL, Lamberth K, Buus S, Brunak S, Lund O
Protein Sci. 12(5):1007-17, 2003 |
PubMed
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Prediction of human protein function according to Gene Ontology categories
Jensen LJ, Gupta R, Stærfeldt HH, Brunak S
Bioinformatics 19(5):635-42, 2003 |
PubMed
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NESbase version 1.0: a database of nuclear export signals
La Cour T, Gupta R, Rapacki K, Skriver K, Poulsen FM, Brunak S
Nucleic Acids Res. 31(1):393-6, 2003 |
PubMed
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2002
Genmanipuleret virus angriber kræftceller
Hansen DA, Larsen DH, Jakobsen RK
Information, 08-26 - s. 6, 2002 |
bibliotek.dk
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Web-based Tools for Vaccine Design
Lund O, Nielsen M, Kesmir C, Christensen JK, Lundegaard C, Worning P, Brunak S
HIV Molecular Immunology, pp. 45-51, 2002 |
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Prediction of protein function from sequence derived protein features
Jensen LJ
Ph.D. thesis, 2002 |
Relevant URL
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Gene and motif finding in prokaryotic DNA using hidden Markov models
Larsen TS
Ph.D. thesis, 2002 |
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Phylogenetic and Functional Analysis of the Bacteriophage P1 Single-Stranded DNA-Binding Protein
Bendtsen JD, Nilsson AS, Lehnherr H
J. Virol. 76(19):9695-701, 2002 |
PubMed
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Comparative Genomics of Pseudomonas aeruginosa PAO1 and Pseudomonas putida KT2440: Orthologs, Codon Usage, REP Elements and Oligonucleotide Motif Signatures
Weinel C, Ussery DW, Ohlsson H, Sicheritz-Ponten T, Kiewitz C, Tümmler B
Genome Letters, 1, 175-187, 2002 |
Genome Letters website
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Hyperstructures, genome analysis and I-cells
Amar P, Ballet P, Barlovatz-Meimon G, Benecke A, Bernot G, Bouligand Y, Bourguine P, Delaplace F, Delosme JM, Demarty M, Fishov I, Fourmentin-Guilbert J, Fralick J, Giavitto JL, Gleyse B, Godin C, Incitti R, Kepes F, Lange C, Le Sceller L, Loutellier C, Michel O, Molina F, Monnier C, Natowicz R, Norris V, Orange N, Pollard H, Raine D, Ripoll P, Rouviere-Yaniv J, Saier M Jr, Soler P, Tambourin P, Thellier M, Tracqui P, Ussery D, Vincent JC, Vannier JP, Wiggins P, Zemirline A
Acta Biotheor. 50(4):357-73, 2002 |
PubMed
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Roles of PucR, GlnR, and TnrA in regulating expression of the Bacillus subtilis ure P3 promoter
Brandenburg JL, Wray LV Jr, Beier L, Jarmer H, Saxild HH, Fisher SH
J. Bacteriol. 184(21):6060-4, 2002 |
PubMed
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Prediction of novel archaeal enzymes from sequence-derived features
Jensen LJ, Skovgaard M, Brunak S
Protein Sci. 11(12):2894-8, 2002 |
PubMed
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Nucleotide sequence database policies
Brunak S, Danchin A, Hattori M, Nakamura H, Shinozaki K, Matise T, Preuss D
Science 298(5597):1333, 2002 |
PubMed
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A new non-linear normalization method for reducing variability in DNA microarray experiments
Workman C, Jensen LJ, Jarmer H, Berka R, Gautier L, Nielsen HB, Saxild HH, Nielsen C, Brunak S, Knudsen S
Genome Biol. 3(9):research0048, 2002 |
PubMed
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DNA Microarray analysis of fim mutations in Escherichia coli
Schembri MA, Ussery D, Workman C, Hasman H, Klemm P
Mol. Genet. Genomics 267(6):721-9, 2002 |
PubMed
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The Atlas Visualisation of Genome-wide Information
Skovgaard M, Jensen LJ, Friis C, Stærfeldt H-H, Worning P, Brunak S, Ussery D
Methods in Microbiology, 33, 49-63, 2002 |
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RNA Secondary Structure and Sequence Conservation in C1 Region of Human Immunodeficiency Virus Type 1 env Gene
Peleg O, Brunak S, Trifonov EN, Nevo E, Bolshoy A
AIDS Res. Hum. Retroviruses 18(12):867-78, 2002 |
PubMed
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Neural network predicts sequence of TP53 gene based on DNA chip
Spicker S, Wikman F, Lu ML, Cordon-Cardo C, Workman C, Orntoft TF, Brunak S, Knudsen S
Bioinformatics 18(8):1133-4, 2002 |
PubMed
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Clustering Patterns of Cytotoxic T-Lymphocyte Epitopes in Human Immunodeficiency Virus Type 1 (HIV-1) Proteins Reveal Imprints of Immune Evasion on HIV-1 Global Variation
Yusim K, Kesmir C, Gaschen B, Addo MM, Altfeld M, Brunak S, Chigaev A, Detours V, Korber BT
J. Virol. 76(17):8757-68, 2002 |
PubMed
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Mean-field approaches to independent component analysis
Højen-Sørensen PA, Winther O, Hansen LK
Neural Comput 14(4):889-918, 2002 |
PubMed
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Avoiding cross hybridization by choosing nonredundant targets on cDNA arrays
Nielsen HB, Knudsen S
Bioinformatics 18(2):321-2, 2002 |
PubMed
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Bias of purine stretches in sequenced chromosomes
Ussery D, Soumpasis DM, Brunak S, Stærfeldt HH, Worning P, Krogh A
Comput. Chem. 26(5):531-41, 2002 |
PubMed
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Prediction of human protein function from post-translational modifications and localization features
Jensen LJ, Gupta R, Blom N, Devos D, Tamames J, Kesmir C, Nielsen H, Stærfeldt HH, Rapacki K, Workman C, Andersen CAF, Knudsen S, Krogh A, Valencia A, Brunak S
J. Mol. Biol. 319(5):1257-65, 2002 |
PubMed
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Prediction of proteasome cleavage motifs by neural networks
Kesmir C, Nussbaum AK, Schild H, Detours V, Brunak S
Protein Eng. 15(4):287-96, 2002 |
PubMed
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Gene expression analysis and gene regulation: from DNA microarrays to comparative genomics
Workman C
Ph.D. thesis, 2002 |
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Inheritance and organisation of the mitochondiral genome differ between two Saccharomyces
Petersen RF, Langkjær RB, Hvidfeldt J, Gartner J, Palmen W, Ussery DW, Piskur J
Indian J. Biochem. Biophys. 12(1):21-3, 2002 |
PubMed
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Continuum secondary structure captures protein flexibility
Anderson CAF, Palmer AG, Brunak S
Structure 10(2):175-84, 2002 |
PubMed
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Visualisation and Significance of DNA Structural Motifs in the Campylobacter jejuni genome
Petersen L, On SLW, Ussery D
Genome Letters, 1, 16-25, 2002 |
Relevant URL
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Transcription Analysis of the Bacillus subtilis PucR Regulon and Identification of a cis-Acting Sequence Required PucR-Regulated Expression of Genes Involved in Purine Catabolism
Beier L, Nygaard P, Jarmer H, Saxild HH
J. Bacteriol. 184(12):3232-41, 2002 |
PubMed
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Transcriptome analysis documents induced competence of Bacillus subtilis during nitrogen limiting conditions
Jarmer H, Berka R, Knudsen S, Saxild HH
FEMS Microbiol. Lett. 206(2):197-200, 2002 |
PubMed
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The genome sequence of Schizosaccharomyces pombe
Wood V, Gwilliam R, Rajandream M-A, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, Baker S, Basham D, Bowman S, Brooks K, Brown D, Brown S, Chillingworth T, Churcher C, Collins M, Connor R, Cronin A, Davis P, Feltwell T, Fraser A, Gentles S, Goble A, Hamlin N, Harris D, Hidalgo J, Hodgson G, Holroyd S, Hornsby T, Howarth S, Huckle EJ, Hunt S, Jagels K, James K, Jones L, Jones M, Leather S, McDonald S, McLean J, Moule S, Mungall K, Murphy L, Niblett D, Odell C, Oliver K, O'Neil S, Pearson D, Quail MA, Rabbinowitsch E, Rutherford K, Rutter S, Saunders D, Seeger K, Sharp S, Skelton J, Simmonds M, Squares R, Squares S, Stevens K, Taylor K, Taylor RG, Walsh S, Warren T, Whitehead S, Woodward J, Volckaert G, Aert R, Robben J, Grymonprez B, Weltjens I, Vanstreels E, Rieger M, Schäfer M, Muller-Auer S, Gabel C, Fuchs M, Fritzc C, Holzer E, Moestl D, Hilbert H, Borzym K, Langer I, Beck A, Lehrach H, Reinhardt R, Pohl TM, Eger P, Zimmermann W, Wedler H, Wambutt R, Purnelle B, Goffeau A, Cadieu E, Dréano S, Gloux S, Lelaure V, Mottier S, Galibert F, Aves SJ, Xiang Z, Hunt C, Moore K, Hurst SM, Lucas M, Rochet M, Gaillardin C, Tallada VA, Garzon A, Thode G, Daga RR, Cruzado L, Jimenez J, Sanchez M, del Rey F, Dominguez A, Revuelta JL, Moreno S, Armstrong J, Forsburg S, Cerrutti L, Lowe T, McCombie WR, Paulsen I, Potashkin J, Shpakovski GV, Ussery D, Barrell BG, Nurse P
Nature 415(6874):871-80, 2002 |
PubMed
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Evaluation of potential regulatory elements identified as DNase I hypersensitive sites in the CFTR gene
Phylactides M, Rowntree R, Nuthall H, Ussery D, Wheeler A, Harris A
Eur. J. Biochem. 269(2):553-9, 2002 |
PubMed
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Variety identification of wheat using mass spectrometry with neural networks and the influence of mass spectra processing prior to neural network analysis
Aagaard Sørensen H, Sperotto MM, Petersen M, Kesmir C, Radzikowski L, Jacobsen S, Søndergaard I
Rapid Commun. Mass Spectrom. 16(12):1232-7, 2002 |
PubMed
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Reproducibility of transcriptome analyses using oligonucleotide microarrays: an interlaboratory comparison of chemostat cultures of Saccharomyces cerevisiae
Piper M, Daran-Lapujade P, Bro C, Regenberg B, Knudsen S, Nielsen J, Pronk J
Biochem. J. 150(3):405-11, 2002 |
PubMed
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Prediction of glycosylation across the human proteome and the correlation to protein function
Gupta R, Brunak S
Pac Symp Biocomput:310-22, 2002 |
PubMed
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2001
Evolutionary and immunological implications of contemporary HIV-1 variation
Korber B, Gaschen B, Yusim K, Thakallapally R, Kesmir C, Detours V
Br. Med. Bull. 58:19-42, 2001 |
PubMed
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Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes
Krogh A, Larsson B, von Heijne G, Sonnhammer ELL
J. Mol. Biol. 305(3):567-80, 2001 |
PubMed
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A phylogenomic approach to microbial evolution
Sicheritz-Pontén T, Andersson SGE
Nucleic Acids Res. 29(2):545-52, 2001 |
PubMed
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Genome Organisation and Chromatin Structure in Escherichia coli
Ussery D, Larsen TS, Wilkes KT, Friis C, Worning P, Krogh A, Brunak S
Biochimie 83(2):201-12, 2001 |
PubMed
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Protein secondary structure: category assignment and predictability
Andersen CAF, Bohr H, Brunak S
FEBS Lett. 507(1):6-10, 2001 |
PubMed
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Quantitative predictions of peptide binding to MHC class I molecules using specificity matrices and anchor-stratified calibrations
Lauemoller SL, Holm A, Hilden J, Brunak S, Holst Nissen M, Stryhn A, Østergaard Pedersen L, Buus S
Tissue Antigens 57(5):405-14, 2001 |
PubMed
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Recognition of environmental and genetic effects on barley phenolic fingerprints by neural networks
Gorodkin J, Sogaard B, Bay H, Doll H, Kolster P, Brunak S
Comput. Chem. 25(3):301-7, 2001 |
PubMed
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Flexibility of the genetic code with respect to DNA structure
Baisnee PF, Baldi P, Brunak S, Pedersen AG
Bioinformatics 17(3):237-48, 2001 |
PubMed
PDF
Publication download
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Identification and design of p53-derived HLA-A2-binding peptides with increased CTL immunogenicity
Petersen TR, Buus S, Brunak S, Nissen MH, Sherman LA, Claesson MH
Scand. J. Immunol. 53(4):357-64, 2001 |
PubMed
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Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18
Parkhill J, Dougan G, James KD, Thomson NR, Pickard D, Wain J, Churcher C, Mungall KL, Bentley SD, Holden MT, Sebaihia M, Baker S, Basham D, Brooks K, Chillingworth T, Connerton P, Cronin A, Davis P, Davies RM, Dowd L, White N, Farrar J, Feltwell T, Hamlin N, Haque A, Hien TT, Holroyd S, Jagels K, Krogh A, Larsen TS, Leather S, Moule S, O\\\'Gaora P, Parry C, Quail M, Rutherford K, Simmonds M, Skelton J, Stevens K, Whitehead S, Barrell BG
Nature 413(6858):848-52, 2001 |
PubMed
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Sigma A recognition sites in the Bacillus subtilis genome
Jarmer H, Larsen TS, Krogh A, Saxild HH, Brunak S, Knudsen S
Microbiology (Reading, Engl.) 147:2417-24, 2001 |
PubMed
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On the total number of genes and their length distribution in complete microbial genomes
Skovgaard M, Jensen LJ, Brunak S, Ussery D, Krogh A
Trends Genet. 17(8):425-8, 2001 |
PubMed
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Proceedings of ISMB
Brunak S, Krogh A (eds.)
Bioinformatics, 17, 2001 |
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Identification of gene expression patterns in superficial and invasive human bladder cancer
Thykjaer T, Workman C, Kruhoffer M, Demtroder K, Wolf H, Andersen LD, Frederiksen CM, Knudsen S, Ørntoft TF
Cancer Res. 61(6):2492-9, 2001 |
PubMed
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Definition of the Bacillus subtilis PurR operator sequence using genetic and bioinformatic tools and expansion of the PurR regulon with glyA, guaC, pbuG, xpt-pbuX, yqhZ-folD and pbuO
Saxild HH, Bruntedt K, Nielsen KI, Jarmer H, Nygaard P
J. Bacteriol. 183(21):6175-83, 2001 |
PubMed
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Enrichment of regulatory signals in conserved non-coding genomic sequence
Levy S, Hannenhalli S, Workman C
Bioinformatics 17(10):871-7, 2001 |
PubMed
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On the estimation of number of events required for saturation mutagenesis of large genomes
Phogat SK, Gupta R, Burma PK, Sen K, Pental D
Curr. Sci., 80, 823-824, 2001 |
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ISMB2001 - Proceedings for the Ninth international Conference on Intelligent Systems for Molecular Biology
Brunak S, Gallison F, Gribskov M, Krogh A, Pedersen AG, Rouze P, Stormo G, Tramontano A (eds.)
Bioinformatics, 17, Suppl. 1, 2001 |
TOC
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Prediction of glycosylation sites in proteomes: from post-translational modifications to protein function
Gupta R
Ph.D. thesis, 2001 |
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Protein Structure and the Diversity of Hydrogen Bonds
Andersen CAF
Ph.D. thesis, 2001 |
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The Stealth Creationists
Ussery DW
Skeptic, 8, 72-74, 2001 |
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Orphan protein function and its relation to glycosylation
Gupta R, Jensen LJ, Brunak S
Ernst Schering Research Foundation Proceedings, 38, Chapter 13, Springer-Verlag, 2001 |
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2000
Kan mælkeproteiner styrke vores immunforsvar?
Brix S, Barkholt V, Frokiaer H
Mælkeritidende, 13/14:364-366 (2000)., 2000 |
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Caleosins: Ca2+-binding proteins associated with lipid bodies
Næsted H, Frandsen GI, Jauh G, Hernandez-Pinzon I, Nielsen HB, Murphy DJ, Rogers JC, Mundy J
Plant Mol. Biol. 44(4):463-76, 2000 |
PubMed
Relevant URL
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Promiscuous and specific phospholipid binding by domains in ZAC, a membrane-associated Arabidopsis protein with an ARF GAP zinc finger and a C2 domain
Jensen RB, Lykke-Andersen K, Frandsen GI, Nielsen HB, Haseloff J, Jespersen HM, Mundy J, Skriver K
Plant Mol. Biol. 44(6):799-814, 2000 |
PubMed
Relevant URL
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In vivo protection of nigral dopamine neurons by lentiviral gene transfer of the novel GDNF-family member neublastin/artemin
Rosenblad C, Gronborg M, Hansen C, Blom N, Meyer M, Johansen J, Dago L, Kirik D, Patel UA, Lundberg C, Trono D, Bjorklund A, Johansen TE
Mol. Cell. Neurosci. 15(2):199-214, 2000 |
PubMed
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Identifying cytotoxic T cell epitopes from genomic and proteomic information: "The human MHC project"
Lauemøller SL, Kesmir C, Corbet SL, Fomsgaard A, Holm A, Claesson MH, Brunak S, Buus S
Rev Immunogenet 2(4):477-91, 2000 |
PubMed
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Predicting subcellular localization of proteins based on their N-terminal amino acid sequence
Emmanuelsson O, Nielsen H, Brunak S, von Heijne G
J. Mol. Biol. 300(4):1005-16, 2000 |
PubMed
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Computational methods in molecular biology, (Book review)
Brunak S
Trends in Genetics, 16, 97-98, 2000 |
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Prediction of protein secondary structure at 80% accuracy
Petersen TN, Lundegaard C, Nielsen M, Bohr H, Brunak S, Gippert GP, Lund O
Proteins 41(1):17-20, 2000 |
PubMed
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Matching protein beta-sheet partners by feedforward and recurrent neural networks
Baldi P, Pollastri G, Andersen CA, Brunak S
Proc Int Conf Intell Syst Mol Biol 8:25-36, 2000 |
PubMed
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Using database matches with HMMgene for automated gene detection in Drosophila
Krogh A
Genome Res. 10(4):523-8, 2000 |
PubMed
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Arabidopsis MAP Kinase 4 Negatively Regulates Systemic Acquired Resistance
Petersen M, Brodersen P, Naested H, Andreasson E, Lindhart U, Johansen B, Nielsen HB, Lacy M, Austin MJ, Parker JE, Sharma SB, Klessig DF, Martienssen R, Mattsson O, Jensen AB, Mundy J
Cell 103(7):1111-20, 2000 |
PubMed
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Efficient Identification and Analysis of Substructures in Proteins Using the Kappa-Tau Framework: Left Turns and Helix c-cap Motifs
Soumpasis DM, Strahm MC
J. Biomol. Struct. Dyn. 17(6):965-79, 2000 |
PubMed
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Visualization of pathogenicity regions in bacteria
Friis C, Jensen LJ, Ussery DW
Genetica 108(1):47-51, 2000 |
PubMed
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A DNA structural atlas for Escherichia coli
Pedersen AG, Jensen LJ, Stærfeldt H, Brunak S, Ussery DW
J. Mol. Biol. 299(4):907-30, 2000 |
PubMed
Publication download
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Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation
Jensen LJ, Knudsen S
Bioinformatics 16(4):326-33, 2000 |
PubMed
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The frequency of mutators in populations of Escherichia coli
Boe L, Danielsen M, Knudsen S, Petersen JB, Maymann J, Jensen PR
Mutat. Res. 448(1):47-55, 2000 |
PubMed
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A Classification of Possible Routes of Darwinian Evolution
Thornhill RH, Ussery DW
J. Theor. Biol. 203(2):111-6, 2000 |
PubMed
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Assessing the Accuracy of Prediction Algorithms for Classification: An Overview
Baldi P, Brunak S, Chauvin Y, Nielsen H, Andersen CAF
Bioinformatics 16(5):412-24, 2000 |
PubMed
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Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima
Worning P, Jensen LJ, Nielson KE, Brunak S, Ussery DW
Nucleic Acids Res. 28(3):706-9, 2000 |
PubMed
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env Sequences of Simian Immunodeficiency Viruses from Chimpanzees in Cameroon Are Strongly Related to Those of Human Immunodeficiency Virus Group N from the Same Geographic Area
Corbet S, Müller-Trutwin MC, Versmisse P, Delarue S, Ayouba A, Lewis J, Brunak S, Martin P, Brun-Vezinet F, Simon F, Barré-Sinoussi F, Mauclére P
J. Virol. 74(1):529-34, 2000 |
PubMed
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Improving the odds in discriminating
Frimurer TM, Bywater R, Nærum L, Nørskov Lauritsen L, Brunak S
Journal of Chemical Information and Computer Sciences 40(6):1315-24, 2000 |
PubMed
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1999
From sequence to sorting: Prediction of signal peptides
Nielsen H
PhD thesis, 1999 |
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ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites
Emanuelsson O, Nielsen H, von Heijne G
Protein Sci. 8(5):978-84, 1999 |
PubMed
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A mathematical model on germinal center kinetics and termination
Kesmir C, De Boer RJ
J. Immunol. 163(5):2463-9, 1999 |
PubMed
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Identification of wheat varieties using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry and an artificial neural network
Bloch HA, Kesmir C, Petersen M, Jacobsen S, Sondergaard II
Rapid Commun. Mass Spectrom. 13(14):1535-9, 1999 |
PubMed
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No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution
Workman C, Krogh A
Nucleic Acids Res. 27(24):4816-22, 1999 |
PubMed
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Competition between Sec- and TAT-dependent protein translocation in Escherichia coli
Cristóbal S, de Gier J-W, Nielsen H, von Heijne G
The EMBO Journal . 18(11):2982-90, 1999 |
PubMed
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Sequence and structure-based prediction of eukaryotic protein phosphorylation sites
Blom N, Gammeltoft S, Brunak S
J. Mol. Biol. 294(5):1351-62, 1999 |
PubMed
|
Three views of microbial genomes
Jensen LJ, Friis C, Ussery DW
Res. Microbiol. 150:773-7, 1999 |
PubMed
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Structural Basis for Triplet Repeat Disorders: A Computational Analysis
Baldi P, Brunak S, Chauvin Y, Pedersen AG
Bioinformatics 15(11):918-29, 1999 |
PubMed
Publication download
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The biology of eukaryotic promoter prediction - a review
Pedersen AG, Baldi P, Chauvin Y, Brunak S
Comput. Chem. 23:191-207, 1999 |
PubMed
Publication download
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Modeling regulatory networks with weight matrices
Weaver D, Workman C, Stormo GD
Pac Symp Biocomput:112-23, 1999 |
PubMed
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Exploiting the past and the future in protein secondary structure prediction
Baldi P, Brunak S, Frasconi P, Pollastri G, Soda G
Bioinformatics 15(11):937-46, 1999 |
PubMed
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Characterization of enzymatically induced aggregation of Casein icelles in natural concentration by in situ static light scattering and ultra low shear viscosimetry
Lehner D, Worning P, Fritz G, Ogendal L, Bauer R, Glatter O
J Colloid Interface Sci 213(2):445-456, 1999 |
PubMed
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Measures on Hidden Markov Models
Lyngsø RB, Pedersen CNS, Nielsen H
BRICS Report Series, RS-99-6, February, 1999 |
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Scanning the available Dictyostelium discoideum proteome for O-linked GlcNAc glycosylation sites using neural networks
Gupta R, Jung E, Gooley AA, Williams KL, Brunak S, Hansen J
Glycobiology 9(10):1009-22, 1999 |
PubMed
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MatrixPlot: visualizing sequence constraints
Gorodkin J, Stærfeldt HH, Lund O, Brunak S
Bioinformatics 15(9):769-70, 1999 |
PubMed
|
Nosocomial HIV-transmission in an outpatient clinic detected by epidemiological and phylogenetic analyses
Katzenstein TL, Jørgensen LB, Permin H, Hansen J, Nielsen C, Machuca R, Gerstoft J
AIDS 13(13):1737-44, 1999 |
PubMed
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Using Sequence Motifs for Enhanced Neural Network Prediction of Protein Distance Constraints
Gorodkin J, Lund O, Andersen CA, Brunak S
Proc Int Conf Intell Syst Mol Biol:95-105, 1999 |
PubMed
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Metrics and Similarity Measures for Hidden Markov Models
Lyngsø RB, Pedersen CNS, Nielsen H
Proc Int Conf Intell Syst Mol Biol:178-86, 1999 |
PubMed
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Promoter 2.0: for the Recognition of PolII Promoter Sequences and
Knudsen S
Bioinformatics 15(5):356-61, 1999 |
PubMed
|
Hidden neural networks
Krogh A, Riis SK
Neural Comput 11(2):541-63, 1999 |
PubMed
|
Environmental Influences on DNA Curvature
Ussery DW, Higgins CF, Bolshoy A
J. Biomol. Struct. Dyn. 16(4):811-23, 1999 |
PubMed
|
Machine learning approaches to the prediction of signal peptides and other protein sorting signal (review)
Nielsen H, Brunak S, von Heijne G
Protein Eng. 12(1):3-9, 1999 |
PubMed
|
O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins
Gupta R, Birch H, Rapacki K, Brunak S, Hansen JE
Nucleic Acids Res. 27(1):370-2, 1999 |
PubMed
|
A Biochemist's Response to the Biochemical Challenge to Evolution
Ussery DW
Bios, 70, 40-45, 1999 |
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PhosphoBase, a database of phosphorylation sites: release 2.0
Kreegipuu A, Blom N, Brunak S
Nucleic Acids Res. 27(1):237-9, 1999 |
PubMed
|
1998
DNA Structure in Human RNA Polymerase II Promoters
Pedersen AG, Baldi P, Chauvin Y, Brunak S
J. Mol. Biol. 281(4):663-73, 1998 |
PubMed
Publication download
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Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
Cole ST et al (Krogh A)
Nature 393(6685):537-44, 1998 |
PubMed
|
The effect of the lacY gene on the induction of IPTG inducible promoters, studied in Eschericia coli and Pseudomonas fluorescens
Hansen LH, Knudsen S, Sorensen SJ
Curr. Microbiol. 36(6):341-7, 1998 |
PubMed
|
Computational analyses and annotations of the Arabidopsis peroxidase gene family
Østergaard L, Pedersen AG, Jespersen HM, Brunak S, Welinder KG
FEBS Lett. 433:98-102, 1998 |
PubMed
Publication download
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DNA: Structure and Function
Sinden RR, Pearson CE, Potaman VN, Ussery DW
in R.D. Verma (ed.), ``Advances in Genome Biology'', 5, 1-141, 1998 |
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Gene finding: putting the parts together
Krogh A
in M.J. Bishop (ed.), ``Guide to Human Genome Computing'', Academic Press, 261-274, 1998 |
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An Introduction to Hidden Markov Models for Biological Sequences
Krogh A
in S.L. Salzberg, D.B. Searls and S. Kasif (eds.), ``Computational Methods in Molecular Biology'', Elsevier, 45-63, 1998 |
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Prediction of signal peptides and signal anchors by a hidden Markov model
Nielsen H, Krogh A
Proc Int Conf Intell Syst Mol Biol 6:122-30, 1998 |
PubMed
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A hidden Markov model for predicting transmembrane helices in protein sequences
Sonnhammer ELL, von Heijne G, Krogh A
Proc Int Conf Intell Syst Mol Biol 6:175-82, 1998 |
PubMed
|
Computational Applications of DNA Structural Scales
Baldi P, Brunak S, Chauvin Y, Gorodkin J, Pedersen AG
Proc Int Conf Intell Syst Mol Biol 6:35-42, 1998 |
PubMed
Publication download
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Statistical analysis of protein kinase specificity determinants
Kreegipuu A, Blom N, Brunak S, Järv J
FEBS Letters, 430, 45-50, 1998 |
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Comparisons of DNA mediated immunization procedures to surface glycoproteins of Human Immunodeficiency Virus type 1 and Hepatitis B virus
Fomsgaard A, Vedel Nielsen H, Johansson K, Nielsen C, Machuca R, Bruun L, Hansen J, Buus S
APMIS 106(6):636-46, 1998 |
PubMed
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Improved humoral and cellular immune responses against the gp120 V3 loop of HIV-1 following genetic immunization with a chimeric DNA vaccine encoding the V3 inserted into the Hepatitis B surface antigen (HBsAg)
Fomsgaard A, Vedel Nielsen H, Johansson K, Nielsen C, Machuca R, Bruun L, Hansen J, Buus S
Scand. J. Immunol. 47(4):289-95, 1998 |
PubMed
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PhosphoBase: a database of phosphorylation sites
Blom N, Kreegipuu A, Brunak S
Nucleic Acids Res. 26(1):382-6, 1998 |
PubMed
|
O-GLYCBASE Version 3.0 - A revised database of O-glycosylated proteins
Hansen JE, Lund O, Nilsson J, Rapacki K, Brunak S
Nucleic Acids Res. 26(1):387-9, 1998 |
PubMed
|
NetOglyc: Prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility
Hansen JE, Lund O, Tolstrup N, Gooley AA, Williams KL, Brunak S
Glycoconj. J. 15(2):115-30, 1998 |
PubMed
|
1997
Relation between phylogeny of African green monkey CD4 genes and their respective Simian Immunodeficiency Virus genes
Fomsgaard A, Muller-Trutwin M, Diop O, Hansen J, Mathiot C, Barre-Sinoussi F, Allen JS
J. Med. Primatol. 26(3):120-8, 1997 |
PubMed
|
Displaying the information contents of structural RNA alignments: the structure logos
Gorodkin J, Heyer LJ, Brunak S, Stormo GD
Comput. Appl. Biosci. 13(6):583-6, 1997 |
PubMed
|
Hidden Markov models for human genes: periodic patterns in exon sequences
Baldi P, Brunak S, Chauvin Y, Krogh A
Proc Int Conf Intell Syst Mol Biol 3:30-8, 1997 |
PubMed
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Finding the most significant common sequences and structure motifs in a set of RNA sequences
Gorodkin J, Heyer LJ, Stormo GD
Nucleic Acids Res. 25(18):3724-32, 1997 |
PubMed
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A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
Nielsen H, Engelbrecht J, Brunak S, von Heijne G
Int J Neural Syst 8:581-99, 1997 |
PubMed
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Hidden neural networks: a framework for HMM/NN hybrids
Riis SK, Krogh A
Neural Comput 11(2):541-63, 1997 |
PubMed
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Hierarchical organization of aggregated protein molecules
Bohr H, Kühle A, Sørensen AH, Bohr J
Zeitschrift f. Physik D, 40, 513-515, 1997 |
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The implication of topology for protein structure and aggregation
Bohr J, Bohr H
Zeitschrift f. Physik D, 40, 186-189, 1997 |
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Towards a classification of protein folds
Bohr H, Lindgård PA
Phys. Rev. E, 56, 4497, 1997 |
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Packing of protein structures in clusters with magic numbers
Lindgård PA, Bohr H
Zeitschrift f. Physik D, 40, 236-239, 1997 |
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Density functional and neural network analysis of hydration effects and spectroscopic and structural correlations in small peptides and amino acids
Bohr H, Jalkanen K, Suhai S
in Theoretical and Computational Methods in Genome Research, S. Suhaí (ed.), Plenum Press, N.Y., 255-278, 1997 |
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An update of the DEF database of protein fold class predictions
Reczko M, Karras D, Bohr H
Nucleic Acids Res. 25(1):235, 1997 |
PubMed
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Protein distance constraints predicted by neural networks and probability density functions
Lund O, Frimand K, Gorodkin J, Bohr H, Bohr J, Hansen J, Brunak S
Protein Eng. 10(11):1241-8, 1997 |
PubMed
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Coherent topological phenomena in protein folding
Bohr H, Brunak S, Bohr J
Fold Des 2(3):S15-8, 1997 |
PubMed
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Enhancement of the nucleosomal pattern in sequences of lower complexity
Bolshoy A, Shapiro K, Trifonov EN, Ioshikhes I
Nucleic Acids Res. 25(16):3248-54, 1997 |
PubMed
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A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites
Tolstrup N, Rouzé P, Brunak S
Nucleic Acids Res. 25(15):3159-63, 1997 |
PubMed
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Prediction of N-terminal protein sorting signals
Claros MG, Brunak S, von Heijne G
Curr. Opin. Struct. Biol. 7(3):394-8, 1997 |
PubMed
|
Relation between phylogeny of African green monkey CD4 genes and their respective Simian Immunodeficiency Virus genes
Fomsgaard A, Muller-Trutwin M, Diop O, Hansen J, Mathiot C, Barre-Sinoussi F, Allen JS
J. Med. Primatol., 26, 120-128, 1997 |
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Kissing loops hide premature termination codons in pre-mRNA of selenoprotein genes and in genes containing programmed ribosomal frameshifts
Knudsen S, Brunak S
RNA 3(7):697-701, 1997 |
PubMed
|
Finding Common Sequence and Structure Motifs in a Set of RNA Sequences
Gorodkin J, Heyer LJ, Stormo G
Proc Int Conf Intell Syst Mol Biol 5:120-3, 1997 |
PubMed
|
Two Methods for Improving Performance of a HMM and their Application for Gene Finding
Krogh A
Proc Int Conf Intell Syst Mol Biol 5:179-86, 1997 |
PubMed
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Neural Network Prediction of Translation Initiation Sites in Eukaryotes: Perspectives for EST and Genome analysis
Pedersen AG, Nielsen H
Proc Int Conf Intell Syst Mol Biol 5:226-33, 1997 |
PubMed
Publication download
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O-glycbase version 2.0 - A revised database of O-glycosylated proteins
Hansen JE, Lund O, Rapacki K, Brunak S
Nucleic Acids Res. 25(1):278-82, 1997 |
PubMed
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Molecular Wring Resonances in Chain Molecules
Bohr H, Brunak S, Bohr J
Bioelectromagnetics 18(2):187-9, 1997 |
PubMed
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Protein Folding and Wring Resonances
Bohr J, Bohr H, Brunak S
Biophys. Chem. 63:97-105, 1997 |
PubMed
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Non-linear backpropagation: doing back-propagation without derivatives of the activation function
Hertz JA, Krogh A, Lautrup B, Lehmann T
IEEE Trans Neural Netw 8(6):1321-7, 1997 |
PubMed
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Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
Nielsen H, Engelbrecht J, Brunak S, von Heijne G
Protein Eng. 10(1):1-6, 1997 |
PubMed
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Simulated Annealing and the Complexity of Protein Conformations
Bohr H, Brunak S
in Proceedings of the Workshop on Statistical Mechanics, DTH, June 1987, eds: H. Bohr and O.G. Mouritsen, 1997 |
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1996
Protein structure and the sequential structure of mRNA: alpha-helix and beta-sheet signals at the nucleotide level
Brunak S, Engelbrecht J
Proteins 25(2):237-52, 1996 |
PubMed
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Cleavage site analysis in picornaviral polyproteins: Discovering cellular targets with neural networks
Blom N, Hansen J, Blaas D, Brunak S
Protein Sci. 5(11):2203-16, 1996 |
PubMed
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Relationship between protein structure and geometrical constraints
Lund O, Hansen J, Brunak S, Bohr J
Protein Sci. 5(11):2217-25, 1996 |
PubMed
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Magic numbers in protein structures
Lindgård PA, Bohr H
Phys. Rev. Lett. 77(4):779-782, 1996 |
PubMed
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Naturally occurring nucleosome positioning signals in human exons and introns
Baldi P, Brunak S, Chauvin Y, Krogh A
J. Mol. Biol. 263(4):503-10, 1996 |
PubMed
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Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models
Pedersen AG, Baldi P, Brunak S, Chauvin Y
Proc Int Conf Intell Syst Mol Biol 4:182-91, 1996 |
PubMed
Publication download
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Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information
Korning PG, Hebsgaard SM, Tolstrup N, Engelbrecht J, Rouzé P, Brunak S
Nucleic Acids Res. 24(17):3439-52, 1996 |
PubMed
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The Formation of Protein Structure
Bohr J, Bohr H, Brunak S
Europhysics News, 27, 50-54, 1996 |
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Distance distributions in proteins: A six parameter representation
Reese MG, Lund O, Bohr J, Bohr H, Hansen JE, Brunak S
Protein Eng. 9(9):733-40, 1996 |
PubMed
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Prediction of the secondary structure of HIV-1 gp120
Hansen JE, Lund O, Nielsen JO, Brunak S, Hansen J-ES
Proteins 25(1):1-11, 1996 |
PubMed
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Protein structure and the sequential structure of mRNA: alpha-helix and beta-sheet signals at the nucleotide level
Brunak S, Engelbrecht J
Proteins, 25, 237-252, 1996 |
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O-glycbase - A revised database of O-glycosylated proteins
Hansen JE, Lund O, Nielsen JO, Hansen J-ES, Brunak S
Nucleic Acids Res.24, 248-252, 1996 |
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Defining a similarity threshold for a functional protein sequence pattern: The signal peptide cleavage site
Nielsen H, Engelbrecht J, von Heijne G, Brunak S
Proteins 24(2):165-77, 1996 |
PubMed
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Update on protein structure prediction: results of the 1995 IRBM workshop
Hubbard T, Tramontano A, Hansen J, Vinals C, Fjellstrom O, Ribas de Pouplana L, the rest of the workshop team
Fold Des 1(3):R55-63, 1996 |
PubMed
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The gntP Gene of Escherichia coli Involved in Gluconate Uptake
Klemm P, Tong S, Nielsen H, Conway T
J. Bacteriol. 178(1):61-7, 1996 |
PubMed
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Cleaning the GenBank Arabidopsis thaliana data set
Korning PG, Hebsgaard SM, Rouzé P, Brunak S
Nucleic Acids Res. 24(2):316-20, 1996 |
PubMed
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1995
Prediction of hypervariable CDR-H3 loop structures in antibodies
Reczko M, Martin ACR, Bohr H, Suhai S
Protein Eng. 8(4):389-95, 1995 |
PubMed
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Increased adhesion as a mechanism of antibody-dependent and antibody-independent complement-mediated enhancement of human immunodeficiency virus infection
Lund O, Hansen J, Sørensen AM, Mosekilde E, Nielsen JO, Hansen J-ES
J. Virol. 69(4):2393-400, 1995 |
PubMed
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Receptor Function of CD4 Structures from African Green Monkey and Pig-Tail Macaque for Simian Immunodeficiency Virus, SIVsm, SIVagm, and Human Immunodeficiency Virus Type-1
Fomsgaard A, Johnson PR, Nielsen C, Novembre FJ, Hansen J, Goldstein S, Hirsch VM
Viral Immunol. 8(3):121-33, 1995 |
PubMed
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Patterns of Protein Conformations
Bohr H, Brunak S
in ``The Pattern Book - Fractals, Art and Nature'', Clifford A. Pickover (ed.), 6-9, World Scientific, 1995 |
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Pruning of a large network by optimal brain damage and surgeon: An example from biological sequence analysis
Tolstrup N
Int J Neural Syst 6(1):31-42, 1995 |
PubMed
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Resonator driven protein folding: the implication of topology for protein structure and folding
Bohr J, Bohr H, Brunak S
in Protein folds --- a distance-based approach, eds. H. Bohr and S. Brunak, 243-252, CRC Press, 1995 |
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How many protein fold classes are to be found?
Lindgård PA, Bohr H
in Protein folds -- a distance-based approach, H Bohr and S Brunak (eds.), 98-102, CRC Press, 1995 |
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Investigations of Escherichia coli promoter sequences with artificial neural networks: New signals discovered upstream of the transcriptional startpoint
Pedersen AG, Engelbrecht J
Proc Int Conf Intell Syst Mol Biol 3:292-9, 1995 |
PubMed
Publication download
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Periodic sequence patterns in human exons
Baldi P, Brunak S, Chauvin Y, Engelbrecht J, Krogh A
Proc Int Conf Intell Syst Mol Biol 3:30-8, 1995 |
PubMed
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Analysis of Eukaryotic Promoter Sequences reveals a systematically occurring CT-signal
Larsen NI, Engelbrecht J, Brunak S
Nucleic Acids Res. 23(7):1223-30, 1995 |
PubMed
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Prediction of O-glycosylation of mammalian proteins: Specificity patterns of UDP-GalNAc:-polypeptide N-acetylgalactosaminyltransferase
Hansen JE, Lund O, Engelbrecht J, Bohr H, Nielsen JO, Hansen JES, Brunak S
Biochem. J.:801-13, 1995 |
PubMed
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1994
Neural network model of the genetic code is strongly correlated to the GES scale of amino acid transfer free energies
Tolstrup N, Toftgård J, Engelbrecht J, Brunak S
J. Mol. Biol. 243(5):816-20, 1994 |
PubMed
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Structure and geometry of proteins and membranes: a physical view
Bohr H
100 pp. Lecture notes for College in biophysics: experimental and theoretical aspects of biomolecules, International Center for Theoretical Physics, Trieste, Italien, 26/9 - 14/10, 1994 |
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Glycosylation and protein conformation
Clausen H, Hansen JE, Lund O, Rapacki K, Clausen H, Mosekilde E, Nielsen JO, Hansen JES
in Protein structure by distance analysis, H. Bohr and S. Brunak (eds.), 247-254, IOS Press & Ohmsha, 1994 |
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Recurrent networks for protein distance matrix prediction
Bohr H, Reczko M
in Protein structure by distance analysis, H. Bohr and S. Brunak (eds.), 87-97, IOS Press & Ohmsha, 1994 |
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Growth of domains in distance geometry through protein folding
Bohr H, Wang J, Wolynes P
in Protein Structure by Distance Analysis, eds. H. Bohr and S. Brunak, 98-109, IOS Press & Ohmsha, 1994 |
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Viscous trees and Voronoi structure formation in expanding systems
Bohr J, Brunak S, Nørretranders T
Europhysics Lett., 25, 245-251, 1994 |
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Neural network model of the genetic code is strongly correlated to the GES scale of amino acid transfer free energies
Tolstrup N, Toftgaard J, Engelbrecht J, Brunak S
J. Mol. Biol., 243, 816-820, (Cover illustration), 1994 |
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Correlation between protein secondary structure and the mRNA nucleotide sequence
Brunak S, Engelbrecht J, Kesmir C
in ``Protein Structure by Distance Analysis'', H. Bohr and S. Brunak (eds.), 327-334, IOS Press, Amsterdam, 1994 |
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The DEF data base of sequence based protein fold class predictions
Reczko M, Bohr H
Nucleic Acids Res. 22(17):3616-9, 1994 |
PubMed
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Hidden Markov Models for Human Genes
Baldi P, Brunak S, Chauvin Y, Engelbrecht J, Krogh A
in Advances in Neural Information Processing Systems, 6, 761-768, Morgan Kaufmann Pub, 1994 |
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1993
Predictive Recognition of Signal Peptides Using Artificial Neural Networks
Nielsen H
M.Sc. thesis, 1993 |
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Protein structures from distance inequalities
Bohr J, Bohr H, Brunak S, Cotterill RMJ, Fredholm H, Lautrup B, Petersen SB
J. Mol. Biol., 231, 861-869, 1993 |
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Computational Biosequence Analysis by Neural Networks
Brunak S, Engelbrecht J
Proceedings of the "Workshop on Physics and Computation, PhysComp 92", October 2-4, 1992, Dallas, Texas, 111-115, IEEE Computer Society Press, 1993 |
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Doing sequence analysis by inspecting the order in which neural networks learn
Brunak S
Proceedings of ``Computation of Biomolecular Structures - Achievements, Problems and Perspectives'', March 5-10, 1990, eds: D.M. Soumpasis & T.M. Jovin, 43-54, Springer Verlag, Berlin, 1993 |
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1992
Multiple Alignment Using Simulated Annealing: Branch Point Definition in Human mRNA Splicing
Lukashin AV, Engelbrecht J, Brunak S
Nucleic Acids Res. 20, 2511-2516, 1992 |
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G/C rich tract in 5' end of human introns
Engelbrecht J, Knudsen S, Brunak S
J. Mol. Biol., 227, 108-113, 1992 |
|
1991
Neural networks applied to protein structure
Bohr H, Bohr J, Brunak S, Cotterill RMJ, Fredholm H, Lautrup B, Petersen SB
in ``Advances in Biomolecular Simulations'', AIP Conference proceedings 239, 293-310, 1991 |
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Non-linearities in training sets identified by inspecting the order in which neural networks learn
Brunak S
in ``Neural Networks: from Biology to High Energy Physics'', Proceedings of the workshop held in Elba International Physics Center - Italy, June 5-14, 1991, eds. O. Benhar, C. Bosio, P. del Giudice and E. Tabet, 277-288, ETS Editrice, 1991 |
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Neural networks applied to the study of protein sequences and protein structures
Fredholm H, Bohr H, Bohr J, Brunak S, Cotterill RMJ, Lautrup B, Petersen SB
Site-Directed Mutagenesis and Protein Engineering, ed. M.R. El-Gewely, Elsevier Science Publishers B.V., pages 41-46, 1991 |
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Prediction of human mRNA donor and acceptor sites from the DNA sequence
Brunak S, Engelbrecht J, Knudsen S
J. Mol. Biol., 220, 49-65, 1991 |
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1990
Training neural networks to analyse biological sequences
Petersen SB, Bohr H, Bohr J, Brunak S, Cotterill RMJ, Fredholm H, Lautrup B
Trends Biotechnol., 11, 304-308, 1990 |
|
Neural Network Detects Errors in the assignment of pre-mRNA splice sites
Brunak S, Engelbrecht J, Knudsen S
Nucleic Acids Res., 18, 4797-4801, 1990 |
|
Cleaning up gene databases
Brunak S, Engelbrecht J, Knudsen S
Nature, 343, 123, 1990 |
|
A novel approach to prediction of the 3-dimensional structures of protein backbones by neural networks
Bohr H, Bohr J, Brunak S, Cotterill RMJ, Fredholm H, Lautrup B, Petersen SB
FEBS Letters, 261, 43-46, 1990 |
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Analysis of the secondary structure of the human immunodeficiency virus (HIV) proteins p17, gp120 and gp41 by computer modelling based on neural network methods
Adreassen H, Bohr H, Bohr J, Brunak S, Bugge T, Cotterill RMJ, Jacobsen C, Kusk P, Lautrup B, Petersen SB, Særmark T, Ulrich K
Journal of AIDS, 3, 615-622, 1990 |
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1989
Linjedeling med et neuralt netværk
Brunak S, Lautrup B
Skrifter om Anvendt and Matematisk Lingvistik, 14, 55-74, (Paper on hyphenation in refereed Danish linguistic journal.), 1989 |
|
A Travelling Salesman Approach to Protein Conformation
Bohr H, Brunak S
Complex Systems, 3, 9-28,(Cover illustration), 1989 |
|
1988
Linjedeling med TeX
Lautrup B, Brunak S
Skrifter om Anvendt and Matematisk Lingvistik, 13, 63-80, (Paper on hyphenation in refereed Danish linguistic journal.), 1988 |
|
Protein secondary structure and homology by neural networks
Bohr H, Bohr J, Brunak S, Cotterill RMJ, Lautrup B, Nørskov L, Olsen OH, Petersen SB
FEBS Letters, 241, 223-228, 1988 |
|
Books
Predicting Subcellular Localization of Proteins by Bioinformatic Algorithms
Nielsen H
Part of the series Current Topics in Microbiology and Immunology pp 1-30, 2016 |
DOI
|
The Genome of Trichomonas vaginalis
Carlton JM, Malik SB, Sullivan SA, Sicheritz-Ponten T, Tang P, Hirt RP
Anaerobic Parasitic Protozoa: Genomics and Molecular Biology, Chapter 3, 2010 |
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Methods for building quantitative structure-activity relationship (QSAR) descriptors and predictive models for computer-aided design of antimicrobial peptides
Taboureau O
Methods Mol. Biol. 618:77-86 doi:10.1007/978-1-60761-594-1_6, 2010 |
PubMed
|
Genome comparison of bacterial pathogens
Wassenaar TM, Bohlin J, Binnewies TT, Ussery DW
chapter 1 in Genome Dynamics, volume 6 - Microbial Pathogenomics, (Karger AG publishers, Basel), 2009 |
|
Tools for comparison of bacterial genomes
Wassenaar TM, Binnewies TT, Hallin PF, Ussery DW
Microbiology of Hydrocarbons, Oils, Lipids, and Derived Compounds, (Springer-Verlag, Heidelberg, Germany), 2009 |
|
The genus Burkholderia: analysis of 56 genomic sequences
Ussery DW, Kiil K, Lagesen K, Sicheritz-Ponten T, Bohlin J, Wassenaar TM
Genome Dyn 6:140-57 doi:10.1159/000235768, 2009 |
PubMed
|
COMPUTING FOR COMPARATIVE GENOMICS: Bioinformatics for Microbiologists
Ussery DW, Borini S, Wassenaar TM
Springer, Series: Computational Biology , Vol. 8, 2008 |
Springer, to be published in autumn 2008
|
Genome Diversity of Pseudomonas aeruginosa
Klockgether J, Würdemann D, Wiehlmann L, Binnewies TT, Ussery DW, Tümmler B
Chapter 2 in Pseudomonas: Genomics and Molecular Biology, (Edited by: Pierre Cornelis, Caister Academic Press, 2008), 2008 |
Link to publisher
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Comparative Genomics of Pseudomonas
Kiil K, Binnewies TT, Willenbrock H, Hansen SK, Yang L, Jelsbak L, Ussery DW, Friis C
Chapter 1 in Pseudomonas: Model Organism, Pathogen, Cell Factory, (Edited by: B. H. A. Rehm, Wiley-VCH, 2008), 2008 |
Link to publisher
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Signal peptides and protein localization prediction
Nielsen H
Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, M.J. Dunn, L.B. Jorde, P.F.R. Little, S. Subramaniam (eds.), Wiley, 2005 |
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Immunological Bioinformatics
Lund O, Nielsen M, Lundegaard C, Kesmir C, Brunak S
MIT Press, 312 pages, 2005 |
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A Biologist's Guide to Analysis of DNA Microarray Data, 2nd edition
Knudsen S
John Wiley & Sons, New York, 2004 |
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DNA Structure: A-, B-, and Z-DNA Families
Ussery D
The Encyclopedia of Life Sciences, (Macmillan Publishers, London), 2002 |
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A Biologist's Guide to Analysis of DNA Microarray Data, 1st edition
Knudsen S
John Wiley & Sons, New York, 2002 |
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Genome Sequence Databases
Ussery DW, Brunak S
Encyclopedia of Genetics, S. Brenner and J.H. Miller (eds.), Academic Press, 2001 |
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DNA Denaturation
Ussery DW
Encyclopedia of Genetics, S. Brenner and J.H. Miller (eds.), Academic Press, 2001 |
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Bidirectional Dynamics for Protein Secondary Structure Prediction
Baldi P, Brunak S, Frasconi P, Pollastri G, Soda G
Sequence Learning - Paradigms, Algorithms, and Applications, R. Sun and C. Lee Giles (eds.), 80-104, Springer Verlag, 2001 |
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Bioinformatics: The Machine Learning Approach, 2nd edition
Baldi P, Brunak S
MIT Press, 360 pages, 2001 |
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Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
Durbin R, Eddy S, Krogh A, Mitchison GJ
Cambridge University Press, 350 pages, 1998 |
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Bioinformatics: The Machine Learning Approach
Baldi P, Brunak S
MIT Press, 360 pages, 1998 |
Details
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Protein Folds: A Distance Based Approach
Bohr H, Brunak S (eds.)
CRC Press, Boca Raton, 318 pages, 1995 |
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Protein Structure by Distance Analysis
Bohr H, Brunak S (eds.)
IOS Press, Amsterdam, 352 pages, 1994 |
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Neuronale Netze: Die nächste Computer-Revolution
Brunak S, Lautrup B, (translated by Malte Heim)
Carl Hanser Verlag, 160 pages, 1993 |
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Neural Networks - Computers with Intuition
Brunak S, Lautrup B
World Scientific Publishing, 178 pages, 1990 |
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Neurale Netværk - Computere med Intuition
Brunak S, Lautrup B
Nysyn, Munksgaards Forlag, 160 pages (3 printings), 1988 |
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