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2013
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
Am J Clin Nutr. 2013 May 1. [Epub ahead of print], 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 Physiol. 2013 Apr;161(4):1783-94. doi: 10.1104/pp.112.210773. Epub 2013 Feb 27., 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 Mol Biol. 2013;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, Vol. 31, No. 7, 2013, p. 20971-972., 2013 |
PubMed
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Biasogram: Visualization of Confounding Technical Bias in Gene Expression Data
Krzystanek M, Szallasi Z, Eklund A
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
EMBO J. 2013 Apr 12. 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
J. Phys. Chem. 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., 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
Am J Respir Crit Care Med., 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 Health Dis., 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
J Agric Food Chem, 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 Biol, 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
J. Chem. Inf. Model., 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 Rep. 2013 Jan 30. pii: S2211-1247(13)00010-7. 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. 2013 Jan 29, 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 Mol Biol. 2013, 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
Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):E99-E107. doi: 10.1073/pnas.1205532110. Epub 2012 Dec 17, 2013 |
PubMed
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2012
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 Biol Evol. 2012 Jan;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 Biol Evol. 2012 Jan;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
J Proteomics. 2012 Dec 7, 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. 2012 Sep 28;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
Int J Androl. 2012 Jun, 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 Res. 2012 Nov 26, 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 Biol Evol. 2012 Dec 3, 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. 2012 Oct 24. [Epub ahead of print], 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
J Immunol Methods. 2012 Sep 25. pii: S0022-1759(12)00287-6. doi: 10.1016/j.jim.2012.09.005. [Epub ahead of print], 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
J Biol Chem. 2012 Oct 1. [Epub ahead of print], 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 Discov. 2012 Apr;2(4):366-75. Epub 2012 Mar 22., 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. 2012 Sep 28. [Epub ahead of print], 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. 2012 Sep 14;13(1):235. [Epub ahead of print], 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. 2012 Sep 18. doi: 10.1111/j.1365-2052.2012.02400.x. [Epub ahead of print], 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
Nat Biotechnol. 2012 Sep 10;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, Jose MG, 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. 2012 Aug 6. [Epub ahead of print], 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 optimum temperature based on genome sequences
Jensen DB, Vest TC, Hallin PF, Pedersen AG, Ussery D
BMC Genomics, 2012 |
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Mutational properties of amino acid residues: implications for evolvability of phosphorylatable residues
Creixell P, Schoof EM, Tan CS, Linding R
Philos Trans R Soc Lond B Biol Sci. 2012 Sep 19;367(1602):2584-93, 2012 |
PubMed
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Two novel methods for using genome sequences to infer taxonomy
Ussery DW, Gordon SV
Microbiology. 2012 Jun;158(Pt 6):1414. Epub 2012 Apr 13, 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. 2012 Jul 16. 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. 2012;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., 2012, 134 (29), pp 12198–12208, 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. 2012;7(6):e39360. Epub 2012 Jun 21., 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. 2012 May 24;19(3):365-79. Print 2012 Jun., 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. 2012 Mar 2;335(6072):1103-6., 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
J. Clin. Micobiol. 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., 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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2011
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. 2011 Mar 1;71(5):1858-70., 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. 2011 Jul;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
J Pathol. 2012 Feb;226(3):482-94. doi: 10.1002/path.2998. Epub 2011 Oct 19., 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
Nuture 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, 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, 8:785-786, 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, 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
Circulation Cardiovascular Genetics, 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, Aug 17, 2011 |
PubMed
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BDDCS Applied to Over 900 Drugs
Benet LZ, Broccatelli F, Oprea TI
AAPS J, Aug 5, 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, July 27, 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., July 9, 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., August 2, 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, July 28, 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, June 25th, 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, Jun 30, 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, June 22, 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, June 17, 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. June 11, 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 Health Dis., June 10, 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, February, 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, July, 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
Inflam Bowel Dis., February 18, 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, May, 2011 |
PubMed
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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
International journal of andrology. 2012 Feb;35(1):25-40. doi: 10.1111/j.1365-2605.2011.01150.x. Epub 2011 Jun 9., 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, June 4, 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, May 20, 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) Feb, 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, April 23, 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, April 2, 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
Proc Natl Acad Sci U S A, May 3, 2011 |
PubMed
Relevant URL
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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, May 12, 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
Int Arch Allergy Appl Immunol, April 2, 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, April 11, 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 Research, January 26, 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, February 18, 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, January 2011, 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
Journal of Immunology, January 15, 2011 |
PubMed
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Bistability in autoimmune diseases
Rapin N, Mosekilde E, Lund O
Autoimmunity, January 19, 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
Microbial Ecology, January 11, 2011 |
PubMed
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2010
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. 2010 Sep 7;5(9):e12586, 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
Philos Transact A Math Phys Eng Sci, June 13, 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, May 7, 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
Malaria Journal, June 16, 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, September 14, 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, October 31, 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 Communications, December 21, 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
Clinical and Vaccine Immunology, December 22, 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
J Proteome Res, November 5, 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, 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, December 1, 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, October 27, 2010 |
PubMed
Read article
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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, 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., November 11, 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, November 22, 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, November 30, 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, Nov 16, 2010 |
PubMed
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Ethicity and Stratum Corneum Ceramides
Jungersted JM, Høgh J, Hellgren LI, Jemec G & Agner T
British Journal of Dermatology, 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, October 27, 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, 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 Research, Nov 13, 2010 |
PubMed
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Prediction of epitopes using neural network based methods
Lundegaard C, Lund O, Nielsen M
Journal of Immunological Methods, Oct 31, 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 Research, Nov 3, 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 Computational Biology, 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, 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, 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, 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
Sci Transl Med, 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, 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, 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, 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
Developmental Dynamics, 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
Biotechnology Adv, 2010 |
PubMed
Read abstract
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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, 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 Research, 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 Physiol, 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 Dermatitis, 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, 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 Computational Biology, 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, 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, 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., 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., 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
Journal of Cell Biochemistry, 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, 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, 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, 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
Brief Bioinform., 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, 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
The Plant Journal, 2010 |
PubMed
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Comparison of 61 Sequenced Escherichia coli Genomes Microbial Ecology
Lukjancenko O, Wassenaar TM, Ussery DW
Microb. Ecol., 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., 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, 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, 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, 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, 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, 157:395-400, 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, 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
Transl Med 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, 2010 |
PubMed
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MHC Class II epitope predictive algorithms
Nielsen M, Lund O, Buus S, Lundegaard C
Immunology, 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, April 16, 2010, 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 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, 2010 Apr 17, 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, 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: 350-353, 2010 |
PubMed
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NetCTLpan: pan-specific MHC class I pathway epitope predictions
Stranzl T, Larsen MV, Lundegaard C, Nielsen M
Immunogenetics, 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, 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
J Immunol, 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
Sci Signal 12;3(104):ra3, 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):21-27, 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
The PLoS ONE, 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, 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, Volume 464 Number 7285 pp7-132, 2010 |
PubMed
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., 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, 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. 17;5(2):e9272, 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: 911-918. DOI: 10.1111/j.1398-9995.2010.02326, 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, 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 11:99doi: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.Chapter 18:Unit18.17, 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 11 Feb;463(7282):757-62, 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: 338-350. 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 Res. 38(Database issue):D699-702, 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
Sci Signal. 12;3(104):ra3, 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
Nat Med, 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
J Clin Oncol, 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 Jan 19;11(1):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
Journal of Molecular Microbiology and Biotechnology, 18:63-73 in the press, 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 Science, 1190: 42-49, 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 Pharmacology and Physiology, 23:62-67, 2010 |
PubMed
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Comparative Genomics of Green Sulfur Bacteria
Davenport C, Ussery DW, Tümmler B
Photosynthesis Research, 103: in the press, 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 Journal, 24:1128-38. DOI: 10.1096/fj.09-139410, 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
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 Research, 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 |
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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 |
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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
Ann NY Acad Sci, 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. Epub 2009 Jan 28, 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, 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, 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 15;25(10):1293-9, 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
Bioinformatics1;25(9):1125-31, 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, 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 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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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
J. Biol Chem, 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 Res. 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, 2009 |
PubMed
Read abstract
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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
Journal of Theoretical Biology, 261:100-106, 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, 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: 2341-7, 2009 |
PubMed
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The transcriptionally active regions in the genome of Bacillus subtilis
Rasmussen S, Nielsen HB, Jarmer H
Mol Micro 73: 1043-57, 2009 |
PubMed
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Microbial comparative pan-genomics using binomial mixture models
Snipen L, Almøy T, Ussery DW
BMC Genomics. ;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 Structural Biology, 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, 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, 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, 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(1):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, 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 Evolutionary Biology, 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, 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, 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, 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
Proc Natl Acad Sci U S A;106(21):8671-6, 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 (in press), 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
BRIEFINGS IN BIOINFORMATICS. VOL 10. NO 3. 330^340, 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, obesity & metabolism, 2009 Feb;11 Suppl 1:60-6, 2009 |
PubMed
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Genetic Tools and Algorithms for Gene Discovery in Major Congenital Anomalies
Donahoe PK, Noonan KM, Lage K
Birth defects research. Part A, Clinical and molecular teratology, 2009 Jan;85(1):6-12, 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
Experimental and Molecular;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, 2009;527:299-310, 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
Clinical and Experimental Immunology, 2009 Mar;155(3):441-6., 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 Genetics and Biology, Volume 46, Issue 1, Supplement , March 2009, Pages S14-S18, Thematic Issue: Aspergillus Genomics and Beyond., 2009 |
PubMed
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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. 2009;4(2):e4428, 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
Molecular Pharmaceutics, 2009 Jan-Feb;6(1):144-57, 2009 |
PubMed
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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 metabolism and disposition: the biological fate of chemicals, March ;37(3):658-64. Epub 2008 Dec 4, 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, January ;49(1):43-52, 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
Journal of Biological Chemistry, Feb 12., 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, 2009, 7 January, 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 61(1):1-13, 2009 |
PubMed
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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, 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. 15;7(24):3947-8. Epub 2008 Dec 17, 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, 2008 Mar;57(1):32-7. Epub 2007 Aug 1, 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
Toxicological sciences : an official journal of the Society of Toxicology, 2008 Apr;102(2):444-54. Epub 2008 Jan 4, 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, 2008 Feb 27;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, 2008 May;26(5):541-7, 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
Malaria Journal, 2008 Jun 6;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
Antimicrobial agents and chemotherapy, 2008 Jul;52(7):2616-25. Epub 2008 Apr 14, 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
The British Journal of Nutrition, 2008 Jul;100(1):120-9. Epub 2008 Jan 2, 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, 2008 Sep;148(1):212-22. Epub 2008 Jul 3, 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
Breas Cancer Research, 2008;10(5):214. Epub 2008 Oct 31, 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
Proceedings of the National Academy of Sciences of the United States of America, 2008 Dec 30;105(52):20870-5. Epub 2008 Dec 22, 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. 2008 Dec 3, 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. 2008;153(10):1833-44, 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. 2008;9(6):403. Epub 2008 Jun 23, 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
Molecular Nutrition and Food Research, 52:1140-1146., 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
Am. J. Clin. Nutr., 88:1232-1241, 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, Metabolism and Disposition (DMD), December 4, 2008; 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
Journal of Experimental Botany, 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, 2008 Sep 2;1(35):ra2, 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. 2008 Sep 4. [Epub ahead of print], 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. 2008 Aug;15(4):187-93., 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, 26:541-547, (2008), 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, 49:104 (2008). doi:10.1371/journal.pcbi.1000057, 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, 279:523-534, (2008)., 2008 |
PubMed
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Investigations of oligonucleotide usage variance within and between prokaryotes
Bohlin J, Skjerve E, Ussery D
PLoS Computational Biology, 4:e1000057 (2008), 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 - A Journal of Integrative Biology, 12:157-160, (2008), 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. 2008 Sep 3. [Epub ahead of print], 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. 2008 Aug 22;4(8):e1000163, 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. 2008 Aug;5(4):371-86, 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. 2008 Jun 30;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. 2008 Jun 4;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 Physiol. 2008 Jul 3, 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 2008 (16):2214-21, 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: 200-212., 2008 |
PubMed
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Lipids and skin barrier function--a clinical perspective
Jungersted JM, Hellgren LI, Jemec GB, Agner T
Contact Dermatitis 58: 255-262., 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. 2008 May;27(5):251-6., 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. 2008 Mar;10(3):614-25 and Mol Genet Genomics, 279:523-534, (2008), 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 4:363-71 (2008), 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. 2008 Jun 19., 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. 2008 Vol. 124 (4):489-503, 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. 2008 Jul 4;4(7):e1000107, 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. 2008 Jul 1;36(Web Server issue):W513-8. Epub 2008 May 31., 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. 2008 Jul 1;36(Web Server issue):W509-12. Epub 2008 May 7., 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. 2008 Jun 1;24(11):1397-8. Epub 2008 Apr 14, 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 and QSAR in Environmental Research, 19, 167-177, 2008, 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, 11;22(11):1299-303, 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):1214-1224, 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. 2008 Feb 15;4(2):e42, 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. 2008 Mar 19;3(3):e1831, 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
J Immunol.,2008 Apr 1;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, 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., 4;9(2):R26, 2008 |
PubMed
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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,25;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,4;5(1):117-127, 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,28;9(1):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, 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. 2008 Feb;123(2):197-208, 2008 |
PubMed
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2007
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, 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 276:83-92,(2007)., 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 (Sept. 2007), 2007 |
PubMed
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Synthesis of structured phospholipids by immobilized phospholipase A2 catalyzed acidolysis
Vikbjerg A, Mu H, Xu X
J. Biotechnol., 128:545-554, 2007 |
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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, Leukotrienes and Essential Fatty Acids, 76: 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
J. Agric. Food Chem., 55, 7615 -7619, 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. 2007 Dec 26;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:R267 (2007), 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
Journal of Experimental Botany 2007 58(14):3987-3995; doi:10.1093/jxb/erm254, 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, 23:3265-75, 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,31;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., 28;8(11):R253, 2007 |
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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 |
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Jarmer H
DTU-avisen, 27 April, nr. 5, 2007 |
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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 |
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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,1;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
Advances in Parasitology, 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 (in press), 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. 6;51(3):535-546, 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
Int Immunol., 19(12):1319-1327, 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. Sep 19;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. Jul 18, 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 3:325, 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. Jul 4;8(1):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. Jan 12;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 in Molecular Biology, 3;2(1):12, 2007 |
PubMed
PDF
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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. Aug 29;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
J Biol Chem. Sep 18, 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. Jul;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 |
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Probe Selection for DNA Microarrays using OligoWiz
Wernersson R, Juncker AS, Nielsen HB
Nature Protocols, vol. 2, no. 11, p. 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. Jul 1;23(13):i387-91, 2007 |
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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
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MaxAlign: maximizing usable data in an alignment
Gouveia-Oliveira R, Sackett PW, Pedersen AG
BMC Bioinformatics. Aug 28;8(1):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. Aug 1;2: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 |
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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 (in press), 2007 |
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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 |
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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 Research 35:3100-3108,(2007)., 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 Physiol., 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., (in press), 2007 |
PubMed
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Prediction of protein phosphorylation sites in yeast
Ingrell CR, Miller ML, Jensen ON, Blom N
Bioinformatics, 1;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 |
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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. (in press), 2007 |
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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
Nature Biotechnol., 25 (3), 309-16, 2007 |
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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. Wildlife Dis., 43(3), 345-352, 2007 |
PubMed
Publication download
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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 Research, doi:10.1093/nar/gkl1098, 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), 107-115, 2007 |
PubMed
Publication download
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2006
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., 6;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. Jul 1;34(Web Server issue):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. Jul 1;34(Web Server issue):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
Chem. Phys. 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
Journal of Bacteriology, 188:7713-7721, 2006 |
PubMed
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Leaner and Meaner Genomes in Escherichia coli
Ussery DW
GenomeBiology, 7:237, 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 Biology, 7, R114, 2006 |
PubMed
|
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 (in press), 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
Chem. Inf. Model., 46, 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 vol. 16 no. 9, 844-853, 2006 |
PubMed
|
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 Pathogens, 2 (11):e124, 2006 |
PubMed
PDF
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Protein Evolution is Faster Outside the Cell
Julenius K, Pedersen AG
Mol. Biol. Evol., 23 (11), 2039-2048, 2006 |
PubMed
PDF
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The genomic code: inferring Vibrionaceae niche specialization
Reen FJ, Almagro-Moreno S, Ussery D et al
Nature Reviews Microbiology 4, 697-704, 2006 |
PubMed
|
Distinct developmental defense activations in barley embryos identified by transcriptome profiling
Nielsen ME, Lok F, Nielsen HB
Plant molecular biology, 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, 832-839, 2006 |
PubMed
PDF
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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, 135-44, 2006 |
PubMed
|
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, 261-77, 2006 |
PubMed
|
Improved method for predicting linear B-cell epitopes
Larsen JE, Lund O, Nielsen M
Immunome Res, 2: 2, 2006 |
PubMed
|
A Wiring of the Human Nucleolus
Hinsby AM, Kiemer L, Karlberg EO, Lage K, Fausboll A, Juncker AS, Andersen JS, Mann M, Brunak S
Molecular Cell, 22, 285-295, 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, 152(Pt 3): 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
Experimental neurology, 198(2):427-37, 2006 |
PubMed
|
Crosstalk
Mundy J, Nielsen HB, Brodersen P
Trends plant Sci, 11, 63-64, 2006 |
PubMed
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Origin of Replication in Circular Prokaryotic Chromosomes
Worning P, Jensen LJ, Hallin PF, Stærfeldt HH, Ussery DW
Environ Microbiol, 8, 353-61, 2006 |
PubMed
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2005
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 Biology, 2005 |
PubMed
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High throughput production of mouse monoclonal antibodies using antigen microarrays
De Masi F, Chiarella P, Wilhelm H, Massimi M, Bullard B
Proteomics, 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.,14;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., 151(Pt 4):1013-6, 2005 |
PubMed
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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: 1778-1798, 2005 |
PubMed
|
Selection of proteins for human MHC class II presentation
Jiang L, Lund O, Tan JQ
Cell Mol Immunol, 2, 49-56, 2005 |
PubMed
|
Extracytoplasmic function sigma factors in Pseudomona syringae
Oguiza JA, Kiil K, Ussery DW
Trends Microbiology, 13(12):565-8, 2005 |
PubMed
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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, 151, 1013-1016, 2005 |
PubMed
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Genome update: Prediction of secreted proteins in 225 bacterial proteomes
Bendtsen JD, Binnewies TT, Hallin PF, Sicheritz-Pontén T, Ussery DW
Microbiology, 151, 1725-1727, 2005 |
PubMed
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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
Bacteriology, 187, 4992-4999, 2005 |
PubMed
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Genome update: Prediction of membrane proteins in prokaryotic genomes
Bendtsen JD, Binnewies TT, Hallin PF, Ussery DW
Microbiology, 151, 2119-2121, 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-SGM, 151, 3147-3150, 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
Applied and environmental microbiology, 71, 6465-6472, 2005 |
PubMed
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A comparison study: Applying segmentation to array CGH data for downstream analyses
Willenbrock H, Fridlyand J
Bioinformatics, 21, 4084-4091, 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, 151, 3447-3452, 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, 14, 70, 2005 |
PubMed
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Integrating protein annotation resources through the Distributed Annotation System
Olason PI
Nucleic Acids research, 33, 468-470, 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, 1191-201, 2005 |
PubMed
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Non-classical protein secretion in bacteria
Bendtsen J, Kiemer L, Fausboll A, Brunak S
BMC Microbiol, 5,58, 2005 |
PubMed
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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, 84-93, 2005 |
PubMed
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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, 326-36, 2005 |
PubMed
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Crystal ball. Systems biology: in the broadest sense of the word
Ussery DW, de Lichtenberg U, Jensen LJ
Environmental Microbiology, 7, 482-83, 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 |
|
Prediction and Analysis of Protein Motifs
Kiemer L
Ph.D. thesis, 2005 |
|
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, 2295-2303, 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, 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
J Clin Microbiol, 43, 1099-104, 2005 |
PubMed
Publication download
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OligoWiz 2.0 - Integrating sequence feature annotation into the design of microarray probes
Wernersson R, Nielsen HB
Nucleic Acids, 33, 611-5, 2005 |
PubMed
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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
EMBO Journal, 24, 2579-89, 2005 |
PubMed
|
Prediction of twin-arginine signal peptides
Bendtsen JD, Nielsen H, Widdick D, Palmer T, Brunak S
BMC Bioinformatics, 2,6, 167, 2005 |
PubMed
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FeatureExtract--extraction of sequence annotation made easy
Wernersson R
Nucleic Acids Res, 33(Web Server issue), W567-9, 2005 |
PubMed
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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, 1;21, 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, 1;21, 1164-71, 2005 |
PubMed
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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, 24;433, 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, 91, 2005 |
PubMed
|
Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates
Jonsdottir SO, Jorgensen FS, Brunak S
Bioinformatics, 15;21, 2145-60, 2005 |
PubMed
|
Genome Update: proteome comparisons
Binnewies TT, Hallin PF, Staerfeldt HH, Ussery DW
Microbiology, 151, 1-4, 2005 |
PubMed
|
Genome update: 2D clustering of bacterial genomes
Willenbrock H, Binnewies TT, Hallin PF, Ussery DW
Microbiology, 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, 151, 633-7, 2005 |
PubMed
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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, 856-64, 2005 |
PubMed
|
Dynamic Complex Formation During the Yeast Cell Cycle
de Lichtenberg U, Jensen LJ, Brunak S, Bork P
Science, 307, 724-727, 2005 |
PubMed
|
2004
Alternative mapping of probes to genes for affymetrix chips
Gautier L, Møller M, Friis-Hansen L, Knudsen L
BioMed Central, August 14th, 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
British J Nutr, 91:725-732 (2004), 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. Jun 22;5:79, 2004 |
PubMed
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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, 634-48, 2004 |
PubMed
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Biological Sequence Analysis of Archeal Genomes
Skovgaard M
Ph.D. thesis, 2004 |
|
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, 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
J Biol Chem, 2;279, 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, 22;339, 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, 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, 797-810, 2004 |
PubMed
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Genome update: correlation of bacterial genomic properties
Hallin PF, Coenye T, Binnewies TT, Jarmer H, Staerfeldt HH, Ussery DW
Microbiology, 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
Comparative and Functional Genomics 5, 459-470, 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, 153-164, 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 150, 3519-21, 2004 |
PubMed
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Genome Update: alignment
Ussery DW, Jensen MS, Poulsen TR, Hallin PF
Microbiology 150, 2491-3, 2004 |
PubMed
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NetAcet: prediction of N-terminal acetylation sites
Kiemer L, Bendtsen JB, Blom N
Bioinformatics, 1;21, 1269-70, 2004 |
PubMed
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Chromatin architecture and gene expression in Escherichia coli
Willenbrock H, Ussery DW
Genome Biology, 5, 252, 2004 |
PubMed
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Genome update: chromosome atlases
Hallin PF, Binnewies TT, Ussery DW
Microbiology, 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
Molecular Genetics Genomics, 272, 173-80, 2004 |
PubMed
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Genome update: promoter profiles
Ussery DW, Tindbaek N, Hallin PF
Microbiology, 150, 2791-3, 2004 |
PubMed
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Genome update: alignment of bacterial chromosomes
Ussery DW, Jensen MS, Poulsen TR, Hallin PF
Microbiology, 150, 2491-3, 2004 |
PubMed
|
Genome Update: annotation quality in sequenced microbial genomes
Ussery DW, Hallin PF
Microbiology, 150, 2015-7, 2004 |
PubMed
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CBS genome atlas database: a dynamic storage for bioinformatic results and sequence data
Hallin PF, Ussery DW
Bioinformatics, 12;20, 3682-6, 2004 |
PubMed
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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
Journal of Cell Science, 117, 4807-4818, 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, 1;21, 687-8, 2004 |
PubMed
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Analysis and prediction of leucine-rich nuclear export signals
La Cour T, Kiemer L, Mølgaard A, Gupta R, Skriver K, Brunak S
Protein Engineering Design and Selection, 17, 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, 20,770-6, 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 Engineering Design and Selection, 17, 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, 6;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, 16;340, 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
J Proteome Research 426-33, 2004 |
PubMed
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Genome Update: tRNAs in sequenced microbial genomes
Ussery DW, Hallin PF, Lagesen K, Wassenaar TM
Microbiology, 150, 1603-6, 2004 |
PubMed
|
Genome update: rRNAs in sequenced microbial genomes
Ussery DW, Hallin PF, Lagesen K, Coenye T
Microbiology, 150, 1113-5, 2004 |
PubMed
|
TXTGate: profiling gene groups with text-based information
Glenisson P, Coessens B, Van Vooren S, Mathys J, Moreau Y, De Moor B
Genome Biology, 5, 43, 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, 1;5, 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, 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
Journal of Immunology, 172, 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, 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
Immunology Letters, 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, 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
Artificial intelligence in medicine, 30, 257-81, 2004 |
PubMed
|
A first glimpse into the pattern and scale of gene transfer in Apicomplexa
Huang J, Mullapudi N, Sicheritz-Ponten T, Kissinger JC
International Journal of Parasitology, 34, 265-74, 2004 |
PubMed
|
Genome Update: AT content in sequenced prokaryotic genomes
Ussery DW, Hallin PF
Microbiology, 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
Journal of Microbiological Methods, 57, 123-33, 2004 |
PubMed
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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
Journal of Biological Chemistry, 279, 13461-8, 2004 |
PubMed
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Genome Update: length distributions of sequenced prokaryotic genomes
Ussery DW, Hallin PF
Microbiology, 150, 513-16, 2004 |
PubMed
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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, 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, 307-315, 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, 12;20, 1388-97, 2004 |
PubMed
|
Analysis and recognition of 5' UTR intron splice sites in human pre-mRNA
Eden E, Brunak S
Nucleic Acids Research, 32, 1131-1142, 2004 |
PubMed
|
Genome Update: 161 prokaryotic genomes sequenced, and counting
Ussery DW
Microbiology, 150, 261-263, 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
Molecular Microbiology, 51,15-32, 2004 |
PubMed
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2003
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, 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, 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, 3;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, 437-49, 2003 |
PubMed
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MUTAGEN: Multi-User Tool for Annotating GENomes
Brugger K, Redder P, Skovgaard M
Bioinformatics, 19, 2480-1, 2003 |
PubMed
|
The sigma54 regulon (sigmulon) of Pseudomonas putida
Cases I, Ussery DW, de Lorenzo V
Environmental Microbiology, 5, 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 Computation, 15, 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, 149, 3043-3045, 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, 378-384, 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, 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, 3471-76, 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, 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, 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, 2409-2421, 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 Science,12, 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, 781-787, 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, 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, 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, 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
Journal of Cancer Research and Clinical Oncology, 129,263-271, 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, 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, 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, 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 Science, 12, 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, 635-642, 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., 31,393-6, 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
Journal of Virology, 76, 9695-9701, 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
vActa Biotheor, 50, 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, 6060-4, 2002 |
PubMed
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Prediction of novel archaeal enzymes from sequence-derived features
Jensen LJ, Skovgaard M, Brunak S
Protein Science, 11, 2894-2898, 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, 1312-13, 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, research0048.1-0048.16, 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
Molecular Genetics and Genomics, 267, 721-729, 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, 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, 1133-1134, 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, 8757-8768, 2002 |
PubMed
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Mean-field approaches to independent component analysis
Højen-Sørensen PA, Winther O, Hansen LK
Neural Comput., 14, 889-918, 2002 |
PubMed
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Avoiding cross hybridization by choosing nonredundant targets on cDNA arrays
Nielsen HB, Knudsen S
Bioinformatics, 18, 321-322, 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
Computers and Chemistry, 26, 531-541, 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, 1257-1265, 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, 287-296, 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
J. Mol. Biol., 318, 627-636, 2002 |
PubMed
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Continuum secondary structure captures protein flexibility
Anderson CAF, Palmer AG, Brunak S
Structure, 10,175-184, 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, 3232-3241, 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 Microbiology letters, 206, 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, 871-880, 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, 553-559, 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 Comm. Mass Spectrom., 16, 1232-1237, 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
Journal of Biological Chemistry, 277, 37001-37008, 2002 |
PubMed
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Prediction of glycosylation across the human proteome and the correlation to protein function
Gupta R, Brunak S
PSB-2002 Proceedings, Pacific Symposium on Biocomputing 310-322, 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, (review), 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, 567-580, 2001 |
PubMed
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A phylogenomic approach to microbial evolution
Sicheritz-Pontén T, Andersson SGE
Nucleic Acids Res., 29, 545-552, 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, 202-212 (cover illustration), 2001 |
PubMed
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Protein secondary structure: category assignment and predictability
Andersen CAF, Bohr H, Brunak S
FEBS Letters, 507, 6-1, 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, 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, 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, 237-248, 2001 |
PubMed
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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, 357-364, 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, 848-852, 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, 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, 425-428, 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., 61,2492-2499, 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, 6175-6183, 2001 |
PubMed
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Enrichment of regulatory signals in conserved non-coding genomic sequence
Levy S, Hannenhalli S, Workman C
Bioinformatics, 17, 871-877, 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 Molecular Biology (2000) 44: 463–476, 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 (2000) Dec;44(6):799, 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, 199-214 (Erratum in: Mol Cell Neurosci 2001, 18, 332-3), 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. Immunogenetics, 2, 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, 1005-1016, 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, 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
Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology, 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, 523-528, 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, 1111-1120, 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. Struc. Dyn., 17, 965-979, 2000 |
PubMed
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Visualization of pathogenicity regions in bacteria
Friis C, Jensen LJ, Ussery DW
Genetica, 108, 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, 907-930, 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, 326-333, 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, 47-55, 2000 |
PubMed
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A Classification of Possible Routes of Darwinian Evolution
Thornhill RH, Ussery DW
J. Theor. Biol., 203, 111-116, 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, 412-424, 2000 |
PubMed
|
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, 706-709, 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, 529-534, 2000 |
PubMed
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Improving the odds in discriminating
Frimurer TM, Bywater R, Nærum L, Nørskov Lauritsen L, Brunak S
J. Chem. Inf. Comp. Sci., 40, 1315-1324, 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 Science., 8, 978-984, 1999 |
PubMed
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A mathematical model on germinal center kinetics and termination
Kesmir C, De Boer RJ
J. Immunol., 163(5), 2463-2469, 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, 1535-1539, 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, 4816-4822, 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
EMBO Journal, 18, 2982-2990, 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, 1351-1362, 1999 |
PubMed
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Three views of microbial genomes
Jensen LJ, Friis C, Ussery DW
Res. Microbiol., 150, 773-777, 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, 918-929, 1999 |
PubMed
Publication download
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The biology of eukaryotic promoter prediction - a review
Pedersen AG, Baldi P, Chauvin Y, Brunak S
Comp Chem, 23, 191-207, 1999 |
PubMed
Publication download
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Modeling regulatory networks with weight matrices
Weaver D, Workman C, Stormo GD
Proceedings of The Pacific Symposium on Biocomputing (PSB\'99), 112-123, 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, 937-946, 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, 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, 1009-1022, 1999 |
PubMed
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MatrixPlot: visualizing sequence constraints
Gorodkin J, Stærfeldt HH, Lund O, Brunak S
Bioinformatics, 15 769-770, 1999 |
PubMed
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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, 1737-1744, 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
Proceedings of the seventh international conference on Intelligent Systems for Molecular Biology (ISMB \'99), AAAI Press, 95-105, 1999 |
PubMed
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Metrics and Similarity Measures for Hidden Markov Models
Lyngsø RB, Pedersen CNS, Nielsen H
Proceedings of the seventh international conference on Intelligent Systems for Molecular Biology (ISMB \'99), AAAI Press, 178-186, 1999 |
PubMed
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Promoter 2.0: for the Recognition of PolII Promoter Sequences and
Knudsen S
Bioinformatics, 15, 356-361, 1999 |
PubMed
|
Hidden neural networks
Krogh A, Riis SK
Neural Comput., 11, 541-563, 1999 |
PubMed
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Environmental Influences on DNA Curvature
Ussery DW, Higgins CF, Bolshoy A
J. Biomol. Struct. Dyn., 16, 811-824, 1999 |
PubMed
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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, 3-9, 1999 |
PubMed
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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, 370-372, 1999 |
PubMed
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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, 237-239, 1999 |
PubMed
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1998
DNA Structure in Human RNA Polymerase II Promoters
Pedersen AG, Baldi P, Chauvin Y, Brunak S
J. Mol. Biol., 281, 663-673, 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, 537-544, 1998 |
PubMed
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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, 341-347, 1998 |
PubMed
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Computational analyses and annotations of the Arabidopsis peroxidase gene family
Østergaard L, Pedersen AG, Jespersen HM, Brunak S, Welinder KG
FEBS Letters, 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
Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB98), 122-130, 1998 |
PubMed
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A hidden Markov model for predicting transmembrane helices in protein sequences
Sonnhammer ELL, von Heijne G, Krogh A
Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB98), 175-182, 1998 |
PubMed
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Computational Applications of DNA Structural Scales
Baldi P, Brunak S, Chauvin Y, Gorodkin J, Pedersen AG
Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB98), 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, 636-646, 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, 289-295, 1998 |
PubMed
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PhosphoBase: a database of phosphorylation sites
Blom N, Kreegipuu A, Brunak S
Nucleic Acids Res., 26, 384-386, 1998 |
PubMed
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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, 387-389, 1998 |
PubMed
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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
Glycocon. J., 15, 115-130, 1998 |
PubMed
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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, 120-128, 1997, 1997 |
PubMed
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Displaying the information contents of structural RNA alignments: the structure logos
Gorodkin J, Heyer LJ, Brunak S, Stormo GD
Comput. Appl. Biosci., 13, 583-586, 1997 |
PubMed
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Hidden Markov models for human genes: periodic patterns in exon sequences
Baldi P, Brunak S, Chauvin Y, Krogh A
in Theoretical and Computational Methods in Genome Research, S. Suhai (ed.), Plenum Press, N.Y., 15-32, 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, 3724-3732, 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. Neur. Sys., 8, 581-599, 1997 |
PubMed
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Hidden neural networks: a framework for HMM/NN hybrids
Riis SK, Krogh A
Proceedings of ICASSP \'97, 4, IEEE, New York, 3233-3236, 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, 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, 1241-1248, 1997 |
PubMed
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Coherent topological phenomena in protein folding
Bohr H, Brunak S, Bohr J
Folding & Design, 2, 15-18, 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, 3248-3254, 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, 3159-3163, 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, 394-398, 1997 |
PubMed
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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, 697-701, 1997 |
PubMed
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Finding Common Sequence and Structure Motifs in a Set of RNA Sequences
Gorodkin J, Heyer LJ, Stormo G
Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology (ISMB97), 120-123, 1997 |
PubMed
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Two Methods for Improving Performance of a HMM and their Application for Gene Finding
Krogh A
Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology (ISMB97), 179-186, 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
Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology (ISMB97), 226-233, 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
Nucl. Acids Res., 25, 278-282, 1997 |
PubMed
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Molecular Wring Resonances in Chain Molecules
Bohr H, Brunak S, Bohr J
Bioelectromagnetics, 18, 187-189, 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 Transactions on Neural Networks, 8, 1321-1327, 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, 1-6, 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, 237-252, 1996, 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, 2203-2216, 1996 |
PubMed
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Relationship between protein structure and geometrical constraints
Lund O, Hansen J, Brunak S, Bohr J
Protein Sci., 5, 2217-2225, 1996 |
PubMed
|
Magic numbers in protein structures
Lindgård PA, Bohr H
Phys. Rev. Lett., 77, 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, 503-510, 1996 |
PubMed
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Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models
Pedersen AG, Baldi P, Brunak S, Chauvin Y
Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology (ISMB96), 182-191, 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, 3439-3452, 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, 733-740, 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, 1-11, 1996 |
PubMed
|
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, 165-177, 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
Folding and Design, 1, R55-R63, (Review), 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. of Bacteriol, 178, 61-67, 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, 316-320, 1996 |
PubMed
|
1995
Prediction of hypervariable CDR-H3 loop structures in antibodies
Reczko M, Martin ACR, Bohr H, Suhai S
Protein Eng., 8, 389-395, 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, 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, 121-133, 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 Sys., 6, 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
Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology (ISMB95), AAAI Press, 292-299, 1995 |
PubMed
Publication download
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Periodic sequence patterns in human exons
Baldi P, Brunak S, Chauvin Y, Engelbrecht J, Krogh A
Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology (ISMB95), AAAI Press, 30-38, 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, 1223-1230, 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., 308, 801-813, 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. 1994 Nov 11;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, 3616-3619, 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 |
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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 |
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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 |
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Cleaning up gene databases
Brunak S, Engelbrecht J, Knudsen S
Nature, 343, 123, 1990 |
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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 |
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A Travelling Salesman Approach to Protein Conformation
Bohr H, Brunak S
Complex Systems, 3, 9-28,(Cover illustration), 1989 |
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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 |
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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 |
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Books
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, 2010 |
PubMed
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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 |
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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 |
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The genus Burkholderia: analysis of 56 genomic sequences
Ussery DW, Kiil K, Lagesen K, Sicheritz-Ponten T, Bohlin J, Wassenaar TM
Microbial Pathogenomics,Karger AG publishers, Basel, 2009 |
PubMed
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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
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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 |
Details
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A Biologist's Guide to Analysis of DNA Microarray Data, 2nd edition
Knudsen S
John Wiley & Sons, New York, 2004 |
Details
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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 |
Details
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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 |
Details
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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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