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2014 (66) 2013 (76) 2012 (71) 2011 (72) 2010 (111) 2009 (70) 2008 and before (551) Books (24)

2014

    Solid-phase synthesis and biological evaluation of N-dipeptido L-homoserine lactones as quorum sensing activators.
    Hansen MR, Le Quement ST, Jakobsen TH, Skovstrup S, Taboureau O, Tolker-Nielsen T, Givskov M, Nielsen TE
    Chembiochem. 2014 Feb 10;15(3):460-5. doi: 10.1002/cbic.201300533., 2014
    PubMed
    Proteome reference maps of the Lotus japonicus nodule and root.
    Dam S, Dyrlund TF, Ussatjuk A, Jochimsen B, Nielsen K, Goffard N, Ventosa M, Lorentzen A, Gupta V, Andersen SU, Enghild JJ, Ronson CW, Roepstorff P, Stougaard J
    Proteomics. 2014 Feb;14(2-3):230-40., 2014
    PubMed
    Oxidative stress response pathways: Fission yeast as archetype.
    Papadakis MA, Workman CT
    Critical Reviews in Microbiology. 2014 Feb 27, 2014
    PubMed
    RNA-protein interactions: an overview
    Re A, Joshi T, Kulberkyte E, Morris Q, Workman CT
    Methods in Molecular Biology 2014;1097:491-521., 2014
    PubMed
    Colony morphology and transcriptome profiling of Pseudomonas putida KT2440 and its mutants deficient in alginate or all EPS synthesis under controlled matric potentials.
    Gulez G, Altintas A, Fazli M, Dechesne A, Workman CT, Tolker-Nielsen T, Smets BF
    Microbiologyopen. 2014 Jun 10., 2014
    PubMed
    Synthetic promoter library for modulation of actinorhodin production in Streptomyces coelicolor A3(2).
    Sohoni SV, Fazio A, Workman CT, Mijakovic I, Lantz AE
    PLoS One. 2014 Jun 25;9(6):e99701, 2014
    PubMed
    Lysine deacetylase inhibition prevents diabetes by chromatin-independent immunoregulation and β-cell protection.
    Christensen DP, Gysemans C, Lundh M, Dahllöf MS, Noesgaard D, Schmidt SF, Mandrup S, Birkbak N, Workman CT, Piemonti L, Blaabjerg L, Monzani V, Fossati G, Mascagni P, Paraskevas S, Aikin RA, Billestrup N, Grunnet LG, Dinarello CA, Mathieu C, Mandrup-Poulsen T
    PNAS, Proceedings of the National Academy of Sciences 2014 Jan 21;111(3):1055-9., 2014
    PubMed
    STAT3 induction of miR-146b forms a feedback loop to inhibit the NF-κB to IL-6 signaling axis and STAT3-driven cancer phenotypes
    Xiang M, Birkbak NJ, Vafaizadeh V, Walker SR, Yeh JE, Liu S, Kroll Y, Boldin M, Taganov K, Groner B, Richardson AL, Frank DA
    Science Signaling. 2014 Jan 28;7(310):ra11, 2014
    PubMed
    An elevated pro-inflammatory cytokine profile in multiple chemical sensitivity.
    Dantoft TM, Elberling J, Brix S, Szecsi PB, Vesterhauge S, Skovbjerg S
    Psychoneuroendocrinology. 2014 Feb;40:140-50., 2014
    PubMed
    Multiparametric bioinformatics distinguish the CD4/CD8 ratio as a suitable laboratory predictor of combined T cell pathogenesis in HIV infection.
    Buggert M, Frederiksen J, Noyan K, Svärd J, Barqasho B, Sönnerborg A, Lund O, Nowak P, Karlsson AC
    Journal of Immunology 2014 Mar 1;192(5):2099-108., 2014
    PubMed
    Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica.
    Leekitcharoenphon P, Nielsen EM, Kaas RS, Lund O, Aarestrup FM
    PLoS One. 2014 Feb 4;9(2):e87991., 2014
    PubMed
    Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli.
    Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, Aarestrup FM
    Journal of Clinical Microbiology. 2014 May;52(5):1501-10, 2014
    PubMed
    In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing
    Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O, Villa L, Møller Aarestrup F, Hasman H
    Antimicrobial Agents and Chemotherapy. 2014 Jul;58(7):3895-903., 2014
    PubMed
    Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.
    Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto JM, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Doré J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Léonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sørensen S, Tap J, Tims S, Ussery DW, Yamada T; MetaHIT Consortium, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD Nat Biotechnol
    Nature Biotechnology. 2014 Jul 6., 2014
    PubMed
    T-bet and Eomes Are Differentially Linked to the Exhausted Phenotype of CD8+ T Cells in HIV Infection
    Buggert M, Tauriainen J, Yamamoto T, Frederiksen J, Ivarsson MA, Michaëlsson J, Lund O, Hejdeman B, Jansson M, Sönnerborg A, Koup RA, Betts MR, Karlsson AC
    PLoS Pathogens 2014 Jul 17;10(7):e1004251, 2014
    PubMed
    NetFCM: A semi-automated web-based method for flow cytometry data analysis
    Frederiksen J, Buggert M, Karlsson AC, Lund O
    Cytometry A. 2014 Jul 18., 2014
    PubMed
    Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms.
    Kaas RS, Leekitcharoenphon P, Aarestrup FM, Lund O
    PLoS One. 2014 Aug 11;9(8):e104984, 2014
    PubMed
    Acute and perinatal-programming effects of a fat-rich diet on rat muscle mitochondrial function and hepatic lipid accumulation.
    Hellgren LI, Jensen RI, Waterstradt MS, Quistorff B, Lauritzen L
    Acta Obstetricia et Gynecologica Scandinavica . 2014 Jul 22., 2014
    PubMed
    Natural mannosylation of HIV-1 gp120 imposes no immunoregulatory effects in primary human plasmacytoid dendritic cells
    Søndergaard JN, Vinner L, Brix S
    Molecular Immunology 2014 Jun;59(2):180-7., 2014
    PubMed
    NetMHCstab - predicting stability of peptide-MHC-I complexes; impacts for cytotoxic T lymphocyte epitope discovery
    Jørgensen KW, Rasmussen M, Buus S, Nielsen M
    Immunology. 2014 Jan;141(1):18-26., 2014
    PubMed
    Temporal disease trajectories condensed from population-wide registry data covering 6.2 million patients
    Jensen AB1, Moseley PL2, Oprea TI3, Ellesøe SG4, Eriksson R1, Schmock H5, Jensen PB4, Jensen LJ4, Brunak S1
    Nature Communication. 2014 Jun 24;5:4022., 2014
    PubMed
    An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.
    Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, Dechene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D Jr, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, de Bakker PI, Duzkale H, Dworzy Ski P, Fairbrother W, Francioli L, Funke BH, Giovanni MA, Handsaker RE, Lage K, Lebo MS, Lek M, Leshchiner I, Macarthur DG, McLaughlin HM, Murray MF, Pers TH, Polak PP, Raychaudhuri S, Rehm HL, Soemedi R, Stitziel NO, Vestecka S, Supper J, Gugenmus C, Klocke B, Hahn A, Schubach M, Menzel M, Biskup S, Freisinger P, Deng M, Braun M, Perner S, Smith RJ, Andorf JL, Huang J, Ryckman K, Sheffield VC, Stone EM, Bair T, Black-Ziegelbein EA, Braun TA, Darbro B, Deluca AP, Kolbe DL, Scheetz TE, Shearer AE, Sompallae R, Wang K, Bassuk AG, Edens E, Mathews K, Moore SA, Shchelochkov OA, Trapane P, Bossler A, Campbell CA, Heusel JW, Kwitek A, Maga T, Panzer K, Wassink T, Van Daele D, Azaiez H, Booth K, Meyer N, Segal MM, Williams MS, Tromp G, White P, Corsmeier D, Fitzgerald-Butt S, Herman G, Lamb-Thrush D, McBride KL, Newsom D, Pierson CR, Rakowsky AT, Maver A, Lovre IL, Palanda IA, Peterlin B, Torkamani A, Wedell A, Huss M, Alexeyenko A, Lindvall JM, Magnusson M, Nilsson D, Stranneheim H, Taylan F, Gilissen C, Hoischen A, van Bon B, Yntema H, Nelen M, Zhang W, Sager J, Zhang L, Blair K, Kural D, Cariaso M, Lennon GG, Javed A, Agrawal S, Ng PC, Sandhu KS, Krishna S, Veeramachaneni V, Isakov O, Halperin E, Friedman E, Shomron N, Glusman G, Roach JC, Caballero J, Cox HC, Mauldin D, Ament SA, Rowen L, Richards DR, Lucas FA, Gonzalez-Garay ML, Caskey CT, Bai Y, Huang Y, Fang F, Zhang Y, Wang Z, Barrera J, Garcia-Lobo JM, González-Lamuño D, Llorca J, Rodriguez MC, Varela I, Reese MG, De La Vega FM, Kiruluta E, Cargill M, Hart RK, Sorenson JM, Lyon GJ, Stevenson DA, Bray BE, Moore BM, Eilbeck K, Yandell M, Zhao H, Hou L, Chen X, Yan X, Chen M, Li C, Yang C, Gunel M, Li
    Genome Biology. 2014 Mar 25;15(3):R53, 2014
    PubMed
    Biological insights from 108 schizophrenia-associated genetic loci.
    Ripke S, Neale BM, Corvin A, Walters JT, Farh KH, Holmans PA, Lee P, Bulik-Sullivan B, Collier DA, Huang H, Pers TH, Agartz I, Agerbo E, Albus M, Alexander M, Amin F, Bacanu SA, Begemann M, Belliveau RA Jr, Bene J, Bergen SE, Bevilacqua E, Bigdeli TB, Black DW, Bruggeman R, Buccola NG, Buckner RL, Byerley W, Cahn W, Cai G, Campion D, Cantor RM, Carr VJ, Carrera N, Catts SV, Chambert KD, Chan RC, Chen RY, Chen EY, Cheng W, Cheung EF, Chong SA, Cloninger CR, Cohen D, Cohen N, Cormican P, Craddock N, Crowley JJ, Curtis D, Davidson M, Davis KL, Degenhardt F, Del Favero J, Demontis D, Dikeos D, Dinan T, Djurovic S, Donohoe G, Drapeau E, Duan J, Dudbridge F, Durmishi N, Eichhammer P, Eriksson J, Escott-Price V, Essioux L, Fanous AH, Farrell MS, Frank J, Franke L, Freedman R, Freimer NB, Friedl M, Friedman JI, Fromer M, Genovese G, Georgieva L, Giegling I, Giusti-Rodríguez P, Godard S, Goldstein JI, Golimbet V, Gopal S, Gratten J, de Haan L, Hammer C, Hamshere ML, Hansen M, Hansen T, Haroutunian V, Hartmann AM, Henskens FA, Herms S, Hirschhorn JN, Hoffmann P, Hofman A, Hollegaard MV, Hougaard DM, Ikeda M, Joa I, Julià A, Kahn RS, Kalaydjieva L, Karachanak-Yankova S, Karjalainen J, Kavanagh D, Keller MC, Kennedy JL, Khrunin A, Kim Y, Klovins J, Knowles JA, Konte B, Kucinskas V, Ausrele Kucinskiene Z, Kuzelova-Ptackova H, Kähler AK, Laurent C, Keong JL, Lee SH, Legge SE, Lerer B, Li M, Li T, Liang KY, Lieberman J, Limborska S, Loughland CM, Lubinski J, Lönnqvist J, Macek M Jr, Magnusson PK, Maher BS, Maier W, Mallet J, Marsal S, Mattheisen M, Mattingsdal M, McCarley RW, McDonald C, McIntosh AM, Meier S, Meijer CJ, Melegh B, Melle I, Mesholam-Gately RI, Metspalu A, Michie PT, Milani L, Milanova V, Mokrab Y, Morris DW, Mors O, Murphy KC, Murray RM, Myin-Germeys I, Müller-Myhsok B, Nelis M, Nenadic I, Nertney DA, Nestadt G, Nicodemus KK, Nikitina-Zake L, Nisenbaum L, Nordin A, O\'Callaghan E, O\'Dushlaine C, O\'Neill FA, Oh SY, Olincy A, Olsen L, Van Os J, Pantelis C, Papadimit
    Nature. 2014 Jul 24;511(7510):421-7., 2014
    PubMed
    Genome-wide association analyses identify variants in developmental genes associated with hypospadias.
    Geller F, Feenstra B, Carstensen L, Pers TH, van Rooij IA, Körberg IB, Choudhry S, Karjalainen JM, Schnack TH, Hollegaard MV, Feitz WF, Roeleveld N, Hougaard DM, Hirschhorn JN, Franke L, Baskin LS, Nordenskjöld A, van der Zanden LF, Melbye M
    Nature Genetics. 2014 Aug 10., 2014
    PubMed
    Tracking Genomic Cancer Evolution for Precision Medicine: The Lung TRACERx Study.
    Jamal-Hanjani M, Hackshaw A, Ngai Y, Shaw J, Dive C, Quezada S, Middleton G, de Bruin E, Le Quesne J, Shafi S, Falzon M, Horswell S, Blackhall F, Khan I, Janes S, Nicolson M, Lawrence D, Forster M, Fennell D, Lee SM, Lester J, Kerr K, Muller S, Iles N, Smith S, Murugaesu N, Mitter R, Salm M, Stuart A, Matthews N, Adams H, Ahmad T, Attanoos R, Bennett J, Birkbak NJ, Booton R, Brady G, Buchan K, Capitano A, Chetty M, Cobbold M, Crosbie P, Davies H, Denison A, Djearman M, Goldman J, Haswell T, Joseph L, Kornaszewska M, Krebs M, Langman G, MacKenzie M, Millar J, Morgan B, Naidu B, Nonaka D, Peggs K, Pritchard C, Remmen H, Rowan A, Shah R, Smith E, Summers Y, Taylor M, Veeriah S, Waller D, Wilcox B, Wilcox M, Woolhouse I, McGranahan N, Swanton C
    PLoS Biology. 2014 Jul 8;12(7):e1001906, 2014
    PubMed
    Enhancing Reproducibility in Cancer Drug Screening: How Do We Move Forward?
    Hatzis C, Bedard PL, Birkbak NJ, Beck AH, Aerts HJ, Stern DF, Shi L, Clarke R, Quackenbush J, Haibe-Kains B
    Cancer Research. 2014 Aug 1;74(15):4016-4023, 2014
    PubMed
    Systematic Evaluation of the Prognostic Impact and Intratumour Heterogeneity of Clear Cell Renal Cell Carcinoma Biomarkers.
    Gulati S, Martinez P, Joshi T, Birkbak NJ, Santos CR, Rowan AJ, Pickering L, Gore M, Larkin J, Szallasi Z, Bates PA, Swanton C, Gerlinger M
    European Urology. 2014 Jul 18. pii: S0302-2838(14)00627-7., 2014
    PubMed
    Genomic profiling of thousands of candidate polymorphisms predicts risk of relapse in 778 Danish and German childhood acute lymphoblastic leukemia patients.
    Wesolowska A, Borst L, Dalgaard MD, Yadav R, Rasmussen KK, Wehner PS, Rasmussen M, Orntoft TF, Nordentoft I, Koehler R, Bartram CR, Schrappe M, Sicheritz-Ponten T, Gautier L, Marquart H, Madsen HO, Brunak S, Stanulla M, Gupta R, Schmiegelow K
    Leukemia. 2014 Jul 3., 2014
    PubMed
    Discovery of biomarkers for glycaemic deterioration before and after the onset of type 2 diabetes: rationale and design of the epidemiological studies within the IMI DIRECT Consortium.
    Koivula RW, Heggie A, Barnett A, Cederberg H, Hansen TH, Koopman AD, Ridderstråle M, Rutters F, Vestergaard H, Gupta R, Herrgård S, Heymans MW, Perry MH, Rauh S, Siloaho M, Teare HJ, Thorand B, Bell J, Brunak S, Frost G, Jablonka B, Mari A, McDonald TJ, Dekker JM, Hansen T, Hattersley A, Laakso M, Pedersen O, Koivisto V, Ruetten H, Walker M, Pearson E, Franks PW; DIRECT Consortium
    Diabetologia. 2014 Jun;57(6):1132-42., 2014
    PubMed
    Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis.
    Wesolowska A, Bahl MI, Carvalho V, Kristiansen K, Sicheritz-Pontén T, Gupta R, Licht TR
    Microbiome. 2014 Jun 5;2:19, 2014
    PubMed
    NutriChem: a systems chemical biology resource to explore the medicinal value of plant-based foods
    Jensen K, Panagiotou G, Kouskoumvekaki I
    Nucleic Acids Research, Database issue, 2014
    Nucleic Acids Research
    MR1-restricted MAIT cells display ligand discrimination and pathogen selectivity through distinct T cell receptor usage
    Gold MC, McLaren JE, Reistetter JA, Smyk-Pearson S, Ladell K, Swarbrick GM, Yu YY, Hansen TH, Lund O, Nielsen M, Gerritsen B, Kesmir C, Miles JJ, Lewinsohn DA, Price DA, Lewinsohn DM
    Journal of Experimental Medicine. 2014 Jul 28;211(8):1601-10., 2014
    PubMed
    An integrated catalog of reference genes in the human gut microbiome
    Junhua Li, Huijue Jia, Xianghang Cai, Huanzi Zhong, Qiang Feng, Shinichi Sunagawa, Manimozhiyan Arumugam, Jens Roat Kultima, Edi Prifti, Trine Nielsen, Agnieszka Sierakowska Juncker, Chaysavanh Manichanh, Bing Chen, Wenwei Zhang, Florence Levenez, Juan Wang, Xun Xu, Liang Xiao, Suisha Liang, Dongya Zhang, Zhaoxi Zhang, Weineng Chen, Hailong Zhao, Jumana Yousuf Al-Aama, Sherif Edris, Huanming Yang, Jian Wang, Torben Hansen, Henrik Bjørn Nielsen, Søren Brunak, Karsten Kristiansen, Francisco Guarner, Oluf Pedersen, Joel Doré, Dusko Ehrlich S, MetaHIT Consortium, Peer Bork & Jun Wang
    Nature Biotechnology. 2014 Jul 6, 2014
    PubMed
    Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
    Bjørn Nielsen H, Mathieu Almeida, Agnieszka Sierakowska Juncker, Simon Rasmussen, Junhua Li, Shinichi Sunagawa, Damian R Plichta, Laurent Gautier, Anders G Pedersen, Emmanuelle Le Chatelier, Eric Pelletier, Ida Bonde, Trine Nielsen, Chaysavanh Manichanh, Manimozhiyan Arumugam, Jean-Michel Batto, Marcelo B Quintanilha dos Santos, Nikolaj Blom, Natalia Borruel, Kristoffer S Burgdorf, Fouad Boumezbeur, Francesc Casellas, Joël Doré, Piotr Dworzynski, Francisco Guarner, Torben Hansen, Falk Hildebrand, Rolf S Kaas, Sean Kennedy, Karsten Kristiansen, Jens Roat Kultima, Pierre Léonard, Florence Levenez, Ole Lund, Bouziane Moumen, Denis Le Paslier, Nicolas Pons, Oluf Pedersen, Edi Prifti, Junjie Qin, Jeroen Raes, Søren Sørensen, Julien Tap, Sebastian Tims, David W Ussery, Takuji Yamada, MetaHIT Consortium, Pierre Renault, Thomas Sicheritz-Ponten, Peer Bork, Jun Wang, Søren Brunak & S Dusko Ehrlich
    Nature Biotechnology. 2014 Jul 6., 2014
    PubMed
    Improving Biotech Education through Gamified Laboritory Simulations.
    Bonde M, Makransky G, Wandall J, Larsen MV, Morsing M, Jarmer H & Sommer M
    Nature Biotechnology. 2014 Jul 8;32(7):694-7., 2014
    PubMed
    Exploring Mechanisms of Diet-Colon Cancer Associations through Candidate Molecular Interaction Networks.
    Westergaard D, Li J, Jensen K, Kouskoumvekaki I, Panagiotou G
    BMC Genomics. 2014 May 17;15:380, 2014
    PubMed
    NetTepi: an integrated method for the prediction of T cell epitopes
    Trolle T, Nielsen M
    Immunogenetics. 2014 Aug;66(7-8):449-56., 2014
    PubMed
    LocTree3 prediction of localization.
    Goldberg T, Hecht M, Hamp T, Karl T, Yachdav G, Ahmed N, Altermann U, Angerer P, Ansorge S, Balasz K, Bernhofer M, Betz A, Cizmadija L, Do KT, Gerke J, Greil R, Joerdens V, Hastreiter M, Hembach K, Herzog M, Kalemanov M, Kluge M, Meier A, Nasir H, Neumaier U, Prade V, Reeb J, Sorokoumov A, Troshani I, Vorberg S, Waldraff S, Zierer J, Nielsen H, Rost B
    Nucleic Acids Research. 2014 Jul;42(Web Server issue):W350-5., 2014
    PubMed
    A DNA binding-site landscape and regulatory network analysis for the family of NAC stress response transcription factors in Arabidopsis thaliana.
    Lindemose S, Jensen KM, Van de Velde Jan, O’Shea C, Heyndrickx KS, Workman CT, Vandepoele Klaas, Skriver K, De Masi F
    Nucleic Acids Research. 2014 Aug 1;42(12):7681-93., 2014
    PubMed
    KinomeXplorer: an integrated platform for kinome biology studies
    Horn H, Schoof EM, Kim J, Robin X, Miller ML, Diella F, Palma A, Cesareni G, Jensen LJ, Linding R
    Nature Methods. 2014 Jun;11(6):603-4., 2014
    PubMed
    Software-supported USER cloning strategies for site-directed mutagenesis and DNA assembly
    Genee HJ, Bonde MT, Bagger FO, Jespersen JB, Sommer MOA, Wernersson R, Olsen LR
    ACS Synthetic Biology . 2014 May 9., 2014
    PubMed
    Use of \"one-pot, mix-and-read\" peptide-MHC class I tetramers and predictive algorithms to improve detection of cytotoxic T lymphocyte responses in cattle.
    Svitek N, Hansen AM, Steinaa L, Saya R, Awino E, Nielsen M, Buus S, Nene V
    Veterinary Research. 2014 Apr 28;45:50., 2014
    PubMed
    Identification and HLA-Tetramer-Validation of Human CD4+ and CD8+ T Cell Responses against HCMV Proteins IE1 and IE2.
    Braendstrup P, Mortensen BK, Justesen S, Osterby T, Rasmussen M, Hansen AM, Christiansen CB, Hansen MB, Nielsen M, Vindeløv L, Buus S, Stryhn A
    PLoS One. 2014 Apr 23;9(4):e94892., 2014
    PubMed
    Identification of odorant-receptor interactions by global mapping of the human odorome.
    Audouze K, Tromelin A, Le Bon AM, Belloir C, Petersen RK, Kristiansen K, Brunak S, Taboureau O
    PLoS One. 2014 Apr 2;9(4):e93037., 2014
    PubMed
    Towards in vivo regulon kinetics: PurR activation by PRPP during purine depletion in Lactococcus lactis
    Jendresen CB, Dimitrov P, Gautier L, Lui M, Martinussen J, Kilstrup M
    Microbiology. 2014 Jul;160(Pt 7):1321-31, 2014
    PubMed
    Children with asthma by school age display aberrant immune responses to pathogenic airway bacteria as infants.
    Larsen JM, Brix S, Thysen AH, Birch S, Rasmussen MA, Bisgaard H
    Journal of Allergy and Clinical Immunology. 2014 Apr;133(4):1008-13, 2014
    PubMed
    Lactate dehydrogenase as a selection criterion for ipilimumab treatment in metastatic melanoma
    Kelderman S, Heemskerk B, van Tinteren H, van den Brom RR, Hospers GA, van den Eertwegh AJ, Kapiteijn EW, de Groot JW, Soetekouw P, Jansen RL, Fiets E, Furness AJ, Renn A, Krzystanek M, Szallasi Z, Lorigan P, Gore ME, Schumacher TN, Haanen JB, Larkin JM, Blank CU
    Cancer Immunology, Immunotherapy . 2014 May;63(5):449-58., 2014
    PubMed
    Polychlorinated dibenzo-p-dioxins, furans, and biphenyls (PCDDs/PCDFs and PCBs) in breast milk and early childhood growth and IGF1.
    Wohlfahrt-Veje C, Audouze K, Brunak S, Antignac JP, le Bizec B, Juul A, Skakkebæk NE, Main KM
    Reproduction. 2014 Mar 2;147(4):391-9., 2014
    PubMed
    Benchmarking of Methods for Genomic Taxonomy.
    Larsen MV, Cosentino S, Lukjancenko O, Saputra D, Rasmussen S, Hasman H, Sicheritz-Pontén T, Aarestrup FM, Ussery DW, Lund O
    Journal of Clinical Microbiology. 2014 May;52(5):1529-39., 2014
    PubMed
    Applying the ResFinder and VirulenceFinder web-services for easy identification of acquired antibiotic resistance and E. coli virulence genes in bacteriophage and prophage nucleotide sequences.
    Kleinheinz KA, Joensen KG, Larsen MV
    Bacteriophage. 2014 Jan 1;4(1):e27943., 2014
    PubMed
    Applicability of computational systems biology in toxicology.
    Kongsbak K, Hadrup N, Audouze K, Vinggaard AM
    Basic & Clinical Pharmacology & Toxicology . 2014 Jul;115(1):45-9., 2014
    PubMed
    Host genome variations and risk of infections during induction treatment for childhood acute lymphoblastic leukaemia.
    Lund B, Wesolowska A, Lausen B, Borst L, Rasmussen KK, Müller K, Klungland H, Gupta R, Schmiegelow K
    European Journal of Haematology. 2014 Apr;92(4):321-30., 2014
    PubMed
    Archival Bone Marrow Samples: Suitable for Multiple Biomarker Analysis?
    Lund B, Wesolowska A, Lausen B, Borst L, Rasmussen KK, Müller K, Klungland H, Gupta R, Schmiegelow K
    Diagnostic Molecular Pathology . 2014 Jan 30., 2014
    PubMed
    The genome of a Late Pleistocene human from a Clovis burial site in western Montana.
    Rasmussen M, Anzick SL, Waters MR, Skoglund P, DeGiorgio M, Stafford TW Jr, Rasmussen S, Moltke I, Albrechtsen A, Doyle SM, Poznik GD, Gudmundsdottir V, Yadav R, Malaspinas AS, White SS 5th, Allentoft ME, Cornejo OE, Tambets K, Eriksson A, Heintzman PD, Karmin M, Korneliussen TS, Meltzer DJ, Pierre TL, Stenderup J, Saag L, Warmuth VM, Lopes MC, Malhi RS, Brunak S, Sicheritz-Ponten T, Barnes I, Collins M, Orlando L, Balloux F, Manica A, Gupta R, Metspalu M, Bustamante CD, Jakobsson M, Nielsen R, Willerslev E
    Nature. 2014 Feb 13;506(7487):225-9., 2014
    PubMed
    Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European.
    Olalde I, Allentoft ME, Sánchez-Quinto F, Santpere G, Chiang CW, DeGiorgio M, Prado-Martinez J, Rodríguez JA, Rasmussen S, Quilez J, Ramírez O, Marigorta UM, Fernández-Callejo M, Prada ME, Encinas JM, Nielsen R, Netea MG, Novembre J, Sturm RA, Sabeti P, Marquès-Bonet T, Navarro A, Willerslev E, Lalueza-Fox C
    Nature. 2014 Mar 13;507(7491):225-8, 2014
    PubMed
    Improved pan-specific MHC class I peptide-binding predictions using a novel representation of the MHC-binding cleft environment.
    Carrasco Pro S, Zimic M, Nielsen M
    Tissue Antigens. 2014 Feb;83(2):94-100., 2014
    PubMed
    Tolerance of Whole-Genome Doubling Propagates Chromosomal Instability and Accelerates Cancer Genome Evolution
    Dewhurst SM, McGranahan N, Burrell RA, Rowan AJ, Grönroos E, Endesfelder D, Joshi T, Mouradov D, Gibbs P, Ward RL, Hawkins NJ, Szallasi Z, Sieber OM, Swanton C
    Cancer Discovery. 2014 Feb;4(2):175-85., 2014
    PubMed
    Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions.
    Kim Y, Sidney J, Buus S, Sette A, Nielsen M, Peters B
    BMC Bioinformatics, 2014
    PubMed
    DNA secondary structures are associated with recombination in major Plasmodium falciparum variable surface antigen gene families
    Sander AF, Lavstsen T, Rask TS, Lisby M, Salanti A, Fordyce SL, Jespersen JS, Carter R, Deitsch KW, Theander TG, Pedersen AG, Arnot DE
    Nucleic Acids Research, 2014
    PubMed
    Relevant URL
    Bacterial diversity in snow on North Pole ice floes.
    Hauptmann AL, Stibal M, Bælum J, Sicheritz-Pontén T, Brunak S, Bowman JS, Hansen LH, Jacobsen CS, Blom N
    Extremophiles. 2014 Jun 21, 2014
    PubMed
    Springer Link
    Prenatal undernutrition and postnatal overnutrition are associated with permanent changes in hepatic metabolism markers and fatty acid composition in sheep.
    Hou L, Hellgren LI, Kongsted AH, Vaag A, Nielsen MO
    Acta Physiologica, 2014
    PubMed
    Effects of pregnancy on obesity-induced inflammation in a mouse model of fetal programming.
    Ingvorsen C, Thysen AH, Fernandez-Twinn DS, Nordby P, Nielsen KF, Ozanne SE, Brix S, Hellgren LI
    Nature - International Journal of Obesity, 2014
    PubMed
    Effects on metabolic markers are modified by PPARG2 and COX2 polymorphisms in infants randomized to fish oil.
    Harslof LB, Damsgaard CT, Hellgren LI, Andersen AD, Vogel U, Lauritzen L
    Genes & Nutrition 9(3):396 doi:10.1007/s12263-014-0396-4, 2014
    PubMed
    Large-scale analysis of B-cell epitopes on influenza virus hemagglutinin – implications for cross-reactivity of neutralizing antibodies
    Sun J, Kudahl UJ, Simon C, Cao Z, Reinherz EL, Brusic V
    Frontiers In Immunology, 2014
    PubMed
    Integrated Text Mining and Chemoinformatics Analysis Associates Diet to Health Benefit at Molecular Level
    Jensen K, Panagiotou G, Kouskoumvekaki I
    PLOS Computational Biology, 2014
    Relevant URL
    A genome-wide association study identifies CDHR3 as a susceptibility locus for early childhood asthma with severe exacerbations.
    Bønnelykke K, Sleiman P, Nielsen K, Kreiner-Møller E, Mercader JM, Belgrave D, den Dekker HT, Husby A, Sevelsted A, Faura-Tellez G, Mortensen LJ, Paternoster L, Flaaten R, Mølgaard A, Smart DE, Thomsen PF, Rasmussen MA, Bonàs-Guarch S, Holst C, Nohr EA, Yadav R, March ME, Blicher T, Lackie PM, Jaddoe VW, Simpson A, Holloway JW, Duijts L, Custovic A, Davies DE, Torrents D, Gupta R, Hollegaard MV, Hougaard DM, Hakonarson H, Bisgaard H
    Nature Genetics. 46(1):51-5 doi:10.1038/ng.2830, 2014
    PubMed

2013

    Personalized network-based treatments in oncology.
    Robin X, Creixell P, Radetskaya O, Santini CC, Longden J, Linding R
    Nature Clinical Pharmacology & Therapeutics . 2013 Dec;94(6):646-50., 2013
    PubMed
    The SH2 domain interaction landscape.
    Tinti M, Kiemer L, Costa S, Miller ML, Sacco F, Olsen JV, Carducci M, Paoluzi S, Langone F, Workman CT, Blom N, Machida K, Thompson CM, Schutkowski M, Brunak S, Mann M, Mayer BJ, Castagnoli L, Cesareni G
    Cell Reports. 2013 Apr 25;3(4):1293-305., 2013
    PubMed
    Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing.
    Zankari E, Hasman H, Kaas RS, Seyfarth AM, Agersø Y, Lund O, Larsen MV, Aarestrup FM
    Journal of Antimicrobial Chemotherapy. 2013 Apr;68(4):771-7., 2013
    PubMed
    PathogenFinder--distinguishing friend from foe using bacterial whole genome sequence data
    Cosentino S, Voldby Larsen M, Møller Aarestrup F, Lund O
    PLoS One. 2013 Oct 28;8(10):e77302., 2013
    PubMed
    Low-bandwidth and non-compute intensive remote identification of microbes from raw sequencing reads.
    Gautier L, Lund O
    PLoS One. 2013 Dec 31;8(12):e83784, 2013
    PubMed
    BlockLogo: Visualization of peptide and sequence motif conservation
    Olsen LR, Kudahl UJ, Simon C, Sun J, Schönbach C, Reinherz EL, Zhang GL, Brusic V
    Journal of Immunological Methods :37-44 doi:10.1016/j.jim.2013.08.014, 2013
    PubMed
    Detection of serological biomarkers by proximity extension assay for detection of colorectal
    Thorsen SB, Lundberg M, Villablanca A, Christensen SL, Belling K, Nielsen BS, Knowles M, Gee N, Nielsen HJ, Brünner N, Christensen IJ, Frederiksson S, Stenvang J, Assarsson E
    Journal of Translational Medicine 11:253 doi:10.1186/1479-5876-11-253, 2013
    PubMed
    Targeting of conserved gag-epitopes in early HIV infection is associated with lower plasma viral load and slower CD4(+) T cell depletion.
    Perez CL, Milush JM, Buggert M, Eriksson EM, Larsen MV, Liegler T, Hartogensis W, Bacchetti P, Lund O, Hecht FM, Nixon DF, Karlsson AC
    AIDS Research and Human Retroviruses 29(3):602-12 doi:10.1089/AID.2012.0171, 2013
    PubMed
    Rapid whole genome sequencing for the detection and characterization of microorganisms directly from clinical samples.
    Hasman H, Saputra D, Sicheritz-Ponten T, Lund O, Svendsen CA, Frimodt-Møller N, Aarestrup FM
    Journal of Clinical Microbiology. 52(1):139-46 doi:10.1128/JCM.02452-13, 2013
    PubMed
    Adipose tissue trans-fatty acids and changes in body weight and waist circumference.
    Hansen CP, Berentzen TL, Ostergaard JN, Dahm CC, Hellgren LI, Schmidt EB, Tjønneland A, Sørensen TI, Overvad K, Jakobsen MU
    British Journal of Nutrition 111(7):1283-91 doi:10.1017/S0007114513003747, 2013
    PubMed
    Epithelial entry rather than the ensuing systemic immune response determines the pathogenicity of two Salmonella enterica serovar Typhimurium strains in a mouse model.
    Brandt R, Petersen A, Brix S, Licht TR, Frøkiær H
    Microbes and Infection 15(13):911-9 doi:10.1016/j.micinf.2013.08.004, 2013
    PubMed
    Complete genes may pass from food to human blood
    Spisák S, Solymosi N, Ittzés P, Bodor A, Kondor D, Vattay G, Barták BK, Sipos F, Galamb O, Tulassay Z, Szallasi Z, Rasmussen S, Sicheritz-Ponten T, Brunak S, Molnar B, Csabai I
    PLoS ONE 8(7):e69805 doi:10.1371/journal.pone.0069805, 2013
    PubMed
    wKinMut: An integrated tool for the analysis and interpretation of mutations in human protein kinases
    Izarzugaza JMG, Vazquez M, Pozo A, Valencia A
    BMC Bioinformatics 2013, 14:345, 2013
    BMC Bioinformatics - biomedcentral
    Deep phenotyping of the unselected COPSAC2010 birth cohort study.
    Bisgaard H, Vissing NH, Carson CG, Bischoff AL, Følsgaard NV, Kreiner-Møller E, Chawes BL, Stokholm J, Pedersen L, Bjarnadóttir E, Thysen AH, Nilsson E, Mortensen LJ, Olsen SF, Schjørring S, Krogfelt KA, Lauritzen L, Brix S, Bønnelykke K
    Clinical & Experimental Allergy 43(12):1384-94 doi:10.1111/cea.12213, 2013
    PubMed
    The comparison of thrombocytosis and platelet-lymphocyte ratio as potential prognostic markers in colorectal cancer
    Baranyai Z, Krzystanek M, Jósa V, Dede K, Ágoston E, Szász AM, Sinkó D, Szarvas V, Salamon F, Eklund AC, Szallasi Z, Jakab F
    Thrombosis and Haemostasis, 2013
    Schattauer
    Computational optimisation of targeted DNA sequencing for cancer detection
    Martinez P, McGranahan N, Birkbak NJ, Gerlinger M, Swanton C
    Scientific Reports 3:3309 doi:10.1038/srep03309, 2013
    PubMed
    Inconsistency in large pharmacogenomic studies
    Haibe-Kains B, El-Hachem N, Birkbak NJ, Jin AC, Beck AH, Aerts HJWL, Quackenbush J
    Nature (2013/11/27 ) doi:10.1038/nature12831, 2013
    Nature
    Whole-Exome Sequencing of 2,000 Danish Individuals and the Role of Rare Coding Variants in Type 2 Diabetes
    Lohmueller KE, Sparsø T, Li Q, Andersson E, Korneliussen T, Albrechtsen A, Banasik K, Grarup N, Hallgrimsdottir I, Kiil K, Kilpeläinen TO, Krarup NT, Pers TH, Sanchez G, Hu Y, DeGiorgio M, Jørgensen T, Sandbæk A, Lauritzen T, Brunak S, Kristiansen K, Li Y, Hansen T, Wang J, Nielsen R, Pedersen O
    AJHG, The American Journal of Human Genetics - Cell 2013, 2013
    AJHG
    Bacterial natural transformation by highly fragmented and damaged DNA
    Overballe-Petersen S, Harms K, Orlando LA, Mayar JV, Rasmussen S, Dahl TW, Rosing MT, Poole AM, Sicheritz-Ponten T, Brunak S, Inselmann S, de Vries J, Wackernagel W, Pybus OG, Nielsen R, Johnsen PJ, Nielsen KM, Willerslev E
    PNAS, Proceedings of the National Academy of Sciences U.S.A. 110(49):19860-5 doi:10.1073/pnas.1315278110, 2013
    PubMed
    Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans
    Raghavan M, Skoglund P, Graf KE, Metspalu M, Albrechtsen A, Moltke I, Rasmussen S, Stafford Jr TW, Orlando L, Metspalu E, Karmin M, Tambets K, Rootsi S, Magi R, Campos PF, Balanovska E, Balanovsky O, Khusnutdinova E, Litvinov S, Osipova LP, Fedorova SA, Voevoda MI, DeGiorgio M, Sicheritz-Ponten T, Brunak S, Demeshchenko S, Kivisild T, Villems R, Nielsen R, Jakobsson M, Willerslev E
    Nature, 2013/11/20/online, 10.1038/nature12736, 2013
    Nature
    HELQ promotes RAD51 paralogue-dependent repair to avert germ cell loss and tumorigenesis.
    Adelman CA, Lolo RL, Birkbak NJ, Murina O, Matsuzaki K, Horejsi Z, Parmar K, Borel V, Skehel JM, Stamp G, D\\\'Andrea A, Sartori AA, Swanton C, Boulton SJ
    Nature 502(7471):381-4 doi:10.1038/nature12565, 2013
    PubMed
    Tumor Mutation Burden Forecasts Outcome in Ovarian Cancer with BRCA1 or BRCA2 Mutations
    Birkbak NJ, Kochupurakkal B, Izarzugaza JMG, Eklund AC, Li Y, Liu J, Szallasi Z, Matulonis UA, Richardson AL, Iglehart JD, Wang ZC
    Research Article | published 12 Nov 2013 | PLOS ONE 10.1371/journal.pone.0080023, 2013
    PLOS ONE
    Metagenomic species profiling using universal phylogenetic marker genes.
    Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Doré J, Ehrlich SD, Stamatakis A, Bork P
    Nature Methods 10(12):1196-9 doi:10.1038/nmeth.2693, 2013
    PubMed
    Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes.
    Barah P, Jayavelu ND, Rasmussen S, Nielsen HB, Mundy J, Bones AM
    BMC Genomics 14:722 doi:10.1186/1471-2164-14-722, 2013
    PubMed
    Mapping Condition Dependent Regulation of Lipid Metabolism in Saccharomyces cerevisiae.
    Jewett MC, Workman CT, Nookaew I, Pizarro FA, Agosin E, Hellgren LI, Nielsen J
    G3 (Bethesda) 3(11):1979-95 doi:10.1534/g3.113.006601, 2013
    PubMed
    A nondegenerate code of deleterious variants in mendelian Loci contributes to complex disease risk.
    Blair DR, Lyttle CS, Mortensen JM, Bearden CF, Jensen AB, Khiabanian H, Melamed R, Rabadan R, Bernstam EV, Brunak S, Jensen LJ, Nicolae D, Shah NH, Grossman RL, Cox NJ, White KP, Rzhetsky A
    Cell 155(1):70-80 doi:10.1016/j.cell.2013.08.030, 2013
    PubMed
    Relevant URL
    Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics
    Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümü? ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M
    Science, 2013
    Relevant URL
    Evaluation of peptide selection approaches for epitope-based vaccine design
    Schubert B, Lund O, Nielsen M
    Tissue Antigens, 82: 243–251. doi: 10.1111/tan.12199, 2013
    Relevant URL
    A computational approach to mechanistic and predictive toxicology of pesticides
    Kongsbak K, Vinggaard AM, Hadrup N, Audouze K
    ALTEX 31(1):11-22 doi:10.14573/altex.1304241, 2013
    PubMed
    Relevant URL
    A computational approach to chemical etiologies of diabetes
    Audouze K, Brunak S, Grandjean P
    Scientific Reports 2013, 2013
    Relevant URL
    The effect of network biology on drug toxicology
    Gautier L, Taboureau O, Audouze K
    Expert Opinion on Drug Metabolism & Toxicology 9(11):1409-18 doi:10.1517/17425255.2013.820704, 2013
    PubMed
    Prediction of Disease Causing Non-Synonymous SNPs by the Artificial Neural Network Predictor NetDiseaseSNP
    Johansen MB, Izarzugaza JM, Brunak S, Petersen TN, Gupta R
    PLoS ONE 8(7):e68370 doi:10.1371/journal.pone.0068370, 2013
    PubMed
    Richness of human gut microbiome correlates with metabolic markers.
    Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jørgensen T, Brandslund I, Nielsen HB, Juncker AS, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Clément K, Doré J, Kleerebezem M, Kristiansen K, Renault P, Sicheritz-Ponten T, de Vos WM, Zucker JD, Raes J, Hansen T; MetaHIT consortium, Bork P, Wang J, Ehrlich SD, Pedersen O, Guedon E, Delorme C, Layec S, Khaci G, van de Guchte M, Vandemeulebrouck G, Jamet A, Dervyn R, Sanchez N, Maguin E, Haimet F, Winogradski Y, Cultrone A, Leclerc M, Juste C, Blottière H, Pelletier E, LePaslier D, Artiguenave F, Bruls T, Weissenbach J, Turner K, Parkhill J, Antolin M, Manichanh C, Casellas F, Boruel N, Varela E, Torrejon A, Guarner F, Denariaz G, Derrien M, van Hylckama Vlieg JE, Veiga P, Oozeer R, Knol J, Rescigno M, Brechot C, M\\\'Rini C, Mérieux A, Yamada T
    Nature 500(7464):541-6 doi:10.1038/nature12506, 2013
    PubMed
    ATAF1 transcription factor directly regulates abscisic acid biosynthetic gene NCED3 in Arabidopsis thaliana.
    Jensen MK, Lindemose S, Masi Fd, Reimer JJ, Nielsen M, Perera V, Workman CT, Turck F, Grant MR, Mundy J, Petersen M, Skriver K
    FEBS Open Bio 3:321-7 doi:10.1016/j.fob.2013.07.006, 2013
    PubMed
    Effects of butter from mountain-pasture grazing cows on risk markers of the metabolic syndrome compared with conventional Danish butter: a randomized controlled study.
    Werner LB, Hellgren LI, Raff M, Jensen SK, Petersen RA, Drachmann T, Tholstrup T
    Lipids in Health and Disease 12:99 doi:10.1186/1476-511X-12-99, 2013
    PubMed
    Whey protein reduces early life weight gain in mice fed a high-fat diet.
    Tranberg B, Hellgren LI, Lykkesfeldt J, Sejrsen K, Jeamet A, Rune I, Ellekilde M, Nielsen DS, Hansen AK
    PLoS ONE 8(8):e71439 doi:10.1371/journal.pone.0071439, 2013
    PubMed
    Computational approaches to identify functional genetic variants in cancer genomes.
    International Cancer Genome Consortium Mutation Pathways, Consequences Subgroup of the Bioinformatics Analyses Working Group, Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N
    Nature Methods 10(8):723-9 doi:10.1038/nmeth.2562, 2013
    PubMed
    Global characterization of signalling networks associated with tamoxifen resistance in breast cancer.
    Browne BC, Hochgräfe F, Wu J, Millar EK, Barraclough J, Stone A, McCloy RA, Lee CS, Roberts C, Ali NA, Boulghourjian A, Schmich F, Linding R, Farrow L, Gee JM, Nicholson RI, O\\\'Toole SA, Sutherland RL, Musgrove EA, Butt AJ, Daly RJ
    FEBS Journal . 280(21):5237-57 doi:10.1111/febs.12441, 2013
    PubMed
    TIMP1 overexpression mediates resistance of MCF-7 human breast cancer cells to fulvestrant and down-regulates progesterone receptor expression.
    Bjerre C, Vinther L, Belling KC, Würtz SO, Yadav R, Lademann U, Rigina O, Do KN, Ditzel HJ, Lykkesfeldt AE, Wang J, Nielsen HB, Brünner N, Gupta R, Schrohl AS, Stenvang J
    Tumour Biology. 34(6):3839-51 doi:10.1007/s13277-013-0969-7, 2013
    PubMed
    TIMP-1 increases expression and phosphorylation of proteins associated with drug resistance in breast cancer cells.
    Hekmat O, Munk S, Fogh L, Yadav R, Francavilla C, Horn H, Wurtz SO, Schrohl AS, Damsgaard B, Romer MU, Belling K, Jensen NF, Gromova I, Bekker-Jensen DB, Moreira JM, Jensen LJ, Gupta R, Lademann U, Brunner N, Olsen JV, Stenvang J
    Journal of Proteome Research. 12(9):4136-51 doi:10.1021/pr400457u, 2013
    PubMed
    Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics.
    Kouskoumvekaki I, Shublaq N, Brunak S
    Briefings in Bioinformatics, 2013
    PubMed
    Concordance of gene expression in human protein complexes reveals tissue specificity and pathology
    Börnigen D, Pers TH, Thorrez L, Huttenhower C, Moreau Y, Brunak S
    Nucleic Acids Research. 41(18):e171 doi:10.1093/nar/gkt661, 2013
    PubMed
    Relevant URL
    NetMHCIIpan-3.0, a common pan-specific MHC class II prediction method including all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ
    Karosiene E, Rasmussen M, Blicher T, Lund O, Buus S, Nielsen M
    Immunogenetics 65(10):711-24 doi:10.1007/s00251-013-0720-y, 2013
    PubMed
    MicroRNA profiling in ocular adnexal lymphoma: A role for MYC and NFKB1 mediated dysregulation of microRNA expression in aggressive disease.
    Hother C, Rasmussen P, Joshi T, Reker D, Ralfkiaer U, Workman C, Heegaard S, Ralfkiaer E, Grønbæk K
    Investigative Ophthalmology & Visual Science. 54(8):5169-75 doi:10.1167/iovs.13-12272, 2013
    PubMed
    Meta-analysis of genome-wide association studies identifies ten loci influencing allergic sensitization
    Bønnelykke K, Matheson MC, Pers TH, Granell R, Strachan DP, Alves AC, Linneberg A, Curtin JA, Warrington NM, Standl M, Kerkhof M, Jonsdottir I, Bukvic BK, Kaakinen M, Sleimann P, Thorleifsson G, Thorsteinsdottir U, Schramm K, Baltic S, Kreiner-Møller E, Simpson A, St Pourcain B, Coin L, Hui J, Walters EH, Gupta R, et al
    Nature Genetics (2013), 2013
    Relevant URL
    The piRNAs forge an immune system for the genome.
    Muller S, Raman Pandey R, Pillai RS
    International Journal of Medical Sciences (Paris) 29(5):487-94 doi:10.1051/medsci/2013295011, 2013
    PubMed
    Relevant URL
    Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.
    Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert M, Cappellini E, Petersen B, Moltke I, Johnson PL, Fumagalli M, Vilstrup JT, Raghavan M, Korneliussen T, Malaspinas AS, Vogt J, Szklarczyk D, Kelstrup CD, Vinther J, Dolocan A, Stenderup J, Velazquez AM, Cahill J, Rasmussen M, Wang X, Min J, Zazula GD, Seguin-Orlando A, Mortensen C, Magnussen K, Thompson JF, Weinstock J, Gregersen K, Røed KH, Eisenmann V, Rubin CJ, Miller DC, Antczak DF, Bertelsen MF, Brunak S, Al-Rasheid KA, Ryder O, Andersson L, Mundy J, Krogh A, Gilbert MT, Kjær K, Sicheritz-Ponten T, Jensen LJ, Olsen JV, Hofreiter M, Nielsen R, Shapiro B, Wang J, Willerslev E
    Nature 499(7456):74-8 doi:10.1038/nature12323, 2013
    PubMed
    Relevant URL
    MHCcluster, a method for functional clustering of MHC molecules
    Thomsen MCF, Lundegaard C, Buus S, Lund O, Nielsen M
    Immunogenetics 65(9):655-65 doi:10.1007/s00251-013-0714-9, 2013
    PubMed
    Relevant URL
    SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments
    Jessen L, Hoof I, Lund O, Nielsen M
    Nucleic Acids Research 2013; doi: 10.1093/nar/gkt497, 2013
    Relevant URL
    Pre- and early-postnatal nutrition modify gene and protein expressions of muscle energy metabolism markers and phospholipid Fatty Acid composition in a muscle type specific manner in sheep.
    Hou L, Kongsted AH, Ghoreishi SM, Takhtsabzy TK, Friedrichsen M, Hellgren LI, Kadarmideen HN, Vaag A, Nielsen MO
    PLoS ONE 8(6):e65452 doi:10.1371/journal.pone.0065452, 2013
    PubMed
    Relevant URL
    Parallel evolution of tumor subclones mimics diversity between tumors.
    Martinez P, Birkbak NJ, Gerlinger M, McGranahan N, Burrell R, Rowan A, Joshi T, Fisher R, Larkin J, Szallasi Z, Swanton C
    The Journal of Pathology. 230(4):356-64 doi:10.1002/path.4214, 2013
    PubMed
    Relevant URL
    Transcriptome profiling of mice testes following low dose irradiation
    Belling KC, Tanaka M, Dalgaard MD, Nielsen JE, Nielsen HB, Brunak S, Almstrup K, Leffers H
    Reproductive Biology and Endocrinology 2013, 2013
    Relevant URL
    MISTIC: mutual information server to infer coevolution
    Simonetti FL, Teppa E, Chernomoretz A, Nielsen M, Buslje CM
    Nucleic Acids Research. (2013), 2013
    Relevant URL
    MetaRanker 2.0: a web server for prioritization of genetic variation data
    Pers TH, Dworzynski P, Thomas C, Lage K, Brunak S
    Nucleic Acids Research, 2013
    Relevant URL
    Mutations in FGF17, IL17RD, DUSP6, SPRY4, and FLRT3 Are Identified in Individuals with Congenital Hypogonadotropic Hypogonadism.
    Miraoui H, Dwyer A, Sykiotis GP, Plummer L, Chung W, Feng B, Beenken A, Clarke J, Pers TH, Dworzynski P, Keefe K, Niedziela M, Raivio T, Crowley Jr WF, Seminara SB, Quinton R, Hughes VA, Kumanov P, Young J, Yialamas MA, Hall JE, Van Vliet G, Chanoine JP, Rubenstein J, Mohammadi M, Tsai PS, Sidis Y, Lage K, Pitteloud N
    AJHG, The American Journal of Human Genetics - Cell. 92(5):725-43 doi:10.1016/j.ajhg.2013.04.008, 2013
    PubMed
    Relevant URL
    The CIN4 chromosomal instability qPCR classifier defines tumor aneuploidy and stratifies outcome in grade 2 breast cancer.
    Szász AM, Li Q, Eklund AC, Sztupinszki Z, Rowan A, Tõkés AM, Székely B, Kiss A, Szendrõi M, Gyõrffy B, Szállási Z, Swanton C, Kulka J
    PLoS ONE 8(2):e56707 doi:10.1371/journal.pone.0056707, 2013
    PubMed
    Relevant URL
    Deconvoluting complex tissues for expression quantitative trait locus-based analyses.
    Seo JH, Li Q, Fatima A, Eklund A, Szallasi Z, Polyak K, Richardson AL, Freedman ML
    Philosophical Transactions of the Royal Society B: Biological Sciences. 368(1620):20120363 doi:10.1098/rstb.2012.0363, 2013
    PubMed
    Relevant URL
    Regulatory coordination between two major intracellular homeostatic systems: heat shock response and autophagy
    Dokladny K, Zuhl MN, Mandell M, Bhattacharya D, Schneider S, Deretic V, Moseley PL
    The Journal of Biological Chemistry. 288(21):14959-72 doi:10.1074/jbc.M113.462408, 2013
    PubMed
    Relevant URL
    FADS genotype and diet are important determinants of DHA status: a cross-sectional study in Danish infants.
    Harsløf LB, Larsen LH, Ritz C, Hellgren LI, Michaelsen KF, Vogel U, Lauritzen L
    The American Journal of Clinical Nutrition. 97(6):1403-10 doi:10.3945/ajcn.113.058685, 2013
    PubMed
    Transcriptome responses to combinations of stresses in Arabidopsis.
    Rasmussen S, Barah P, Suarez-Rodriguez MC, Bressendorff S, Friis P, Costantino P, Bones AM, Nielsen HB, Mundy J
    Plant Physiology 161(4):1783-94 doi:10.1104/pp.112.210773, 2013
    PubMed
    Targeted metabolic engineering guided by computational analysis of single-nucleotide polymorphisms (SNPs).
    Udatha DB, Rasmussen S, Sicheritz-Pontén T, Panagiotou G
    Methods in Molecular Biology . 985:409-28 doi:10.1007/978-1-62703-299-5_20, 2013
    PubMed
    Prognostic and Predictive Markers in Metastatic Renal Cell Carcinoma
    Khattak MA, Bakr F, Krzystanek M, Szallasi Z, Gerlinger M, Santos C, Swanton C, Pickering LM, Gore ME, Larkin JM
    Journal of Clinical Oncology. 31(7):971-2 doi:10.1200/JCO.2012.46.9353, 2013
    PubMed
    Biasogram: Visualization of Confounding Technical Bias in Gene Expression Data
    Krzystanek M, Szallasi Z, Eklund AC
    PLOS ONE, April 16 2013, 2013
    Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology
    Steentoft C, Vakhrushev SY, Joshi HJ, Kong Y, Vester-Christensen MB, Schjoldager KT, Lavrsen K, Dabelsteen S, Pedersen NB, Marcos-Silva L, Gupta R, Paul Bennett E, Mandel U, Brunak S, Wandall HH, Levery SB, Clausen H
    The EMBO Journal . 32(10):1478-88 doi:10.1038/emboj.2013.79, 2013
    PubMed
    Predictions of Phase Separation in Three-Component Lipid Membranes by the MARTINI Force Field.
    Davis RS, Kumar PBS, Sperotto MM, Laradji M
    The Journal of Physical Chemistry B, 117, 4072.4080 (2013), 2013
    Relevant URL
    HExpoChem: a systems biology resource to explore human exposure to chemicals.
    Taboureau O, Jacobsen UP, Kalhauge C, Edsgärd D, Rigina O, Gupta R, Audouze K
    Bioinformatics 29(9):1231-2 doi:10.1093/bioinformatics/btt112, 2013
    PubMed
    Pathogenic bacteria colonizing the airways in asymptomatic neonates stimulates topical inflammatory mediator release.
    Følsgaard NV, Schjørring S, Chawes BL, Rasmussen MA, Krogfelt KA, Brix S, Bisgaard H
    American Journal of Respiratory and Critical Care Medicine . 187(6):589-95 doi:10.1164/rccm.201207-1297OC, 2013
    PubMed
    Relevant URL
    Phytanic acid stimulates glucose uptake in a model of skeletal muscles, the primary porcine myotubes.
    Che BN, Oksbjerg N, Hellgren LI, Nielsen JH, Young JF
    Lipids in Health and Disease 12:14 doi:10.1186/1476-511X-12-14, 2013
    PubMed
    Content and distribution of phytanic acid diastereomers in organic milk as affected by feed composition
    Che BN, Kristensen T, Nebel C, Dalsgaard TK, Hellgren LI, Young JF, Larsen MK
    Journal of Agricultural and Food Chemistry . 61(1):225-30 doi:10.1021/jf304079r, 2013
    PubMed
    CMG-biotools, a free workbench for basic Comparative Microbial Genomics
    Vesth T, Lagesen K, Acar O, Ussery D
    PLoS ONE, in the press, 2013
    Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes
    Alsmark C, Foster PG, Sicheritz-Ponten T, Nakjang S, Embley TM, Hirt RP
    Genome Biology. 14(2):R19, 2013
    PubMed
    Discovery of a Novel Selective PPAR Ligand with Partial Agonist Binding Properties by Integrated in Silico in Vitro Work Flow
    Kouskoumvekaki I, Petersen RK, Fratev F, Taboureau O, Nielsen TE, Oprea TI, Sonne S, Flindt E, Jónsdóttir SO, Kristiansen K
    Journal of Chemical Information and Modeling 53(4):923-37 doi:10.1021/ci3006148, 2013
    PubMed
    In Vivo SILAC-Based Proteomics Reveals Phosphoproteome Changes during Mouse Skin Carcinogenesis
    Zanivan S, Meves A, Behrendt K, Schoof EM, Neilson LJ, Cox J, Tang HR, Kalna G, van Ree JH, van Deursen JM, Trempus CS, Machesky LM, Linding R, Wickström SA, Fässler R, Mann M
    Cell Reports 3(2):552-66 doi:10.1016/j.celrep.2013.01.003, 2013
    PubMed
    In silico peptide-binding predictions of passerine MHC class I reveal similarities across distantly related species, suggesting convergence on the level of protein function
    Follin E, Karlsson M, Lundegaard C, Nielsen M, Wallin S, Paulsson K, Westerdahl H
    Immunogenetics 65(4):299-311 doi:10.1007/s00251-012-0676-3, 2013
    PubMed
    Bioinformatics Identification of Antigenic Peptide: Predicting the Specificity of Major MHC Class I and II Pathway Players
    Lund O, Karosiene E, Lundegaard C, Larsen MV, Nielsen M
    Methods in Molecular Biology . 960:247-60 doi:10.1007/978-1-62703-218-6_19, 2013
    PubMed
    Accurate prediction of secondary metabolite gene clusters in filamentous fungi
    Andersen MR, Nielsen JB, Klitgaard A, Petersen LM, Zachariasen M, Hansen TJ, Blicher LH, Gotfredsen CH, Larsen TO, Nielsen KF, Mortensen UH
    PNAS, Proceedings of the National Academy of Sciences U.S.A. 110(1):E99-107 doi:10.1073/pnas.1205532110, 2013
    PubMed

2012

    Differential protein pathways in 1,25-dihydroxyvitamin d(3) and dexamethasone modulated tolerogenic human dendritic cells.
    Ferreira GB, Kleijwegt FS, Waelkens E, Lage K, Nikolic T, Hansen DA, Workman CT, Roep BO, Overbergh L, Mathieu C
    Journal of Proteome Research. 2012 Feb 3;11(2):941-71, 2012
    PubMed
    Transcriptome dynamics of Pseudomonas putida KT2440 under water stress.
    Gülez G, Dechesne A, Workman CT, Smets BF
    Applied and Environmental Microbiology. 2012 Feb;78(3):676-83, 2012
    PubMed
    Gene prioritization for livestock diseases by data integration.
    Jiang L, Sørensen P, Thomsen B, Edwards SM, Skarman A, Røntved CM, Lund MS, Workman CT
    Physiological Genomics. 2012 Mar 1;44(5):305-17, 2012
    PubMed
    Multilocus sequence typing of total-genome-sequenced bacteria.
    Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Sicheritz-Pontén T, Ussery DW, Aarestrup FM, Lund O
    Journal of Clinical Microbiology 2012 Apr;50(4):1355-61., 2012
    PubMed
    Identification of a novel UTY-encoded minor histocompatibility antigen.
    Mortensen BK, Rasmussen AH, Larsen ME, Larsen MV, Lund O, Braendstrup P, Harndahl M, Rasmussen M, Buus S, Stryhn A, Vindeløv L
    Scandinavian Journal of Immunology . 2012 Aug;76(2):141-50., 2012
    PubMed
    Structural analysis of B-cell epitopes in antibody:protein complexes.
    Kringelum JV, Nielsen M, Padkjær SB, Lund O
    Molecular Immunology 2013 Jan;53(1-2):24-34, 2012
    PubMed
    Characterization of HIV-specific CD4+ T cell responses against peptides selected with broad population and pathogen coverage.
    Buggert M, Norström MM, Czarnecki C, Tupin E, Luo M, Gyllensten K, Sönnerborg A, Lundegaard C, Lund O, Nielsen M, Karlsson AC
    PLoS One. 2012;7(7):e39874, 2012
    PubMed
    The cancer exome generated by alternative mRNA splicing dilutes predicted HLA class I epitope density.
    Stranzl T, Larsen MV, Lund O, Nielsen M, Brunak S
    PLoS One. 2012;7(9):e38670, 2012
    PubMed
    Integrating genome-based informatics to modernize global disease monitoring, information sharing, and response.
    Aarestrup FM, Brown EW, Detter C, Gerner-Smidt P, Gilmour MW, Harmsen D, Hendriksen RS, Hewson R, Heymann DL, Johansson K, Ijaz K, Keim PS, Koopmans M, Kroneman A, Lo Fo Wong D, Lund O, Palm D, Sawanpanyalert P, Sobel J, Schlundt J
    Emerging Infectious Diseases. 2012 Nov;18(11):e1., 2012
    PubMed
    Reliable B cell epitope predictions: impacts of method development and improved benchmarking.
    Kringelum JV, Lundegaard C, Lund O, Nielsen M
    PLoS Comput Biol. 2012 Dec;8(12):e1002829., 2012
    PubMed
    Mycobacterium leprae virulence-associated peptides are indicators of exposure to M. leprae in Brazil, Ethiopia and Nepal.
    Bobosha K, Tang ST, van der Ploeg-van Schip JJ, Bekele Y, Martins MV, Lund O, Franken KL, Khadge S, Pontes MA, Gonçalves Hde S, Hussien J, Thapa P, Kunwar CB, Hagge DA, Aseffa A, Pessolani MC, Pereira GM, Ottenhoff TH, Geluk A
    Mem. Inst. Oswaldo Cruz:112-23 pii:S0074-02762012000900018, 2012
    PubMed
    Identification of acquired antimicrobial resistance genes
    Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, Aarestrup FM, Larsen MV
    Journal of Antimicrobial Chemotherapy. 67(11):2640-4 doi:10.1093/jac/dks261, 2012
    PubMed
    snpTree-a web-server to identify and construct SNP trees from whole genome sequence data
    Leekitcharoenphon P, Kaas RS, Thomsen MCF, Friis C, Rasmussen S, Aarestrup FM
    BMC Genomics:S6 doi:10.1186/1471-2164-13-S7-S6, 2012
    PubMed
    Polyclonality of concurrent natural populations of Alteromonas macleodii.
    Gonzaga A, Martin-Cuadrado AB, López-Pérez M, Megumi Mizuno C, García-Heredia I, Kimes NE, Lopez-García P, Moreira D, Ussery D, Zaballos M, Ghai R, Rodriguez-Valera F
    Genome Biology and Evolution 4(12):1360-74 doi:10.1093/gbe/evs112, 2012
    PubMed
    Polyclonality of concurrent natural populations of Alteromonas macleodii.
    Gonzaga A, Martin-Cuadrado AB, López-Pérez M, Megumi Mizuno C, García-Heredia I, Kimes NE, Lopez-García P, Moreira D, Ussery D, Zaballos M, Ghai R, Rodriguez-Valera F
    Genome Biology and Evolution 4(12):1360-74 doi:10.1093/gbe/evs112, 2012
    PubMed
    PROTEINCHALLENGE: Crowd sourcing in proteomics analysis and software development
    Martin SF, Falkenberg H, Dyrlund TF, Khoudoli GA, Mageean CJ, Linding R
    Journal of Proteomics 88:41-6 doi:10.1016/j.jprot.2012.11.014, 2012
    PubMed
    A comparative analysis of the intestinal metagenomes present in guinea pigs
    Hildebrand F, Ebersbach T, Nielsen HB, Li X, Sonne SB, Bertalan M, Dimitrov P, Madsen L, Qin J, Wang J, Raes J, Kristiansen K, Licht TR
    BMC Genomics 13:514 doi:10.1186/1471-2164-13-514, 2012
    PubMed
    Association between chemical pattern in breast milk and congenital cryptorchidism: modelling of complex human exposures
    Krysiak-Baltyn K, Toppari J, Skakkebaek NE, Jensen TS, Virtanen HE, Schramm KW, Shen H, Vartiainen T, Kiviranta H, Taboureau O, Audouze K, Brunak S, Main KM
    International Journal of Andrology . 35(3):294-302 doi:10.1111/j.1365-2605.2012.01268.x, 2012
    PubMed
    ChemProt-2.0: visual navigation in a disease chemical biology database
    Kim Kjærulff S, Wich L, Kringelum J, Jacobsen UP, Kouskoumvekaki I, Audouze K, Lund O, Brunak S, Oprea TI, Taboureau O
    Nucleic Acids Research. 41:D464-9 doi:10.1093/nar/gks1166, 2012
    PubMed
    Polyclonality of concurrent natural populations of Alteromonas macleodii
    Gonzaga A, Martin-Cuadrado AB, López-Pérez M, Mizuno CM, García-Heredia I, Kimes NE, Lopez-García P, Moreira D, Ussery D, Zaballos M, Ghai R, Rodriguez-Valera F
    Genome Biology and Evolution 4(12):1360-74 doi:10.1093/gbe/evs112, 2012
    PubMed
    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
    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
    Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach
    Andreatta M, Lund O, Nielsen M
    Bioinformatics 29(1):8-14 doi:10.1093/bioinformatics/bts621, 2012
    PubMed
    Relevant URL
    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
    Isolation of IL-12p70-competent human monocyte-derived dendritic cells
    Søndergaard JN, Brix S
    Journal of Immunological Methods 386:112-6 doi:10.1016/j.jim.2012.09.005, 2012
    PubMed
    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
    Hyperactivity of the Ero1á oxidase elicits endoplasmic reticulum stress but no broad antioxidant response
    Hansen HG, Schmidt JD, Soeltoft CL, Ramming T, Geertz-Hansen HM, Christensen B, Sorensen ES, Juncker AS, Appenzeller-Herzog C, Ellgaard L
    The Journal of Biological Chemistry. 287(47):39513-23 doi:10.1074/jbc.M112.405050, 2012
    PubMed
    Telomeric allelic imbalance indicates defective DNA repair and sensitivity to DNA-damaging agents
    Birkbak NJ, Wang ZC, Kim JY, Eklund AC, Li Q, Tian R, Bowman-Colin C, Li Y, Greene-Colozzi A, Iglehart JD, Tung N, Ryan PD, Garber JE, Silver DP, Szallasi Z, Richardson AL
    Cancer Discovery 2(4):366-75 doi:10.1158/2159-8290.CD-11-0206, 2012
    PubMed
    Profiles of genomic instability in high-grade serous ovarian cancer predict treatment outcome
    Wang ZC, Birkbak NJ, Culhane AC, Drapkin R, Fatima A, Tian R, Schwede M, Alsop K, Daniels KE, Piao H, Liu J, Etemadmoghadam D, Miron A, Salvesen HB, Mitchell G, Defazio A, Quackenbush J, Berkowitz RS, Iglehart JD, Bowtell DD; for the Australian Ovarian Cancer Study Group, Matulonis UA
    Clin. Cancer Res. 18(20):5806-15 doi:10.1158/1078-0432.CCR-12-0857, 2012
    PubMed
    Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction
    Teppa E, Wilkins AD, Nielsen M, Marino Buslje C
    BMC Bioinformatics 13:235 doi:10.1186/1471-2105-13-235, 2012
    PubMed
    Identification of peptides from foot-and-mouth disease virus structural proteins bound by class I swine leukocyte antigen (SLA) alleles, SLA-1*0401 and SLA-2*0401
    Pedersen LE, Harndahl M, Nielsen M, Patch JR, Jungersen G, Buus S, Golde WT
    Anim. Genet. 44(3):251-8 doi:10.1111/j.1365-2052.2012.02400.x, 2012
    PubMed
    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
    Navigating cancer network attractors for tumor-specific therapy
    Creixell P, Schoof EM, Erler JT, Linding R
    Nature Biotechnology 30(9):842-8 doi:10.1038/nbt.2345, 2012
    PubMed
    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
    Interpretation of the consequences of mutations in protein kinases: combined use of bioinformatics and text mining
    Izarzugaza JM, Krallinger M, Valencia A
    Front. Physio. 3:323. doi: 10.3389/fphys.2012.00323, 2012
    Relevant URL
    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
    Campylobacter fetus subspecies: Comparative genomics and prediction of potential virulence targets
    Ali A, Soares SC, Santos AR, Guimarães LC, Barbosa E, Almeida SS, Abreu VA, Carneiro AR, Ramos RT, Bakhtiar SM, Hassan SS, Ussery DW, On S, Silva A, Schneider MP, Lage AP, Miyoshi A, Azevedo V
    Gene 508(2):145-56 doi:10.1016/j.gene.2012.07.070, 2012
    PubMed
    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
    Bayesian prediction of bacterial growth temperature range based on genome sequences
    Jensen DB, Vest TC, Hallin PF, Pedersen AG, Ussery D
    BMC Genomics, 2012
    PubMed
    Relevant URL
    Mutational properties of amino acid residues: implications for evolvability of phosphorylatable residues
    Creixell P, Schoof EM, Tan CS, Linding R
    Philosophical Transactions of the Royal Society B: Biological Sciences. 367(1602):2584-93 doi:10.1098/rstb.2012.0076, 2012
    PubMed
    Two novel methods for using genome sequences to infer taxonomy
    Ussery DW, Gordon SV
    Microbiology (Reading, Engl.) 158:1414 doi:10.1099/mic.0.059816-0, 2012
    PubMed
    LeuO is a global regulator of gene expression in Salmonella enterica serovar Typhimurium
    Dillon SC, Espinosa E, Hokamp K, Ussery DW, Casadesús J, Dorman CJ
    Mol. Microbiol. 85(6):1072-89 doi:10.1111/j.1365-2958.2012.08162.x, 2012
    PubMed
    Cells, shared memory and breaking the PTM code
    Creixell P, Linding R
    Mol. Syst. Biol. 8:598 doi:10.1038/msb.2012.33, 2012
    PubMed
    Flip-Flop of Steroids in Phospholipid Bilayers: Effects of the Chemical Structure on Transbilayer Diffusion
    Parisio G, Sperotto MM, Ferrarini A
    J. Am. Chem. Soc. 134(29):12198-208 doi:10.1021/ja304007t, 2012
    PubMed
    A Steered Molecular Dynamics Study of Binding and Translocation Processes in the GABA Transporter.
    Skovstrup S, David L, Taboureau O, Jørgensen FS
    PLoS ONE 7(6):e39360 doi:10.1371/journal.pone.0039360, 2012
    PubMed
    Relevant URL
    MicroRNA expression profiling of carcinoma in situ cells of the testis
    Novotny GW, Belling KC, Bramsen JB, Nielsen JE, Bork-Jensen J, Almstrup K, Sonne SB, Kjems J, Rajpert-De Meyts E, Leffers H
    Endocr. Relat. Cancer 19(3):365-79 doi:10.1530/ERC-11-0271, 2012
    PubMed
    Relevant URL
    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
    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
    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
    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
    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
    Network Medicine Strikes a Blow against Breast Cancer
    Erler JT, Linding R
    Cell, volume 149, issue 4, 2012
    Relevant URL
    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
    Ceramide profile in hypohidrotic ectodermal dysplasia.
    Jungersted JM, Høgh JK, Hellgren LI, Agner T, Jemec GB
    Clin Exp Dermatol, 2012
    Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.
    Nicolas P, Mäder U, Dervyn E, Rochat T, Leduc A, Pigeonneau N, Bidnenko E, Marchadier E, Hoebeke M, Aymerich S, Becher D, Bisicchia P, Botella E, Delumeau O, Doherty G, Denham EL, Fogg MJ, Fromion V, Goelzer A, Hansen A, Härtig E, Harwood CR, Homuth G, Jarmer H, Jules M, Klipp E, Le Chat L, Lecointe F, Lewis P, Liebermeister W, March A, Mars RA, Nannapaneni P, Noone D, Pohl S, Rinn B, Rügheimer F, Sappa PK, Samson F, Schaffer M, Schwikowski B, Steil L, Stülke J, Wiegert T, Devine KM, Wilkinson AJ, van Dijl JM, Hecker M, Völker U, Bessières P, Noirot P
    Science 335(6072):1103-6 doi:10.1126/science.1206848, 2012
    PubMed
    Relevant URL
    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
    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
    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
    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
    Multilocus Sequence Typing of Total Genome Sequenced Bacteria
    Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H et al
    Journal of Clinical Microbiology. 2012. 50(4): 1355-1361., 2012
    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
    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
    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
    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
    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
    The impact of network biology in pharmacology and toxicology
    Panagiotou G, Taboureau O
    SAR QSAR Environ Res., 2012
    Relevant URL
    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
    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
    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
    Prediction of drug efficacy for cancer treatment based on comparative analysis of chemosensitivity and gene expression data
    Wan P, Li Q, Larsen JE, Eklund AC, Parlesak A, Rigina O, Nielsen SJ, Björkling F, Jónsdóttir SÓ
    Bioorg. Med. Chem. 20(1):167-76 doi:10.1016/j.bmc.2011.11.019, 2012
    PubMed
    Relevant URL
    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

2011

    Immune system simulation online.
    Rapin N, Lund O, Castiglione F
    Bioinformatics. 2011 Jul 15;27(14):2013-4., 2011
    PubMed
    Human leukocyte antigen (HLA) class I restricted epitope discovery in yellow fever and dengue viruses: importance of HLA binding strength
    Lund O, Nascimento EJ, Maciel M Jr, Nielsen M, Larsen MV, Lundegaard C, Harndahl M, Lamberth K, Buus S, Salmon J, August TJ, Marques ET Jr
    PLoS One. 2011;6(10):e26494, 2011
    PubMed
    Chromosomal instability confers intrinsic multidrug resistance
    Lee AJ, Endesfelder D, Rowan AJ, Walther A, Birkbak NJ, Futreal PA, Downward J, Szallasi Z, Tomlinson IP, Howell M, Kschischo M, Swanton C
    Cancer Res. 71(5):1858-70 doi:10.1158/0008-5472.CAN-10-3604, 2011
    PubMed
    A breast cancer meta-analysis of two expression measures of chromosomal instability reveals a relationship with younger age at diagnosis and high risk histopathological variables
    Endesfelder D, McGranahan N, Birkbak NJ, Szallasi Z, Kschischo M, Graham TA, Swanton C
    Oncotarget 2(7):529-37, 2011
    PubMed
    CERT depletion predicts chemotherapy benefit and mediates cytotoxic and polyploid-specific cancer cell death through autophagy induction
    Lee AJ, Roylance R, Sander J, Gorman P, Endesfelder D, Kschischo M, Jones NP, East P, Nicke B, Spassieva S, Obeid LM, Birkbak NJ, Szallasi Z, McKnight NC, Rowan AJ, Speirs V, Hanby AM, Downward J, Tooze SA, Swanton C
    The Journal of Pathology. 226(3):482-94 doi:10.1002/path.2998, 2011
    PubMed
    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
    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
    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
    PSICQUIC and PSISCORE - Accessing and Scoring Molecular Interactions
    Aranda B, Rigina O, et al
    Nature Methods, 2011
    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
    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
    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
    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
    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
    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
    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
    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
    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
    Jetset: selecting the optimal microarray probe set to represent a gene
    Li Q, Birkbak NJ, Gyorffy B, Szallasi Z, Eklund AC
    BMC Bioinformatics 12:474 doi:10.1186/1471-2105-12-474, 2011
    PubMed
    SignalP 4.0: discriminating signal peptides from transmembrane regions
    Petersen TN, Brunak S, von Heijne G, Nielsen H
    Nature Methods 8(10):785-6 doi:10.1038/nmeth.1701, 2011
    PubMed
    Relevant URL
    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
    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
    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
    An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia
    Rasmussen M, Guo X, Wang Y, Lohmueller KE, Rasmussen S, Albrechtsen A, Skotte L, Lindgren S, Metspalu M, Jombart T, Kivisild T, Zhai W, Eriksson A, Manica A, Orlando L, De La Vega F, Tridico S, Metspalu E, Nielsen K, Ávila-Arcos MA, Moreno-Mayar JV, Muller C, Dortch J, Gilbert MTP, Lund O, Wesolowska A, Karmin M, Weinert LA, Wang B, Li J, Tai S, Xiao F, Hanihara T, van Driem G, Jha AR, Ricaut FX, de Knijf P, Migliano AB, Gallego-Romero I, Kristiansen K, Lambert DM, Brunak S, Forster P, Brinkmann B, Nehlich O, Bunce M, Richards M, Gupta R, Bustamante CD, Krogh A, Foley RA, Lahr MM, Balloux F, Sichertitz-Pontén T, Villems R, Nielsen R, Jun W, Willerslev E
    Science 334(6052):94-8 doi:10.1126/science.1211177, 2011
    PubMed
    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
    NetMHCcons: a consensus method for the major histocompatibility complex class I predictions
    Karosiene E, Lundegaard C, Lund O, Nielsen M
    Immunogenetics, 2011
    Relevant URL
    Protein Interaction-Based Genome-Wide Analysis of Incident Coronary Heart Disease
    Jensen MK, Pers TH, Dworzynski P, Girman CJ, Brunak S, Rimm EB
    Circ Cardiovasc Genet 4(5):549-56 doi:10.1161/CIRCGENETICS.111.960393, 2011
    PubMed
    Relevant URL
    Application of Computational Systems Biology to Explore Environmental Toxicity Hazards
    Audouze K, Grandjean P
    Environ. Health Perspect. 119(12):1754-9 doi:10.1289/ehp.1103533, 2011
    PubMed
    BDDCS Applied to Over 900 Drugs
    Benet LZ, Broccatelli F, Oprea TI
    AAPS J 13(4):519-47 doi:10.1208/s12248-011-9290-9, 2011
    PubMed
    International Dairy Journal
    Bonomi F, Sørensen RB, Favalli S, Ferranti P, Fierro O, Frøkier H, Ragg E, Lametti S
    Elsevier, April 26, 2011
    Defining the Pseudomonas Genus: Where Do We Draw the Line with Azotobacter?
    Özen AI, Ussery DW
    Springer, July 13, 2011
    Relevant URL
    Effect of industrially produced trans fat on markers of endothelial dysfunction and systemic inflammation: evidence from a randomized trial in overweight women
    Bendsen NT, Stender S, Szecsi PB, Pedersen SB, Basu S, Hellgren LI, Newman JW, Larsen TM, Haugaard SB, Astrup A
    J. Lipid Res. 52(10):1821-8 doi:10.1194/jlr.M014738, 2011
    PubMed
    The Effect of Dietary Fish Oil in addition to Lifestyle Counselling on Lipid Oxidation and Body Composition in Slightly Overweight Teenage Boys
    Pedersen MH, Mølgaard C, Hellgren LI, Matthiessen J, Holst JJ, Lauritzen L
    J Nutr Metab 2011:348368 doi:10.1155/2011/348368, 2011
    PubMed
    Relationship of Extreme Chromosomal Instability with Long-term Survival in a Retrospective Analysis of Primary Breast Cancer
    Roylance R, Endesfelder D, Gorman P, Burrell RA, Sander J, Tomlinson I, Hanby AM, Speirs V, Richardson AL, Birkbak NJ, Eklund AC, Downward J, Szallasi Z, Kschischo M, Swanton C
    Cancer Epidemiol. Biomarkers Prev. 20(10):2183-94 doi:10.1158/1055-9965.EPI-11-0343, 2011
    PubMed
    Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response
    Li Q, Eklund AC, Birkbak NJ, Desmedt C, Haibe-Kains B, Sotiriou C, Symmans WF, Pusztai L, Brunak S, Richardson AL, Szallasi Z
    BMC Bioinformatics 12:310 doi:10.1186/1471-2105-12-310, 2011
    PubMed
    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
    Cost-effective multiplexing before capture allows screening of 25 000 clinically relevant SNPs in childhood acute lymphoblastic leukemia
    Wesolowska A, Dalgaard MD, Borst L, Gautier L, Bak M, Weinhold N, Nielsen BF, Helt LR, Audouze K, Nersting J, Tommerup N, Brunak S, Sicheritz-Ponten T, Leffers H, Schmiegelow K, Gupta R
    Leukemia 25(6):1001-6 doi:10.1038/leu.2011.32, 2011
    PubMed
    Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene
    Bowman JS, Rasmussen S, Blom N, Deming JW, Rysgaard S, Sicheritz-Ponten T
    ISME J 6(1):11-20 doi:10.1038/ismej.2011.76, 2011
    PubMed
    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
    Muscle ceramide content is similar after 3 weeks\\\' consumption of fat or carbohydrate diet in a crossover design in patients with type 2 diabetes
    Helge JW, Tobin L, Drachmann T, Hellgren LI, Dela F, Galbo H
    Eur. J. Appl. Physiol. 112(3):911-8 doi:10.1007/s00421-011-2041-x, 2011
    PubMed
    A Randomized Controlled Intervention with Fish Oil versus Sunflower Oil from 9 to 18 Months of Age - Exploring Changes in Growth and Skinfold Thicknesses
    Andersen AD, Michaelsen KF, Hellgren LI, Trolle E, Lauritzen L
    Pediatr. Res. 70(4):368-74 doi:10.1038/pr.2011.593, 2011
    PubMed
    Using Tag-Neighbors for Query Expansion in Medical Information Retrieval
    Durao F, Bayyapu K, Guandong X, Dolog P, Lage R
    Am J Ment Defic 80(4):388-93, 2011
    PubMed
    http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?reload=true&arnumber=5772324
    FARO server: Meta-analysis of gene expression by matching gene expression signatures to a compendium of public gene expression data
    Manijak MP, Nielsen HB
    BMC Res Notes 4:181 doi:10.1186/1756-0500-4-181, 2011
    PubMed
    Effect of dairy fat on plasma phytanic acid in healthy volunteers - A randomized controlled study
    Werner LB, Hellgren LI, Raff M, Jensen SK, Petersen RA, Drachmann T, Tholstrup T
    Lipids in Health and Disease 10:95 doi:10.1186/1476-511X-10-95, 2011
    PubMed
    Probiotika
    Nielsen OH, Brix S, Kjeldsen HC, Johannessen T, Løge I
    Sundhed.dk, March, 2011
    Diversion of flux toward sesquiterpene production in Saccharomyces cerevisiae by fusion of host and heterologous enzymes
    Albertsen L, Chen Y, Bach LS, Rattleff S, Maury J, Brix S, Nielsen J, Mortensen UH
    Appl. Environ. Microbiol. 77(3):1033-40 doi:10.1128/AEM.01361-10, 2011
    PubMed
    Quantification of specific E. coli in gut mucosa from Crohn\'s disease patients
    Jensen SR, Fink LN, Struve C, Sternberg C, Andersen JB, Brynskov J, Nielsen OH, Brix S
    J. Microbiol. Methods 86(1):111-4 doi:10.1016/j.mimet.2011.04.002, 2011
    PubMed
    Are NOD2 polymorphisms linked to a specific disease endophenotype of Crohn’s Disease?
    Jensen SR, Nielsen OH, Brix S
    Inflamm. Bowel Dis. 17(11):2392-401 doi:10.1002/ibd.21656, 2011
    PubMed
    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
    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
    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
    Effects of topical corticosteroid and tacrolimus on ceramides and irritancy to sodium lauryl sulphate in healthy skin
    Jungersted JM, Høgh JK, Hellegren LI, Jemec GB, Agner T
    Acta Derm. Venereol. 91(3):290-4 doi:10.2340/00015555-1064, 2011
    PubMed
    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 . 35(1):25-40 doi:10.1111/j.1365-2605.2011.01150.x, 2011
    PubMed
    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
    The Salmonella enterica Pan-genome
    Jacobsen A, Hendriksen RS, Aaresturp FM, Ussery DW, Friis C
    Microb. Ecol. 62(3):487-504 doi:10.1007/s00248-011-9880-1, 2011
    PubMed
    PINTA: a web server for network-based gene prioritization from expression data
    Nitsch D, Tranchevent LC, Gonçalves JP, Vogt JK, Madeira SC, Moreau Y
    Nucleic Acids Research. 39:W334-8 doi:10.1093/nar/gkr289, 2011
    PubMed
    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
    Mycobacterial species as case-study of comparative genome analysis
    Zakham F, Belayachi L, Ussery D, Akrim M, Benjouad A, El Aouad R, Ennaji MM
    Cell. Mol. Biol. (Noisy-le-grand):OL1462-9, 2011
    PubMed
    Revealing the beneficial effect of protease supplementation to high gravity beer fermentations using \"-omics\" techniques
    Piddocke MP, Fazio A, Vongsangnak W, Wong ML, Heldt-Hansen HP, Workman C, Nielsen J, Olsson L
    Microb. Cell Fact. 10:27 doi:10.1186/1475-2859-10-27, 2011
    PubMed
    In silico Predictions of hERG Channel Blockers in Drug Discovery: From Ligand-Based and Target-Based Approaches to Systems Chemical Biology
    Taboureau O, Jørgensen FS
    Comb. Chem. High Throughput Screen. 14(5):375-87, 2011
    PubMed
    Evolutionary dynamics of bacteria in a human host environment
    Yang L, Jelsbak L, Marvig RL, Damkiær S, Workman CT, Rau MH, Hansen SK, Folkesson A, Johansen HK, Ciofu O, Høiby N, Sommer MO, Molin S
    Proceedings of the National Academy of Sciences U.S.A. 108(18):7481-6 doi:10.1073/pnas.1018249108, 2011
    PubMed
    Relevant URL
    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
    Enterotypes of the human gut microbiome
    Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J; MetaHIT Consortium, Antolín M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Mérieux A, Melo Minardi R, M\'rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, Bork P
    Nature 473(7346):174-80 doi:10.1038/nature09944, 2011
    PubMed
    Correlation of sCD23 release and immunoglobulin (E, A, G, M) synthesis by peripheral blood lymphocytes of atopic patients
    Bujanowski-Weber J, Knöller I, Pfeil T, Luther H, Altmeyer P, König W
    International Archives of Allergy and Immunology . 92(2):113-8, 2011
    PubMed
    Meta-analysis of heterogeneous data sources for genome-scale identification of risk genes in complex phenotypes
    Pers TH, Hansen NT, Lage K, Koefoed P, Dworzynski P, Miller ML, Flint TJ, Mellerup E, Dam H, Andreassen OA, Djurovic S, Melle I, Børglum AD, Werge T, Purcell S, Ferreira MA, Kouskoumvekaki I, Workman CT, Hansen T, Mors O, Brunak S
    Genet. Epidemiol. 35(5):318-32 doi:10.1002/gepi.20580, 2011
    PubMed
    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
    Paradoxical relationship between chromosomal instability and survival outcome in cancer
    Birkbak NJ, Eklund AC, Li Q, McClelland SE, Endesfelder D, Tan P, Tan IB, Richardson AL, Szallasi Z, Swanton C
    Cancer Res. 71(10):3447-52 doi:10.1158/0008-5472.CAN-10-3667, 2011
    PubMed
    Using a structural and logics systems approach to infer bHLH DNA binding specificity determinants
    De Masi F, Grove CA, Vedenko A, Alibés A, Gisselbrecht SS, Serrano L, Bulyk ML, Walhout AJ
    Nucleic Acids Research. 39(11):4553-63 doi:10.1093/nar/gkr070, 2011
    PubMed
    Functional analysis of frequently expressed Chinese rhesus macaque MHC class I molecules Mamu-A1*02601 and Mamu-B*08301 reveals HLA-A2 and HLA-A3 supertypic specificities
    Southwood S, Solomon C, Hoof I, Rudersdorf R, Sidney J, Peters B, Wahl A, Hawkins O, Hildebrand W, Mothé BR, Sette A
    Immunogenetics 63(5):275-90 doi:10.1007/s00251-010-0502-8, 2011
    PubMed
    Genome-Based In Silico Identification of New Mycobacterium tuberculosis Antigens Activating Polyfunctional CD8+ T Cells in Human Tuberculosis
    Tang ST, van Meijgaarden KE, Caccamo N, Guggino G, Klein MR, van Weeren P, Kazi F, Stryhn A, Zaigler A, Sahin U, Buus S, Dieli F, Lund O, Ottenhoff TH
    The Journal of Immunology. 186(2):1068-80 doi:10.4049/jimmunol.1002212, 2011
    PubMed
    Bistability in autoimmune diseases
    Rapin N, Mosekilde E, Lund O
    Autoimmunity 44(4):256-60 doi:10.3109/08916934.2010.523233, 2011
    PubMed
    A Closer Look at Bacteroides: Phylogenetic Relationship and Genomic Implications of a Life in the Human Gut
    Karlsson FH, Ussery DW, Nielsen J, Nookaew I
    Microb. Ecol. 61(3):473-85 doi:10.1007/s00248-010-9796-1, 2011
    PubMed

2010

    Early adaptive developments of Pseudomonas aeruginosa after the transition from life in the environment to persistent colonization in the airways of human cystic fibrosis hosts.
    Rau MH, Hansen SK, Johansen HK, Thomsen LE, Workman CT, Nielsen KF, Jelsbak L, Høiby N, Yang L, Molin S
    Environmental Microbiology . 2010 Jun;12(6):1643-58., 2010
    PubMed
    Lazarus1, a DUF300 protein, contributes to programmed cell death associated with Arabidopsis acd11 and the hypersensitive response
    Malinovsky FG, Brodersen P, Fiil BK, McKinney LV, Thorgrimsen S, Beck M, Nielsen HB, Pietra S, Zipfel C, Robatzek S, Petersen M, Hofius D, Mundy J
    PLoS ONE 5(9):e12586 doi:10.1371/journal.pone.0012586, 2010
    PubMed
    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
    ImmunoGrid: towards agent-based simulations of the human immune system at a natural scale
    Halling-Brown M, Pappalardo F, Rapin N, Zhang P, Alemani D, Emerson A, Castiglione F, Duroux P, Pennisi M, Miotto O, Churchill D, Rossi E, Moss DS, Sansom CE, Bernaschi M, Lefranc MP, Brunak S, Lund O, Motta S, Lollini PL, Murgo A, Palladini A, Basford KE, Brusic V, Shepherd AJ
    Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences 368(1920):2799-815 doi:10.1098/rsta.2010.0067, 2010
    PubMed
    HLA class I binding 9mer peptides from influenza A virus induce CD4 T cell responses
    Wang M, Larsen MV, Nielsen M, Harndahl M, Justesen S, Dziegiel MH, Buus S, Tang ST, Lund O, Claesson MH
    PLoS ONE 5(5):e10533 doi:10.1371/journal.pone.0010533, 2010
    PubMed
    Plasmodium falciparum population dynamics in a cohort of pregnant women in Senegal
    Guitard J, Andersen P, Ermont C, Gnidehou S, Fievet N, Lund O, Deloron P, Ndam NT
    Malar. J. 9:165 doi:10.1186/1475-2875-9-165, 2010
    PubMed
    Identification of CD8+ T cell epitopes in the West Nile virus polyprotein by reverse-immunology using NetCTL
    Larsen MV, Lelic A, Parsons R, Nielsen M, Hoof I, Lamberth K, Loeb MB, Buus S, Bramson J, Lund O
    PLoS ONE 5(9):e12697 doi:10.1371/journal.pone.0012697, 2010
    PubMed
    MULTIPRED2: a computational system for large-scale identification of peptides predicted to bind to HLA supertypes and alleles
    Zhang GL, Deluca DS, Keskin DB, Chitkushev L, Zlateva T, Lund O, Reinherz EL, Brusic V
    Journal of Immunological Methods 374:53-61 doi:10.1016/j.jim.2010.11.009, 2010
    PubMed
    Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains
    Canelas AB, Harrison N, Fazio A, Zhang J, Pitkänen JP, van den Brink J, Bakker BM, Bogner L, Bouwman J, Castrillo JI, Cankorur A, Chumnanpuen P, Daran-Lapujade P, Dikicioglu D, van Eunen K, Ewald JC, Heijnen JJ, Kirdar B, Mattila I, Mensonides FI, Niebel A, Penttilä M, Pronk JT, Reuss M, Salusjärvi L, Sauer U, Sherman D, Siemann-Herzberg M, Westerhoff H, de Winde J, Petranovic D, Oliver SG, Workman CT, Zamboni N, Nielsen J
    Nature Communication 1:145 doi:10.1038/ncomms1150, 2010
    PubMed
    An Inordinate Fondness of Bacteria - a review of Signature in the Cell by Stephen Meyer
    Ussery DW
    NCSE Reports, 2010
    One Small Step for Bacteria, or One Giant Leap for Mankind?
    Ussery DW
    Journal of Cosmology, 2010
    Read article
    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
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    Induction of foot-and-mouth disease virus (FMDV) specific cytotoxic T cell killing by vaccination
    Patch JR, Pedersen LE, Toka FN, Moreas M, Grubman MJ, Nielsen M, Jungersen G, Buus S, Golde WT
    Clin. Vaccine Immunol. 18(2):280-8 doi:10.1128/CVI.00417-10, 2010
    PubMed
    Proteome analysis of pod and seed development in the model legume Lotus japonicus
    Nautrup-Pedersen G, Dam S, Laursen BS, Siegumfeldt AL, Nielsen K, Goffard N, Stærfeldt HH, Friis C, Sato S, Tabata S, Lorentzen A, Roepstorff P, Stougaard J
    Rev Esp Enferm Dig 78(4):205-9, 2010
    PubMed
    An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators
    Gautier L
    BMC Bioinformatics, 2010
    Strain M4-5 Isolated From Human Colonic Flora Attenuates Intestinal Inflammation
    Avram-Hananel L, Stock J, Parlesak A, Bode C, Schwartz B, Durans E
    Dis. Colon Rectum 53(12):1676-86 doi:10.1007/DCR.0b013e3181f4b148, 2010
    PubMed
    Minimising Immunohistochemical False Negative ER Classification Using a Complementary 23 Gene Expression Signature of ER Status
    Li Q, Eklund AC, Juul N, Haibe-Kains B, Workman CT, Richardson AL, Szallasi Z, Swanton C
    PLoS ONE 5(12):e15031 doi:10.1371/journal.pone.0015031, 2010
    PubMed
    In Silico Prediction of Human Pathogenicity in the γ-Proteobacteria
    Andreatta M, Nielsen M, Møller Aarestrup F, Lund O
    PLoS ONE 5(10):e13680 doi:10.1371/journal.pone.0013680, 2010
    PubMed
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    Comparative analysis of a large panel of non-starch polysaccharides reveals structures with selective regulatory properties in dendritic cells
    Wismar R, Brix S, Lærke HN, Frøkiær H
    Mol Nutr Food Res 55(3):443-54 doi:10.1002/mnfr.201000230, 2010
    PubMed
    Pharmacophore-driven identification of PPARã agonists from natural sources
    Petersen RK, Christensen KB, Assimopoulou AN, Fretté X, Papageorgiou VP, Kristiansen K, Kouskoumvekaki I
    J. Comput. Aided Mol. Des. 25(2):107-16 doi:10.1007/s10822-010-9398-5, 2010
    PubMed
    Peptide binding predictions for HLA DR, DP and DQ molecules
    Wang P, Sidney J, Kim Y, Sette A, Lund O, Nielsen M, Peters B
    BMC Bioinformatics 11:568 doi:10.1186/1471-2105-11-568, 2010
    PubMed
    NetTurnP - Neural Network Prediction of Beta-turns by Use of Evolutionary Information and Predicted Protein Sequence Features
    Petersen B, Lundegaard C, Petersen TN
    PLoS ONE 5(11):e15079 doi:10.1371/journal.pone.0015079, 2010
    PubMed
    NetTurnP
    HLArestrictor-a tool for patient-specific predictions of HLA restriction elements and optimal epitopes within peptides
    Erup Larsen M, Kloverpris H, Stryhn A, Koofhethile CK, Sims S, Ndung\'u T, Goulder P, Buus S, Nielsen M
    Immunogenetics 63(1):43-55 doi:10.1007/s00251-010-0493-5, 2010
    PubMed
    Ethicity and Stratum Corneum Ceramides
    Jungersted JM, Høgh J, Hellgren LI, Jemec G & Agner T
    Br. J. Dermatol. 163(6):1169-73 doi:10.1111/j.1365-2133.2010.10080.x, 2010
    PubMed
    Transcriptome differentiation along the dorso-ventral axis in laser-captured microdissected rat hippocampal granular cell layer
    Christensen T, Bisgaard CF, Nielsen HB, Wiborg O
    Neuroscience 170(3):731-41 doi:10.1016/j.neuroscience.2010.07.016, 2010
    PubMed
    Many Putative Endocrine Disruptors Inhibit Prostaglandin Synthesis
    Kristensen DM, Skalkam ML, Audouze K, Lesné L, Desdoits-Lethimonier C, Frederiksen H, Brunak S, Skakkebaek NE, Jégou B, Hansen JB, Junker S, Leffers H
    Environ. Health Perspect. 119(4):534-41 doi:10.1289/ehp.1002635, 2010
    PubMed
    NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure
    Nielsen M, Justesen S, Lund O, Lundegaard C, Buus S
    Immunome Res 6:9 doi:10.1186/1745-7580-6-9, 2010
    PubMed
    Prediction of epitopes using neural network based methods
    Lundegaard C, Lund O, Nielsen M
    Journal of Immunological Methods 374:26-34 doi:10.1016/j.jim.2010.10.011, 2010
    PubMed
    State of the art and challenges in sequence based T-cell epitope prediction
    Lundegaard C, Hoof I, Lund O, Nielsen M
    Immunome Res:S3 doi:10.1186/1745-7580-6-S2-S3, 2010
    PubMed
    Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic Residue Identification
    Buslje CM, Teppa E, Doménico TD, Delfino JM, Nielsen M
    PLoS Comput. Biol. 6(11):e1000978 doi:10.1371/journal.pcbi.1000978, 2010
    PubMed
    Read article
    Novel insights into the global proteome responses of insulin-producing INS-1E cells to different degrees of endoplasmic reticulum stress
    D\\\'Hertog W, Maris M, Ferreira GB, Verdrengh E, Lage K, Hansen DA, Cardozo AK, Workman CT, Moreau Y, Eizirik DL, Waelkens E, Overbergh L, Mathieu C
    Journal of Proteome Research. 9(10):5142-52 doi:10.1021/pr1004086, 2010
    PubMed
    BioXSD: the common data-exchange format for everyday bioinformatics web services
    Kalas M, Puntervoll P, Joseph A, Bartaseviciute E (Karosiene published as Bartaseviciute), Töpfer A, Venkataraman P, Pettifer S, Bryne JC, Ison J, Blanchet C, Rapacki K, Jonassen I
    Bioinformatics 26(18):i540-6 doi:10.1093/bioinformatics/btq391, 2010
    PubMed
    ChemProt: a disease chemical biology database
    Taboureau O, Nielsen SK, Audouze K, Weinhold N, Edsgärd D, Roque FS, Kouskoumvekaki I, Bora A, Curpan R, Jensen TS, Brunak S, Oprea TI
    Nucleic Acids Research. 39:D367-72 doi:10.1093/nar/gkq906, 2010
    PubMed
    PGC-1{alpha}, A Potential Therapeutic Target for Early Intervention in Parkinson\\\\\\\'s Disease
    Zheng B, Liao Z, Locascio JJ, Lesniak KA, Roderick SS, Watt ML, Eklund AC, Zhang-James Y, Kim PD, Hauser MA, Grünblatt E, Moran LB, Mandel SA, Riederer P, Miller RM, Federoff HJ, Wüllner U, Papapetropoulos S, Youdim MB, Cantuti-Castelvetri I, Young AB, Vance JM, Davis RL, Hedreen JC, Adler CH, Beach TG, Graeber MB, Middleton FA, Rochet JC, Scherzer CR
    Science Translational Medicine 2(52):52ra73 doi:10.1126/scitranslmed.3001059, 2010
    PubMed
    Autoimmunity in Arabidopsis acd11 Is Mediated by Epigenetic Regulation of an Immune Receptor
    Palma K, Thorgrimsen S, Malinovsky FG, Fiil BK, Nielsen HB, Brodersen P, Hofius D, Petersen M, Mundy J
    PLoS Pathog. 6(10):e1001137 doi:10.1371/journal.ppat.1001137, 2010
    PubMed
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    Equitoxic Doses of 5-Azacytidine and 5-Aza-2ŒDeoxycytidine Induce Diverse Immediate and Overlapping Heritable Changes in the Transcriptome
    Qiu X, Hother C, Ralfkiær UM, Søgaard A, Lu Q, Workman CT, Liang G, Jones PA, Grønbæk K
    PLoS ONE 5(9) doi:10.1371/journal.pone.0012994, 2010
    PubMed
    Insight into Antigenic Diversity of VAR2CSA-DBL5å Domain from Multiple Plasmodium falciparum Placental Isolates
    Gnidehou S, Jessen L, Gangnard S, Ermont C, Triqui C, Quiviger M, Guitard J, Lund O, Deloron P, Ndam NT
    PLoS ONE 5(10) doi:10.1371/journal.pone.0013105, 2010
    PubMed
    Ultrastructural and molecular distinctions between the porcine inner cell mass and epiblast reveal unique pluripotent cell states
    Hall VJ, Jacobsen JV, Rasmussen MA, Hyttel P
    Dev. Dyn. 239(11):2911-20 doi:10.1002/dvdy.22424, 2010
    PubMed
    The interplay of descriptor-based computational analysis with pharmacophore modeling builds the basis for a novel classification scheme for feruloyl esterases
    Udatha DB, Kouskoumvekaki I, Olsson L, Panagiotou G
    Biotechnol. Adv. 29(1):94-110 doi:10.1016/j.biotechadv.2010.09.003, 2010
    PubMed
    Read abstract
    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
    The Genome Atlas Resource
    Qureshi M, Rotenberg E, Staerfeldt HH, Hansson L, Ussery DW
    CSBio 2010 Proceedings, 115: 149-158, 2010
    Combining substrate specificity analysis with support vector classifiers reveals feruloyl esterase as a phylogenetically informative protein group
    Olivares R, Sunner H, Frisvad JC, Olsson L, Nielsen J, Panagiotou G
    PLoS ONE 5(9):e12781 doi:10.1371/journal.pone.0012781, 2010
    PubMed
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    Antioxidant properties of modified rutin esters by DPPH, reducing power, iron chelation and human low density lipoprotein assays
    Lue BM, Nielsen NS, Jacobsen C, Hellgren LI, Guo Z, Xu XB
    Food Chemistry, 123:221-230, 2010
    Changes in skin barrier during treatment with systemic alitretinoin: focus on skin susceptibility and stratum corneum ceramides
    Jungersted JM, Hogh JK, Hellgren LI, Jemec GB, Agner T
    Arch. Dermatol. Res. 302(9):653-6 doi:10.1007/s00403-010-1057-0, 2010
    PubMed
    Improved glucose tolerance after intensive life style intervention occurs without changes in muscle ceramide or triacylglycerol in morbidly obese subjects
    Helge JW, Stallknecht B, Drachmann T, Hellgren LI, Jimenez-Jimenez R, Andersen JL, Richelsen B, Bruun JM
    Acta Physiologica 201(3):357-64 doi:10.1111/j.1748-1716.2010.02180.x, 2010
    PubMed
    Skin barrier response to occlusion of healthy and irritated skin: Differences in trans-epidermal water loss, erythema and stratum corneum lipids
    Jungersted JM, Hogh JK, Hellgren LI, Jemec GB, Agner T
    Contact Derm. 63(6):313-9 doi:10.1111/j.1600-0536.2010.01773.x, 2010
    PubMed
    Twenty-eight divergent polysaccharide loci specifying within and amongst strain capsule diversity in three strains of Bacteroides fragilis
    Patrick S, Blakely GW, Houston S, Moore J, Abratt VR, Bertalan M, Cerdeño-Tárraga AM, Quail MA, Corton N, Corton C, Bignell A, Barron A, Clark L, Bentley SD, Parkhill J
    Microbiology (Reading, Engl.) 156:3255-69 doi:10.1099/mic.0.042978-0, 2010
    PubMed
    Plasmodium falciparum Erythrocyte Membrane Protein 1 Diversity in Seven Genomes – Divide and Conquer
    Rask TS, Hansen DA, Theander TG, Pedersen AG, Lavstsen T
    PLoS Comput. Biol. 6(9) doi:10.1371/journal.pcbi.1000933, 2010
    PubMed
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    Country-specific chemical signatures of persistent environmental compounds in breast milk
    Krysiak-Baltyn K, Toppari J, Skakkebaek NE, Jensen TS, Virtanen HE, Schramm KW, Shen H, Vartiainen T, Kiviranta H, Taboureau O, Brunak S, Main KM
    International Journal of Andrology . 33(2):270-8 doi:10.1111/j.1365-2605.2009.00996.x, 2010
    PubMed
    The EMBRACE web service collection
    Pettifer S, Ison J, Kalas M, Thorne D, McDermott P, Jonassen I, Liaquat A, Fernández JM, Rodriguez JM; INB-Partners, Pisano DG, Blanchet C, Uludag M, Rice P, Bartaseviciute E (Karosiene published as Bartaseviciute), Rapacki K, Hekkelman M, Sand O, Stockinger H, Clegg AB, Bongcam-Rudloff E, Salzemann J, Breton V, Attwood TK, Cameron G, Vriend G
    Nucleic Acids Research. 38:W683-8 doi:10.1093/nar/gkq297, 2010
    PubMed
    Genomic comparisons of Brucella spp. and closely related bacteria using base compositional and proteome based methods
    Bohlin J, Snipen L, Cloeckaert A, Lagesen K, Ussery D, Kristoffersen AB, Godfroid J
    BMC Evol. Biol. 10:249 doi:10.1186/1471-2148-10-249, 2010
    PubMed
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    Predictive biomarker discovery through the parallel integration of clinical trial and functional genomics datasets
    Swanton C, Larkin JM, Gerlinger M, Eklund AC, Howell M, Stamp G, Downward J, Gore M, Futreal PA, Escudier B, Andre F, Albiges L, Beuselinck B, Oudard S, Hoffmann J, Gyorffy B, Torrance C, Boehme KA, Volkmer H, Toschi L, Nicke B, Beck M, Szallasi Z
    Genome Med 2(8):53 doi:10.1186/gm174, 2010
    PubMed
    Targeting chromosomal instability and tumour heterogeneity in HER2 positive breast cancer
    Burrell RA, Juul N, Johnston SR, Reis-Filho J, Szallasi Z, Swanton C
    J. Cell. Biochem. 111(4):782-90 doi:10.1002/jcb.22781, 2010
    PubMed
    Genomic Characterization of Campylobacter jejuni strain M1
    Friis C, Wassenaar T, Javed M, Snipen L, Lagesen K, Hallin P, Newell D, Toszeghy M, RIdley A, Manning G, Ussery D
    PLoS ONE 5(8):e12253 doi:10.1371/journal.pone.0012253, 2010
    PubMed
    Analysis of intra-genomic GC content homogeneity within prokaryotes
    Bohlin J, Snipen L, Hardy SP, Kristoffersen AB, Lagesen K, Donsvik T, Skjerve E, Ussery DW
    BMC Genomics 11:464 doi:10.1186/1471-2164-11-464, 2010
    PubMed
    Lykke i absurditetens tidsalder
    Schou T
    Dagbladet Information, 3. juni 2010, 2010
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    Mice, men and MHC supertypes
    Lundegaard C
    Expert Rev Vaccines 9(7):713-8 doi:10.1586/erv.10.76, 2010
    PubMed
    Bioinformatics Training: A Review of Challenges, Actions and Support Requirements
    Schneider MV, Watson J, Attwood T, Rother K, Budd A, McDowall J, Via A, Fernandes P, Nyronen T, Blicher T, Jones P, Blatter MC, De Las Rivas J, Phillip Judge D, van der Gool W, Brooksbank C
    Briefings in Bioinformatics 11(6):544-51 doi:10.1093/bib/bbq021, 2010
    PubMed
    Using protein design algorithms to understand the molecular basis of disease caused by protein-DNA interactions: the Pax6 example
    Alibes A, Nadra A, De Masi F, Bulyk M, Serrano L, Stricher F
    Nucleic Acids Research. 38(21):7422-31 doi:10.1093/nar/gkq683, 2010
    PubMed
    Transcriptomes of the desiccation- tolerant resurrection plant Craterostigma plantagineum
    Rodriguez MC, Edsgärd D, Hussain SS, Alquezar D, Rasmussen M, Gilbert T, Nielsen HB, Bartels D, Mundy J
    Plant J. 63(2):212-28 doi:10.1111/j.1365-313X.2010.04243.x, 2010
    PubMed
    Comparison of 61 Sequenced Escherichia coli Genomes Microbial Ecology
    Lukjancenko O, Wassenaar TM, Ussery DW
    Microb. Ecol. 60(4):708-20 doi:10.1007/s00248-010-9717-3, 2010
    PubMed
    Dissecting spatio-temporal protein networks driving human heart development and related disorders
    Lage K, Møllgård K, Greenway S, Wakimoto H, Gorham JM, Workman CT, Bendsen E, Hansen NT, Rigina O, Roque FS, Wiese C, Christoffels VM, Roberts AE, Smoot LB, Pu WT, Donahoe PK, Tommerup N, Brunak S, Seidman CE, Seidman JG, Larsen LA
    Mol. Syst. Biol. 6:381 doi:10.1038/msb.2010.36, 2010
    PubMed
    CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles
    Nielsen M, Lundegaard C, Lund O, Petersen TN
    Nucleic Acids Research. 38:W576-81 doi:10.1093/nar/gkq535, 2010
    PubMed
    Lactobacillus acidophilus induces virus immune defence genes in murine dendritic cells by a Toll-like receptor-2-dependent mechanism
    Weiss G, Rasmussen S, Zeuthen LH, Nielsen BN, Jarmer H, Jespersen L, Frøkiær H
    Immunology 131(2):268-81 doi:10.1111/j.1365-2567.2010.03301.x, 2010
    PubMed
    Bifidobacterium bifidum Actively Changes the Gene Expression Profile Induced by Lactobacillus acidophilus in Murine Dendritic Cells
    Weiss G, Rasmussen S, Nielsen Fink L, Jarmer H, Nøhr Nielsen B, Frøkiær H
    PLoS ONE 5(6):e11065 doi:10.1371/journal.pone.0011065, 2010
    PubMed
    Major histocompatibility complex class I binding predictions as a tool in epitope discovery
    Lundegaard C, Lund O, Buus S, Nielsen M
    Immunology 130(3):309-18 doi:10.1111/j.1365-2567.2010.03300.x, 2010
    PubMed
    Effects of Fish Oil Supplementation on Markers of the Metabolic Syndrome
    Pedersen MH, Mølgaard C, Hellgren LI, Lauritzen L
    J. Pediatr. 157(3):395-400, 400.e1 doi:10.1016/j.jpeds.2010.04.001, 2010
    PubMed
    Homology Modelling of the GABA Transporter and Analysis of Tiagabine Binding.
    Skovstrup S, Taboureau O, Bräuner-Osborne H, Jørgensen FS
    ChemMedChem 5(7):986-1000 doi:10.1002/cmdc.201000100, 2010
    PubMed
    Differential sensitivity of melanoma cell lines with BRAFV600E mutation to the specific raf inhibitor PLX4032
    Søndergaard JN, Nazarian R, Wang Q, Guo D, Hsueh T, Mok S, Sazegar H, MacConaill LE, Barretina JG, Kehoe SM, Attar N, von Euw E, Zuckerman JE, Chmielowski B, Comin-Anduix B, Koya RC, Mischel PS, Lo RS, Ribas A
    J Transl Med 8:39 doi:10.1186/1479-5876-8-39, 2010
    PubMed
    Read article
    Deciphering Diseases and Biological Targets for Environmental Chemicals using Toxicogenomics Networks
    Audouze K, Juncker AS, Roque F, Krysiak-Baltyn K, Weinhold N, Taboureau O, Jensen TS, Brunak S
    PLoS Comput. Biol. 6(5):e1000788 doi:10.1371/journal.pcbi.1000788, 2010
    PubMed
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    MHC Class II epitope predictive algorithms
    Nielsen M, Lund O, Buus S, Lundegaard C
    Immunology 130(3):319-28 doi:10.1111/j.1365-2567.2010.03268.x, 2010
    PubMed
    Computational Immunology Meets Bioinformatics: The Use of Prediction Tools for Molecular Binding in the Simulation of the Immune System
    Rapin N, Lund O, Bernaschi M, Castiglione F
    PLoS ONE 5(4):e9862 doi:10.1371/journal.pone.0009862, 2010
    PubMed
    Read article
    Parallel Genetic and Phenotypic Evolution of DNA Superhelicity in Experimental Populations of Escherichia coli
    Crozat E, Winkworth C, Gaffé J, Hallin PF, Riley MA, Lenski RE, Schneider D
    Mol. Biol. Evol. 27(9):2113-28 doi:10.1093/molbev/msq099, 2010
    PubMed
    Prediction of Glycosylation Sites in Proteins
    Julenius K, Johansen M, Zhang Y, Brunak S, Gupta R
    Bioinformatics for Glycobiology and Glycomics, 2010
    Protein annotation in the era of personal genomics
    Blicher T, Gupta R, Wesolowska A, Jensen LJ, Brunak S
    Curr. Opin. Struct. Biol. 20(3):335-41 doi:10.1016/j.sbi.2010.03.008, 2010
    PubMed
    Metabolic network topology reveals transcriptional regulatory signatures of type 2 diabetes
    Zelezniak A, Pers TH, Soares S, Patti ME, Patil KR
    PLoS Comput. Biol. 6(4):e1000729 doi:10.1371/journal.pcbi.1000729, 2010
    PubMed
    Malaria vaccine design - Identification of epitopes and characterization of antigenic variation in the PfEMP1 family
    Rask TS
    Ph.D. thesis, 2010
    Ceramides and barrier function in healthy skin
    Jungerstedt J, Hellgren LI, Drachmann T, Hoegh JG, Jemec GBE, Agner T
    Acta Derm. Venereol. 90(4):350-3 doi:10.2340/00015555-0894, 2010
    PubMed
    NetCTLpan: pan-specific MHC class I pathway epitope predictions
    Stranzl T, Larsen MV, Lundegaard C, Nielsen M
    Immunogenetics 62(6):357-68 doi:10.1007/s00251-010-0441-4, 2010
    PubMed
    Read abstract
    The Degree of Predicted Minor Histocompatibility Antigen Mismatch Correlates with Poorer Clinical Outcome of Non-myeloablative Allogeneic Hematopoietic Cell Transplantation
    Larsen ME, Kornblit B, Larsen MV, Masmas TN, Nielsen M, Thiim M, Garred P, Stryhn A, Lund O, Buus S, Vindelov L
    Biol. Blood Marrow Transplant. 16(10):1370-81 doi:10.1016/j.bbmt.2010.03.022, 2010
    PubMed
    Interdisciplinary Analysis of HIV-Specific CD8+ T Cell Responses against Variant Epitopes Reveals Restricted TCR Promiscuity
    Hoof I, Pérez CL, Buggert M, Gustafsson RK, Nielsen M, Lund O, Karlsson AC
    The Journal of Immunology. 184(9):5383-91 doi:10.4049/jimmunol.0903516, 2010
    PubMed
    Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis
    Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M
    Science Signaling 3(104):ra3 doi:10.1126/scisignal.2000475, 2010
    PubMed
    Acupuncture Induces a Pro-Inflammatory Immune Response Intensified by a Conditioning-Expectation Effect
    Karst M, Schneidewind D, Scheinichen D, Juettner B, Bernateck M, Molsberger A, Parlesak A, Passie T, Hoy L, Fink M
    Forsch Komplementmed 17(1):21-7 doi:10.1159/000264657, 2010
    PubMed
    The Type 1 Diabetes - HLA Susceptibility Interactome - Identification of HLA Genotype-Specific Disease Genes for Type 1 Diabetes
    Brorsson C, Hansen NT, Bergholdt R, Brunak S, Pociot F
    PLoS ONE 5(3):e9576 doi:10.1371/journal.pone.0009576, 2010
    PubMed
    Read article
    Chemoinformatics-assisted development of new anti-biofilm compounds
    Dürig A, Kouskoumvekaki I, Vejborg RM, Klemm P
    Appl. Microbiol. Biotechnol. 87(1):309-17 doi:10.1007/s00253-010-2471-0, 2010
    PubMed
    Standard operating procedure for computing pangenome trees
    Snipen L, Ussery DW
    Standards in Genomic Sciences, 2010
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    A human gut microbial gene catalogue established by metagenomic sequencing
    Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, MetaHIT Consortium, Bork P, Ehrlich DS & Wang J
    Nature 464(7285):59-65 doi:10.1038/nature08821, 2010
    PubMed
    Nature frontpage
    Assessment of an RNA interference screen-derived mitotic and ceramide pathway metagene as a predictor of response to neoadjuvant paclitaxel for primary triple-negative breast cancer: a retrospective analysis of five clinical trials
    Juul N, Szallasi Z, Eklund AC, Li Q, Burrell RA, Gerlinger M, Valero V, Andreopoulou E, Esteva FJ, Symmans WF, Desmedt C, Haibe-Kains B, Sotiriou C, Pusztai L, Swanton C
    Lancet Oncol. 11(4):358-65 doi:10.1016/S1470-2045(10)70018-8, 2010
    PubMed
    The phosphorylation specificity of B-RAF(WT), B-RAF(D594V), B-RAF(V600E) and B-RAF(K601E) kinases: An in silico study
    Fratev F, Jónsdóttir SO
    J. Mol. Graph. Model. 28(7):598-603 doi:10.1016/j.jmgm.2009.12.005, 2010
    PubMed
    Limitations of Ab Initio Predictions of Peptide Binding to MHC Class II Molecules
    Zhang H, Wang P, Papangelopoulos N, Xu Y, Sette A, Bourne PE, Lund O, Ponomarenko J, Nielsen M, Peters B
    PLoS ONE 5(2):e9272 doi:10.1371/journal.pone.0009272, 2010
    PubMed
    Stratum corneum lipids, skin barrier function and filaggrin mutations in patients with atopic eczema
    Jungersted JM, Scheer H, Mempel M, Baurecht H, Cifuentes L, Høgh JK, Hellgren LI, Jemec GBE, Agner T & Weidinger S
    Allergy 65(7):911-8 doi:10.1111/j.1398-9995.2010.02326.x, 2010
    PubMed
    Read abstract
    OCT4 and downstream factors are expressed in human somatic urogenital epithelia and in culture of epididymal spheres
    Kristensen DM, Nielsen JE, Kalisz M, Dalgaard MD, Audouze K, Larsen ME, Jacobsen GK, Horn T, Brunak S, Skakkebaek NE, Leffers H
    Mol. Hum. Reprod. 16(11):835-45 doi:10.1093/molehr/gaq008, 2010
    PubMed
    Trichomonas vaginalis vast BspA-like gene family: evidence for functional diversity from structural organisation and transcriptomics
    Noel CJ, Diaz N, Sicheritz-Ponten T, Safarikova L, Tachezy J, Tang P, Fiori PL, Hirt RP
    BMC Genomics 11:99 doi:10.1186/1471-2164-11-99, 2010
    PubMed
    The MHC motif viewer: a visualization tool for MHC binding motifs
    Rapin N, Hoof I, Lund O, Nielsen M
    Curr Protoc Immunol:Unit 18.17 doi:10.1002/0471142735.im1817s88, 2010
    PubMed
    Ancient Human Genome Sequence of an Extinct Palaeo-Eskimo
    Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, Metspalu M, Metspalu E, Kivisild T, Gupta R, Bertalan M, Nielsen K, Gilbert MTP, Wang Y, Raghavan M, Campos PF, Kamp HM, Wilson AS, Gledhill A, Tridico S, Bunce M, Lorenzen ED, Binladen J, Guo X, Zhao J, Zhang X, Zhang H, Li Z, Chen M, Orlando L, Kristiansen K, Bak M, Tommerup N, Bendixen C, Pierre TL, Grønnow B, Meldgaard M, Andreasen C, Fedorova SA, Osipova LP, Higham TFG, Ramsey CB, Hansen TV, Nielsen FC, Crawford MH, Brunak S, Sicheritz-Ponten T, Villems R, Nielsen R, Krogh A, Wang J, Willerslev E
    Nature 463(7282):757-62 doi:10.1038/nature08835, 2010
    PubMed
    CD4+ T cell activation is differentially modulated by bacteria-primed dendritic cells, but generally downregulated by n-3 polyunsaturated fatty acids
    Brix S, Lund P, Kjaer TMR, Straarup EM, Hellgren LI, Frøkiær H
    Immunology 129(3):338-50 doi:10.1111/j.1365-2567.2009.03163.x, 2010
    PubMed
    Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results
    Gauthier NP, Jensen LJ, Wernersson R, Brunak S, Jensen TS
    Nucleic Acids Research. 38:D699-702 doi:10.1093/nar/gkp1044, 2010
    PubMed
    Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis
    Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M
    Science Signaling 3(104):ra3 doi:10.1126/scisignal.2000475, 2010
    PubMed
    Amplification of LAPTM4B and YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer
    Li Y, Zou L, Li Q, Haibe-Kains B, Tian R, Li Y, Desmedt C, Sotiriou C, Szallasi Z, Iglehart JD, Richardson AL, Wang ZC
    Nature Medicine. 16(2):214-8 doi:10.1038/nm.2090, 2010
    PubMed
    Efficacy of Neoadjuvant Cisplatin in Triple-Negative Breast Cancer
    Silver DP, Richardson AL, Eklund AC, Wang ZC, Szallasi Z, Li Q, Juul N, Leong CO, Calogrias D, Buraimoh A, Fatima A, Gelman RS, Ryan PD, Tung NM, De Nicolo A, Ganesan S, Miron A, Colin C, Sgroi DC, Ellisen LW, Winer EP, Garber JE
    Journal of Clinical Oncology. 28(7):1145-53 doi:10.1200/JCO.2009.22.4725, 2010
    PubMed
    The Thousandth Genome – A Cautionary Tale
    Lagesen K, Ussery DW, Wassenaar TM
    Microbiology 156:603-609, 2010
    Lactobacillus acidophilus induces a slow but more sustained chemokine and cytokine response in naive foetal enterocytes compared to commensal Escherichia coli
    Zeuthen LH, Fink LN, Metzdorff SB, Kristensen MB, Licht TR, Nellemann C, Frokiaer H
    BMC Immunol. 11:2 doi:10.1186/1471-2172-11-2, 2010
    PubMed
    Genomic Analysis of Two-Component Signal Transduction Proteins in Basidiomycetes
    Lavín JL, Ramírez L, Ussery DW, Pisabarro AG, Oguiza JA
    J. Mol. Microbiol. Biotechnol. 18(2):63-73 doi:10.1159/000277654, 2010
    PubMed
    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
    Phytanic acid: An overlooked bioactive fatty acid in dairy products?
    Lars I Hellgren
    Annals of the New York Academy of Sciences. 1190:42-9 doi:10.1111/j.1749-6632.2009.05254.x, 2010
    PubMed
    Validation of Cyanoacrylate Method for Collection of Stratum Corneum in Human Skin for Lipid Analysis
    Jungersted JM, Hellgren LI, Drachmann T, Jemec GBE, Agner T
    Skin Pharmacol Physiol 23(2):62-7 doi:10.1159/000265676, 2010
    PubMed
    Read abstract
    Comparative Genomics of Green Sulfur Bacteria
    Davenport C, Ussery DW, Tümmler B
    Photosyn. Res. 104:137-52 doi:10.1007/s11120-009-9515-2, 2010
    PubMed
    Lipid assymetry in plant plasma membranes: phosphate deficiency-induced phospholipid replacement is restricted to the cytosolic leaflet
    Tjällström H, Hellgren LI, Wieslander Å & Sandelius AS
    FASEB J. 24(4):1128-38 doi:10.1096/fj.09-139410, 2010
    PubMed
    Mutational mapping and modeling of the binding site for (S)-citalopram in the human serotonin transporter
    Andersen J, Olsen L, Hansen KB, Taboureau O, Jorgensen FS, Jorgensen AM, Bang-Andersen B, Egebjerg J, Stromgaard K, Kristensen AS
    The Journal of Biological Chemistry, 2010
    PubMed
    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

2009

    Predicting functionality of protein-DNA interactions by integrating diverse evidence.
    Ucar D, Beyer A, Parthasarathy S, Workman CT
    Bioinformatics. 2009 Jun 15;25(12):i137-44., 2009
    PubMed
    IL-1 receptor antagonism and muscle gene expression in patients with type 2 diabetes.
    Berchtold LA, Larsen CM, Vaag A, Faulenbach M, Workman CT, Kruhøffer M, Donath M, Mandrup-Poulsen T
    European Cytokine Network . 2009 Jun;20(2):81-7., 2009
    PubMed
    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
    High-Resolution DNA Binding Specificity Analysis of Yeast Transcription Factors
    Zhu C, Byers K, McCord RP, Shi Z, Berger MF, Newburger D, Saulrieta K, Smith Z, Shah M, Radhakrishnan M, Phillipakis AA, Hu Y, De Masi F, Pacek M, Rolfs A, Murthy TVS, LaBaer J, Bulyk ML
    Genome Res. 19(4):556-66 doi:10.1101/gr.090233.108, 2009
    PubMed
    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
    Bioinformatics and simulation of the immune system
    Rapin N
    Ph.D. thesis, 2009
    Integrative analyses of complex phenotypes
    Hansen NT
    Ph.D. thesis, 2009
    Prediction and analysis of MHC class I binding specificities beyond humans
    Hoof I
    Ph.D. thesis, 2009
    Degenerate Peptide Specificity of MHC Molecules and T cell Receptors in Immunodominance and Tolerance
    Frankild S
    Ph.D. thesis, 2009
    Systems biology analysis of pre-mRNA splicing and alternative splicing, and its role in cancers
    Wang K
    Ph.D.thesis, 2009
    Bioinformatics Analysis of Peptide:Protein Binding
    Zhang H
    Ph.D. thesis, 2009
    Computational tools and Interoperability in Comparative Genomics
    Hallin PF
    Ph.D. thesis, 2009
    Analysis of gene expression profiles of microdissected cell populations indicates that testicular carcinoma in situ is an arrested gonocyte
    Sonne SB, Almstrup K, Dalgaard M, Juncker AS, Edsgard D, Ruban L, Harrison NJ, Schwager C, Abdollahi A, Huber PE, Brunak S, Gjerdrum LM, Moore HD, Andrews PW, Skakkebaek NE, Rajpert-De Meyts E, Leffers H
    Cancer Res. 15;69(12):5241-50., 2009
    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
    Dietary fibers as immunoregulatory compounds in health and disease
    Wismar R, Brix S, Frøkiær H, Lærke HN
    Annals of the New York Academy of Sciences, 2009
    Pseudomonas aeruginosa quorum-sensing signal molecules interfere with dendritic cell-induced T-cell proliferation
    Skindersoe ME, Zeuthen LH, Brix S, Fink LN, Lazenby J, Whittall C, Williams P, Diggle SP, Froekiaer H, Cooley M, Givskov M
    FEMS Immunol. Med. Microbiol. 55(3):335-45 doi:10.1111/j.1574-695X.2008.00533.x, 2009
    PubMed
    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
    Phosphatidylcholine reverses ethanol-induced increase in transepithelial endotoxin permeability and abolishes transepithelial leukocyte activation
    Mitzscherling K, Volynets V, Parlesak A
    Alcohol. Clin. Exp. Res. 33(3):557-62 doi:10.1111/j.1530-0277.2008.00869.x, 2009
    PubMed
    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
    An online survival analysis tool to rapidly assess the effect of 22,277 genes on breast cancer prognosis using microarray data of 1,809 patients
    Györffy B, Lanczky A, Eklund AC, Denkert C, Budczies J, Li Q, Szallasi Z
    Breast Cancer Res. Treat. 123(3):725-31 doi:10.1007/s10549-009-0674-9, 2009
    PubMed
    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
    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
    The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding
    Zhang H, Lund O, Nielsen M
    Bioinformatics 25(10):1293-9 doi:10.1093/bioinformatics/btp137, 2009
    PubMed
    Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information
    Buslje CM, Santos J, Delfino JM, Nielsen M
    Bioinformatics 25(9):1125-31 doi:10.1093/bioinformatics/btp135, 2009
    PubMed
    Stretches of alternating pyrimidine/ purines and purines are respectively linked with pathogenicity and growth temperature in prokaryotes
    Bohlin J, Hardy SP, Ussery DW
    BMC Genomics 10:346 doi:10.1186/1471-2164-10-346, 2009
    PubMed
    Read article
    Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization
    Aron C Eklund; Pia Friis; Rasmus Wernersson; Zoltan Szallasi
    Nucleic Acids Research. 38(4):e27 doi:10.1093/nar/gkp1116, 2009
    PubMed
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    Transcriptomic variation in a coral reveals pathways of clonal organisation
    Line K Bay, Bjørn Nielsen H, Hanne Jarmer, Francois Seneca, Madeleine J H van Oppe
    Marine Genomics, 2009
    Read abstract
    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
    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
    The Immune Epitope Database 2.0
    Vita R, Zarebski L, Greenbaum JA, Emami H, Hoof I, Salimi N, Damle R, Sette A, Peters B
    Nucleic Acids Research. 2009 Nov 11, 2009
    Genomic taxonomy of vibrios
    Thompson CC, Vicente AC, Souza RC, Vasconcelos AT, Vesth T, Alves N Jr, Ussery DW, Iida T, Thompson FL
    BMC Evol. Biol. 9:258 doi:10.1186/1471-2148-9-258, 2009
    PubMed
    Read abstract
    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
    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
    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
    Higher variability in the number of sexual partners in males can contribute to a higher prevalence of sexually transmitted diseases in females
    Gouveia-Oliveira R, Pedersen AG
    J. Theor. Biol. 261(1):100-6 doi:10.1016/j.jtbi.2009.06.028, 2009
    PubMed
    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
    An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction.
    Nielsen M, Lund O
    BMC bioinformatics, 2009
    Impaired uptake and/or utilisation of leucine is suppressed by the SPT15-300 allele of the TATA binding protein gene.
    Baerends RJ, Qiu JL, Rasmussen S, Nielsen HB, Brandt A
    Appl. Environ. Microbiol. 75(19):6055-61 doi:10.1128/AEM.00989-09, 2009
    PubMed
    Transcriptional landscape estimation from tiling array data using a model of signal shift and drift.
    Nicolas P, Leduc A, Robin S, Rasmussen S, Jarmer H, Bessières P
    Bioinformatics 25(18):2341-7 doi:10.1093/bioinformatics/btp395, 2009
    PubMed
    The transcriptionally active regions in the genome of Bacillus subtilis
    Rasmussen S, Nielsen HB, Jarmer H
    Mol. Microbiol. 73(6):1043-57 doi:10.1111/j.1365-2958.2009.06830.x, 2009
    PubMed
    Microbial comparative pan-genomics using binomial mixture models
    Snipen L, Almøy T, Ussery DW
    BMC Genomics 10:385 doi:10.1186/1471-2164-10-385, 2009
    PubMed
    An in silico study of the molecular basis of B-RAF activation and conformational stability
    Fratev FF, Jónsdóttir SÓ
    BMC Struct. Biol. 9:47 doi:10.1186/1472-6807-9-47, 2009
    PubMed
    Link to publication
    Expression profiling of human genetic and protein interaction networks in type 1 diabetes
    Bergholdt R, Brorsson C, Lage K, Nielsen JH, Brunak S, Pociot F
    PLoS ONE 4(7):e6250 doi:10.1371/journal.pone.0006250, 2009
    PubMed
    Proteome analysis demonstrates profound alterations in human dendritic cell nature by TX527, an analogue of vitamin D
    Ferreira GB, van Etten E, Lage K, Hansen DA, Moreau Y, Workman CT, Waer M, Verstuyf A, Waelkens E, Overbergh L, Mathieu C
    Proteomics 9(14):3752-64 doi:10.1002/pmic.200800848, 2009
    PubMed
    The validation and assessment of machine learning: a game of prediction from high-dimensional data
    Pers TH, Albrechtsen A, Holst C, Sørensen TI, Gerds TA
    PLoS ONE 4(8):e6287 doi:10.1371/journal.pone.0006287, 2009
    PubMed
    A generic method for assignment of reliability scores applied to solvent accessibility predictions
    Petersen B, Petersen TN, Andersen P, Nielsen M, Lundegaard C
    BMC Struct. Biol. 9:51 doi:10.1186/1472-6807-9-51, 2009
    PubMed
    InterMap3D: predicting and visualizing co-evolving protein residues
    Gouveia-Oliveira R, Roque FS, Wernersson R, Sicheritz-Ponten T, Sackett PW, Mølgaard A, Pedersen AG
    Bioinformatics 25(15):1963-5 doi:10.1093/bioinformatics/btp335, 2009
    PubMed
    PDF
    Evolution of the leukotoxin promoter in genus Mannheimia
    Larsen J, Pedersen AG, Davies R, Kuhnert P, Frey J, Christensen H, Bisgaard M, Olsen J
    BMC Evol. Biol. 9:121 doi:10.1186/1471-2148-9-121, 2009
    PubMed
    PDF
    Controlled indole-3-acetaldoxime production through ethanol-induced expression of CYP79B2
    Mikkelsen MD, Fuller VL, Hansen BG, Nafisi M, Olsen CE, Nielsen HB, Halkier BA
    Planta 229(6):1209-17 doi:10.1007/s00425-009-0907-5, 2009
    PubMed
    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
    Genome-wide gene expression profiling of SCID mice with T-cell-mediated Colitis
    Brudzewsky D, Pedersen AE, Claesson MH, Gad M, Kristensen NN, Lage K, Jensen T, Tommerup N, Larsen LA, Knudsen S, Tümer Z
    Scand. J. Immunol. 69(5):437-46 doi:10.1111/j.1365-3083.2009.02243.x, 2009
    PubMed
    Evaluation of microarray preprocessing algorithms based on concordance with rt-PCR in clinical samples
    Gyorffy B, Molnar B, Lage H, Szallasi Z, Eklund AC
    PLoS ONE 4(5):e5645 doi:10.1371/journal.pone.0005645, 2009
    PubMed
    Chromosomal instability determines taxane response
    Swanton C, Nicke B, Schuett M, Eklund AC, Ng C, Li Q, Hardcastle T, Lee A, Roy R, East P, Kschischo M, Endesfelder D, Wylie P, Kim SN, Chen JG, Howell M, Ried T, Habermann JK, Auer G, Brenton JD, Szallasi Z, Downward J
    PNAS, Proceedings of the National Academy of Sciences U.S.A. 106(21):8671-6 doi:10.1073/pnas.0811835106, 2009
    PubMed
    Macrophages and Adipocytes in Human Obesity: Adipose Tissue Gene Expression and Insulin Sensitivity during Calorie Restriction and Weight Stabilization
    Capel F, Klimcáková E, Viguerie N, Roussel B, Vítková M, Kováciková M, Polák J, Kovácová Z, Galitzky J, Maoret JJ, Hanácek J, Pers TH, Bouloumié A, Stich V, Langin D
    Diabetes 58(7):1558-67 doi:10.2337/db09-0033, 2009
    PubMed
    ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization
    Pappalardo F, Halling-Brown MD, Rapin N, Zhang P, Alemani D, Emerson A, Paci P, Duroux P, Pennisi M, Palladini A, Miotto O, Churchill D, Rossi E, Shepherd AJ, Moss DS, Castiglione F, Bernaschi M, Lefranc MP, Brunak S, Motta S, Lollini PL, Basford KE, Brusic V
    Brief. Bioinformatics 10(3):330-40 doi:10.1093/bib/bbp014, 2009
    PubMed
    Identification of T1D susceptibility genes within the MHC region by combining protein interaction networks and SNP genotyping data
    Brorsson C, Hansen NT, Lage K, Bergholdt R, Brunak S, Pociot F; Diabetes Genetics Consortium
    Diabetes Obes Metab:60-6 doi:10.1111/j.1463-1326.2008.01004.x, 2009
    PubMed
    Genetic Tools and Algorithms for Gene Discovery in Major Congenital Anomalies
    Donahoe PK, Noonan KM, Lage K
    Birth Defects Res. Part A Clin. Mol. Teratol. 85(1):6-12 doi:10.1002/bdra.20546, 2009
    PubMed
    Expression analyses of human cleft palate tissue suggest a role for osteopontin and immune related factors in palatal development
    Jakobsen LP, Borup R, Vestergaard J, Larsen LA, Lage K, Maroun LL, Kjaer I, Niemann CU, Andersen M, Knudsen MA, Møllgård K, Tommerup N
    Exp. Mol. Med. 41(2):77-85, 2009
    PubMed
    Kinase-specific prediction of protein phosphorylation sites.
    Miller ML, Blom N
    Methods in Molecular Biology . 527:299-310, x doi:10.1007/978-1-60327-834-8_22, 2009
    PubMed
    High-affinity human leucocyte antigen class I binding variola-derived peptides induce CD4+ T cell responses more than 30 years post-vaccinia virus vaccination
    Wang M, Tang ST, Lund O, Dziegiel MH, Buus S, Claesson MH
    Clin. Exp. Immunol. 155(3):441-6 doi:10.1111/j.1365-2249.2008.03856.x, 2009
    PubMed
    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
    Analysis and prediction of gene splice sites in four Aspergillus genomes
    Wang K, Ussery DW, Brunak S
    Fungal Genet. Biol.:S14-8 doi:10.1016/j.fgb.2008.09.010, 2009
    PubMed
    Fatness-associated FTO gene variant increases mortality independent of fatness--in cohorts of Danish men
    Zimmermann E, Kring SI, Berentzen TL, Holst C, Pers TH, Hansen T, Pedersen O, Sørensen TI, Jess T
    PLoS ONE 4(2):e4428 doi:10.1371/journal.pone.0004428, 2009
    PubMed
    Molecular basis of inactive B-RAF(WT) and B-RAF(V600E) ligand inhibition, selectivity and conformational stability: an in silico study.
    Fratev F, Jónsdóttir SO, Mihaylova E, Pajeva I
    Mol. Pharm. 6(1):144-57 doi:10.1021/mp8001107, 2009
    PubMed
    Classification of cytochrome P450 1A2 inhibitors and noninhibitors by machine learning techniques.
    Vasanthanathan P, Taboureau O, Oostenbrink C, Vermeulen NP, Olsen L, Jørgensen FS
    Drug Metab. Dispos. 37(3):658-64 doi:10.1124/dmd.108.023507, 2009
    PubMed
    Virtual screening and prediction of site of metabolism for cytochrome P450 1A2 ligands.
    Vasanthanathan P, Hritz J, Taboureau O, Olsen L, Jørgensen FS, Vermeulen NP, Oostenbrink C
    Journal of Chemical Information and Modeling 49(1):43-52 doi:10.1021/ci800371f, 2009
    PubMed
    Location of the antidepressant binding site in the serotonin transporter: Importance of SER438 in recognition of citalopram and tricyclic antidepressants.
    Andersen J, Taboureau O, Hansen KB, Olsen L, Egebjerg J, Strømgaard K, Kristensen AS
    The Journal of Biological Chemistry 284(15):10276-84 doi:10.1074/jbc.M806907200, 2009
    PubMed
    The proteome of seed development in the model legume Lotus japonicus.
    Dam S, Laursen BS, Ornfelt JH, Jochimsen B, Stærfeldt HH, Friis C, Nielsen K, Goffard N, Besenbacher S, Krusell L, Sato S, Tabata S, Thogersen IB, Enghild JJ, Stougaard J
    Plant Physiology. 149(3):1325-40 doi:10.1104/pp.108.133405, 2009
    PubMed
    Pan-specific MHC class I predictors: A benchmark of HLA class I pan-specific prediction methods
    Zhang H, Lundegaard C, Nielsen M
    Bioinformatics 25(1):83-9 doi:10.1093/bioinformatics/btn579, 2009
    PubMed
    NetMHCpan, a method for MHC class I binding prediction beyond humans.
    Hoof I, Peters B, Sidney J, Pedersen LE, Sette A, Lund O, Buus S, Nielsen M
    Immunogenetics 61(1):1-13 doi:10.1007/s00251-008-0341-z, 2009
    PubMed

2008

    Contributions to the study of coevolution, at micro and macroscales
    Gouveia-Oliveira R
    Ph.D. thesis, 2008
    Linear motifs in phosphorylation-dependent signalling
    Miller ML
    Ph.D. thesis, 2008
    Bioinformatics and systems biology of human diseases
    Lage K
    Ph.D. thesis, 2008
    Concordance of exon array and real-time PCR assessment of gene expression following cancer cell cytotoxic drug exposure
    Lee AJ, East P, Pepper S, Nicke B, Szallasi Z, Eklund AC, Downward J, Swanton C
    Cell Cycle 7(24):3947-8, 2008
    PubMed
    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
    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
    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
    Occurrence of multiple infections with different Borrelia burgdorferi genospecies in Danish Ixodes ricinus nymphs
    Vennestrøm J, Egholm H, Jensen PM
    Parasitology International . 57(1):32-7, 2008
    PubMed
    Integration of clinical chemistry, expression, and metabolite data leads to better toxicological class separation
    Spicker JS, Brunak S, Frederiksen KS, Toft H
    Toxicol. Sci. 102(2):444-54 doi:10.1093/toxsci/kfn001, 2008
    PubMed
    Protein abundance profiling of the Escherichia coli cytosol
    Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D
    BMC Genomics 9:102 doi:10.1186/1471-2164-9-102, 2008
    PubMed
    The minimum information about a genome sequence (MIGS) specification
    Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A
    Nature Biotechnology. 26(5):541-7 doi:10.1038/nbt1360, 2008
    PubMed
    Identification of glycosaminoglycan binding regions in the Plasmodium falciparum encoded placental sequestration ligand, VAR2CSA
    Resende M, Nielsen MA, Dahlbäck M, Ditlev SB, Andersen P, Sander AF, Ndam NT, Theander TG, Salanti A
    Malar. J. 7:104 doi:10.1186/1475-2875-7-104, 2008
    PubMed
    Whole-genome pyrosequencing of an epidemic multidrug-resistant Acinetobacter baumannii strain belonging to the European clone II group
    Iacono M, Villa L, Fortini D, Bordoni R, Imperi F, Bonnal RJ, Sicheritz-Ponten T, De Bellis G, Visca P, Cassone A, Carattoli A
    Antimicrob. Agents Chemother. 52(7):2616-25 doi:10.1128/AAC.01643-07, 2008
    PubMed
    Dietary soya saponins increase gut permeability and play a key role in the onset of soyabean-induced enteritis in Atlantic salmon ( Salmo salar L.)
    Knudsen D, Jutfelt F, Sundh H, Sundell K, Koppe W, Frøkiaer H
    Br. J. Nutr. 100(1):120-9 doi:10.1017/S0007114507886338, 2008
    PubMed
    Arabidopsis mitogen-activated protein kinase kinases MKK1 and MKK2 have overlapping functions in defense signaling mediated by MEKK1, MPK4, and MKS1
    Qiu JL, Zhou L, Yun BW, Nielsen HB, Fiil BK, Petersen K, Mackinlay J, Loake GJ, Mundy J, Morris PC
    Plant Physiology. 148(1):212-22 doi:10.1104/pp.108.120006, 2008
    PubMed
    Functional genomic analysis of drug sensitivity pathways to guide adjuvant strategies in breast cancer
    Swanton C, Szallasi Z, Brenton JD, Downward J
    Breast Cancer Res. 10(5):214 doi:10.1186/bcr2159, 2008
    PubMed
    A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes
    Lage K, Hansen NT, Karlberg EO, Eklund AC, Roque F, Donahoe PK, Szallasi Z, Jensen TS, Brunak S
    Proc. Natl. Acad. Sci. U.S.A. 105(52):20870-5 doi:10.1073/pnas.0810772105, 2008
    PubMed
    NetPhosBac - A predictor for Ser/Thr phosphorylation sites in bacterial proteins.
    Miller ML, Soufi B, Jers C, Blom N, Macek B, Mijakovic I
    Proteomics 9(1):116-25 doi:10.1002/pmic.200800285, 2008
    PubMed
    MHC-I-restricted epitopes conserved among variola and other related orthopoxviruses are recognized by T cells 30 years after vaccination
    Tang ST, Wang M, Lamberth K, Harndahl M, Dziegiel MH, Claesson MH, Buus S, Lund O
    Arch. Virol. 153(10):1833-44 doi:10.1007/s00705-008-0194-7, 2008
    PubMed
    Circular reasoning rather than cyclic expression
    Jensen LJ, de Lichtenberg U, Jensen TS, Brunak S, Bork P
    Genome Biol. 9(6):403 doi:10.1186/gb-2008-9-6-403, 2008
    PubMed
    Bioavailability of omega-3 long-chain polyunsaturated fatty acids from foods
    Mu H
    Supplement to AgroFood industry hi-tech, 19 (4), 24-26, 2008
    Butter blend containing fish oil does not affect cholesterol absorption in a single meal study in humans
    Overgaard J, Porsgaard T, Guo Z, Lauritzen L, Mu H
    Mol Nutr Food Res 52(10):1140-6 doi:10.1002/mnfr.200700484, 2008
    PubMed
    Comparison of 3 ad libitum diets for weight-loss maintenance, risk of cardiovascular disease, and diabetes: A 6-mo randomized, controlled trial
    Due A, Larsen TM, Mu H, Hermansen K, Stender S, Astrup A
    The American Journal of Clinical Nutrition. 88(5):1232-41, 2008
    PubMed
    Staphylokokkens ømme punkt.
    Jarmer HO
    Dynamo, November 2008, 2008
    Classification of Cytochrome P450 1A2 Inhibitors and Non-Inhibitors by Machine Learning Techniques
    Vasanthanathan P, Taboureau O, Oostenbrink C, Vermeulen NPE, Olsen L, Jorgensen FS
    Drug Metab. Dispos. 37(3):658-64 doi:10.1124/dmd.108.023507, 2008
    PubMed
    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
    A pathway-specific microarray analysis highlights the complex and co-ordinated transcriptional networks of the developing grain of field-grown barley
    Hansen M, Friis C, Bowra S, Holm PB, Vincze E
    J. Exp. Bot. 60(1):153-67 doi:10.1093/jxb/ern270, 2008
    PubMed
    Relevant URL
    Linear motif atlas for phosphorylation-dependent signaling.
    Miller ML, Jensen LJ, Diella F, Jørgensen C, Tinti M, Li L, Hsiung M, Parker SA, Bordeaux J, Sicheritz-Ponten T, Olhovsky M, Pasculescu A, Alexander J, Knapp S, Blom N, Bork P, Li S, Cesareni G, Pawson T, Turk BE, Yaffe MB, Brunak S, Linding R
    Science Signaling 1(35):ra2 doi:10.1126/scisignal.1159433, 2008
    PubMed
    Fedtsyrebalance påvirker livsstilssygdomme og allergi
    Hellgren LI, Brix S
    FoodDTU, nr. 44, maj (2008)., 2008
    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
    The peptide-binding specificity of HLA-A*3001 demonstrates membership of the HLA-A3 supertype
    Lamberth K, Røder G, Harndahl M, Nielsen M, Lundegaard C, Schafer- Nielsen C, Lund O, Buus S
    Immunogenetics 60(11):633-43 doi:10.1007/s00251-008-0317-z, 2008
    PubMed
    Adjuvant auricular electroacupuncture and autogenic training in rheumatoid arthritis: a randomized controlled trial. Auricular acupuncture and autogenic training in rheumatoid arthritis.
    Bernateck M, Becker M, Schwake C, Hoy L, Passie T, Parlesak A, Fischer MJ, Fink M, Karst M
    Forsch Komplementmed 15(4):187-93 doi:10.1159/000141929, 2008
    PubMed
    Towards a richer description of our complete collection of genomes and metagenomes: the ’Minimum Information about a Genome Sequence’ (MIGS) specification
    Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuolii SV, Ashburner M, Axelrod N, Baldauf S, Boore SBJ, Cochrane G, Cole J, Dawyndt P, Vos PD, dePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister A, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Moxon R, Nelson K, Parkhill J, Proctor L, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery DW, Vaughan B, Ward N, Whetzel T, Wilson G, Wipat A
    Nature Biotechnology. 26(5):541-7 doi:10.1038/nbt1360, 2008
    PubMed
    Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes
    Bohlin J, Skjerve E, Ussery DW
    BMC Genomics 9:104 doi:10.1186/1471-2164-9-104, 2008
    PubMed
    BMC Genomics link
    Transcriptomics and adaptive genomics of the asymptomatic bacteria Escherichia coli strain 83972
    Hancock V, Seshasayee AS, Ussery DW, Luscombe NM, Klemm P
    Mol. Genet. Genomics 279(5):523-34 doi:10.1007/s00438-008-0330-9, 2008
    PubMed
    Investigations of oligonucleotide usage variance within and between prokaryotes
    Bohlin J, Skjerve E, Ussery D
    PLoS Comput. Biol. 4(4):e1000057 doi:10.1371/journal.pcbi.1000057, 2008
    PubMed
    PLoS Computational Biology link
    Toward a Standards-Compliant Genomic and Metagenomic Publication Record
    Garrity GM, Field D, Kyrpides N, Hirschman L, Sansone SA, Angiuoli S, Cole JR, Glöckner FO, Kolker E, Kowalchuk G, Moran MA, Ussery D, White O
    OMICS 12(2):157-60 doi:10.1089/omi.2008.A2B2, 2008
    PubMed
    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
    MHC motif viewer
    Rapin N, Hoof I, Lund O, Nielsen M
    Immunogenetics 60(12):759-65 doi:10.1007/s00251-008-0330-2, 2008
    PubMed
    Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq.
    Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT, Hinton JC, Vogel J
    PLoS Genet. 4(8):e1000163 doi:10.1371/journal.pgen.1000163, 2008
    PubMed
    The complete genome sequence and analysis of the human pathogen Campylobacter lari
    Miller WG, Wang G, Binnewies TT, Parker CT
    Foodborne Pathog. Dis. 5(4):371-86 doi:10.1089/fpd.2008.0101, 2008
    PubMed
    Molecular analysis of the emergence of pandemic Vibrio parahaemolyticus
    Boyd EF, Cohen AL, Naughton LM, Ussery DW, Binnewies TT, Stine OC, Parent MA
    BMC Microbiol. 8:110 doi:10.1186/1471-2180-8-110, 2008
    PubMed
    The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571
    Lee KB, De Backer P, Aono T, Liu CT, Suzuki S, Suzuki T, Kaneko T, Yamada M, Tabata S, Kupfer DM, Najar FZ, Wiley GB, Roe B, Binnewies TT, Ussery DW, D’Haeze WD, Herder JD, Gevers D, Vereecke D, Holsters M, Oyaizu H
    BMC Genomics 9:271 doi:10.1186/1471-2164-9-271, 2008
    PubMed
    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
    Arabidopsis MAP Kinase Kinases MKK1 and MKK2 have overlapping functions in defense signalling mediated by MEKK1, MPK4 and MKS1.
    Qiu J, Nielsen HB, Fiil BK, Petersen K, MacKinlay J, Loake G, Mundy J, Morris PC
    Plant Physiology. 148(1):212-22 doi:10.1104/pp.108.120006, 2008
    PubMed
    Relevant URL
    Arabidopsis MAP Kinase 4 regulates gene expression via transcription factor release in the nucleus
    Qiu J, Fiil BK, Petersen K, Nielsen HB, Botanga CJ, Thorgrimsen S, Lichota J, Brodersen P, Grasser KD, Mattsson O, Glazebrook J, Mundy J, Petersen M
    The EMBO Journal . 27(16):2214-21 doi:10.1038/emboj.2008.147, 2008
    PubMed
    Relevant URL
    Influence of dietary fatty acids on endocannabinoid and N-acylethanolamine levels in rat brain, liver and small intestine
    Artmann A, Petersen G, Hellgren LI, Boberg J, Skonberg C, Nellemann C, Hansen SH, Hansen HS
    Biochim. Biophys. Acta 1781(4):200-12 doi:10.1016/j.bbalip.2008.01.006, 2008
    PubMed
    Lipids and skin barrier function--a clinical perspective
    Jungersted JM, Hellgren LI, Jemec GB, Agner T
    Contact Derm. 58(5):255-62 doi:10.1111/j.1600-0536.2008.01320.x, 2008
    PubMed
    Kinetic study of sphingomyelin hydrolysis for ceramide production.
    Zhang L, Hellgren LI, Xu X
    Journal of Molecular Catalysis B: Enzymatic 51: 93-99., 2008
    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
    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
    GLI1 is involved in cell cycle regulation and proliferation of NT2 embryonal carcinoma stem cells
    Vestergaard J, Lind-Thomsen A, Pedersen MW, Jarmer HO, Bak M, Hasholt L, Tommerup N, Tümer Z, Larsen LA
    DNA Cell Biol. 27(5):251-6 doi:10.1089/dna.2007.0625, 2008
    PubMed
    Global features of the Alcanivorax borkumensis SK2 genome
    Reva ON, Hallin PF, Willenbrock H, Sicheritz-Ponten T, Tummler B, Ussery DW
    Environ. Microbiol. 10(3):614-25, 2008
    PubMed
    The genome BLASTatlas-a GeneWiz extension for visualization ofwhole-genome homology
    Hallin PF, Binnewies TT, Ussery DW
    Mol Biosyst 4(5):363-71 doi:10.1039/b717118h, 2008
    PubMed
    Dendritic Cells from Peyer\'s Patches and Mesenteric Lymph Nodes Differ from Spleen Dendritic Cells in their Response to Commensal Gut Bacteria
    Fink LN, Frøkiær H
    Scand. J. Immunol. 68(3):270-9 doi:10.1111/j.1365-3083.2008.02136.x, 2008
    PubMed
    Toll-like receptor 2 and nucleotide-binding oligomerization domain-2 play divergent roles in the recognition of gut-derived lactobacilli and bifidobacteria in dendritic cells
    Zeuthen LH, Fink LN, Frøkiær H
    Immunology 124(4):489-502 doi:10.1111/j.1365-2567.2007.02800.x, 2008
    PubMed
    Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan
    Nielsen M, Lundegaard C, Blicher T, Peters B, Sette A, Justesen S, Buus S, Lund O
    PLoS Comput. Biol. 4(7):e1000107 doi:10.1371/journal.pcbi.1000107, 2008
    PubMed
    Immune epitope database analysis resource (IEDB-AR)
    Zhang Q, Wang P, Kim Y, Haste-Andersen P, Beaver J, Bourne PE, Bui HH, Buus S, Frankild S, Greenbaum J, Lund O, Lundegaard C, Nielsen M, Ponomarenko J, Sette A, Zhu Z, Peters B
    Nucleic Acids Res. 36:W513-8 doi:10.1093/nar/gkn254, 2008
    PubMed
    NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11
    Lundegaard C, Lamberth K, Harndahl M, Buus S, Lund O, Nielsen M
    Nucleic Acids Res. 36:W509-12 doi:10.1093/nar/gkn202, 2008
    PubMed
    Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers
    Lundegaard C, Lund O, Nielsen M
    Bioinformatics 24(11):1397-8 doi:10.1093/bioinformatics/btn128, 2008
    PubMed
    Prediction of pH-dependent solubility of Histone Deacetylase (HDAC)inhibitors
    Kouskoumvekaki I, Hansen NT, Björkling F, Vadlamudi SM, Jónsdóttir SÓ
    SAR QSAR Environ Res 19:167-77 doi:10.1080/10629360701843367, 2008
    PubMed
    Humans with chimpanzee-like major histocompatibility complex-specificities control HIV-1 infection
    Hoof I, Kesmir C, Lund O, Nielsen M
    AIDS 22(11):1299-303 doi:10.1097/QAD.0b013e328302f39f, 2008
    PubMed
    Alternative splicing in colon, bladder, and prostate cancer identified by exon-array analysis
    Thorsen K, Sørensen KD, Brems-Eskildsen AS, Modin C, Gaustadnes M, Hein AMK, Kruhøffer M, Laurberg S, Borre M, Wang K, Brunak S, Krainer AR, Tørring N, Dyrskjøt L, Andersen CL, Ørntoft TF
    Mol. Cell Proteomics 7(7):1214-24 doi:10.1074/mcp.M700590-MCP200, 2008
    PubMed
    Structural Insight into Epitopes in the Pregnancy-Associated Malaria Protein VAR2CSA
    Andersen P, Nielsen MA, Resende M, Rask TS, Dahlbäck M, Theander T, Lund O, Salanti A
    PLoS Pathog. 4(2):e42 doi:10.1371/journal.ppat.0040042, 2008
    PubMed
    Amino acid similarity accounts for T cell cross-reactivity and for \\\'holes\\\' in the T cell repertoire
    Frankild S, de Boer RJ, Lund O, Nielsen M, Kesmir C
    PLoS ONE 3(3):e1831 doi:10.1371/journal.pone.0001831, 2008
    PubMed
    Broadly Immunogenic HLA Class I Supertype-Restricted Elite CTL Epitopes Recognized in a Diverse Population Infected with Different HIV-1 Subtypes
    Pérez CL, Larsen MV, Gustafsson R, Norström MM, Atlas A, Nixon DF, Nielsen M, Lund O, Karlsson AC
    The Journal of Immunology. 180(7):5092-100, 2008
    PubMed
    Obesity - a social and physical risk
    Parlesak A, Krömker D
    J Dtsch Dermatol Ges 6(6):442-9 doi:10.1111/j.1610-0387.2008.06572.x, 2008
    PubMed
    Correction of technical bias in clinical microarray data improves concordance with known biological information
    Eklund AC, Szallasi Z
    Genome Biol. 9(2):R26 doi:10.1186/gb-2008-9-2-r26, 2008
    PubMed
    Web
    Phylogenetic relationships between Sarcocystis species from reindeer and other Sarcocystidae deduced from ssu rRNA gene sequences
    Dahlgren SS, Gouveia-Oliveira R, Gjerde B
    Vet. Parasitol. 151(1):27-35, 2008
    PubMed
    hERG Classification Model Based on a Combination of Support Vector Machine Method and GRIND Descriptors
    Li Q, Jørgensen FS, Oprea T, Brunak S, Taboureau O
    Mol. Pharm. 5(1):117-27 doi:10.1021/mp700124e, 2008
    PubMed
    Identification of biomarkers for genotyping Aspergilli using non-linear methods for clustering and classification
    Kouskoumvekaki I, Yang Z, Jonsdottir SO, Olsson L, Panagiotou G
    BMC Bioinformatics 9:59 doi:10.1186/1471-2105-9-59, 2008
    PubMed
    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
    Effect of gender on lipid-induced insulin resistance in obese subjects
    Vistisen B, Hellgren LI, Vadset T, Scheede-Bergdahl C, Helge JW, Dela F, Stallknecht B
    Eur. J. Endocrinol. 158(1):61-8 doi:10.1530/EJE-07-0493, 2008
    PubMed
    Epithelial cells prime the immune response to an array of gut-derived commensals towards a tolerogenic phenotype through distinct actions of thymic stromal lymphopoietin and transforming growth factor-beta
    Zeuthen LH, Fink LN, Frokiaer H
    Immunology 123(2):197-208, 2008
    PubMed

2007

    DASS: efficient discovery and p-value calculation of substructures in unordered data.
    Hollunder J, Friedel M, Beyer A, Workman CT, Wilhelm T
    Bioinformatics. 2007 Jan 1;23(1):77-83., 2007
    PubMed
    Integration of biological networks and gene expression data using Cytoscape.
    Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD
    Nature Protocols. 2007;2(10):2366-82., 2007
    PubMed
    Prediction of T-cell Epitopes for Therapeutic and Prophylactic Vaccines
    Larsen MV
    Ph.D. thesis, 2007
    Prediction and identification of B-cell epitopes using protein structure information
    Andersen PH
    Ph.D. thesis, 2007
    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
    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
    Characterization of near full-length genomes of HIV type 1 strains in Denmark: basis for a universal therapeutic vaccine
    Andresen BS, Vinner L, Tang ST, Bragstad K, Kronborg G, Gerstoft J, Corbet S, Fomsgaard A
    AIDS Res. Hum. Retroviruses 23(11):1442-8 doi:10.1089/aid.2007.0111, 2007
    PubMed
    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
    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
    Identification of putative noncoding RNA genes in the Burkholderia cenocepacia J2315 genome
    Coenye T, Drevinek P, Mahenthiralingam E, Shah SA, Gill RT, Vandamme P, Ussery DW
    FEMS Microbiol. Lett. 276(1):83-92, 2007
    PubMed
    Comparative genomic analysis of two-component regulatory proteins in Pseudomonas syringae
    Lavin JL, Kiil K, Resano O, Ussery DW, Oguiza JA
    BMC Genomics 8:397, 2007
    PubMed
    Link to article
    Synthesis of structured phospholipids by immobilized phospholipase A2 catalyzed acidolysis
    Vikbjerg A, Mu H, Xu X
    J. Biotechnol. 128(3):545-54, 2007
    PubMed
    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
    Increased lipids in non-lipogenic tissues are indicators of the severity of type 2 diabetes in mice
    Campbell JA, Hansen HS, Mu H, Mølgaard P
    Prostaglandins Leukot. Essent. Fatty Acids 76(1):9-18, 2007
    PubMed
    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
    Butter blend containing fish oil improves the level of n-3 fatty acids in biological tissues of hamster
    Porsgaard T, Overgaard J, Krogh AL, Jensen MB, Guo Z, Mu H
    Journal of Agricultural and Food Chemistry . 55(18):7615-9, 2007
    PubMed
    The Complete Genome Sequence and Analysis of the EpsilonproteobacteriumArcobacter butzleri
    Miller WG, Parker CT, Rubenfield M, Mendz GL, Wosten MM, Ussery DW, Stolz JF, Binnewies TT, Hallin PF, Wang G, Malek JA, Rogosin A, Stanker LH, Mandrell RE
    PLoS ONE 2(12):e1358, 2007
    PubMed
    Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray
    Willenbrock H, Hallin PF, Wassenaar TM, Ussery DW
    Genome Biol. 8(12):R267, 2007
    PubMed
    Antisense-mediated suppression of C-hordein biosynthesis in the barley grain results in correlated changes in the transcriptome, protein profile, and amino acid composition
    Hansen M, Lange M, Friis C, Dionisio G, Holm PB, Vincze E
    J. Exp. Bot. 58(14):3987-95, 2007
    PubMed
    Modeling the adaptive immune system: predictions and simulations
    Lundegaard C, Lund O, Kesmir C, Brunak S, Nielsen M
    Bioinformatics 23(24):3265-75, 2007
    PubMed
    Forsg med ny online eksamensform i \\
    Wernersson R
    DTU Avisen, 2007
    Computational Analysis and Modeling of Bacterial Pathogenesis
    Binnewies TT
    PhD thesis, 2007
    Kemoinformatik: Lær computeren at finde nye lægemidler
    Kouskoumvekaki I, Hansen NT, Jónsdóttir SÓ
    Dansk Kemi, 88(8),23-25, 2007
    Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction
    Larsen MV, Lundegaard C, Lamberth K, Buus S, Lund O, Nielsen M
    BMC Bioinformatics 8:424, 2007
    PubMed
    Integrative analysis for finding genes and networks involved in diabetes and other complex diseases
    Bergholdt R, Størling ZM, Lage K, Karlberg EO, Olason PI, Aalund M, Nerup J, Brunak S, Workman CT, Pociot F
    Genome Biol. 8(11):R253, 2007
    PubMed
    Proteomics analysis of cytokine-induced dysfunction and death in insulin-producing INS-1E cells: new insights into the pathways involved
    Hertog W, Overbergh L, Lage K, Ferreira GB, Maris M, Gysemans C, Flamez D, Cardozo AK, Van den Bergh G, Schoofs L, Arckens L, Moreau Y, Hansen DA, Eizirik DL, Waelkens E, Mathieu C
    Mol. Cell Proteomics 6(12):2180-99, 2007
    PubMed
    Kamp med og mod bakterier
    Jarmer H
    DTU-avisen, 27 April, nr. 5, 2007
    Det er ikke bare et fedt
    Hellgren LI
    Dansk Kemi, 88:14-6, 2007
    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
    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
    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
    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
    Evolution of cell cycle control: same molecular machines, different regulation
    de Lichtenberg U, Jensen TS, Brunak S, Bork P, Jensen LJ
    Cell Cycle 6(15):1819-25, 2007
    PubMed
    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
    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
    Structure and Content of the Entamoeba histolytica Genome
    Clark CG, Alsmark UCM, Tazreiter M, Saito Y, Nakano, Ali V, Marion S, Weber C, Mukherjee C, Bruchhaus I, Tannich E, Leippe M, Sicheritz-Ponten T, Foster PG, Samuelson J, Noël CJ, Hirt RP, Embley TM, Gilchrist CA, Mann BJ, Singh U, Ackers JP, Bhattacharya S, Bhattacharya S, Lohia A, Guillén N, Duchêne M, Nozaki T, Hall N
    Adv. Parasitol. 65:51-190, 2007
    PubMed
    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
    Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2
    Miller ML, Hanke S, Hinsby AM, Friis C, Brunak S, Mann M, Blom N
    Mol. Cell Proteomics 7(1):181-92, 2007
    PubMed
    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
    Human antigen-presenting cells respond differently to gut-derived probiotic bacteria but mediate similar strain-dependent NK and T cell activation
    Fink LN, Zeuthen LH, Ferlazzo G, Frøkiær H
    FEMS Immunol. Med. Microbiol. 51(3):535-46, 2007
    PubMed
    Distinct gut-derived lactic acid bacteria elicit divergent dendritic cell-mediated NK cell responses
    Fink LN, Zeuthen LH, Christensen HR, Morandi B, Frøkiær H, Ferlazzo G
    International Immunology. 19(12):1319-27, 2007
    PubMed
    HLA Alleles Associated with Slow Progression to AIDS Truly Prefer to Present HIV-1 p24
    Borghans JA, Molgaard A, de Boer RJ, Kesmir C
    PLoS ONE 2(9):e920, 2007
    PubMed
    Branchio-Oto-Renal Syndrome: Detection of EYA1 and SIX1 mutations in five out of six Danish families by combining linkage, sequencing and MLPA analyses
    Sanggaard KM, Kjaer KW, Eiberg H, Rendtorff ND, Johnsen T, Gimsing S, Dyrmose J, Nielsen KO, Lage K, Tranebjærg L
    Eur. J. Hum. Genet. 15(11):1121-31, 2007
    PubMed
    Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina
    Arvas MM, Kivioja T, Mitchell A, Saloheimo M, Ussery DW, Penttila M, Oliver S
    BMC Genomics 8:325, 2007
    PubMed
    Dice & DNA
    Wernersson R
    BioScience Education e-journal, (in press), 2007
    Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method
    Nielsen M, Lundegaard C, Lund O
    BMC Bioinformatics 8:238, 2007
    PubMed
    Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis
    Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, Wortman JR, Bidwell SL, Alsmark UC, Besteiro S, Sicheritz-Ponten T, Noel CJ, Dacks JB, Foster PG, Simillion C, Van de Peer Y, Miranda-Saavedra D, Barton GJ, Westrop GD, Müller S, Dessi D, Fiori PL, Ren Q, Paulsen I, Zhang H, Bastida-Corcuera FD, Simoes-Barbosa A, Brown MT, Hayes RD, Mukherjee M, Okumura CY, Schneider R, Smith AJ, Vanacova S, Villalvazo M, Haas BJ, Pertea M, Feldblyum TV, Utterback TR, Shu CL, Osoegawa K, de Jong PJ, Hrdy I, Horvathova L, Zubacova Z, Dolezal P, Malik SB, Logsdon JM Jr, Henze K, Gupta A, Wang CC, Dunne RL, Upcroft JA, Upcroft P, White O, Salzberg SL, Tang P, Chiu CH, Lee YS, Embley TM, Coombs GH, Mottram JC, Tachezy J, Fraser-Liggett CM, Johnson PJ
    Science 315(5809):207-12, 2007
    PubMed
    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
    Finding Coevolving Amino acid Residues using Row and Column Weighing of Mutual Information and Multi-Dimensional Amino acid Representation
    Gouveia-Oliveira R, Pedersen AG
    Algorithms Mol Biol 2:12, 2007
    PubMed
    PDF
    NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence
    Nielsen M, Lundegaard C, Blicher T, Lamberth K, Harndahl M, Justesen S, Roder G, Peters B, Sette A, Lund O, Buus S
    PLoS ONE 2(8):e796, 2007
    PubMed
    Structure-function analysis of the ER oxidoreductase TMX3 reveals inter-domain stabilization of the N-terminal redox-active domain
    Haugstetter J, Maurer MA, Blicher T, Pagac M, Wider G, Ellgaard L
    The Journal of Biological Chemistry. 282(46):33859-67, 2007
    PubMed
    The essential YycFG two-component system controls cell wall metabolism in Bacillus subtilis
    Bisicchia P,Noone D,Lioliou E,Howell A,Quigley S,Jensen T,Jarmer H,Devine KM
    Mol. Microbiol. 65(1):180-200, 2007
    PubMed
    CycleBase.org - a comprehensive multi-organism online database of cell-cycle experiments
    Gauthier NP, Jensen TS, de Lichtenberg U, Wernersson R, Larsen ME, Brunak S
    Nucleic Acids Res. (in press), 2007
    Web
    Probe Selection for DNA Microarrays using OligoWiz
    Wernersson R, Juncker AS, Nielsen HB
    Nat Protoc 2(11):2677-91, 2007
    PubMed
    SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation
    Panitz F, Stengaard H, Hornshøj H, Gorodkin J, Hedegaard J, Cirera S, Thomsen B, Madsen LB, Høj A, Vingborg RK, Zahn B, Wang X, Wang X, Wernersson R, Jørgensen CB, Scheibye-Knudsen K, Arvin T, Lumholdt S, Sawera M, Green T, Nielsen BJ, Havgaard JH, Brunak S, Fredholm M, Bendixen C
    Bioinformatics 23(13):i387-91, 2007
    PubMed
    Web
    Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags
    Gorodkin J, Cirera S, Hedegaard J, Gilchrist MJ, Panitz F, Jørgensen C, Scheibye-Knudsen K, Arvin T, Lumholdt S, Sawera M, Green T, Nielsen BJ, Havgaard JH, Rosenkilde C, Wang J, Li H, Li R, Liu B, Hu S, Dong W, Li W, Yu J, Wang J, Staerfeldt HH, Wernersson R, Madsen LB, Thomsen B, Hornshøj H, Bujie Z, Wang X, Wang X, Bolund L, Brunak S, Yang H, Bendixen C, Fredholm M
    Genome Biol. 8(4):R45, 2007
    PubMed
    Web
    MaxAlign: maximizing usable data in an alignment
    Gouveia-Oliveira R, Sackett PW, Pedersen AG
    BMC Bioinformatics 8:312, 2007
    PubMed
    PDF
    Functional Associations by Response Overlap (FARO), a functional genomics approach matching gene expression phenotypes
    Nielsen HB, Mundy J, Willenbrock H
    PLoS ONE 2(7):e676, 2007
    PubMed
    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
    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
    PDF
    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
    A high-quality catalog of the Drosophila melanogaster proteome
    Brunner E, Ahrens CH, Mohanty S, Baetschmann H, Loevenich S, Potthast F, Deutsch EW, Panse C, de Lichtenberg U, Rinner O, Lee H, Pedrioli PG, Malmstrom J, Koehler K, Schrimpf S, Krijgsveld J, Kregenow F, Heck AJ, Hafen E, Schlapbach R, Aebersold R
    Nat. Biotechnol. 25(5):576-83, 2007
    PubMed
    The implications of alternative splicing in the ENCODE protein complement
    Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PI, Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA, Lopez G, Sadowski MI, Watson JD, Fariselli P, Rossi I, Nagy A, Wang K, Storling Z, Orsini M, Assenov Y, Blankenburg H, Huthmacher C, Ramirez F, Schlicker A, Denoued F, Jones P, Kerrien S, Orchard S, Antonarakis SE, Reymond A, Birney E, Brunak S, Casadio R, Guigo R, Harrow J, Hermjakob H, Jones DT, Lengauer T, Orengo CA, Patthy L, Thornton JM, Tramontano A, Valencia A
    Proc. Natl. Acad. Sci. U.S.A. 104(13):5495-500, 2007
    PubMed
    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
    Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88
    Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, Turner G, de Vries RP, Albang R, Albermann K, Andersen MR, Bendtsen JD, Benen JA, van den Berg M, Breestraat S, Caddick MX, Contreras R, Cornell M, Coutinho PM, Danchin EG, Debets AJ, Dekker P, van Dijck PW, van Dijk A, Dijkhuizen L, Driessen AJ, d\'Enfert C, Geysens S, Goosen C, Groot GS, de Groot PW, Guillemette T, Henrissat B, Herweijer M, van den Hombergh JP, van den Hondel CA, van der Heijden RT, van der Kaaij RM, Klis FM, Kools HJ, Kubicek CP, van Kuyk PA, Lauber J, Lu X, van der Maarel MJ, Meulenberg R, Menke H, Mortimer MA, Nielsen J, Oliver SG, Olsthoorn M, Pal K, van Peij NN, Ram AF, Rinas U, Roubos JA, Sagt CM, Schmoll M, Sun J, Ussery D, Varga J, Vervecken W, van de Vondervoort PJ, Wedler H, Wosten HA, Zeng AP, van Ooyen AJ, Visser J, Stam H
    Nat. Biotechnol. 25(2):221-31, 2007
    PubMed
    Prediction of highly expressed genes in microbes based on chromatin accessibility
    Willenbrock H, Ussery DW
    BMC Mol. Biol. 8:11, 2007
    PubMed
    Link to BMC Molecular Biology file
    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
    RNAmmer: consistent and rapid annotation of ribosomal RNA genes
    Lagesen K, Hallin P, Rødland EA, Stærfeldt HH, Rognes T, Ussery DW
    Nucleic Acids Res. 35(9):3100-8, 2007
    PubMed
    Genome-wide analysis of the Arabidopsis leaf transcriptome reveals interaction of phosphate and sugar metabolism
    Muller R, Morant M, Jarmer H, Nilsson L, Nielsen TH
    Plant Physiology. 143(1):156-71, 2007
    PubMed
    Midbrain expression of Delta-like 1 homologue is regulated by GDNF and is associated with dopaminergic differentiation
    Christophersen NS, Gronborg M, Petersen TN, Fjord-Larsen L, Jorgensen JR, Juliusson B, Blom N, Rosenblad C, Brundin P
    Exp. Neurol. 204(2):791-801, 2007
    PubMed
    Prediction of protein phosphorylation sites in yeast
    Ingrell CR, Miller ML, Jensen ON, Blom N
    Bioinformatics 23(7):895-7, 2007
    PubMed
    Human pregnancy-associated malaria-specific B cells target polymorphic, conformational epitopes in VAR2CSA
    Barfod L, Bernasconi NL, Dahlback M, Jarrossay D, Andersen PH, Salanti A, Ofori MF, Turner L, Resende M, Nielsen MA, Theander TG, Sallusto F, Lanzavecchia A, Hviid L
    Mol. Microbiol. 63(2):335-47, 2007
    PubMed
    Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools
    Greenbaum JA, Andersen PH, Blythe M, Bui HH, Cachau RE, Crowe J, Davies M, Kolaskar AS, Lund O, Morrison S, Mumey B, Ofran Y, Pellequer JL, Pinilla C, Ponomarenko JV, Raghava GP, van Regenmortel MH, Roggen EL, Sette A, Schlessinger A, Sollner J, Zand M, Peters B
    J. Mol. Recognit. 20(2):75-82, 2007
    PubMed
    A human phenome-interactome network of protein complexes implicated in genetic disorders
    Lage K, Karlberg EO, Storling ZM, Olason PI, Pedersen AG, Rigina O, Hinsby AM, Tumer Z, Pociot F, Tommerup N, Moreau Y, Brunak S
    Nat. Biotechnol. 25(3):309-16, 2007
    PubMed
    Identification of a novel Mannheimia granulomatis lineage from pathological lesions in roe deer (Capreolus capreolus)
    Bojesen AM, Larsen J, Pedersen AG, Mörner T, Mattson R, Bisgaard M
    J. Wildl. Dis. 43(3):345-52, 2007
    PubMed
    Publication download
    Improving comparability between microarray probe signals by thermodynamic intensity correction
    Bruun GM, Wernersson R, Juncker AS, Willenbrock H, Nielsen HB
    Nucleic Acids Res. 35(7):e48, 2007
    PubMed
    Web
    Investigating Signs of Recent Evolution in the Pool of Pro-viral DNA during Years of Successful HAART
    Mens H, Pedersen AG, Jørgensen LB, Hue S, Gerstoft J, Katzenstein TL
    AIDS Res. Hum. Retroviruses 23(1):107-15, 2007
    PubMed
    Publication download

2006

    A systems approach to mapping DNA damage response pathways.
    Workman CT, Mak HC, McCuine S, Tagne JB, Agarwal M, Ozier O, Begley TJ, Samson LD, Ideker T
    Science. 2006 May 19;312(5776):1054-9., 2006
    PubMed
    Integrated assessment and prediction of transcription factor binding.
    Beyer A, Workman C, Hollunder J, Radke D, Möller U, Wilhelm T, Ideker T
    PLoS Computational Biology. 2006 Jun 16;2(6):e70., 2006
    PubMed
    Barley genes in action: Transcriptome analysis of developing barley embryos
    Nielsen ME
    Ph.D. thesis, 2006
    DNA Microarrays in Comparative Genomics and Transcriptomics
    Willenbrock H
    Ph.D. thesis, 2006
    Dynamics of chromosome segregation in bacteria
    Nielsen HJ
    Ph.D. thesis, 2006
    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
    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
    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
    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
    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
    Insights into the quality of DnaA boxes and their cooperativity
    Hansen FG, Christensen BB, Nielsen CB, Atlung T
    J. Mol. Biol. 355(1):85-95, 2006
    PubMed
    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
    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
    FeatureMap3D - a tool to map protein features and sequence conservation onto homologous structures in the PDB
    Wernersson R, Rapacki K, Staerfeldt HH, Sackett PW, Mølgaard A
    Nucleic Acids Res. 34:W84-8, 2006
    PubMed
    Web
    Virtual Ribosome - a comprehensive DNA translation tool with support for integration of sequence feature annotation
    Wernersson R
    Nucleic Acids Res. 34:W385-8, 2006
    PubMed
    Web
    Mesoscopic Simulations of Biological Membranes
    Smit B, Kranenburg K, Sperotto MM, Venturoli M
    Lect. Notes Phys. 704, 259-286, 2006
    Modelling of proteins in membranes
    Sperotto MM, May S, Baumgaertner A
    Chemistry and Physics of Lipids 141:2-29, 2006
    PubMed
    Mesoscopic Models of Biological Membranes
    Venturoli M, Sperotto MM, Kranenburg M, Smit B
    Physics Reports, 437: 1-54, 2006
    TAP-Independent MHC Class I Presentation
    Larsen MV, Nielsen M, Weinzierl A, Lund O
    Curr Immunol Rev, 2, 233-245, 2006
    Opening the pan-genomics box
    Read T, Ussery DW
    Current Opinion in Microbiology, 9:496-498, 2006
    Design of a 7 Genomes Escherichia coli Microarray for Comparative Genomic Profiling
    Willenbrock H, Petersen A, Sekse C, Kiil K, Wasteson Y, Ussery DW
    J. Bacteriol. 188(22):7713-21, 2006
    PubMed
    Leaner and Meaner Genomes in Escherichia coli
    Ussery DW
    Genome Biol. 7(10):237, 2006
    PubMed
    An environmental signature for 323 microbial genomes based on codon adaptation indices
    Willenbrock H, Friis C, Juncker AS, Ussery DW
    Genome Biol. 7(12):R114, 2006
    PubMed
    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
    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
    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
    The validity of predicted T-cell epitopes
    Lundegaard C, Nielsen M, Lund O
    Trends Biotechnol. 24(12):537-8, 2006
    PubMed
    CTL epitopes for influenza A including the H5N1 bird flu; genome-, pathogen-, and HLA-wide screening
    Wang M, Lamberth K, Harndahl M, Roder G, Stryhn A, Larsen MV, Nielsen M, Lundegaard C, Tang ST, Dziegiel MH, Rosenkvist J, Pedersen AE, Buus S, Claesson MH, Lund O
    Vaccine 25(15):2823-31, 2006
    PubMed
    Prediction of pH-Dependent Aqueous Solubility of Druglike Molecules
    Hansen NT, Kouskoumvekaki I, Jørgensen FS, Brunak S, Jónsdóttir SÓ
    J Chem Inf Model 46(6):2601-9, 2006
    PubMed
    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
    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
    Analysis and prediction of mammalian protein glycation
    Johansen MB, Kiemer L, Brunak S
    Glycobiology 16(9):844-53, 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
    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
    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
    Epitope mapping and topographic analysis of VAR2CSA DBL3X involved in P. falciparum placental sequestration
    Dahlbäck M, Rask TS, Andersen PH, Nielsen MA, Ndam NT, Resende M, Turner L, Deloron P, Lund O, Pedersen AG, Hviid L, Theander TG, Salanti A
    PLoS Pathog. 2(11):e124, 2006
    PubMed
    PDF
    Protein Evolution is Faster Outside the Cell
    Julenius K, Pedersen AG
    Mol. Biol. Evol. 23(11):2039-48, 2006
    PubMed
    PDF
    The genomic code: inferring Vibrionaceae niche specialization
    Reen FJ, Almagro-Moreno S, Ussery D et al
    Nat. Rev. Microbiol. 4(9):697-704, 2006
    PubMed
    Distinct developmental defense activations in barley embryos identified by transcriptome profiling
    Nielsen ME, Lok F, Nielsen HB
    Plant Mol. Biol. 61:589-601, 2006
    PubMed
    Identification of Tn5397-like and Tn916-like transposons and diversity of the tetracycline resistance gene tet(M) in enterococci from humans, pigs and poultry
    Agersø Y, Pedersen AG, Aarestrup FM
    Journal of Antimicrobial Chemotherapy. 57(5):832-9, 2006
    PubMed
    PDF
    Transcriptome analysis of FSH and FSH variant stimulation in granulosa cells from IVM patients reveals novel regulated genes
    Perlman S, Bouquin T, van den Hazel B, Jensen TH, Schambye HT, Knudsen S, Okkels JS
    Mol. Hum. Reprod. 12(3):135-44, 2006
    PubMed
    The more the merrier: comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast
    Marguerat S, Jensen TS, de Lichtenberg U, Wilhelm BT, Jensen LJ, Bahler J
    Yeast 23(4):261-77, 2006
    PubMed
    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
    Mol. Cell 22(2):285-95, 2006
    PubMed
    Structural features of fungal genomes
    Wanchanthuek P, Hallin PF, Gouveia-Oliveira R, Ussery DW
    Topics in Current Genetics, 15, 47-77, 2006
    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
    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
    Genome update: purine strand bias in 280 bacterial genomes
    Champ PC, Binnewies TT, Nielsen N, Zinman G, Kiil K, Wu H, Bohlin J, Ussery DW
    Microbiology (Reading, Engl.) 152:579-83, 2006
    PubMed
    Identification of novel genes regulated in the developing human ventral mesencephalon
    Jorgensen JR, Juliusson B, Henriksen KF, Hansen C, Knudsen S, Petersen TN, Blom N, Seiger A, Wahlberg LU
    Exp. Neurol. 198(2):427-37, 2006
    PubMed
    Crosstalk
    Mundy J, Nielsen HB, Brodersen P
    Trends Plant Sci. 11(2):63-4, 2006
    PubMed
    Origin of Replication in Circular Prokaryotic Chromosomes
    Worning P, Jensen LJ, Hallin PF, Stærfeldt HH, Ussery DW
    Environ. Microbiol. 8(2):353-61, 2006
    PubMed

2005

    enoLOGOS: a versatile web tool for energy normalized sequence logos.
    Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, Benos PV
    Nucleic Acids Research. 2005 Jul 1;33(Web Server issue):W389-92., 2005
    PubMed
    Preprocessing High-density Oligonucleotide Arrays
    Bolstad B, Irizarry R, Gautier L, Wu Z
    Statistics for Biology and Health, Springer, 2005
    Relevant URL
    Systematic discovery of new recognition peptides mediating protein interaction netoworks
    Neduva V, Linding R, Su-Angrand I, Stark A, De Masi F, Gibson T, Lewis J, Serrano L, Russell R
    PLoS Biol. 3(12):e405, 2005
    PubMed
    High throughput production of mouse monoclonal antibodies using antigen microarrays
    De Masi F, Chiarella P, Wilhelm H, Massimi M, Bullard B, Ansorge W, Sawyer A
    Proteomics 5(16):4070-81, 2005
    PubMed
    Integrating protein feature based predictions into S ystems Biology
    Fausbøll A
    Ph.D. thesis, 2005
    Interactions between milk proteins and the immune system: modulation of nonspecific and antigen-specific immune responses
    Brix S
    ISBN: 87-991021-0-2, 2005
    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
    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
    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
    Maternal transfer of oral tolerance to ingested soy proteins
    Christensen HR, Brix S, Frokiaer H
    Immunology, 116:61-61 Suppl. 1 Dec (2005), 2005
    The 3\' region of human papillomavirus type 16 early mRNAs decrease expression
    Vinther J, Rosenstierne MW, Kristiansen K, Norrild B
    BMC Infect. Dis. 5:83, 2005
    PubMed
    Genome Update: Protein secretion systems in 225 bacterial genomes
    Binnewies TT, Bendtsen JD, Hallin PF, Nielsen N, Wassenaar TM, Pedersen MB, Klemm P, Ussery DW
    Microbiology (Reading, Engl.) 151:1013-6, 2005
    PubMed
    Simulation studies of protein-induced bilayer deformations, and lipid-induced protein tilting, on a mesoscopic model for lipid bilayers with embedded proteins
    Venturoli M, Smit B, Sperotto MM
    Biophys. J. 88(3):1778-98, 2005
    PubMed
    Selection of proteins for human MHC class II presentation
    Jiang L, Lund O, Tan JQ
    Cell. Mol. Immunol. 2(1):49-56, 2005
    PubMed
    Extracytoplasmic function sigma factors in Pseudomona syringae
    Oguiza JA, Kiil K, Ussery DW
    Trends Microbiol. 13(12):565-8, 2005
    PubMed
    Genome opdate: Protein secretion systems in 225 bacterial genomes
    Bennewies TT, Bendtsen JD, Hallin PF, Nielsen N, Wassenaar TM, Pedersen MB, Klemm P, Ussery DW
    Microbiology (Reading, Engl.) 151:1013-6, 2005
    PubMed
    Genome update: Prediction of secreted proteins in 225 bacterial proteomes
    Bendtsen JD, Binnewies TT, Hallin PF, Sicheritz-Pontén T, Ussery DW
    Microbiology (Reading, Engl.) 151:1725-7, 2005
    PubMed
    The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota
    Chen LM, Brugger K, Skovgaard M, Redder P, She QX, Torarinsson E, Greve B, Awayez M, Zibat A, Klenk HP, Garrett RA
    J. Bacteriol. 187(14):4992-9, 2005
    PubMed
    Genome update: Prediction of membrane proteins in prokaryotic genomes
    Bendtsen JD, Binnewies TT, Hallin PF, Ussery DW
    Microbiology (Reading, Engl.) 151:2119-21, 2005
    PubMed
    Alcohol-induced surface attachment of Listeria monocytogenes: Which mechanisms lie behind?
    Knudsen B, Jarmer H, Knochel S, Gravesen A
    Biotechnology, 118, 158-158, 2005
    Temporal interactome for the eukaryotic cell cycle by data integration
    Brunak S
    Biotechnology, 118, 7-8, 2005
    Genome update: Sigma factors in 240 bacterial genomes
    Kiil K, Binnewies TT, Sicheritz-Pontén T, Willenbrock H, Hallin PF, Wassenaart TM, Ussery DW
    Microbiology (Reading, Engl.) 151:3147-50, 2005
    PubMed
    Improvement of galactose uptake in Saccharomyces cerevisiae through overexpression of phosphoglucomutase: Example of transcript analysis as a tool in inverse metabolic engineering
    Bro C, Knudsen S, Regenberg B, Olsson L, Nielsen J
    Appl. Environ. Microbiol. 71(11):6465-72, 2005
    PubMed
    A comparison study: Applying segmentation to array CGH data for downstream analyses
    Willenbrock H, Fridlyand J
    Bioinformatics 21(22):4084-91, 2005
    PubMed
    Genome update: Distribution of two.component trensduction systems in 250 bacterial genomes
    Kiil K, Ferchaud JB, David C, Binnewies T, Wu H, Sicheritz-Pontén T, Willenbrock H, Ussery DW
    Microbiology (Reading, Engl.) 151:3447-52, 2005
    PubMed
    Genetic evolution of HIV in patients remaining on a stable HAART regimen despite insufficient viral suppression
    Kristiansen TB, Pedersen AG, Eugen-Olsen J, Katzenstein TL, Lundgren JD
    Scand. J. Infect. Dis. 37:890-901, 2005
    PubMed
    Publication download
    Presence of a functional but dispensable Nuclear Export Signal in the HTLV-2 Tax protein
    Chevalier SA, Meertens L, Calattini S, Gessain A, Kiemer L, Mahieux R
    Retrovirology 2:70, 2005
    PubMed
    Integrating protein annotation resources through the Distributed Annotation System
    Olason PI
    Nucleic Acids Res. 33:W468-70, 2005
    PubMed
    New weakly expressed cell cycle-regulated genes in yeast
    Hansen B, Schmidt P, Fausboll A, de Lichtenberg U, Wernersson R, Skøt Jensen T, Nielsen HB, Knudsen S, Brunak S
    Yeast 22(15):1191-201, 2005
    PubMed
    Non-classical protein secretion in bacteria
    Bendtsen J, Kiemer L, Fausboll A, Brunak S
    BMC Microbiol. 5:58, 2005
    PubMed
    Identification and analysis of 21 novel disease-causing amino acid substitutions in the conserved part of ATP7A
    Moller LB, Bukrinsky JT, Molgaard A, Paulsen M, Lund C, Tumer Z, Larsen S, Horn N
    Hum. Mutat. 26(2):84-93, 2005
    PubMed
    The design and implementation of the immune epitope database and analysis resource
    Peters B, Sidney J, Bourne P, Bui HH, Buus S, Doh G, Fleri W, Kronenberg M, Kubo R, Lund O, Nemazee D, Ponomarenko JV, Sathiamurthy M, Schoenberger SP, Stewart S, Surko P, Way S, Wilson S, Sette A
    Immunogenetics 57(5):326-36, 2005
    PubMed
    Crystal ball. Systems biology: in the broadest sense of the word
    Ussery DW, de Lichtenberg U, Jensen LJ
    Environ. Microbiol. 7(4):482-3, 2005
    PubMed
    A Systems Biology Investigation and Comparison of the Cell Cycle in Eukaryotic Cells
    Jensen TS
    Ph.D. thesis, 2005
    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(8):2295-303, 2005
    PubMed
    Limited Inter- and Intra-patient Sequence Diversity of the Genetic Lineage A human metapneumovirus fusion gene
    Winther TN, Madsen CD, Pedersen AG, von Linstow ML, Eugen-Olsen J, Hogh B
    Virus Genes 31(1):89-97, 2005
    PubMed
    Publication download
    Characterization of rotavirus strains in a Danish population: high frequency of mixed infections and diversity within the VP4 gene of P [8] strains
    Fischer TK, Eugen-Olsen J, Pedersen AG, Molbak K, Bottiger B, Rostgaard K, Nielsen NM
    Journal of Clinical Microbiology. 43(3):1099-104, 2005
    PubMed
    Publication download
    OligoWiz 2.0 - Integrating sequence feature annotation into the design of microarray probes
    Wernersson R, Nielsen HB
    The EMBO Journal . 24(14):2579-89, 2005
    PubMed
    The MAP kinase substrate MKS1 is a regulator of plant defense responses
    Andreasson E, Jenkins T, Brodersen P, Thorgrimsen S, Petersen NH, Zhu S, Qiu JL, Micheelsen P, Rocher A, Petersen M, Newman MA, Nielsen HB, Hirt H, Somssich I, Mattsson O, Mundy J
    The EMBO Journal . 24(14):2579-89, 2005
    PubMed
    Prediction of twin-arginine signal peptides
    Bendtsen JD, Nielsen H, Widdick D, Palmer T, Brunak S
    BMC Bioinformatics 6:167, 2005
    PubMed
    FeatureExtract--extraction of sequence annotation made easy
    Wernersson R
    Nucleic Acids Res. 33:W567-9, 2005
    PubMed
    Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing
    Wernersson R, Schierup MH, Jorgensen FG, Gorodkin J, Panitz F, Staerfeldt HH, Christensen OF, Mailund T, Hornshoj H, Klein A, Wang J, Liu B, Hu S, Dong W, Li W, Wong GK, Yu J, Wang J, Bendixen C, Fredholm M, Brunak S, Yang H, Bolund L
    BMC Genomics 6:70, 2005
    PubMed
    Implementation of a gene expression index cal-culation method based on the PDNN model
    Nielsen HB, Gautier L, Knudsen S
    Bioinformatics 21(5):687-8, 2005
    PubMed
    Comparison of computational methods for the identification of cell cycle-regulated genes
    de Lichtenberg U, Jensen LJ, Fausboll A, Jensen TS, Bork P, Brunak S
    Bioinformatics 21(7):1164-71, 2005
    PubMed
    The genome of the protist parasite Entamoeba histolytica
    Loftus B, Anderson I, Davies R, Alsmark UC, Samuelson J, Amedeo P, Roncaglia P, Berriman M, Hirt RP, Mann BJ, Nozaki T, Suh B, Pop M, Duchene M, Ackers J, Tannich E, Leippe M, Hofer M, Bruchhaus I, Willhoeft U, Bhattacharya A, Chillingworth T, Churcher C, Hance Z, Harris B, Harris D, Jagels K, Moule S, Mungall K, Ormond D, Squares R, Whitehead S, Quail MA, Rabbinowitsch E, Norbertczak H, Price C, Wang Z, Guillen N, Gilchrist C, Stroup SE, Bhattacharya S, Lohia A, Foster PG, Sicheritz-Pontén T, Weber C, Singh U, Mukherjee C, El-Sayed NM, Petri WA Jr, Clark CG, Embley TM, Barrell B, Fraser CM, Hall N
    Nature 433(7028):865-8, 2005
    PubMed
    The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage
    Nielsen M, Lundegaard C, Lund O, Kesmir C
    Immunogenetics 57:33-41, 2005
    PubMed
    The Immune Epitope Database and Analysis Resource: From Vision to Blueprint
    Peters B, Sidney J, Bourne P, Bui HH, Buus S, Doh G, Fleri W, Kronenberg M, Kubo R, Lund O, Nemazee D, Ponomarenko JV, Sathiamurthy M, Schoenberger S, Stewart S, Surko P, Way S, Wilson S, Sette A
    PLoS Biol. 3(3):e91, 2005
    PubMed
    Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates
    Jonsdottir SO, Jorgensen FS, Brunak S
    Bioinformatics 21(10):2145-60, 2005
    PubMed
    Genome Update: proteome comparisons
    Binnewies TT, Hallin PF, Staerfeldt HH, Ussery DW
    Microbiology (Reading, Engl.) 151:1-4, 2005
    PubMed
    Genome update: 2D clustering of bacterial genomes
    Willenbrock H, Binnewies TT, Hallin PF, Ussery DW
    Microbiology (Reading, Engl.) 151:333-6, 2005
    PubMed
    Genome update: base skews in 200+ bacterial chromosomes
    Hallin PF, Nielsen N, Devine KM, Binnewies TT, Willenbrock H, Ussery DW
    Microbiology (Reading, Engl.) 151:633-7, 2005
    PubMed
    Lid L11 of the glutamine amidotransferase domain of CTP synthase mediates allosteric GTP activation of glutaminase activity
    Willemoës M, Mølgaard A, Johansson E, Martinussen J
    FEBS Journal. 272(3):856-64, 2005
    PubMed
    Dynamic Complex Formation During the Yeast Cell Cycle
    de Lichtenberg U, Jensen LJ, Brunak S, Bork P
    Science 307(5710):724-7, 2005
    PubMed

2004

    Alternative mapping of probes to genes for affymetrix chips
    Gautier L, Møller M, Friis-Hansen L, Knudsen L
    BMC Bioinformatics 5:111, 2004
    PubMed
    Relevant URL
    Det vi spiser påvirker vores immunforsvar – men hvordan?
    Christensen HR, Kjaer TMR, Brix S, Frokiaer H
    Dansk Kemi, 84:26-27 (2004), 2004
    Immune response in mice to ingested soya protein: antibody production, oral tolerance and maternal transfer
    Christensen HR, Brix S, Frøkiær H
    Br. J. Nutr. 91(5):725-32, 2004
    PubMed
    Lipopolysaccharide contamination of beta-lactoglobulin affects the immune response against intraperitoneally and orally administrated antigen
    Brix S, Kjær TMR, Barkholt V, Frøkiær H
    Int Arch Allergy Immunol, 135:216-220 (2004), 2004
    Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins
    Diella F, Cameron S, Gemünd C, Linding R, Via A, Kuster B, Sicheritz-Pontén T, Blom N, Gibson TJ
    BMC Bioinformatics 5:79, 2004
    PubMed
    DNA bendability and Nucleosome positioning in transcriptional regulation
    Dlakic M, Brunak S, Ussery DW
    DNA Conformation in Transcription, chapter 14, 2004
    Transcriptional profiling of extracellular amino acid in Saccharomyces cerevisiae and the role of St1p and Stp2p
    Eckert-Boulet N, Nielsen PS, Friis C, dos Santos MM, Nielsen J, Kielland-Brandt MC, Regenberg B
    Yeast 21(8):635-48, 2004
    PubMed
    Biological Sequence Analysis of Archeal Genomes
    Skovgaard M
    Ph.D. thesis, 2004
    Analysis and Prediction of Translocation Signals in Eukaryotes and Prokaryotes
    Bendtsen JD
    Ph.D. thesis, 2004
    Integrative Approaches to the Analysis of Microarrays Expression Data: Application to High-density nucleotide Arrays
    Gautier L
    Ph.D. thesis, 2004
    Distribution and characterization of staphylococcal interspersed repeat units (SIRUs) and potential use for strain differentiation
    Hardy KJ, Ussery DW, Oppenheim BA, Hawkey PM
    Microbiology (Reading, Engl.) 150:4045-52, 2004
    PubMed
    Structure-function analysis of the human sialyltransferase ST3Gal I: role of n-glycosylation and a novel conserved sialylmotif
    Jeanneau C, Chazalet V, Auge C, Soumpasis DM, Harduin-Lepers A, Delannoy P, Imberty A, Breton C
    The Journal of Biological Chemistry. 279(14):13461-8, 2004
    PubMed
    QSPR models for various physical properties of carbohydrates based on molecular mechanics and quantum chemical calculations
    Dyekjaer JD, Jonsdottir SO
    Carbohydr. Res. 339(2):269-80, 2004
    PubMed
    ShcA regulates neurite outgrowth stimulated by neural cell adhesion molecule but not by fibroblast growth factor 2: evidence for a distinct fibroblast growth factor receptor response to neural cell adhesion molecule activation
    Hinsby AM, Lundfald L, Ditlevsen DK, Korshunova I, Juhl L, Meakin SO, Berezin V, Bock E
    J. Neurochem. 91(3):694-703, 2004
    PubMed
    Definition of supertypes for HLA molecules using clustering of specificity matrices
    Lund O, Nielsen M, Kesmir C, Pedersen AG, Lundegaard C, Worning P, Sylvester-Hvid C, Lamberth K, Roder G, Justesen S, Buus S, Brunak S
    Immunogenetics 55(12):797-810, 2004
    PubMed
    Genome update: correlation of bacterial genomic properties
    Hallin PF, Coenye T, Binnewies TT, Jarmer H, Staerfeldt HH, Ussery DW
    Microbiology (Reading, Engl.) 150:3899-903, 2004
    PubMed
    Identification of a core set of genes that signifies pathways underlying cardiac hypertrophy
    Strøm CC, Kruhøffer M, Knudsen S, Stensgaard-Hansen F, Jonassen TE, Ørntoft TF, Haunsø S, Sheikh SP
    Comp. Funct. Genomics 5:459-70 doi:10.1002/cfg.428, 2004
    PubMed
    Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites
    Julenius K, Mølgaard A, Gupta R, Brunak S
    Glycobiology 15(2):153-64, 2004
    PubMed
    Genome Update: DNA repeats in bacterial genomes
    Ussery DW, Binnewies TT, Gouveia-Oliveira R, Jarmer H, Hallin PF
    Microbiology (Reading, Engl.) 150:3519-21, 2004
    PubMed
    Genome Update: alignment
    Ussery DW, Jensen MS, Poulsen TR, Hallin PF
    Microbiology (Reading, Engl.) 150:2491-3, 2004
    PubMed
    NetAcet: prediction of N-terminal acetylation sites
    Kiemer L, Bendtsen JB, Blom N
    Bioinformatics 21(7):1269-70, 2004
    PubMed
    Chromatin architecture and gene expression in Escherichia coli
    Willenbrock H, Ussery DW
    Genome Biol. 5(12):252, 2004
    PubMed
    Genome update: chromosome atlases
    Hallin PF, Binnewies TT, Ussery DW
    Microbiology (Reading, Engl.) 150:3091-3, 2004
    PubMed
    Complete DNA sequence of the linear mitochondrial genome of the pathogenic yeast Candida parapsilosis
    Nosek J, Novotna M, Hlavatovicova Z, Ussery DW, Fajkus J, Tomaska L
    Mol. Genet. Genomics 272(2):173-80, 2004
    PubMed
    Genome update: promoter profiles
    Ussery DW, Tindbaek N, Hallin PF
    Microbiology (Reading, Engl.) 150:2791-3, 2004
    PubMed
    Genome update: alignment of bacterial chromosomes
    Ussery DW, Jensen MS, Poulsen TR, Hallin PF
    Microbiology (Reading, Engl.) 150:2491-3, 2004
    PubMed
    Genome Update: annotation quality in sequenced microbial genomes
    Ussery DW, Hallin PF
    Microbiology (Reading, Engl.) 150:2015-7, 2004
    PubMed
    CBS genome atlas database: a dynamic storage for bioinformatic results and sequence data
    Hallin PF, Ussery DW
    Bioinformatics 20(18):3682-6, 2004
    PubMed
    MHC Class I Epitope Binding Prediction Trained on Small Data Sets
    Lundegaard C, Nielsen M, Lamberth K, Worning P, Sylvester-Hvid C, Søren Buus, Brunak S, Lund O
    Lecture Notes in Computer Science, vol 3239, proceeding of ICARIS 2004, 217-225, 2004
    Abstract from Springer-Verlag
    Arabidopsis VARIEGATED 3encodes a chloroplasttargeted, zinc-finger protein required for chloroplast and palisade cell development
    Næsted H, Holm A, Jenkins T, Bjørn Nielsen H, Harris CA, Beale MH, Andersen M, Mant A, Scheller H, Camara B, Mattsson O, Mundy J
    J. Cell. Sci. 117:4807-18, 2004
    PubMed
    Implementation of a gene expression index calculatation method based on the PDNN model
    Bjørn Nielsen H, Gautier L, Knudsen S
    Bioinformatics 21(5):687-8, 2004
    PubMed
    Analysis and prediction of leucine-rich nuclear export signals
    La Cour T, Kiemer L, Mølgaard A, Gupta R, Skriver K, Brunak S
    Protein Eng. Des. Sel. 17(6):527-36, 2004
    PubMed
    Predicting protein structure classes from function predictions
    Sommer I, Rahnenfuhrer J, Domingues FS, de Lichtenberg U, Lengauer T
    Bioinformatics 20(5):770-6, 2004
    PubMed
    Feature-based prediction of non-classical and leaderless protein secretion
    Bendtsen JD, Jensen LJ, Blom N, Von Heijne G, Brunak S
    Protein Eng. Des. Sel. 17(4):349-56, 2004
    PubMed
    Coronavirus 3CLpro proteinase cleavage sites: possible relevance to SARS virus pathology
    Kiemer L, Lund O, Brunak S, Blom N
    BMC Bioinformatics 5:72, 2004
    PubMed
    Improved prediction of signal peptides: SignalP 3,0
    Bendtsen JD, Nielsen H, von Heijne G, Brunak S
    J. Mol. Biol. 340(4):783-95, 2004
    PubMed
    Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry
    Hjerrild M, Stensballe A, Rasmussen TE, Kofoed CB, Blom N, Sicheritz-Ponten T, Larsen MR, Brunak S, Jensen ON, Gammeltoft S
    Journal of Proteome Research. 3(3):426-33, 2004
    PubMed
    Genome Update: tRNAs in sequenced microbial genomes
    Ussery DW, Hallin PF, Lagesen K, Wassenaar TM
    Microbiology (Reading, Engl.) 150:1603-6, 2004
    PubMed
    Genome update: rRNAs in sequenced microbial genomes
    Ussery DW, Hallin PF, Lagesen K, Coenye T
    Microbiology (Reading, Engl.) 150:1113-5, 2004
    PubMed
    TXTGate: profiling gene groups with text-based information
    Glenisson P, Coessens B, Van Vooren S, Mathys J, Moreau Y, De Moor B
    Genome Biol. 5(6):R43, 2004
    PubMed
    Comprehensive analysis of the base composition around the transcription start site in Metazoa
    Aerts S, Thijs G, Dabrowski M, Moreau Y, De Moor B
    BMC Genomics 5(1):34, 2004
    PubMed
    Prediction of immunophenotype, treatment response, and relapse in childhood acute lymphoblastic leukemia using DNA microarrays
    Willenbrock H, Juncker AS, Schmiegelow K, Knudsen S, Ryder LP
    Leukemia 18(7):1270-7, 2004
    PubMed
    The transcriptional activation program of human neutrophils in skin lesions supports their important role in wound healing
    Theilgaard-Monch K, Knudsen S, Follin P, Borregaard N
    J. Immunol. 172(12):7684-93, 2004
    PubMed
    Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence
    Blom N, Sicheritz-Ponten T, Gupta R, Gammeltoft S, Brunak S
    Proteomics 4(6):1633-49, 2004
    PubMed
    Blood cell gene expression profiling in rheumatoid arthritis; Discriminative genes and effect of rheumatoid factor
    Bovin LF, Rieneck K, Workman C, Nielsen H, Sorensen SF, Skjodt H, Florescu A, Brunak S, Bendtzen K
    Immunol. Lett. 93:217-26, 2004
    PubMed
    Representation of protein sequence information by amino acid subalphabets
    Andersen CAF, Brunak S
    AI Magazine, 25, 97-104, 2004
    SARS CTL vaccine candidates; HLA supertype-, genome-wide scanning and biochemical validation
    Sylvester-Hvid C, Nielsen M, Lamberth K, Roder G, Justesen S, Lundegaard C, Worning P, Thomadsen H, Lund O, Brunak S, Buus S
    Tissue Antigens 63(5):395-400, 2004
    PubMed
    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
    Using literature and data to learn Bayesian networks as clinical models of ovarian tumors
    Antal P, Fannes G, Timmerman D, Moreau Y, De Moor B
    Artif Intell Med 30(3):257-81, 2004
    PubMed
    A first glimpse into the pattern and scale of gene transfer in Apicomplexa
    Huang J, Mullapudi N, Sicheritz-Ponten T, Kissinger JC
    Parasitology International . 34(3):265-74, 2004
    PubMed
    Genome Update: AT content in sequenced prokaryotic genomes
    Ussery DW, Hallin PF
    Microbiology (Reading, Engl.) 150:749-52, 2004
    PubMed
    Development of in vitro transposon assisted signal sequence trapping and its use in screening Bacillus halodurans C125 and Sulfolobus solfataricus P2 gene libraries
    Becker F, Schnorr K, Wilting R, Tolstrup N, Bendtsen JD, Olsen PB
    J. Microbiol. Methods 57(1):123-33, 2004
    PubMed
    Structure-function analysis of the human sialyltransferase ST3Gal I
    Jeanneau C, Chazalet V, Auge C, Soumpasis DM, Harduin-Lepers A, Delannoy P, Imberty A, Breton C
    The Journal of Biological Chemistry. 279(14):13461-8, 2004
    PubMed
    Genome Update: length distributions of sequenced prokaryotic genomes
    Ussery DW, Hallin PF
    Microbiology (Reading, Engl.) 150:513-6, 2004
    PubMed
    Heterozygote advantage fails to explain the high degree of polymorphism of the MHC
    De Boer RJ, Borghans JA, Van Boven M, Kesmir C, Weissing FJ
    Immunogenetics 55(11):725-31, 2004
    PubMed
    affy--analysis of Affymetrix GeneChip data at the probe level
    Gautier L, Cope L, Bolstad BM, Irizarry RA
    Bioinformatics 20(3):307-15, 2004
    PubMed
    Improved prediction of MHC class I and II epitopes using a novel Gibbs sampling approach
    Nielsen M, Lundegaard C, Worning P, Sylvester-Hvid C, Lamberth K, Buus S, Brunak S, Lund O
    Bioinformatics 20(9):1388-97, 2004
    PubMed
    Analysis and recognition of 5' UTR intron splice sites in human pre-mRNA
    Eden E, Brunak S
    Nucleic Acids Res. 32(3):1131-42, 2004
    PubMed
    Genome Update: 161 prokaryotic genomes sequenced, and counting
    Ussery DW
    Microbiology (Reading, Engl.) 150:261-3, 2004
    PubMed
    Prediction of proprotein convertase cleavage sites
    Duckert P, Brunak S, Blom N
    Protein Engineering, Design & Selection, 17, 107-112, 2004
    Global regulation of virulence and the stress response by CsrA in the highly adapted human gastric pathogen Helicobacter pylori
    Barnard FM, Loughlin MF, Fainberg HP, Messenger MP, Ussery DW, Williams P, Jenks PJ
    Mol. Microbiol. 51(1):15-32, 2004
    PubMed

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
    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
    Analysis of Gene Expression and Regulatory Networks
    Friis C
    Ph.D. thesis, 2003
    Microarray Data Analysis
    Nielsen HB
    Ph.D. thesis, 2003
    Characterization of incompletely typed rotavirus strains from Guinea-Bissau: identification of G8 and G9 types and a high frequency of mixed infections
    Fischer TK, Page NA, Griffin DD, Eugen-Olsen J, Pedersen AG, Valentiner-Branth P, Mølbak K, Sommerfelt H, Nielsen NM
    Virology 311(1):125-33, 2003
    PubMed
    Publication download
    Modeling of the phase equilibria of polystyrene in methylcyclohexane with semi-empirical quantum mechanical methods I
    Wilczura-Wachnik H, Jonsdottir SO
    J Mol Model 9(2):108-13, 2003
    PubMed
    EasyGene - – a prokaryotic gene finder that ranks ORFs by statistical significance
    Larsen TS, Krogh A
    BMC Bioinformatics 4:21, 2003
    PubMed
    Bioinformatic analysis of functional differences between the immunoproteasome and the constitutive proteasome
    Kesmir C, van Noort V, de Boer RJ, Hogeweg P
    Immunogenetics 55(7):437-49, 2003
    PubMed
    MUTAGEN: Multi-User Tool for Annotating GENomes
    Brugger K, Redder P, Skovgaard M
    Bioinformatics 19(18):2480-1, 2003
    PubMed
    The sigma54 regulon (sigmulon) of Pseudomonas putida
    Cases I, Ussery DW, de Lorenzo V
    Environ. Microbiol. 5(12):1281-93, 2003
    PubMed
    Selecting Informative Data for Developing Peptide-MHC Binding Predictors Using a Query by Committee Approach
    Christensen JK, Lamberth K, Nielsen M, Lundegaard C, Worning P, Lauemøller SL, Buus S, Brunak S, Lund O
    Neural Comput 15(12):2931-42, 2003
    PubMed
    The Plasmid Genome Database
    Molbak L, Tett A, Ussery DW, Wall K, Turner S, Bailey M, Field D
    Microbiology (Reading, Engl.) 149:3043-5, 2003
    PubMed
    Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach
    Buus S, Lauemoller SL, Worning P, Kesmir C, Frimurer T, Corbet S, Fomsgaard A, Hilden J, Holm A, Brunak S
    Tissue Antigens 62(5):378-84, 2003
    PubMed
    Functionality of System Components: Conservation of Protein Function in Protein Feature Space
    Jensen LJ, Ussery DW, Brunak S
    Genome Res. 13(11):2444-9, 2003
    PubMed
    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
    GenePublisher: Automated analysis of DNA microarray data
    Knudsen S, Workman C, Sicheritz-Ponten T, Friis C
    Nucleic Acids Res. 31(13):3471-6, 2003
    PubMed
    Sequence analysis of three mitochondrial DNA molecules reveals interesting differences among Saccharomyces yeasts
    Langkjær RB, Casaregola S, Ussery DW, Gaillardin C, Piskur J
    Nucleic Acids Res. 31(12):3081-91, 2003
    PubMed
    Strand misalignments lead to quasipalindrome correction
    van Noort V, Worning P, Ussery DW, Rosche WA, Sinden RR
    Trends Genet. 19(7):365-9, 2003
    PubMed
    Optimization and immune recognition of multiple novel conserved HLA-A2, human immunodeficiency virus type 1-specific CTL epitopes
    Corbet S, Nielsen HV, Vinner L, Lauemøller S, Therrien D, Tang ST, Kronborg G, Mathiesen L, Chaplin P, Brunak S, Buus S, Fomsgaard A
    J. Gen. Virol. 84:2409-21, 2003
    PubMed
    Prediction of lipoprotein signal peptides in Gram-negative bacteria
    Juncker AS, Willenbrock H, Von Heijne G, Brunak S, Nielsen H, Krogh A
    Protein Sci. 12(8):1652-62, 2003
    PubMed
    Predicting proteasomal cleavage sites: a comparison of available methods
    Saxova P, Buus S, Brunak S, Kesmir C
    International Immunology. 15(7):781-7, 2003
    PubMed
    Plasmodium falciparum merozoite surface protein 1
    Hoessli DC, Poincelet M, Gupta R, Ilangumaran S, Nasir-ud-Din
    Eur. J. Biochem. 270(2):366-75, 2003
    PubMed
    RevTrans: multiple alignment of coding DNA from aligned amino acid sequences
    Wernersson R, Pedersen AG
    Nucleic Acids Res. 31(13):3537-9, 2003
    PubMed
    PDF
    Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays
    Nielsen HB, Wernersson R, Knudsen S
    Nucleic Acids Res. 31(13):3491-6, 2003
    PubMed
    Classification of Dukes´ B and C colorectal cancers using expression arrays
    Frederiksen CM, Knudsen S, Laurberg S, Ørntoft TF
    J. Cancer Res. Clin. Oncol. 129(5):263-71, 2003
    PubMed
    Protein feature based identification of cell cycle regulated proteins in yeast
    de Lichtenberg U, Jensen TS, Jensen LJ, Brunak S
    J. Mol. Biol. 329(4):663-74, 2003
    PubMed
    RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box
    Petersen L, Larsen TS, Ussery DW, On SL, Krogh A
    J. Mol. Biol. 326(5):1361-72, 2003
    PubMed
    Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome
    Jensen LJ, Skovgaard M, Sicheritz-Ponten T, Jørgensen MK, Lundegaard C, Pedersen CC, Petersen N, Ussery D
    BMC Genomics 4(1):12, 2003
    PubMed
    Reliable prediction of T-cell epitopes using neural networks with novel sequence representations
    Nielsen M, Lundegaard C, Worning P, Lauemøller SL, Lamberth K, Buus S, Brunak S, Lund O
    Protein Sci. 12(5):1007-17, 2003
    PubMed
    Prediction of human protein function according to Gene Ontology categories
    Jensen LJ, Gupta R, Stærfeldt HH, Brunak S
    Bioinformatics 19(5):635-42, 2003
    PubMed
    NESbase version 1.0: a database of nuclear export signals
    La Cour T, Gupta R, Rapacki K, Skriver K, Poulsen FM, Brunak S
    Nucleic Acids Res. 31(1):393-6, 2003
    PubMed

2002

    Genmanipuleret virus angriber kræftceller
    Hansen DA, Larsen DH, Jakobsen RK
    Information, 08-26 - s. 6, 2002
    bibliotek.dk
    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
    Prediction of protein function from sequence derived protein features
    Jensen LJ
    Ph.D. thesis, 2002
    Relevant URL
    Gene and motif finding in prokaryotic DNA using hidden Markov models
    Larsen TS
    Ph.D. thesis, 2002
    Phylogenetic and Functional Analysis of the Bacteriophage P1 Single-Stranded DNA-Binding Protein
    Bendtsen JD, Nilsson AS, Lehnherr H
    J. Virol. 76(19):9695-701, 2002
    PubMed
    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
    Hyperstructures, genome analysis and I-cells
    Amar P, Ballet P, Barlovatz-Meimon G, Benecke A, Bernot G, Bouligand Y, Bourguine P, Delaplace F, Delosme JM, Demarty M, Fishov I, Fourmentin-Guilbert J, Fralick J, Giavitto JL, Gleyse B, Godin C, Incitti R, Kepes F, Lange C, Le Sceller L, Loutellier C, Michel O, Molina F, Monnier C, Natowicz R, Norris V, Orange N, Pollard H, Raine D, Ripoll P, Rouviere-Yaniv J, Saier M Jr, Soler P, Tambourin P, Thellier M, Tracqui P, Ussery D, Vincent JC, Vannier JP, Wiggins P, Zemirline A
    Acta Biotheor. 50(4):357-73, 2002
    PubMed
    Roles of PucR, GlnR, and TnrA in regulating expression of the Bacillus subtilis ure P3 promoter
    Brandenburg JL, Wray LV Jr, Beier L, Jarmer H, Saxild HH, Fisher SH
    J. Bacteriol. 184(21):6060-4, 2002
    PubMed
    Prediction of novel archaeal enzymes from sequence-derived features
    Jensen LJ, Skovgaard M, Brunak S
    Protein Sci. 11(12):2894-8, 2002
    PubMed
    Nucleotide sequence database policies
    Brunak S, Danchin A, Hattori M, Nakamura H, Shinozaki K, Matise T, Preuss D
    Science 298(5597):1333, 2002
    PubMed
    A new non-linear normalization method for reducing variability in DNA microarray experiments
    Workman C, Jensen LJ, Jarmer H, Berka R, Gautier L, Nielsen HB, Saxild HH, Nielsen C, Brunak S, Knudsen S
    Genome Biol. 3(9):research0048, 2002
    PubMed
    DNA Microarray analysis of fim mutations in Escherichia coli
    Schembri MA, Ussery D, Workman C, Hasman H, Klemm P
    Mol. Genet. Genomics 267(6):721-9, 2002
    PubMed
    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
    RNA Secondary Structure and Sequence Conservation in C1 Region of Human Immunodeficiency Virus Type 1 env Gene
    Peleg O, Brunak S, Trifonov EN, Nevo E, Bolshoy A
    AIDS Res. Hum. Retroviruses 18(12):867-78, 2002
    PubMed
    Neural network predicts sequence of TP53 gene based on DNA chip
    Spicker S, Wikman F, Lu ML, Cordon-Cardo C, Workman C, Orntoft TF, Brunak S, Knudsen S
    Bioinformatics 18(8):1133-4, 2002
    PubMed
    Clustering Patterns of Cytotoxic T-Lymphocyte Epitopes in Human Immunodeficiency Virus Type 1 (HIV-1) Proteins Reveal Imprints of Immune Evasion on HIV-1 Global Variation
    Yusim K, Kesmir C, Gaschen B, Addo MM, Altfeld M, Brunak S, Chigaev A, Detours V, Korber BT
    J. Virol. 76(17):8757-68, 2002
    PubMed
    Mean-field approaches to independent component analysis
    Højen-Sørensen PA, Winther O, Hansen LK
    Neural Comput 14(4):889-918, 2002
    PubMed
    Avoiding cross hybridization by choosing nonredundant targets on cDNA arrays
    Nielsen HB, Knudsen S
    Bioinformatics 18(2):321-2, 2002
    PubMed
    Bias of purine stretches in sequenced chromosomes
    Ussery D, Soumpasis DM, Brunak S, Stærfeldt HH, Worning P, Krogh A
    Comput. Chem. 26(5):531-41, 2002
    PubMed
    Prediction of human protein function from post-translational modifications and localization features
    Jensen LJ, Gupta R, Blom N, Devos D, Tamames J, Kesmir C, Nielsen H, Stærfeldt HH, Rapacki K, Workman C, Andersen CAF, Knudsen S, Krogh A, Valencia A, Brunak S
    J. Mol. Biol. 319(5):1257-65, 2002
    PubMed
    Prediction of proteasome cleavage motifs by neural networks
    Kesmir C, Nussbaum AK, Schild H, Detours V, Brunak S
    Protein Eng. 15(4):287-96, 2002
    PubMed
    Gene expression analysis and gene regulation: from DNA microarrays to comparative genomics
    Workman C
    Ph.D. thesis, 2002
    Inheritance and organisation of the mitochondiral genome differ between two Saccharomyces
    Petersen RF, Langkjær RB, Hvidfeldt J, Gartner J, Palmen W, Ussery DW, Piskur J
    Indian J. Biochem. Biophys. 12(1):21-3, 2002
    PubMed
    Continuum secondary structure captures protein flexibility
    Anderson CAF, Palmer AG, Brunak S
    Structure 10(2):175-84, 2002
    PubMed
    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
    Transcription Analysis of the Bacillus subtilis PucR Regulon and Identification of a cis-Acting Sequence Required PucR-Regulated Expression of Genes Involved in Purine Catabolism
    Beier L, Nygaard P, Jarmer H, Saxild HH
    J. Bacteriol. 184(12):3232-41, 2002
    PubMed
    Transcriptome analysis documents induced competence of Bacillus subtilis during nitrogen limiting conditions
    Jarmer H, Berka R, Knudsen S, Saxild HH
    FEMS Microbiol. Lett. 206(2):197-200, 2002
    PubMed
    The genome sequence of Schizosaccharomyces pombe
    Wood V, Gwilliam R, Rajandream M-A, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, Baker S, Basham D, Bowman S, Brooks K, Brown D, Brown S, Chillingworth T, Churcher C, Collins M, Connor R, Cronin A, Davis P, Feltwell T, Fraser A, Gentles S, Goble A, Hamlin N, Harris D, Hidalgo J, Hodgson G, Holroyd S, Hornsby T, Howarth S, Huckle EJ, Hunt S, Jagels K, James K, Jones L, Jones M, Leather S, McDonald S, McLean J, Moule S, Mungall K, Murphy L, Niblett D, Odell C, Oliver K, O'Neil S, Pearson D, Quail MA, Rabbinowitsch E, Rutherford K, Rutter S, Saunders D, Seeger K, Sharp S, Skelton J, Simmonds M, Squares R, Squares S, Stevens K, Taylor K, Taylor RG, Walsh S, Warren T, Whitehead S, Woodward J, Volckaert G, Aert R, Robben J, Grymonprez B, Weltjens I, Vanstreels E, Rieger M, Schäfer M, Muller-Auer S, Gabel C, Fuchs M, Fritzc C, Holzer E, Moestl D, Hilbert H, Borzym K, Langer I, Beck A, Lehrach H, Reinhardt R, Pohl TM, Eger P, Zimmermann W, Wedler H, Wambutt R, Purnelle B, Goffeau A, Cadieu E, Dréano S, Gloux S, Lelaure V, Mottier S, Galibert F, Aves SJ, Xiang Z, Hunt C, Moore K, Hurst SM, Lucas M, Rochet M, Gaillardin C, Tallada VA, Garzon A, Thode G, Daga RR, Cruzado L, Jimenez J, Sanchez M, del Rey F, Dominguez A, Revuelta JL, Moreno S, Armstrong J, Forsburg S, Cerrutti L, Lowe T, McCombie WR, Paulsen I, Potashkin J, Shpakovski GV, Ussery D, Barrell BG, Nurse P
    Nature 415(6874):871-80, 2002
    PubMed
    Evaluation of potential regulatory elements identified as DNase I hypersensitive sites in the CFTR gene
    Phylactides M, Rowntree R, Nuthall H, Ussery D, Wheeler A, Harris A
    Eur. J. Biochem. 269(2):553-9, 2002
    PubMed
    Variety identification of wheat using mass spectrometry with neural networks and the influence of mass spectra processing prior to neural network analysis
    Aagaard Sørensen H, Sperotto MM, Petersen M, Kesmir C, Radzikowski L, Jacobsen S, Søndergaard I
    Rapid Commun. Mass Spectrom. 16(12):1232-7, 2002
    PubMed
    Reproducibility of transcriptome analyses using oligonucleotide microarrays: an interlaboratory comparison of chemostat cultures of Saccharomyces cerevisiae
    Piper M, Daran-Lapujade P, Bro C, Regenberg B, Knudsen S, Nielsen J, Pronk J
    Biochem. J. 150(3):405-11, 2002
    PubMed
    Prediction of glycosylation across the human proteome and the correlation to protein function
    Gupta R, Brunak S
    Pac Symp Biocomput:310-22, 2002
    PubMed

2001

    Evolutionary and immunological implications of contemporary HIV-1 variation
    Korber B, Gaschen B, Yusim K, Thakallapally R, Kesmir C, Detours V
    Br. Med. Bull. 58:19-42, 2001
    PubMed
    Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes
    Krogh A, Larsson B, von Heijne G, Sonnhammer ELL
    J. Mol. Biol. 305(3):567-80, 2001
    PubMed
    A phylogenomic approach to microbial evolution
    Sicheritz-Pontén T, Andersson SGE
    Nucleic Acids Res. 29(2):545-52, 2001
    PubMed
    Genome Organisation and Chromatin Structure in Escherichia coli
    Ussery D, Larsen TS, Wilkes KT, Friis C, Worning P, Krogh A, Brunak S
    Biochimie 83(2):201-12, 2001
    PubMed
    Protein secondary structure: category assignment and predictability
    Andersen CAF, Bohr H, Brunak S
    FEBS Lett. 507(1):6-10, 2001
    PubMed
    Quantitative predictions of peptide binding to MHC class I molecules using specificity matrices and anchor-stratified calibrations
    Lauemoller SL, Holm A, Hilden J, Brunak S, Holst Nissen M, Stryhn A, Østergaard Pedersen L, Buus S
    Tissue Antigens 57(5):405-14, 2001
    PubMed
    Recognition of environmental and genetic effects on barley phenolic fingerprints by neural networks
    Gorodkin J, Sogaard B, Bay H, Doll H, Kolster P, Brunak S
    Comput. Chem. 25(3):301-7, 2001
    PubMed
    Flexibility of the genetic code with respect to DNA structure
    Baisnee PF, Baldi P, Brunak S, Pedersen AG
    Bioinformatics 17(3):237-48, 2001
    PubMed
    PDF
    Publication download
    Identification and design of p53-derived HLA-A2-binding peptides with increased CTL immunogenicity
    Petersen TR, Buus S, Brunak S, Nissen MH, Sherman LA, Claesson MH
    Scand. J. Immunol. 53(4):357-64, 2001
    PubMed
    Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18
    Parkhill J, Dougan G, James KD, Thomson NR, Pickard D, Wain J, Churcher C, Mungall KL, Bentley SD, Holden MT, Sebaihia M, Baker S, Basham D, Brooks K, Chillingworth T, Connerton P, Cronin A, Davis P, Davies RM, Dowd L, White N, Farrar J, Feltwell T, Hamlin N, Haque A, Hien TT, Holroyd S, Jagels K, Krogh A, Larsen TS, Leather S, Moule S, O\\\'Gaora P, Parry C, Quail M, Rutherford K, Simmonds M, Skelton J, Stevens K, Whitehead S, Barrell BG
    Nature 413(6858):848-52, 2001
    PubMed
    Sigma A recognition sites in the Bacillus subtilis genome
    Jarmer H, Larsen TS, Krogh A, Saxild HH, Brunak S, Knudsen S
    Microbiology (Reading, Engl.) 147:2417-24, 2001
    PubMed
    On the total number of genes and their length distribution in complete microbial genomes
    Skovgaard M, Jensen LJ, Brunak S, Ussery D, Krogh A
    Trends Genet. 17(8):425-8, 2001
    PubMed
    Proceedings of ISMB
    Brunak S, Krogh A (eds.)
    Bioinformatics, 17, 2001
    Identification of gene expression patterns in superficial and invasive human bladder cancer
    Thykjaer T, Workman C, Kruhoffer M, Demtroder K, Wolf H, Andersen LD, Frederiksen CM, Knudsen S, Ørntoft TF
    Cancer Res. 61(6):2492-9, 2001
    PubMed
    Definition of the Bacillus subtilis PurR operator sequence using genetic and bioinformatic tools and expansion of the PurR regulon with glyA, guaC, pbuG, xpt-pbuX, yqhZ-folD and pbuO
    Saxild HH, Bruntedt K, Nielsen KI, Jarmer H, Nygaard P
    J. Bacteriol. 183(21):6175-83, 2001
    PubMed
    Enrichment of regulatory signals in conserved non-coding genomic sequence
    Levy S, Hannenhalli S, Workman C
    Bioinformatics 17(10):871-7, 2001
    PubMed
    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
    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
    Prediction of glycosylation sites in proteomes: from post-translational modifications to protein function
    Gupta R
    Ph.D. thesis, 2001
    Protein Structure and the Diversity of Hydrogen Bonds
    Andersen CAF
    Ph.D. thesis, 2001
    The Stealth Creationists
    Ussery DW
    Skeptic, 8, 72-74, 2001
    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

2000

    Kan mælkeproteiner styrke vores immunforsvar?
    Brix S, Barkholt V, Frokiaer H
    Mælkeritidende, 13/14:364-366 (2000)., 2000
    Caleosins: Ca2+-binding proteins associated with lipid bodies
    Næsted H, Frandsen GI, Jauh G, Hernandez-Pinzon I, Nielsen HB, Murphy DJ, Rogers JC, Mundy J
    Plant Mol. Biol. 44(4):463-76, 2000
    PubMed
    Relevant URL
    Promiscuous and specific phospholipid binding by domains in ZAC, a membrane-associated Arabidopsis protein with an ARF GAP zinc finger and a C2 domain
    Jensen RB, Lykke-Andersen K, Frandsen GI, Nielsen HB, Haseloff J, Jespersen HM, Mundy J, Skriver K
    Plant Mol. Biol. 44(6):799-814, 2000
    PubMed
    Relevant URL
    In vivo protection of nigral dopamine neurons by lentiviral gene transfer of the novel GDNF-family member neublastin/artemin
    Rosenblad C, Gronborg M, Hansen C, Blom N, Meyer M, Johansen J, Dago L, Kirik D, Patel UA, Lundberg C, Trono D, Bjorklund A, Johansen TE
    Mol. Cell. Neurosci. 15(2):199-214, 2000
    PubMed
    Identifying cytotoxic T cell epitopes from genomic and proteomic information: "The human MHC project"
    Lauemøller SL, Kesmir C, Corbet SL, Fomsgaard A, Holm A, Claesson MH, Brunak S, Buus S
    Rev Immunogenet 2(4):477-91, 2000
    PubMed
    Predicting subcellular localization of proteins based on their N-terminal amino acid sequence
    Emmanuelsson O, Nielsen H, Brunak S, von Heijne G
    J. Mol. Biol. 300(4):1005-16, 2000
    PubMed
    Computational methods in molecular biology, (Book review)
    Brunak S
    Trends in Genetics, 16, 97-98, 2000
    Prediction of protein secondary structure at 80% accuracy
    Petersen TN, Lundegaard C, Nielsen M, Bohr H, Brunak S, Gippert GP, Lund O
    Proteins 41(1):17-20, 2000
    PubMed
    Matching protein beta-sheet partners by feedforward and recurrent neural networks
    Baldi P, Pollastri G, Andersen CA, Brunak S
    Proc Int Conf Intell Syst Mol Biol 8:25-36, 2000
    PubMed
    Using database matches with HMMgene for automated gene detection in Drosophila
    Krogh A
    Genome Res. 10(4):523-8, 2000
    PubMed
    Arabidopsis MAP Kinase 4 Negatively Regulates Systemic Acquired Resistance
    Petersen M, Brodersen P, Naested H, Andreasson E, Lindhart U, Johansen B, Nielsen HB, Lacy M, Austin MJ, Parker JE, Sharma SB, Klessig DF, Martienssen R, Mattsson O, Jensen AB, Mundy J
    Cell 103(7):1111-20, 2000
    PubMed
    Efficient Identification and Analysis of Substructures in Proteins Using the Kappa-Tau Framework: Left Turns and Helix c-cap Motifs
    Soumpasis DM, Strahm MC
    J. Biomol. Struct. Dyn. 17(6):965-79, 2000
    PubMed
    Visualization of pathogenicity regions in bacteria
    Friis C, Jensen LJ, Ussery DW
    Genetica 108(1):47-51, 2000
    PubMed
    A DNA structural atlas for Escherichia coli
    Pedersen AG, Jensen LJ, Stærfeldt H, Brunak S, Ussery DW
    J. Mol. Biol. 299(4):907-30, 2000
    PubMed
    Publication download
    Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation
    Jensen LJ, Knudsen S
    Bioinformatics 16(4):326-33, 2000
    PubMed
    The frequency of mutators in populations of Escherichia coli
    Boe L, Danielsen M, Knudsen S, Petersen JB, Maymann J, Jensen PR
    Mutat. Res. 448(1):47-55, 2000
    PubMed
    A Classification of Possible Routes of Darwinian Evolution
    Thornhill RH, Ussery DW
    J. Theor. Biol. 203(2):111-6, 2000
    PubMed
    Assessing the Accuracy of Prediction Algorithms for Classification: An Overview
    Baldi P, Brunak S, Chauvin Y, Nielsen H, Andersen CAF
    Bioinformatics 16(5):412-24, 2000
    PubMed
    Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima
    Worning P, Jensen LJ, Nielson KE, Brunak S, Ussery DW
    Nucleic Acids Res. 28(3):706-9, 2000
    PubMed
    env Sequences of Simian Immunodeficiency Viruses from Chimpanzees in Cameroon Are Strongly Related to Those of Human Immunodeficiency Virus Group N from the Same Geographic Area
    Corbet S, Müller-Trutwin MC, Versmisse P, Delarue S, Ayouba A, Lewis J, Brunak S, Martin P, Brun-Vezinet F, Simon F, Barré-Sinoussi F, Mauclére P
    J. Virol. 74(1):529-34, 2000
    PubMed
    Improving the odds in discriminating
    Frimurer TM, Bywater R, Nærum L, Nørskov Lauritsen L, Brunak S
    Journal of Chemical Information and Computer Sciences 40(6):1315-24, 2000
    PubMed

1999

    From sequence to sorting: Prediction of signal peptides
    Nielsen H
    PhD thesis, 1999
    Fagre Nye Robotter
    Schou T
    Dagbladet Information, 5 March, 1999
    Kronik i Information, 5. marts 1999: \"Fagre robot-fremtid\"
    ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites
    Emanuelsson O, Nielsen H, von Heijne G
    Protein Sci. 8(5):978-84, 1999
    PubMed
    A mathematical model on germinal center kinetics and termination
    Kesmir C, De Boer RJ
    J. Immunol. 163(5):2463-9, 1999
    PubMed
    Identification of wheat varieties using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry and an artificial neural network
    Bloch HA, Kesmir C, Petersen M, Jacobsen S, Sondergaard II
    Rapid Commun. Mass Spectrom. 13(14):1535-9, 1999
    PubMed
    No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution
    Workman C, Krogh A
    Nucleic Acids Res. 27(24):4816-22, 1999
    PubMed
    Competition between Sec- and TAT-dependent protein translocation in Escherichia coli
    Cristóbal S, de Gier J-W, Nielsen H, von Heijne G
    The EMBO Journal . 18(11):2982-90, 1999
    PubMed
    Sequence and structure-based prediction of eukaryotic protein phosphorylation sites
    Blom N, Gammeltoft S, Brunak S
    J. Mol. Biol. 294(5):1351-62, 1999
    PubMed
    Three views of microbial genomes
    Jensen LJ, Friis C, Ussery DW
    Res. Microbiol. 150:773-7, 1999
    PubMed
    Structural Basis for Triplet Repeat Disorders: A Computational Analysis
    Baldi P, Brunak S, Chauvin Y, Pedersen AG
    Bioinformatics 15(11):918-29, 1999
    PubMed
    Publication download
    The biology of eukaryotic promoter prediction - a review
    Pedersen AG, Baldi P, Chauvin Y, Brunak S
    Comput. Chem. 23:191-207, 1999
    PubMed
    Publication download
    Modeling regulatory networks with weight matrices
    Weaver D, Workman C, Stormo GD
    Pac Symp Biocomput:112-23, 1999
    PubMed
    Exploiting the past and the future in protein secondary structure prediction
    Baldi P, Brunak S, Frasconi P, Pollastri G, Soda G
    Bioinformatics 15(11):937-46, 1999
    PubMed
    Characterization of enzymatically induced aggregation of Casein icelles in natural concentration by in situ static light scattering and ultra low shear viscosimetry
    Lehner D, Worning P, Fritz G, Ogendal L, Bauer R, Glatter O
    J Colloid Interface Sci 213(2):445-456, 1999
    PubMed
    Measures on Hidden Markov Models
    Lyngsø RB, Pedersen CNS, Nielsen H
    BRICS Report Series, RS-99-6, February, 1999
    Scanning the available Dictyostelium discoideum proteome for O-linked GlcNAc glycosylation sites using neural networks
    Gupta R, Jung E, Gooley AA, Williams KL, Brunak S, Hansen J
    Glycobiology 9(10):1009-22, 1999
    PubMed
    MatrixPlot: visualizing sequence constraints
    Gorodkin J, Stærfeldt HH, Lund O, Brunak S
    Bioinformatics 15(9):769-70, 1999
    PubMed
    Nosocomial HIV-transmission in an outpatient clinic detected by epidemiological and phylogenetic analyses
    Katzenstein TL, Jørgensen LB, Permin H, Hansen J, Nielsen C, Machuca R, Gerstoft J
    AIDS 13(13):1737-44, 1999
    PubMed
    Using Sequence Motifs for Enhanced Neural Network Prediction of Protein Distance Constraints
    Gorodkin J, Lund O, Andersen CA, Brunak S
    Proc Int Conf Intell Syst Mol Biol:95-105, 1999
    PubMed
    Metrics and Similarity Measures for Hidden Markov Models
    Lyngsø RB, Pedersen CNS, Nielsen H
    Proc Int Conf Intell Syst Mol Biol:178-86, 1999
    PubMed
    Promoter 2.0: for the Recognition of PolII Promoter Sequences and
    Knudsen S
    Bioinformatics 15(5):356-61, 1999
    PubMed
    Hidden neural networks
    Krogh A, Riis SK
    Neural Comput 11(2):541-63, 1999
    PubMed
    Environmental Influences on DNA Curvature
    Ussery DW, Higgins CF, Bolshoy A
    J. Biomol. Struct. Dyn. 16(4):811-23, 1999
    PubMed
    Machine learning approaches to the prediction of signal peptides and other protein sorting signal (review)
    Nielsen H, Brunak S, von Heijne G
    Protein Eng. 12(1):3-9, 1999
    PubMed
    O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins
    Gupta R, Birch H, Rapacki K, Brunak S, Hansen JE
    Nucleic Acids Res. 27(1):370-2, 1999
    PubMed
    A Biochemist's Response to the Biochemical Challenge to Evolution
    Ussery DW
    Bios, 70, 40-45, 1999
    PhosphoBase, a database of phosphorylation sites: release 2.0
    Kreegipuu A, Blom N, Brunak S
    Nucleic Acids Res. 27(1):237-9, 1999
    PubMed

1998

    DNA Structure in Human RNA Polymerase II Promoters
    Pedersen AG, Baldi P, Chauvin Y, Brunak S
    J. Mol. Biol. 281(4):663-73, 1998
    PubMed
    Publication download
    Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
    Cole ST et al (Krogh A)
    Nature 393(6685):537-44, 1998
    PubMed
    The effect of the lacY gene on the induction of IPTG inducible promoters, studied in Eschericia coli and Pseudomonas fluorescens
    Hansen LH, Knudsen S, Sorensen SJ
    Curr. Microbiol. 36(6):341-7, 1998
    PubMed
    Computational analyses and annotations of the Arabidopsis peroxidase gene family
    Østergaard L, Pedersen AG, Jespersen HM, Brunak S, Welinder KG
    FEBS Lett. 433:98-102, 1998
    PubMed
    Publication download
    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
    Gene finding: putting the parts together
    Krogh A
    in M.J. Bishop (ed.), ``Guide to Human Genome Computing'', Academic Press, 261-274, 1998
    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
    Prediction of signal peptides and signal anchors by a hidden Markov model
    Nielsen H, Krogh A
    Proc Int Conf Intell Syst Mol Biol 6:122-30, 1998
    PubMed
    A hidden Markov model for predicting transmembrane helices in protein sequences
    Sonnhammer ELL, von Heijne G, Krogh A
    Proc Int Conf Intell Syst Mol Biol 6:175-82, 1998
    PubMed
    Computational Applications of DNA Structural Scales
    Baldi P, Brunak S, Chauvin Y, Gorodkin J, Pedersen AG
    Proc Int Conf Intell Syst Mol Biol 6:35-42, 1998
    PubMed
    Publication download
    Statistical analysis of protein kinase specificity determinants
    Kreegipuu A, Blom N, Brunak S, Järv J
    FEBS Letters, 430, 45-50, 1998
    Comparisons of DNA mediated immunization procedures to surface glycoproteins of Human Immunodeficiency Virus type 1 and Hepatitis B virus
    Fomsgaard A, Vedel Nielsen H, Johansson K, Nielsen C, Machuca R, Bruun L, Hansen J, Buus S
    APMIS 106(6):636-46, 1998
    PubMed
    Improved humoral and cellular immune responses against the gp120 V3 loop of HIV-1 following genetic immunization with a chimeric DNA vaccine encoding the V3 inserted into the Hepatitis B surface antigen (HBsAg)
    Fomsgaard A, Vedel Nielsen H, Johansson K, Nielsen C, Machuca R, Bruun L, Hansen J, Buus S
    Scand. J. Immunol. 47(4):289-95, 1998
    PubMed
    PhosphoBase: a database of phosphorylation sites
    Blom N, Kreegipuu A, Brunak S
    Nucleic Acids Res. 26(1):382-6, 1998
    PubMed
    O-GLYCBASE Version 3.0 - A revised database of O-glycosylated proteins
    Hansen JE, Lund O, Nilsson J, Rapacki K, Brunak S
    Nucleic Acids Res. 26(1):387-9, 1998
    PubMed
    NetOglyc: Prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility
    Hansen JE, Lund O, Tolstrup N, Gooley AA, Williams KL, Brunak S
    Glycoconj. J. 15(2):115-30, 1998
    PubMed

1997

    Relation between phylogeny of African green monkey CD4 genes and their respective Simian Immunodeficiency Virus genes
    Fomsgaard A, Muller-Trutwin M, Diop O, Hansen J, Mathiot C, Barre-Sinoussi F, Allen JS
    J. Med. Primatol. 26(3):120-8, 1997
    PubMed
    Displaying the information contents of structural RNA alignments: the structure logos
    Gorodkin J, Heyer LJ, Brunak S, Stormo GD
    Comput. Appl. Biosci. 13(6):583-6, 1997
    PubMed
    Hidden Markov models for human genes: periodic patterns in exon sequences
    Baldi P, Brunak S, Chauvin Y, Krogh A
    Proc Int Conf Intell Syst Mol Biol 3:30-8, 1997
    PubMed
    Finding the most significant common sequences and structure motifs in a set of RNA sequences
    Gorodkin J, Heyer LJ, Stormo GD
    Nucleic Acids Res. 25(18):3724-32, 1997
    PubMed
    A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
    Nielsen H, Engelbrecht J, Brunak S, von Heijne G
    Int J Neural Syst 8:581-99, 1997
    PubMed
    Hidden neural networks: a framework for HMM/NN hybrids
    Riis SK, Krogh A
    Neural Comput 11(2):541-63, 1997
    PubMed
    Hierarchical organization of aggregated protein molecules
    Bohr H, Kühle A, Sørensen AH, Bohr J
    Zeitschrift f. Physik D, 40, 513-515, 1997
    The implication of topology for protein structure and aggregation
    Bohr J, Bohr H
    Zeitschrift f. Physik D, 40, 186-189, 1997
    Towards a classification of protein folds
    Bohr H, Lindgård PA
    Phys. Rev. E, 56, 4497, 1997
    Packing of protein structures in clusters with magic numbers
    Lindgård PA, Bohr H
    Zeitschrift f. Physik D, 40, 236-239, 1997
    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
    An update of the DEF database of protein fold class predictions
    Reczko M, Karras D, Bohr H
    Nucleic Acids Res. 25(1):235, 1997
    PubMed
    Protein distance constraints predicted by neural networks and probability density functions
    Lund O, Frimand K, Gorodkin J, Bohr H, Bohr J, Hansen J, Brunak S
    Protein Eng. 10(11):1241-8, 1997
    PubMed
    Coherent topological phenomena in protein folding
    Bohr H, Brunak S, Bohr J
    Fold Des 2(3):S15-8, 1997
    PubMed
    Enhancement of the nucleosomal pattern in sequences of lower complexity
    Bolshoy A, Shapiro K, Trifonov EN, Ioshikhes I
    Nucleic Acids Res. 25(16):3248-54, 1997
    PubMed
    A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites
    Tolstrup N, Rouzé P, Brunak S
    Nucleic Acids Res. 25(15):3159-63, 1997
    PubMed
    Prediction of N-terminal protein sorting signals
    Claros MG, Brunak S, von Heijne G
    Curr. Opin. Struct. Biol. 7(3):394-8, 1997
    PubMed
    Relation between phylogeny of African green monkey CD4 genes and their respective Simian Immunodeficiency Virus genes
    Fomsgaard A, Muller-Trutwin M, Diop O, Hansen J, Mathiot C, Barre-Sinoussi F, Allen JS
    J. Med. Primatol., 26, 120-128, 1997
    Kissing loops hide premature termination codons in pre-mRNA of selenoprotein genes and in genes containing programmed ribosomal frameshifts
    Knudsen S, Brunak S
    RNA 3(7):697-701, 1997
    PubMed
    Finding Common Sequence and Structure Motifs in a Set of RNA Sequences
    Gorodkin J, Heyer LJ, Stormo G
    Proc Int Conf Intell Syst Mol Biol 5:120-3, 1997
    PubMed
    Two Methods for Improving Performance of a HMM and their Application for Gene Finding
    Krogh A
    Proc Int Conf Intell Syst Mol Biol 5:179-86, 1997
    PubMed
    Neural Network Prediction of Translation Initiation Sites in Eukaryotes: Perspectives for EST and Genome analysis
    Pedersen AG, Nielsen H
    Proc Int Conf Intell Syst Mol Biol 5:226-33, 1997
    PubMed
    Publication download
    O-glycbase version 2.0 - A revised database of O-glycosylated proteins
    Hansen JE, Lund O, Rapacki K, Brunak S
    Nucleic Acids Res. 25(1):278-82, 1997
    PubMed
    Molecular Wring Resonances in Chain Molecules
    Bohr H, Brunak S, Bohr J
    Bioelectromagnetics 18(2):187-9, 1997
    PubMed
    Protein Folding and Wring Resonances
    Bohr J, Bohr H, Brunak S
    Biophys. Chem. 63:97-105, 1997
    PubMed
    Non-linear backpropagation: doing back-propagation without derivatives of the activation function
    Hertz JA, Krogh A, Lautrup B, Lehmann T
    IEEE Trans Neural Netw 8(6):1321-7, 1997
    PubMed
    Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
    Nielsen H, Engelbrecht J, Brunak S, von Heijne G
    Protein Eng. 10(1):1-6, 1997
    PubMed
    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

1996

    Protein structure and the sequential structure of mRNA: alpha-helix and beta-sheet signals at the nucleotide level
    Brunak S, Engelbrecht J
    Proteins 25(2):237-52, 1996
    PubMed
    Cleavage site analysis in picornaviral polyproteins: Discovering cellular targets with neural networks
    Blom N, Hansen J, Blaas D, Brunak S
    Protein Sci. 5(11):2203-16, 1996
    PubMed
    Relationship between protein structure and geometrical constraints
    Lund O, Hansen J, Brunak S, Bohr J
    Protein Sci. 5(11):2217-25, 1996
    PubMed
    Magic numbers in protein structures
    Lindgård PA, Bohr H
    Phys. Rev. Lett. 77(4):779-782, 1996
    PubMed
    Naturally occurring nucleosome positioning signals in human exons and introns
    Baldi P, Brunak S, Chauvin Y, Krogh A
    J. Mol. Biol. 263(4):503-10, 1996
    PubMed
    Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models
    Pedersen AG, Baldi P, Brunak S, Chauvin Y
    Proc Int Conf Intell Syst Mol Biol 4:182-91, 1996
    PubMed
    Publication download
    Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information
    Korning PG, Hebsgaard SM, Tolstrup N, Engelbrecht J, Rouzé P, Brunak S
    Nucleic Acids Res. 24(17):3439-52, 1996
    PubMed
    The Formation of Protein Structure
    Bohr J, Bohr H, Brunak S
    Europhysics News, 27, 50-54, 1996
    Distance distributions in proteins: A six parameter representation
    Reese MG, Lund O, Bohr J, Bohr H, Hansen JE, Brunak S
    Protein Eng. 9(9):733-40, 1996
    PubMed
    Prediction of the secondary structure of HIV-1 gp120
    Hansen JE, Lund O, Nielsen JO, Brunak S, Hansen J-ES
    Proteins 25(1):1-11, 1996
    PubMed
    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
    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
    Defining a similarity threshold for a functional protein sequence pattern: The signal peptide cleavage site
    Nielsen H, Engelbrecht J, von Heijne G, Brunak S
    Proteins 24(2):165-77, 1996
    PubMed
    Update on protein structure prediction: results of the 1995 IRBM workshop
    Hubbard T, Tramontano A, Hansen J, Vinals C, Fjellstrom O, Ribas de Pouplana L, the rest of the workshop team
    Fold Des 1(3):R55-63, 1996
    PubMed
    The gntP Gene of Escherichia coli Involved in Gluconate Uptake
    Klemm P, Tong S, Nielsen H, Conway T
    J. Bacteriol. 178(1):61-7, 1996
    PubMed
    Cleaning the GenBank Arabidopsis thaliana data set
    Korning PG, Hebsgaard SM, Rouzé P, Brunak S
    Nucleic Acids Res. 24(2):316-20, 1996
    PubMed

1995

    Prediction of hypervariable CDR-H3 loop structures in antibodies
    Reczko M, Martin ACR, Bohr H, Suhai S
    Protein Eng. 8(4):389-95, 1995
    PubMed
    Increased adhesion as a mechanism of antibody-dependent and antibody-independent complement-mediated enhancement of human immunodeficiency virus infection
    Lund O, Hansen J, Sørensen AM, Mosekilde E, Nielsen JO, Hansen J-ES
    J. Virol. 69(4):2393-400, 1995
    PubMed
    Receptor Function of CD4 Structures from African Green Monkey and Pig-Tail Macaque for Simian Immunodeficiency Virus, SIVsm, SIVagm, and Human Immunodeficiency Virus Type-1
    Fomsgaard A, Johnson PR, Nielsen C, Novembre FJ, Hansen J, Goldstein S, Hirsch VM
    Viral Immunol. 8(3):121-33, 1995
    PubMed
    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
    Pruning of a large network by optimal brain damage and surgeon: An example from biological sequence analysis
    Tolstrup N
    Int J Neural Syst 6(1):31-42, 1995
    PubMed
    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
    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
    Investigations of Escherichia coli promoter sequences with artificial neural networks: New signals discovered upstream of the transcriptional startpoint
    Pedersen AG, Engelbrecht J
    Proc Int Conf Intell Syst Mol Biol 3:292-9, 1995
    PubMed
    Publication download
    Periodic sequence patterns in human exons
    Baldi P, Brunak S, Chauvin Y, Engelbrecht J, Krogh A
    Proc Int Conf Intell Syst Mol Biol 3:30-8, 1995
    PubMed
    Analysis of Eukaryotic Promoter Sequences reveals a systematically occurring CT-signal
    Larsen NI, Engelbrecht J, Brunak S
    Nucleic Acids Res. 23(7):1223-30, 1995
    PubMed
    Prediction of O-glycosylation of mammalian proteins: Specificity patterns of UDP-GalNAc:-polypeptide N-acetylgalactosaminyltransferase
    Hansen JE, Lund O, Engelbrecht J, Bohr H, Nielsen JO, Hansen JES, Brunak S
    Biochem. J.:801-13, 1995
    PubMed

1994

    Neural network model of the genetic code is strongly correlated to the GES scale of amino acid transfer free energies
    Tolstrup N, Toftgård J, Engelbrecht J, Brunak S
    J. Mol. Biol. 243(5):816-20, 1994
    PubMed
    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
    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
    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
    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
    Viscous trees and Voronoi structure formation in expanding systems
    Bohr J, Brunak S, Nørretranders T
    Europhysics Lett., 25, 245-251, 1994
    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
    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
    The DEF data base of sequence based protein fold class predictions
    Reczko M, Bohr H
    Nucleic Acids Res. 22(17):3616-9, 1994
    PubMed
    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

1993

    Predictive Recognition of Signal Peptides Using Artificial Neural Networks
    Nielsen H
    M.Sc. thesis, 1993
    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
    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
    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

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
    G/C rich tract in 5' end of human introns
    Engelbrecht J, Knudsen S, Brunak S
    J. Mol. Biol., 227, 108-113, 1992

1991

    Neural networks applied to protein structure
    Bohr H, Bohr J, Brunak S, Cotterill RMJ, Fredholm H, Lautrup B, Petersen SB
    in ``Advances in Biomolecular Simulations'', AIP Conference proceedings 239, 293-310, 1991
    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
    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
    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

1990

    Training neural networks to analyse biological sequences
    Petersen SB, Bohr H, Bohr J, Brunak S, Cotterill RMJ, Fredholm H, Lautrup B
    Trends Biotechnol., 11, 304-308, 1990
    Neural Network Detects Errors in the assignment of pre-mRNA splice sites
    Brunak S, Engelbrecht J, Knudsen S
    Nucleic Acids Res., 18, 4797-4801, 1990
    Cleaning up gene databases
    Brunak S, Engelbrecht J, Knudsen S
    Nature, 343, 123, 1990
    A novel approach to prediction of the 3-dimensional structures of protein backbones by neural networks
    Bohr H, Bohr J, Brunak S, Cotterill RMJ, Fredholm H, Lautrup B, Petersen SB
    FEBS Letters, 261, 43-46, 1990
    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

1989

    Linjedeling med et neuralt netværk
    Brunak S, Lautrup B
    Skrifter om Anvendt and Matematisk Lingvistik, 14, 55-74, (Paper on hyphenation in refereed Danish linguistic journal.), 1989
    A Travelling Salesman Approach to Protein Conformation
    Bohr H, Brunak S
    Complex Systems, 3, 9-28,(Cover illustration), 1989

1988

    Linjedeling med TeX
    Lautrup B, Brunak S
    Skrifter om Anvendt and Matematisk Lingvistik, 13, 63-80, (Paper on hyphenation in refereed Danish linguistic journal.), 1988
    Protein secondary structure and homology by neural networks
    Bohr H, Bohr J, Brunak S, Cotterill RMJ, Lautrup B, Nørskov L, Olsen OH, Petersen SB
    FEBS Letters, 241, 223-228, 1988


Books

    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
    Methods for building quantitative structure-activity relationship (QSAR) descriptors and predictive models for computer-aided design of antimicrobial peptides
    Taboureau O
    Methods Mol. Biol. 618:77-86 doi:10.1007/978-1-60761-594-1_6, 2010
    PubMed
    Genome comparison of bacterial pathogens
    Wassenaar TM, Bohlin J, Binnewies TT, Ussery DW
    chapter 1 in Genome Dynamics, volume 6 - Microbial Pathogenomics, (Karger AG publishers, Basel), 2009
    Tools for comparison of bacterial genomes
    Wassenaar TM, Binnewies TT, Hallin PF, Ussery DW
    Microbiology of Hydrocarbons, Oils, Lipids, and Derived Compounds, (Springer-Verlag, Heidelberg, Germany), 2009
    The genus Burkholderia: analysis of 56 genomic sequences
    Ussery DW, Kiil K, Lagesen K, Sicheritz-Ponten T, Bohlin J, Wassenaar TM
    Genome Dyn 6:140-57 doi:10.1159/000235768, 2009
    PubMed
    COMPUTING FOR COMPARATIVE GENOMICS: Bioinformatics for Microbiologists
    Ussery DW, Borini S, Wassenaar TM
    Springer, Series: Computational Biology , Vol. 8, 2008
    Springer, to be published in autumn 2008
    Genome Diversity of Pseudomonas aeruginosa
    Klockgether J, Würdemann D, Wiehlmann L, Binnewies TT, Ussery DW, Tümmler B
    Chapter 2 in Pseudomonas: Genomics and Molecular Biology, (Edited by: Pierre Cornelis, Caister Academic Press, 2008), 2008
    Link to publisher
    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
    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
    Immunological Bioinformatics
    Lund O, Nielsen M, Lundegaard C, Kesmir C, Brunak S
    MIT Press, 312 pages, 2005
    Details
    A Biologist's Guide to Analysis of DNA Microarray Data, 2nd edition
    Knudsen S
    John Wiley & Sons, New York, 2004
    Details
    DNA Structure: A-, B-, and Z-DNA Families
    Ussery D
    The Encyclopedia of Life Sciences, (Macmillan Publishers, London), 2002
    A Biologist's Guide to Analysis of DNA Microarray Data, 1st edition
    Knudsen S
    John Wiley & Sons, New York, 2002
    Details
    Genome Sequence Databases
    Ussery DW, Brunak S
    Encyclopedia of Genetics, S. Brenner and J.H. Miller (eds.), Academic Press, 2001
    DNA Denaturation
    Ussery DW
    Encyclopedia of Genetics, S. Brenner and J.H. Miller (eds.), Academic Press, 2001
    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
    Bioinformatics: The Machine Learning Approach, 2nd edition
    Baldi P, Brunak S
    MIT Press, 360 pages, 2001
    Details
    Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
    Durbin R, Eddy S, Krogh A, Mitchison GJ
    Cambridge University Press, 350 pages, 1998
    Bioinformatics: The Machine Learning Approach
    Baldi P, Brunak S
    MIT Press, 360 pages, 1998
    Details
    Protein Folds: A Distance Based Approach
    Bohr H, Brunak S (eds.)
    CRC Press, Boca Raton, 318 pages, 1995
    Protein Structure by Distance Analysis
    Bohr H, Brunak S (eds.)
    IOS Press, Amsterdam, 352 pages, 1994
    Neuronale Netze: Die nächste Computer-Revolution
    Brunak S, Lautrup B, (translated by Malte Heim)
    Carl Hanser Verlag, 160 pages, 1993
    Neural Networks - Computers with Intuition
    Brunak S, Lautrup B
    World Scientific Publishing, 178 pages, 1990
    Neurale Netværk - Computere med Intuition
    Brunak S, Lautrup B
    Nysyn, Munksgaards Forlag, 160 pages (3 printings), 1988

2014 (66) 2013 (76) 2012 (71) 2011 (72) 2010 (111) 2009 (70) 2008 and before (551) Books (24)