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2013 (15) 2012 (4) 2011 (8) 2010 (15) 2009 (7) 2008 (6) 2007 and before (157) Books (10)

2013

    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 [1932-6203], 2013
    PubMed
    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
    Am J Hum Genet. 2013 - AJHG, 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
    Proc Natl Acad Sci U S A. 2013 Nov 18, 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
    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
    Nat Methods., 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. 2013, 2013
    PubMed
    Relevant URL
    A computational approach to chemical etiologies of diabetes
    Audouze K, Brunak S, Grandjean P
    Scientific Reports 2013, 2013
    Relevant URL
    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. 2013, 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. 2013, 2013
    PubMed
    Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics.
    Kouskoumvekaki I, Shublaq N, Brunak S
    Brief Bioinform. 2013, 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 Res. 2013, 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. 2013, 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
    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
    Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology
    Steentoft C, Vakhrushev SY, Joshi HJ, Kong Y, Vester-Christensen MB, Schjoldager KT, Lavrsen K, Dabelsteen S, Pedersen NB, Marcos-Silva L, Gupta R, Paul Bennett E, Mandel U, Brunak S, Wandall HH, Levery SB, Clausen H
    EMBO J. 2013 Apr 12. doi: 10.1038/emboj.2013.79., 2013
    PubMed

2012

    Association between chemical pattern in breast milk and congenital cryptorchidism: modelling of complex human exposures
    Krysiak-Baltyn K, Toppari J, Skakkebaek NE, Jensen TS, Virtanen HE, Schramm KW, Shen H, Vartiainen T, Kiviranta H, Taboureau O, Audouze K, Brunak S, Main KM
    Int J Androl. 2012 Jun, 2012
    PubMed
    ChemProt-2.0: visual navigation in a disease chemical biology database
    Kim Kjærulff S, Wich L, Kringelum J, Jacobsen UP, Kouskoumvekaki I, Audouze K, Lund O, Brunak S, Oprea TI, Taboureau O
    Nucleic Acids Res. 2012 Nov 26, 2012
    PubMed
    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
    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

    SignalP 4.0: discriminating signal peptides from transmembrane regions
    Petersen TN, Brunak S, von Heijne G, Nielsen H
    Nature Methods, 8:785-786, 2011
    PubMed
    Relevant URL
    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
    An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia
    Rasmussen M, Guo X, Wang Y, Lohmueller KE, Rasmussen S, Albrechtsen A, Skotte L, Lindgren S, Metspalu M, Jombart T, Kivisild T, Zhai W, Eriksson A, Manica A, Orlando L, De La Vega F, Tridico S, Metspalu E, Nielsen K, Ávila-Arcos MA, Moreno-Mayar JV, Muller C, Dortch J, Gilbert MTP, Lund O, Wesolowska A, Karmin M, Weinert LA, Wang B, Li J, Tai S, Xiao F, Hanihara T, van Driem G, Jha AR, Ricaut FX, de Knijf P, Migliano AB, Gallego-Romero I, Kristiansen K, Lambert DM, Brunak S, Forster P, Brinkmann B, Nehlich O, Bunce M, Richards M, Gupta R, Bustamante CD, Krogh A, Foley RA, Lahr MM, Balloux F, Sichertitz-Pontén T, Villems R, Nielsen R, Jun W, Willerslev E
    Science, 2011
    PubMed
    Protein Interaction-Based Genome-Wide Analysis of Incident Coronary Heart Disease
    Jensen MK, Pers TH, Dworzynski P, Girman CJ, Brunak S, Rimm EB
    Circulation Cardiovascular Genetics, 2011
    PubMed
    Relevant URL
    Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response
    Li Q, Eklund AC, Birkbak NJ, Desmedt C, Haibe-Kains B, Sotiriou C, Symmans WF, Pusztai L, Brunak S, Richardson AL, Szallasi Z
    BMC Bioinformatics, July 28, 2011
    PubMed
    Cost-effective multiplexing before capture allows screening of 25 000 clinically relevant SNPs in childhood acute lymphoblastic leukemia
    Wesolowska A, Dalgaard MD, Borst L, Gautier L, Bak M, Weinhold N, Nielsen BF, Helt LR, Audouze K, Nersting J, Tommerup N, Brunak S, Sicheritz-Ponten T, Leffers H, Schmiegelow K, Gupta R
    Leukemia, June 25th, 2011
    PubMed
    Enterotypes of the human gut microbiome
    Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J; MetaHIT Consortium, Antolín M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Mérieux A, Melo Minardi R, M\'rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, Bork P
    Nature, May 12, 2011
    PubMed
    Meta-analysis of heterogeneous data sources for genome-scale identification of risk genes in complex phenotypes
    Pers TH, Hansen NT, Lage K, Koefoed P, Dworzynski P, Miller ML, Flint TJ, Mellerup E, Dam H, Andreassen OA, Djurovic S, Melle I, Børglum AD, Werge T, Purcell S, Ferreira MA, Kouskoumvekaki I, Workman CT, Hansen T, Mors O, Brunak S
    Genet Epidemiol, April 11, 2011
    PubMed

2010

    ImmunoGrid: towards agent-based simulations of the human immune system at a natural scale
    Halling-Brown M, Pappalardo F, Rapin N, Zhang P, Alemani D, Emerson A, Castiglione F, Duroux P, Pennisi M, Miotto O, Churchill D, Rossi E, Moss DS, Sansom CE, Bernaschi M, Lefranc MP, Brunak S, Lund O, Motta S, Lollini PL, Murgo A, Palladini A, Basford KE, Brusic V, Shepherd AJ
    Philos Transact A Math Phys Eng Sci, June 13, 2010
    PubMed
    Many Putative Endocrine Disruptors Inhibit Prostaglandin Synthesis
    Kristensen DM, Skalkam ML, Audouze K, Lesné L, Desdoits-Lethimonier C, Frederiksen H, Brunak S, Skakkebaek NE, Jégou B, Hansen JB, Junker S, Leffers H
    Environ Health Perspect, 2010
    PubMed
    ChemProt: a disease chemical biology database
    Taboureau O, Nielsen SK, Audouze K, Weinhold N, Edsgärd D, Roque FS, Kouskoumvekaki I, Bora A, Curpan R, Jensen TS, Brunak S, Oprea TI
    Nucleic Acids Research, 2010
    PubMed
    Country-specific chemical signatures of persistent environmental compounds in breast milk
    Krysiak-Baltyn K, Toppari J, Skakkebaek NE, Jensen TS, Virtanen HE, Schramm KW, Shen H, Vartiainen T, Kiviranta H, Taboureau O, Brunak S, Main KM
    International Journal of Andrology, 2010
    PubMed
    Dissecting spatio-temporal protein networks driving human heart development and related disorders
    Lage K, Møllgård K, Greenway S, Wakimoto H, Gorham JM, Workman CT, Bendsen E, Hansen NT, Rigina O, Roque FS, Wiese C, Christoffels VM, Roberts AE, Smoot LB, Pu WT, Donahoe PK, Tommerup N, Brunak S, Seidman CE, Seidman JG, Larsen LA
    Mol Syst Biol., 2010
    PubMed
    Deciphering Diseases and Biological Targets for Environmental Chemicals using Toxicogenomics Networks
    Audouze K, Juncker AS, Roque F, Krysiak-Baltyn K, Weinhold N, Taboureau O, Jensen TS, Brunak S
    PLoS Comput Biol 6, 2010
    PubMed
    Read article
    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, 2010 Apr 17, 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
    Sci Signal 12;3(104):ra3, 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
    The PLoS ONE, 2010
    PubMed
    Read article
    A human gut microbial gene catalogue established by metagenomic sequencing
    Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, MetaHIT Consortium, Bork P, Ehrlich DS & Wang J
    Nature, Volume 464 Number 7285 pp7-132, 2010
    PubMed
    Nature frontpage
    OCT4 and downstream factors are expressed in human somatic urogenital epithelia and in culture of epididymal spheres
    Kristensen DM, Nielsen JE, Kalisz M, Dalgaard MD, Audouze K, Larsen ME, Jacobsen GK, Horn T, Brunak S, Skakkebaek NE, Leffers H
    Mol Hum Reprod, 2010
    PubMed
    Ancient Human Genome Sequence of an Extinct Palaeo-Eskimo
    Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, Metspalu M, Metspalu E, Kivisild T, Gupta R, Bertalan M, Nielsen K, Gilbert MTP, Wang Y, Raghavan M, Campos PF, Kamp HM, Wilson AS, Gledhill A, Tridico S, Bunce M, Lorenzen ED, Binladen J, Guo X, Zhao J, Zhang X, Zhang H, Li Z, Chen M, Orlando L, Kristiansen K, Bak M, Tommerup N, Bendixen C, Pierre TL, Grønnow B, Meldgaard M, Andreasen C, Fedorova SA, Osipova LP, Higham TFG, Ramsey CB, Hansen TV, Nielsen FC, Crawford MH, Brunak S, Sicheritz-Ponten T, Villems R, Nielsen R, Krogh A, Wang J, Willerslev E
    Nature 11 Feb;463(7282):757-62, 2010
    PubMed
    Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results
    Gauthier NP, Jensen LJ, Wernersson R, Brunak S, Jensen TS
    Nucleic Acids Res. 38(Database issue):D699-702, 2010
    PubMed
    Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis
    Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M
    Sci Signal. 12;3(104):ra3, 2010
    PubMed

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
    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
    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
    Expression profiling of human genetic and protein interaction networks in type 1 diabetes
    Bergholdt R, Brorsson C, Lage K, Nielsen JH, Brunak S, Pociot F
    PLoS One;4(7):e6250, 2009
    PubMed
    ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization
    Pappalardo F, Halling-Brown MD, Rapin N, Zhang P, Alemani D, Emerson A, Paci P, Duroux P, Pennisi M, Palladini A, Miotto O, Churchill D, Rossi E, Shepherd AJ, Moss DS, Castiglione F, Bernaschi M, Lefranc MP, Brunak S, Motta S, Lollini PL, Basford KE, Brusic V
    BRIEFINGS IN BIOINFORMATICS. VOL 10. NO 3. 330^340, 2009
    PubMed
    Identification of T1D susceptibility genes within the MHC region by combining protein interaction networks and SNP genotyping data
    Brorsson C, Hansen NT, Lage K, Bergholdt R, Brunak S, Pociot F; Diabetes Genetics Consortium
    Diabetes, obesity & metabolism, 2009 Feb;11 Suppl 1:60-6, 2009
    PubMed
    Analysis and prediction of gene splice sites in four Aspergillus genomes
    Wang K, Ussery DW, Brunak S
    Fungal Genetics and Biology, Volume 46, Issue 1, Supplement , March 2009, Pages S14-S18, Thematic Issue: Aspergillus Genomics and Beyond., 2009
    PubMed

2008

    Integration of clinical chemistry, expression, and metabolite data leads to better toxicological class separation
    Spicker JS, Brunak S, Frederiksen KS, Toft H
    Toxicological sciences : an official journal of the Society of Toxicology, 2008 Apr;102(2):444-54. Epub 2008 Jan 4, 2008
    PubMed
    A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes
    Lage K, Hansen NT, Karlberg EO, Eklund AC, Roque F, Donahoe PK, Szallasi Z, Jensen TS, Brunak S
    Proceedings of the National Academy of Sciences of the United States of America, 2008 Dec 30;105(52):20870-5. Epub 2008 Dec 22, 2008
    PubMed
    Circular reasoning rather than cyclic expression
    Jensen LJ, de Lichtenberg U, Jensen TS, Brunak S, Bork P
    Genome Biol. 2008;9(6):403. Epub 2008 Jun 23, 2008
    PubMed
    Linear motif atlas for phosphorylation-dependent signaling.
    Miller ML, Jensen LJ, Diella F, Jørgensen C, Tinti M, Li L, Hsiung M, Parker SA, Bordeaux J, Sicheritz-Ponten T, Olhovsky M, Pasculescu A, Alexander J, Knapp S, Blom N, Bork P, Li S, Cesareni G, Pawson T, Turk BE, Yaffe MB, Brunak S, Linding R
    Science Signaling, 2008 Sep 2;1(35):ra2, 2008
    PubMed
    Alternative splicing in colon, bladder, and prostate cancer identified by exon-array analysis
    Thorsen K, Sørensen KD, Brems-Eskildsen AS, Modin C, Gaustadnes M, Hein AMK, Kruhøffer M, Laurberg S, Borre M, Wang K, Brunak S, Krainer AR, Tørring N, Dyrskjøt L, Andersen CL, Ørntoft TF
    Mol Cell Proteomics;7(7):1214-1224, 2008
    PubMed
    hERG Classification Model Based on a Combination of Support Vector Machine Method and GRIND Descriptors
    Li Q, Jørgensen FS, Oprea T, Brunak S, Taboureau O
    Mol Pharm,4;5(1):117-127, 2008
    PubMed

2007

    Modeling the adaptive immune system: predictions and simulations
    Lundegaard C, Lund O, Kesmir C, Brunak S, Nielsen M
    Bioinformatics, 23:3265-75, 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., 28;8(11):R253, 2007
    PubMed
    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,1;6(15):1819-25, 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 (in press), 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
    SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation
    Panitz F, Stengaard H, Hornshøj H, Gorodkin J, Hedegaard J, Cirera S, Thomsen B, Madsen LB, Høj A, Vingborg RK, Zahn B, Wang X, Wang X, Wernersson R, Jørgensen CB, Scheibye-Knudsen K, Arvin T, Lumholdt S, Sawera M, Green T, Nielsen BJ, Havgaard JH, Brunak S, Fredholm M, Bendixen C
    Bioinformatics. Jul 1;23(13):i387-91, 2007
    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
    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
    The implications of alternative splicing in the ENCODE protein complement
    Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PI, Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA, Lopez G, Sadowski MI, Watson JD, Fariselli P, Rossi I, Nagy A, Wang K, Storling Z, Orsini M, Assenov Y, Blankenburg H, Huthmacher C, Ramirez F, Schlicker A, Denoued F, Jones P, Kerrien S, Orchard S, Antonarakis SE, Reymond A, Birney E, Brunak S, Casadio R, Guigo R, Harrow J, Hermjakob H, Jones DT, Lengauer T, Orengo CA, Patthy L, Thornton JM, Tramontano A, Valencia A
    Proc Natl Acad Sci U S A (in press), 2007
    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
    Nature Biotechnol., 25 (3), 309-16, 2007
    PubMed

2006

    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
    Prediction of pH-Dependent Aqueous Solubility of Druglike Molecules
    Hansen NT, Kouskoumvekaki I, Jørgensen FS, Brunak S, Jónsdóttir SÓ
    Chem. Inf. Model., 46, 2601-9, 2006
    PubMed
    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
    Analysis and prediction of mammalian protein glycation
    Johansen MB, Kiemer L, Brunak S
    Glycobiology vol. 16 no. 9, 844-853, 2006
    PubMed
    A Wiring of the Human Nucleolus
    Hinsby AM, Kiemer L, Karlberg EO, Lage K, Fausboll A, Juncker AS, Andersen JS, Mann M, Brunak S
    Molecular Cell, 22, 285-295, 2006
    PubMed

2005

    Temporal interactome for the eukaryotic cell cycle by data integration
    Brunak S
    Biotechnology, 118, 7-8, 2005
    New weakly expressed cell cycle-regulated genes in yeast
    Hansen B, Schmidt P, Fausboll A, de Lichtenberg U, Wernersson R, Skøt Jensen T, Nielsen HB, Knudsen S, Brunak S
    Yeast, 22, 1191-201, 2005
    PubMed
    Non-classical protein secretion in bacteria
    Bendtsen J, Kiemer L, Fausboll A, Brunak S
    BMC Microbiol, 5,58, 2005
    PubMed
    An integrative approach to CTL epitope prediction: A combined algorithm integrating MHC class I binding, TAP transport
    Larsen MV, Lundegaard C, Lamberth K, Buus S, Brunak S, Lund O, Nielsen M
    Eur J Immunol,35, 2295-2303, 2005
    PubMed
    Prediction of twin-arginine signal peptides
    Bendtsen JD, Nielsen H, Widdick D, Palmer T, Brunak S
    BMC Bioinformatics, 2,6, 167, 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
    Comparison of computational methods for the identification of cell cycle-regulated genes
    de Lichtenberg U, Jensen LJ, Fausboll A, Jensen TS, Bork P, Brunak S
    Bioinformatics, 1;21, 1164-71, 2005
    PubMed
    Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates
    Jonsdottir SO, Jorgensen FS, Brunak S
    Bioinformatics, 15;21, 2145-60, 2005
    PubMed
    Dynamic Complex Formation During the Yeast Cell Cycle
    de Lichtenberg U, Jensen LJ, Brunak S, Bork P
    Science, 307, 724-727, 2005
    PubMed

2004

    DNA bendability and Nucleosome positioning in transcriptional regulation
    Dlakic M, Brunak S, Ussery DW
    DNA Conformation in Transcription, chapter 14, 2004
    Definition of supertypes for HLA molecules using clustering of specificity matrices
    Lund O, Nielsen M, Kesmir C, Pedersen AG, Lundegaard C, Worning P, Sylvester-Hvid C, Lamberth K, Roder G, Justesen S, Buus S, Brunak S
    Immunogenetics, 55, 797-810, 2004
    PubMed
    Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites
    Julenius K, Mølgaard A, Gupta R, Brunak S
    Glycobiology, 15, 153-164, 2004
    PubMed
    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
    Analysis and prediction of leucine-rich nuclear export signals
    La Cour T, Kiemer L, Mølgaard A, Gupta R, Skriver K, Brunak S
    Protein Engineering Design and Selection, 17, 527-36, 2004
    PubMed
    Feature-based prediction of non-classical and leaderless protein secretion
    Bendtsen JD, Jensen LJ, Blom N, Von Heijne G, Brunak S
    Protein Engineering Design and Selection, 17, 349-56, 2004
    PubMed
    Coronavirus 3CLpro proteinase cleavage sites: possible relevance to SARS virus pathology
    Kiemer L, Lund O, Brunak S, Blom N
    BMC Bioinformatics, 6;5, 72, 2004
    PubMed
    Improved prediction of signal peptides: SignalP 3,0
    Bendtsen JD, Nielsen H, von Heijne G, Brunak S
    J Mol biol, 16;340, 783-95, 2004
    PubMed
    Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry
    Hjerrild M, Stensballe A, Rasmussen TE, Kofoed CB, Blom N, Sicheritz-Ponten T, Larsen MR, Brunak S, Jensen ON, Gammeltoft S
    J Proteome Research 426-33, 2004
    PubMed
    Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence
    Blom N, Sicheritz-Ponten T, Gupta R, Gammeltoft S, Brunak S
    Proteomics, 4, 1633-49, 2004
    PubMed
    Blood cell gene expression profiling in rheumatoid arthritis; Discriminative genes and effect of rheumatoid factor
    Bovin LF, Rieneck K, Workman C, Nielsen H, Sorensen SF, Skjodt H, Florescu A, Brunak S, Bendtzen K
    Immunology Letters, 93, 217-26, 2004
    PubMed
    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, 395-400, 2004
    PubMed
    Improved prediction of MHC class I and II epitopes using a novel Gibbs sampling approach
    Nielsen M, Lundegaard C, Worning P, Sylvester-Hvid C, Lamberth K, Buus S, Brunak S, Lund O
    Bioinformatics, 12;20, 1388-97, 2004
    PubMed
    Analysis and recognition of 5' UTR intron splice sites in human pre-mRNA
    Eden E, Brunak S
    Nucleic Acids Research, 32, 1131-1142, 2004
    PubMed
    Prediction of proprotein convertase cleavage sites
    Duckert P, Brunak S, Blom N
    Protein Engineering, Design & Selection, 17, 107-112, 2004

2003

    Selecting Informative Data for Developing Peptide-MHC Binding Predictors Using a Query by Committee Approach
    Christensen JK, Lamberth K, Nielsen M, Lundegaard C, Worning P, Lauemøller SL, Buus S, Brunak S, Lund O
    Neural Computation, 15, 2931-42, 2003
    PubMed
    Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach
    Buus S, Lauemoller SL, Worning P, Kesmir C, Frimurer T, Corbet S, Fomsgaard A, Hilden J, Holm A, Brunak S
    Tissue Antigens, 62, 378-384, 2003
    PubMed
    Functionality of System Components: Conservation of Protein Function in Protein Feature Space
    Jensen LJ, Ussery DW, Brunak S
    Genome Res., 13, 2444-9, 2003
    PubMed
    Optimization and immune recognition of multiple novel conserved HLA-A2, human immunodeficiency virus type 1-specific CTL epitopes
    Corbet S, Nielsen HV, Vinner L, Lauemøller S, Therrien D, Tang ST, Kronborg G, Mathiesen L, Chaplin P, Brunak S, Buus S, Fomsgaard A
    J Gen Virol, 84, 2409-2421, 2003
    PubMed
    Prediction of lipoprotein signal peptides in Gram-negative bacteria
    Juncker AS, Willenbrock H, Von Heijne G, Brunak S, Nielsen H, Krogh A
    Protein Science,12, 1652-62, 2003
    PubMed
    Predicting proteasomal cleavage sites: a comparison of available methods
    Saxova P, Buus S, Brunak S, Kesmir C
    International Immunology, 15, 781-787, 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, 663-74, 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 Science, 12, 1007-17, 2003
    PubMed
    Prediction of human protein function according to Gene Ontology categories
    Jensen LJ, Gupta R, Stærfeldt HH, Brunak S
    Bioinformatics, 19, 635-642, 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., 31,393-6, 2003
    PubMed

2002

    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 novel archaeal enzymes from sequence-derived features
    Jensen LJ, Skovgaard M, Brunak S
    Protein Science, 11, 2894-2898, 2002
    PubMed
    Nucleotide sequence database policies
    Brunak S, Danchin A, Hattori M, Nakamura H, Shinozaki K, Matise T, Preuss D
    Science, 298, 1312-13, 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, research0048.1-0048.16, 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, 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, 1133-1134, 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, 8757-8768, 2002
    PubMed
    Bias of purine stretches in sequenced chromosomes
    Ussery D, Soumpasis DM, Brunak S, Stærfeldt HH, Worning P, Krogh A
    Computers and Chemistry, 26, 531-541, 2002
    PubMed
    Prediction of human protein function from post-translational modifications and localization features
    Jensen LJ, Gupta R, Blom N, Devos D, Tamames J, Kesmir C, Nielsen H, Stærfeldt HH, Rapacki K, Workman C, Andersen CAF, Knudsen S, Krogh A, Valencia A, Brunak S
    J. Mol. Biol., 319, 1257-1265, 2002
    PubMed
    Prediction of proteasome cleavage motifs by neural networks
    Kesmir C, Nussbaum AK, Schild H, Detours V, Brunak S
    Protein Eng., 15, 287-296, 2002
    PubMed
    Continuum secondary structure captures protein flexibility
    Anderson CAF, Palmer AG, Brunak S
    Structure, 10,175-184, 2002
    PubMed
    Prediction of glycosylation across the human proteome and the correlation to protein function
    Gupta R, Brunak S
    PSB-2002 Proceedings, Pacific Symposium on Biocomputing 310-322, 2002
    PubMed

2001

    Genome Organisation and Chromatin Structure in Escherichia coli
    Ussery D, Larsen TS, Wilkes KT, Friis C, Worning P, Krogh A, Brunak S
    Biochimie, 83, 202-212 (cover illustration), 2001
    PubMed
    Protein secondary structure: category assignment and predictability
    Andersen CAF, Bohr H, Brunak S
    FEBS Letters, 507, 6-1, 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, 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, 301-7, 2001
    PubMed
    Flexibility of the genetic code with respect to DNA structure
    Baisnee PF, Baldi P, Brunak S, Pedersen AG
    Bioinformatics, 17, 237-248, 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, 357-364, 2001
    PubMed
    Sigma A recognition sites in the Bacillus subtilis genome
    Jarmer H, Larsen TS, Krogh A, Saxild HH, Brunak S, Knudsen S
    Microbiology, 147, 2417-24, 2001
    PubMed
    On the total number of genes and their length distribution in complete microbial genomes
    Skovgaard M, Jensen LJ, Brunak S, Ussery D, Krogh A
    Trends Genet., 17, 425-428, 2001
    PubMed
    Proceedings of ISMB
    Brunak S, Krogh A (eds.)
    Bioinformatics, 17, 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
    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

    Identifying cytotoxic T cell epitopes from genomic and proteomic information: "The human MHC project"
    Lauemøller SL, Kesmir C, Corbet SL, Fomsgaard A, Holm A, Claesson MH, Brunak S, Buus S
    Rev. Immunogenetics, 2, 477-91, 2000
    PubMed
    Predicting subcellular localization of proteins based on their N-terminal amino acid sequence
    Emmanuelsson O, Nielsen H, Brunak S, von Heijne G
    J. Mol. Biol., 300, 1005-1016, 2000
    PubMed
    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, 17-20, 2000
    PubMed
    Matching protein beta-sheet partners by feedforward and recurrent neural networks
    Baldi P, Pollastri G, Andersen CA, Brunak S
    Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology, 8, 25-36, 2000
    PubMed
    A DNA structural atlas for Escherichia coli
    Pedersen AG, Jensen LJ, Stærfeldt H, Brunak S, Ussery DW
    J. Mol.Biol., 299, 907-930, 2000
    PubMed
    Publication download
    Assessing the Accuracy of Prediction Algorithms for Classification: An Overview
    Baldi P, Brunak S, Chauvin Y, Nielsen H, Andersen CAF
    Bioinformatics, 16, 412-424, 2000
    PubMed
    Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima
    Worning P, Jensen LJ, Nielson KE, Brunak S, Ussery DW
    Nucleic Acids Res., 28, 706-709, 2000
    PubMed
    env Sequences of Simian Immunodeficiency Viruses from Chimpanzees in Cameroon Are Strongly Related to Those of Human Immunodeficiency Virus Group N from the Same Geographic Area
    Corbet S, Müller-Trutwin MC, Versmisse P, Delarue S, Ayouba A, Lewis J, Brunak S, Martin P, Brun-Vezinet F, Simon F, Barré-Sinoussi F, Mauclére P
    J. Virol., 74, 529-534, 2000
    PubMed
    Improving the odds in discriminating
    Frimurer TM, Bywater R, Nærum L, Nørskov Lauritsen L, Brunak S
    J. Chem. Inf. Comp. Sci., 40, 1315-1324, 2000
    PubMed

1999

    Sequence and structure-based prediction of eukaryotic protein phosphorylation sites
    Blom N, Gammeltoft S, Brunak S
    J. Mol. Biol., 294, 1351-1362, 1999
    PubMed
    Structural Basis for Triplet Repeat Disorders: A Computational Analysis
    Baldi P, Brunak S, Chauvin Y, Pedersen AG
    Bioinformatics, 15, 918-929, 1999
    PubMed
    Publication download
    The biology of eukaryotic promoter prediction - a review
    Pedersen AG, Baldi P, Chauvin Y, Brunak S
    Comp Chem, 23, 191-207, 1999
    PubMed
    Publication download
    Exploiting the past and the future in protein secondary structure prediction
    Baldi P, Brunak S, Frasconi P, Pollastri G, Soda G
    Bioinformatics, 15, 937-946, 1999
    PubMed
    Scanning the available Dictyostelium discoideum proteome for O-linked GlcNAc glycosylation sites using neural networks
    Gupta R, Jung E, Gooley AA, Williams KL, Brunak S, Hansen J
    Glycobiology, 9, 1009-1022, 1999
    PubMed
    MatrixPlot: visualizing sequence constraints
    Gorodkin J, Stærfeldt HH, Lund O, Brunak S
    Bioinformatics, 15 769-770, 1999
    PubMed
    Using Sequence Motifs for Enhanced Neural Network Prediction of Protein Distance Constraints
    Gorodkin J, Lund O, Andersen CA, Brunak S
    Proceedings of the seventh international conference on Intelligent Systems for Molecular Biology (ISMB \'99), AAAI Press, 95-105, 1999
    PubMed
    Machine learning approaches to the prediction of signal peptides and other protein sorting signal (review)
    Nielsen H, Brunak S, von Heijne G
    Protein Eng., 12, 3-9, 1999
    PubMed
    O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins
    Gupta R, Birch H, Rapacki K, Brunak S, Hansen JE
    Nucleic Acids Res., 27, 370-372, 1999
    PubMed
    PhosphoBase, a database of phosphorylation sites: release 2.0
    Kreegipuu A, Blom N, Brunak S
    Nucleic Acids Res., 27, 237-239, 1999
    PubMed

1998

    DNA Structure in Human RNA Polymerase II Promoters
    Pedersen AG, Baldi P, Chauvin Y, Brunak S
    J. Mol. Biol., 281, 663-673, 1998
    PubMed
    Publication download
    Computational analyses and annotations of the Arabidopsis peroxidase gene family
    Østergaard L, Pedersen AG, Jespersen HM, Brunak S, Welinder KG
    FEBS Letters, 433, 98-102, 1998
    PubMed
    Publication download
    Computational Applications of DNA Structural Scales
    Baldi P, Brunak S, Chauvin Y, Gorodkin J, Pedersen AG
    Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB98), 35-42, 1998
    PubMed
    Publication download
    Statistical analysis of protein kinase specificity determinants
    Kreegipuu A, Blom N, Brunak S, Järv J
    FEBS Letters, 430, 45-50, 1998
    PhosphoBase: a database of phosphorylation sites
    Blom N, Kreegipuu A, Brunak S
    Nucleic Acids Res., 26, 384-386, 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, 387-389, 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
    Glycocon. J., 15, 115-130, 1998
    PubMed

1997

    Displaying the information contents of structural RNA alignments: the structure logos
    Gorodkin J, Heyer LJ, Brunak S, Stormo GD
    Comput. Appl. Biosci., 13, 583-586, 1997
    PubMed
    Hidden Markov models for human genes: periodic patterns in exon sequences
    Baldi P, Brunak S, Chauvin Y, Krogh A
    in Theoretical and Computational Methods in Genome Research, S. Suhai (ed.), Plenum Press, N.Y., 15-32, 1997
    PubMed
    A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
    Nielsen H, Engelbrecht J, Brunak S, von Heijne G
    Int. J. Neur. Sys., 8, 581-599, 1997
    PubMed
    Protein distance constraints predicted by neural networks and probability density functions
    Lund O, Frimand K, Gorodkin J, Bohr H, Bohr J, Hansen J, Brunak S
    Protein Eng., 10, 1241-1248, 1997
    PubMed
    Coherent topological phenomena in protein folding
    Bohr H, Brunak S, Bohr J
    Folding & Design, 2, 15-18, 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, 3159-3163, 1997
    PubMed
    Prediction of N-terminal protein sorting signals
    Claros MG, Brunak S, von Heijne G
    Curr. Opin. Struct. Biol., 7, 394-398, 1997
    PubMed
    Kissing loops hide premature termination codons in pre-mRNA of selenoprotein genes and in genes containing programmed ribosomal frameshifts
    Knudsen S, Brunak S
    RNA, 3, 697-701, 1997
    PubMed
    O-glycbase version 2.0 - A revised database of O-glycosylated proteins
    Hansen JE, Lund O, Rapacki K, Brunak S
    Nucl. Acids Res., 25, 278-282, 1997
    PubMed
    Molecular Wring Resonances in Chain Molecules
    Bohr H, Brunak S, Bohr J
    Bioelectromagnetics, 18, 187-189, 1997
    PubMed
    Protein Folding and Wring Resonances
    Bohr J, Bohr H, Brunak S
    Biophys. Chem., 63, 97-105, 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, 1-6, 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, 237-252, 1996, 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, 2203-2216, 1996
    PubMed
    Relationship between protein structure and geometrical constraints
    Lund O, Hansen J, Brunak S, Bohr J
    Protein Sci., 5, 2217-2225, 1996
    PubMed
    Naturally occurring nucleosome positioning signals in human exons and introns
    Baldi P, Brunak S, Chauvin Y, Krogh A
    J. Mol. Biol., 263, 503-510, 1996
    PubMed
    Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models
    Pedersen AG, Baldi P, Brunak S, Chauvin Y
    Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology (ISMB96), 182-191, 1996
    PubMed
    Publication download
    Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information
    Korning PG, Hebsgaard SM, Tolstrup N, Engelbrecht J, Rouzé P, Brunak S
    Nucleic Acids Res., 24, 3439-3452, 1996
    PubMed
    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, 733-740, 1996
    PubMed
    Prediction of the secondary structure of HIV-1 gp120
    Hansen JE, Lund O, Nielsen JO, Brunak S, Hansen J-ES
    Proteins, 25, 1-11, 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, 165-177, 1996
    PubMed
    Cleaning the GenBank Arabidopsis thaliana data set
    Korning PG, Hebsgaard SM, Rouzé P, Brunak S
    Nucleic Acids Res., 24, 316-320, 1996
    PubMed

1995

    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
    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
    Periodic sequence patterns in human exons
    Baldi P, Brunak S, Chauvin Y, Engelbrecht J, Krogh A
    Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology (ISMB95), AAAI Press, 30-38, 1995
    PubMed
    Analysis of Eukaryotic Promoter Sequences reveals a systematically occurring CT-signal
    Larsen NI, Engelbrecht J, Brunak S
    Nucleic Acids Res., 23, 1223-1230, 1995
    PubMed
    Prediction of O-glycosylation of mammalian proteins: Specificity patterns of UDP-GalNAc:-polypeptide N-acetylgalactosaminyltransferase
    Hansen JE, Lund O, Engelbrecht J, Bohr H, Nielsen JO, Hansen JES, Brunak S
    Biochem. J., 308, 801-813, 1995
    PubMed

1994

    Neural network model of the genetic code is strongly correlated to the GES scale of amino acid transfer free energies
    Tolstrup N, Toftgård J, Engelbrecht J, Brunak S
    J Mol Biol. 1994 Nov 11;243(5):816-20., 1994
    PubMed
    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
    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

    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

    Immunological Bioinformatics
    Lund O, Nielsen M, Lundegaard C, Kesmir C, Brunak S
    MIT Press, 312 pages, 2005
    Details
    Genome Sequence Databases
    Ussery DW, Brunak S
    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
    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

2013 (15) 2012 (4) 2011 (8) 2010 (15) 2009 (7) 2008 (6) 2007 and before (157) Books (10)