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Søren Brunak

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

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Amino Acid Sequence

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Oligonucleotide Array Sequence Analysis

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Publications

TOP 3
Hansen N T; Brunak S; Altman R B
Generating genome-scale candidate gene lists for pharmacogenomics.
Sonne Si Brask; Almstrup Kristian; Dalgaard Marlene; Juncker Agnieszka Sierakowska; Edsgard Daniel; Ruban Ludmila; Harrison Neil J; Schwager Christian; Abdollahi Amir; Huber Peter E; Brunak Søren; Gjerdrum Lise Mette; Moore Harry D; Andrews Peter W; Skakkebaek Niels E; Rajpert-De Meyts Ewa; Leffers Henrik
Analysis of gene expression profiles of microdissected cell populations indicates that testicular carcinoma in situ is an arrested gonocyte.
Pappalardo Francesco; Halling-Brown Mark D; Rapin Nicolas; Zhang Ping; Alemani Davide; Emerson Andrew; Paci Paola; Duroux Patrice; Pennisi Marzio; Palladini Arianna; Miotto Olivo; Churchill Daniel; Rossi Elda; Shepherd Adrian J; Moss David S; Castiglione Filippo; Bernaschi Massimo; Lefranc Marie-Paule; Brunak Søren; Motta Santo; Lollini Pier-Luigi; Basford Kaye E; Brusic Vladimir
ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization.

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All Publications

2009: Hansen N T; Brunak S; Altman R B
Generating genome-scale candidate gene lists for pharmacogenomics.
Clinical pharmacology and therapeutics 2009;86(2):183-9.
2009: Sonne Si Brask; Almstrup Kristian; Dalgaard Marlene; Juncker Agnieszka Sierakowska; Edsgard Daniel; Ruban Ludmila; Harrison Neil J; Schwager Christian; Abdollahi Amir; Huber Peter E; Brunak Søren; Gjerdrum Lise Mette; Moore Harry D; Andrews Peter W; Skakkebaek Niels E; Rajpert-De Meyts Ewa; Leffers Henrik
Analysis of gene expression profiles of microdissected cell populations indicates that testicular carcinoma in situ is an arrested gonocyte.
Cancer research 2009;69(12):5241-50.
2009: Pappalardo Francesco; Halling-Brown Mark D; Rapin Nicolas; Zhang Ping; Alemani Davide; Emerson Andrew; Paci Paola; Duroux Patrice; Pennisi Marzio; Palladini Arianna; Miotto Olivo; Churchill Daniel; Rossi Elda; Shepherd Adrian J; Moss David S; Castiglione Filippo; Bernaschi Massimo; Lefranc Marie-Paule; Brunak Søren; Motta Santo; Lollini Pier-Luigi; Basford Kaye E; Brusic Vladimir
ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization.
Briefings in bioinformatics 2009;10(3):330-40.
2009: Wang Kai; Ussery David Wayne; Brunak Søren
Analysis and prediction of gene splice sites in four Aspergillus genomes.
Fungal genetics and biology : FG & B 2009;46 Suppl 1():S14-8.
2009: Brorsson C; Hansen N T; Lage K; Bergholdt R; Brunak S; Pociot F;
Identification of T1D susceptibility genes within the MHC region by combining protein interaction networks and SNP genotyping data.
Diabetes, obesity & metabolism 2009;11 Suppl 1():60-6.
2009: Juncker Agnieszka S; Larsen Mette V; Weinhold Nils; Nielsen Morten; Brunak Søren; Lund Ole
Systematic characterisation of cellular localisation and expression profiles of proteins containing MHC ligands.
PloS one 2009;4(10):e7448.
2009: Bergholdt Regine; Brorsson Caroline; Lage Kasper; Nielsen Jens Høiriis; Brunak Søren; Pociot Flemming
Expression profiling of human genetic and protein interaction networks in type 1 diabetes.
PloS one 2009;4(7):e6250.
2008: Lage Kasper; Hansen Niclas Tue; Karlberg E Olof; Eklund Aron C; Roque Francisco S; Donahoe Patricia K; Szallasi Zoltan; Jensen Thomas Skøt; Brunak Søren
A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(52):20870-5.
2008: Thorsen Kasper; Sørensen Karina D; Brems-Eskildsen Anne Sofie; Modin Charlotte; Gaustadnes Mette; Hein Anne-Mette K; Kruhøffer Mogens; Laurberg Søren; Borre Michael; Wang Kai; Brunak Søren; Krainer Adrian R; Tørring Niels; Dyrskjøt Lars; Andersen Claus L; Orntoft Torben F
Alternative splicing in colon, bladder, and prostate cancer identified by exon array analysis.
Molecular & cellular proteomics : MCP 2008;7(7):1214-24.
2008: Spicker Jeppe S; Brunak Søren; Frederiksen Klaus S; Toft Henrik
Integration of clinical chemistry, expression, and metabolite data leads to better toxicological class separation.
Toxicological sciences : an official journal of the Society of Toxicology 2008;102(2):444-54.
2008: Li Qiyuan; Jørgensen Flemming Steen; Oprea Tudor; Brunak Søren; Taboureau Olivier
hERG classification model based on a combination of support vector machine method and GRIND descriptors.
Molecular pharmaceutics 2008;5(1):117-27.
2008: Gauthier Nicholas Paul; Larsen Malene Erup; Wernersson Rasmus; de Lichtenberg Ulrik; Jensen Lars Juhl; Brunak Søren; Jensen Thomas Skøt
Cyclebase.org--a comprehensive multi-organism online database of cell-cycle experiments.
Nucleic acids research 2008;36(Database issue):D854-9.
2008: Miller Martin Lee; Hanke Stefan; Hinsby Anders Mørkeberg; Friis Carsten; Brunak Søren; Mann Matthias; Blom Nikolaj
Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2.
Molecular & cellular proteomics : MCP 2008;7(1):181-92.
2008: Miller Martin Lee; Jensen Lars Juhl; Diella Francesca; Jørgensen Claus; Tinti Michele; Li Lei; Hsiung Marilyn; Parker Sirlester A; Bordeaux Jennifer; Sicheritz-Ponten Thomas; Olhovsky Marina; Pasculescu Adrian; Alexander Jes; Knapp Stefan; Blom Nikolaj; Bork Peer; Li Shawn; Cesareni Gianni; Pawson Tony; Turk Benjamin E; Yaffe Michael B; Brunak Søren; Linding Rune
Linear motif atlas for phosphorylation-dependent signaling.
Science signaling 2008;1(35):ra2.
2008: Jensen Lars Juhl; de Lichtenberg Ulrik; Jensen Thomas Skøt; Brunak Søren; Bork Peer
Circular reasoning rather than cyclic expression.
Genome biology 2008;9(6):403.
2007: Lundegaard Claus; Lund Ole; Kesmir Can; Brunak Søren; Nielsen Morten
Modeling the adaptive immune system: predictions and simulations.
Bioinformatics (Oxford, England) 2007;23(24):3265-75.
2007: Spicker Jeppe S; Pedersen Henrik Toft; Nielsen Henrik Bjørn; Brunak Søren
Analysis of cell death inducing compounds.
Archives of toxicology 2007;81(11):803-11.
2007: Thorn Mette; Wang Mingjun; Kløverpris Henrik; Schmidt Esben G W; Fomsgaard Anders; Wenandy Lynn; Berntsen Annika; Brunak Søren; Buus Søren; Claesson Mogens H
Identification of a new hTERT-derived HLA-A*0201 restricted, naturally processed CTL epitope.
Cancer immunology, immunotherapy : CII 2007;56(11):1755-63.
2007: de Lichtenberg Ulrik; Jensen Thomas Skøt; Brunak Søren; Bork Peer; Jensen Lars Juhl
Evolution of cell cycle control: same molecular machines, different regulation.
Cell cycle (Georgetown, Tex.) 2007;6(15):1819-25.
2007: Panitz Frank; Stengaard Henrik; Hornshøj Henrik; Gorodkin Jan; Hedegaard Jakob; Cirera Susanna; Thomsen Bo; Madsen Lone B; Høj Anette; Vingborg Rikke K; Zahn Bujie; Wang Xuegang; Wang Xuefei; Wernersson Rasmus; Jørgensen Claus B; Scheibye-Knudsen Karsten; Arvin Troels; Lumholdt Steen; Sawera Milena; Green Trine; Nielsen Bente J; Havgaard Jakob H; Brunak Søren; Fredholm Merete; Bendixen Christian
SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation.
Bioinformatics (Oxford, England) 2007;23(13):i387-91.
2007: Lage Kasper; Karlberg E Olof; Størling Zenia M; Olason Páll I; Pedersen Anders G; Rigina Olga; Hinsby Anders M; Tümer Zeynep; Pociot Flemming; Tommerup Niels; Moreau Yves; Brunak Søren
A human phenome-interactome network of protein complexes implicated in genetic disorders.
Nature biotechnology 2007;25(3):309-16.
2007: Bergholdt Regine; Størling Zenia M; Lage Kasper; Karlberg E Olof; Olason Páll I; Aalund Mogens; Nerup Jørn; Brunak Søren; Workman Christopher T; Pociot Flemming
Integrative analysis for finding genes and networks involved in diabetes and other complex diseases.
Genome biology 2007;8(11):R253.
2007: Emanuelsson Olof; Brunak Søren; von Heijne Gunnar; Nielsen Henrik
Locating proteins in the cell using TargetP, SignalP and related tools.
Nature protocols 2007;2(4):953-71.
2006: Hansen Niclas Tue; Kouskoumvekaki Irene; Jørgensen Flemming Steen; Brunak Søren; Jónsdóttir Svava Osk
Prediction of pH-dependent aqueous solubility of druglike molecules.
Journal of chemical information and modeling 2006;46(6):2601-9.
2006: Rapin Nicolas; Kesmir Can; Frankild Sune; Nielsen Morten; Lundegaard Claus; Brunak Søren; Lund Ole
Modelling the human immune system by combining bioinformatics and systems biology approaches.
Journal of biological physics 2006;32(3-4):335-53.
2006: Jensen Lars Juhl; Jensen Thomas Skøt; de Lichtenberg Ulrik; Brunak Søren; Bork Peer
Co-evolution of transcriptional and post-translational cell-cycle regulation.
Nature 2006;443(7111):594-7.
2006: Johansen Morten Bo; Kiemer Lars; Brunak Søren
Analysis and prediction of mammalian protein glycation.
Glycobiology 2006;16(9):844-53.
2006: Hinsby Anders M; Kiemer Lars; Karlberg E Olof; Lage Kasper; Fausbøll Anders; Juncker Agnieszka S; Andersen Jens S; Mann Matthias; Brunak Søren
A wiring of the human nucleolus.
Molecular cell 2006;22(2):285-95.
2006: Neshich Goran; Bourne Philip E; Brunak Søren
ISMB 2006.
PLoS computational biology 2006;2(2):e11.
2006: Regenberg Birgitte; Grotkjaer Thomas; Winther Ole; Fausbøll Anders; Akesson Mats; Bro Christoffer; Hansen Lars Kai; Brunak Søren; Nielsen Jens
Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae.
Genome biology 2006;7(11):R107.
2005: de Lichtenberg Ulrik; Wernersson Rasmus; Jensen Thomas Skøt; Nielsen Henrik Bjørn; Fausbøll Anders; Schmidt Peer; Hansen Flemming Bryde; Knudsen Steen; Brunak Søren
New weakly expressed cell cycle-regulated genes in yeast.
Yeast (Chichester, England) 2005;22(15):1191-201.
2005: Larsen Mette Voldby; Lundegaard Claus; Lamberth Kasper; Buus Søren; Brunak Søren; Lund Ole; Nielsen Morten
An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions.
European journal of immunology 2005;35(8):2295-303.
2005: Jónsdóttir Svava Osk; Jørgensen Flemming Steen; Brunak Søren
Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates.
Bioinformatics (Oxford, England) 2005;21(10):2145-60.
2005: de Lichtenberg Ulrik; Jensen Lars Juhl; Fausbøll Anders; Jensen Thomas S; Bork Peer; Brunak Søren
Comparison of computational methods for the identification of cell cycle-regulated genes.
Bioinformatics (Oxford, England) 2005;21(7):1164-71.
2005: de Lichtenberg Ulrik; Jensen Lars Juhl; Brunak Søren; Bork Peer
Dynamic complex formation during the yeast cell cycle.
Science (New York, N.Y.) 2005;307(5710):724-7.
2005: Julenius Karin; Mølgaard Anne; Gupta Ramneek; Brunak Søren
Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites.
Glycobiology 2005;15(2):153-64.
2005: Bendtsen Jannick D; Kiemer Lars; Fausbøll Anders; Brunak Søren
Non-classical protein secretion in bacteria.
BMC microbiology 2005;5():58.
2005: Bendtsen Jannick Dyrløv; Nielsen Henrik; Widdick David; Palmer Tracy; Brunak Søren
Prediction of twin-arginine signal peptides.
BMC bioinformatics 2005;6():167.
2005: Wernersson Rasmus; Schierup Mikkel H; Jørgensen Frank G; Gorodkin Jan; Panitz Frank; Staerfeldt Hans-Henrik; Christensen Ole F; Mailund Thomas; Hornshøj Henrik; Klein Ami; Wang Jun; Liu Bin; Hu Songnian; Dong Wei; Li Wei; Wong Gane K S; Yu Jun; Wang Jian; Bendixen Christian; Fredholm Merete; Brunak Søren; Yang Huanming; Bolund Lars
Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing.
BMC genomics 2005;6(1):70.
2004: Bendtsen Jannick Dyrløv; Nielsen Henrik; von Heijne Gunnar; Brunak Søren
Improved prediction of signal peptides: SignalP 3.0.
Journal of molecular biology 2004;340(4):783-95.
2004: la Cour Tanja; Kiemer Lars; Mølgaard Anne; Gupta Ramneek; Skriver Karen; Brunak Søren
Analysis and prediction of leucine-rich nuclear export signals.
Protein engineering, design & selection : PEDS 2004;17(6):527-36.
2004: Kiemer Lars; Lund Ole; Brunak Søren; Blom Nikolaj
Coronavirus 3CLpro proteinase cleavage sites: possible relevance to SARS virus pathology.
BMC bioinformatics 2004;5():72.
2004: Blom Nikolaj; Sicheritz-Pontén Thomas; Gupta Ramneek; Gammeltoft Steen; Brunak Søren
Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence.
Proteomics 2004;4(6):1633-49.
2004: Nielsen Morten; Lundegaard Claus; Worning Peder; Hvid Christina Sylvester; Lamberth Kasper; Buus Søren; Brunak Søren; Lund Ole
Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach.
Bioinformatics (Oxford, England) 2004;20(9):1388-97.
2004: Hjerrild Majbrit; Stensballe Allan; Rasmussen Thomas E; Kofoed Christine B; Blom Nikolaj; Sicheritz-Ponten Thomas; Larsen Martin R; Brunak Søren; Jensen Ole N; Gammeltoft Steen
Identification of phosphorylation sites in protein kinase A substrates using artificial neural networks and mass spectrometry.
Journal of proteome research 2004;3(3):426-33.
2004: Bovin Lone Frier; Rieneck Klaus; Workman Christopher; Nielsen Henrik; Sørensen Søren Freiesleben; Skjødt Henrik; Florescu Adrian; Brunak Søren; Bendtzen Klaus
Blood cell gene expression profiling in rheumatoid arthritis. Discriminative genes and effect of rheumatoid factor.
Immunology letters 2004;93(2-3):217-26.
2004: Sylvester-Hvid C; Nielsen M; Lamberth K; Røder G; Justesen S; Lundegaard C; Worning P; Thomadsen H; Lund O; Brunak S; Buus S
SARS CTL vaccine candidates; HLA supertype-, genome-wide scanning and biochemical validation.
Tissue antigens 2004;63(5):395-400.
2004: Bendtsen Jannick Dyrløv; Jensen Lars Juhl; Blom Nikolaj; Von Heijne Gunnar; Brunak Søren
Feature-based prediction of non-classical and leaderless protein secretion.
Protein engineering, design & selection : PEDS 2004;17(4):349-56.
2004: Lund Ole; Nielsen Morten; Kesmir Can; Petersen Anders Gorm; Lundegaard Claus; Worning Peder; Sylvester-Hvid Christina; Lamberth Kasper; Røder Gustav; Justesen Sune; Buus Søren; Brunak Søren
Definition of supertypes for HLA molecules using clustering of specificity matrices.
Immunogenetics 2004;55(12):797-810.
2004: Duckert Peter; Brunak Søren; Blom Nikolaj
Prediction of proprotein convertase cleavage sites.
Protein engineering, design & selection : PEDS 2004;17(1):107-12.
2004: Eden E; Brunak S
Analysis and recognition of 5' UTR intron splice sites in human pre-mRNA.
Nucleic acids research 2004;32(3):1131-42.
2003: Christensen Jens Kaae; Lamberth Kasper; Nielsen Morten; Lundegaard Claus; Worning Peder; Lauemøller Sanne Lise; Buus Søren; Brunak Søren; Lund Ole
Selecting informative data for developing peptide-MHC binding predictors using a query by committee approach.
Neural computation 2003;15(12):2931-42.
2003: Buus S; Lauemøller S L; Worning P; Kesmir C; Frimurer T; Corbet S; Fomsgaard A; Hilden J; Holm A; Brunak S
Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach.
Tissue antigens 2003;62(5):378-84.
2003: Jensen Lars Juhl; Ussery David W; Brunak Søren
Functionality of system components: conservation of protein function in protein feature space.
Genome research 2003;13(11):2444-9.
2003: Corbet Sylvie; Nielsen Henrik Vedel; Vinner Lasse; Lauemoller Sanne; Therrien Dominic; Tang Sheila; Kronborg Gitte; Mathiesen Lars; Chaplin Paul; Brunak Søren; Buus Søren; Fomsgaard Anders
Optimization and immune recognition of multiple novel conserved HLA-A2, human immunodeficiency virus type 1-specific CTL epitopes.
The Journal of general virology 2003;84(Pt 9):2409-21.
2003: Juncker Agnieszka S; Willenbrock Hanni; Von Heijne Gunnar; Brunak Søren; Nielsen Henrik; Krogh Anders
Prediction of lipoprotein signal peptides in Gram-negative bacteria.
Protein science : a publication of the Protein Society 2003;12(8):1652-62.
2003: Saxová Patricia; Buus Søren; Brunak Søren; Kesmir Can
Predicting proteasomal cleavage sites: a comparison of available methods.
International immunology 2003;15(7):781-7.
2003: de Lichtenberg Ulrik; Jensen Thomas S; Jensen Lars J; Brunak Søren
Protein feature based identification of cell cycle regulated proteins in yeast.
Journal of molecular biology 2003;329(4):663-74.
2003: Nielsen Morten; Lundegaard Claus; Worning Peder; Lauemøller Sanne Lise; Lamberth Kasper; Buus Søren; Brunak Søren; Lund Ole
Reliable prediction of T-cell epitopes using neural networks with novel sequence representations.
Protein science : a publication of the Protein Society 2003;12(5):1007-17.
2003: Jensen L J; Gupta R; Staerfeldt H-H; Brunak S
Prediction of human protein function according to Gene Ontology categories.
Bioinformatics (Oxford, England) 2003;19(5):635-42.
2003: la Cour Tanja; Gupta Ramneek; Rapacki Kristoffer; Skriver Karen; Poulsen Flemming M; Brunak Søren
NESbase version 1.0: a database of nuclear export signals.
Nucleic acids research 2003;31(1):393-6.
2002: Jensen Lars Juhl; Skovgaard Marie; Brunak Søren
Prediction of novel archaeal enzymes from sequence-derived features.
Protein science : a publication of the Protein Society 2002;11(12):2894-8.
2002: Yusim Karina; Kesmir Can; Gaschen Brian; Addo Marylyn M; Altfeld Marcus; Brunak Søren; Chigaev Alexandre; Detours Vincent; Korber Bette T
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.
Journal of virology 2002;76(17):8757-68.
2002: Workman Christopher; Jensen Lars Juhl; Jarmer Hanne; Berka Randy; Gautier Laurent; Nielser Henrik Bjørn; Saxild Hans-Henrik; Nielsen Claus; Brunak Søren; Knudsen Steen
A new non-linear normalization method for reducing variability in DNA microarray experiments.
Genome biology 2002;3(9):research0048.
2002: Peleg Ofer; Brunak Søren; Trifonov Edward N; Nevo Eviatar; Bolshoy Alexander
RNA secondary structure and squence conservation in C1 region of human immunodeficiency virus type 1 env gene.
AIDS research and human retroviruses 2002;18(12):867-78.
2002: Spicker Jeppe S; Wikman Friedrik; Lu Ming-Lan; Cordon-Cardo Carlos; Workman Christopher; ØRntoft Torben F; Brunak Søren; Knudsen Steen
Neural network predicts sequence of TP53 gene based on DNA chip.
Bioinformatics (Oxford, England) 2002;18(8):1133-4.
2002: Ussery David; Soumpasis Dikeos Mario; Brunak Søren; Staerfeldt Hans Henrik; Worning Peder; Krogh Anders
Bias of purine stretches in sequenced chromosomes.
Computers & chemistry 2002;26(5):531-41.
2002: Jensen L J; Gupta R; Blom N; Devos D; Tamames J; Kesmir C; Nielsen H; Staerfeldt H H; Rapacki K; Workman C; Andersen C A F; Knudsen S; Krogh A; Valencia A; Brunak S
Prediction of human protein function from post-translational modifications and localization features.
Journal of molecular biology 2002;319(5):1257-65.
2002: Kesmir Can; Nussbaum Alexander K; Schild Hansjörg; Detours Vincent; Brunak Søren
Prediction of proteasome cleavage motifs by neural networks.
Protein engineering 2002;15(4):287-96.
2002: Andersen Claus A F; Palmer Arthur G; Brunak Søren; Rost Burkhard
Continuum secondary structure captures protein flexibility.
Structure (London, England : 1993) 2002;10(2):175-84.
2002: Gupta Ramneek; Brunak Søren
Prediction of glycosylation across the human proteome and the correlation to protein function.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2002;():310-22.
2001: Andersen C A; Bohr H; Brunak S
Protein secondary structure: category assignment and predictability.
FEBS letters 2001;507(1):6-10.
2001: Jarmer H; Larsen T S; Krogh A; Saxild H H; Brunak S; Knudsen S
Sigma A recognition sites in the Bacillus subtilis genome.
Microbiology (Reading, England) 2001;147(Pt 9):2417-24.
2001: Skovgaard M; Jensen L J; Brunak S; Ussery D; Krogh A
On the total number of genes and their length distribution in complete microbial genomes.
Trends in genetics : TIG 2001;17(8):425-8.
2001: Lauemøller S L; Holm A; Hilden J; Brunak S; Holst Nissen M; Stryhn A; Østergaard Pedersen L; Buus S
Quantitative predictions of peptide binding to MHC class I molecules using specificity matrices and anchor-stratified calibrations.
Tissue antigens 2001;57(5):405-14.
2001: Gorodkin J; Søgaard B; Bay H; Doll H; Kølster P; Brunak S
Recognition of environmental and genetic effects on barley phenolic fingerprints by neural networks.
Computers & chemistry 2001;25(3):301-7.
2001: Petersen T R; Buus S; Brunak S; Nissen M H; Sherman L A; Claesson M H
Identification and design of p53-derived HLA-A2-binding peptides with increased CTL immunogenicity.
Scandinavian journal of immunology 2001;53(4):357-64.
2001: Baisnée P F; Baldi P; Brunak S; Pedersen A G
Flexibility of the genetic code with respect to DNA structure.
Bioinformatics (Oxford, England) 2001;17(3):237-48.
2001: Ussery D; Larsen T S; Wilkes K T; Friis C; Worning P; Krogh A; Brunak S
Genome organisation and chromatin structure in Escherichia coli.
Biochimie 2001;83(2):201-12.
2000: Emanuelsson O; Nielsen H; Brunak S; von Heijne G
Predicting subcellular localization of proteins based on their N-terminal amino acid sequence.
Journal of molecular biology 2000;300(4):1005-16.
2000: Pedersen A G; Jensen L J; Brunak S; Staerfeldt H H; Ussery D W
A DNA structural atlas for Escherichia coli.
Journal of molecular biology 2000;299(4):907-30.
2000: Baldi P; Brunak S; Chauvin Y; Andersen C A; Nielsen H
Assessing the accuracy of prediction algorithms for classification: an overview.
Bioinformatics (Oxford, England) 2000;16(5):412-24.
2000: Worning P; Jensen L J; Nelson K E; Brunak S; Ussery D W
Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima.
Nucleic acids research 2000;28(3):706-9.
2000: Corbet S; Müller-Trutwin M C; Versmisse P; Delarue S; Ayouba A; Lewis J; Brunak S; Martin P; Brun-Vezinet F; Simon F; Barre-Sinoussi F; Mauclere P
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.
Journal of virology 2000;74(1):529-34.
2000: Lauemøller S L; Kesmir C; Corbet S L; Fomsgaard A; Holm A; Claesson M H; Brunak S; Buus S
Identifying cytotoxic T cell epitopes from genomic and proteomic information: "The human MHC project.".
Reviews in immunogenetics 2000;2(4):477-91.
2000: Baldi P; Pollastri G; Andersen C A; Brunak S
Matching protein beta-sheet partners by feedforward and recurrent neural networks.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 2000;8():25-36.
1999: Blom N; Gammeltoft S; Brunak S
Sequence and structure-based prediction of eukaryotic protein phosphorylation sites.
Journal of molecular biology 1999;294(5):1351-62.
1999: Baldi P; Brunak S; Frasconi P; Soda G; Pollastri G
Exploiting the past and the future in protein secondary structure prediction.
Bioinformatics (Oxford, England) 1999;15(11):937-46.
1999: Baldi P; Brunak S; Chauvin Y; Pedersen A G
Structural basis for triplet repeat disorders: a computational analysis.
Bioinformatics (Oxford, England) 1999;15(11):918-29.
1999: Gupta R; Jung E; Gooley A A; Williams K L; Brunak S; Hansen J
Scanning the available Dictyostelium discoideum proteome for O-linked GlcNAc glycosylation sites using neural networks.
Glycobiology 1999;9(10):1009-22.
1999: Gorodkin J; Staerfeldt H H; Lund O; Brunak S
MatrixPlot: visualizing sequence constraints.
Bioinformatics (Oxford, England) 1999;15(9):769-70.
1999: Pedersen A G; Baldi P; Chauvin Y; Brunak S
The biology of eukaryotic promoter prediction--a review.
Computers & chemistry 1999;23(3-4):191-207.
1999: Nielsen H; Brunak S; von Heijne G
Machine learning approaches for the prediction of signal peptides and other protein sorting signals.
Protein engineering 1999;12(1):3-9.
1999: Gupta R; Birch H; Rapacki K; Brunak S; Hansen J E
O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins.
Nucleic acids research 1999;27(1):370-2.
1999: Kreegipuu A; Blom N; Brunak S
PhosphoBase, a database of phosphorylation sites: release 2.0.
Nucleic acids research 1999;27(1):237-9.
1999: Gorodkin J; Lund O; Andersen C A; Brunak S
Using sequence motifs for enhanced neural network prediction of protein distance constraints.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1999;():95-105.
1998: Ostergaard L; Pedersen A G; Jespersen H M; Brunak S; Welinder K G
Computational analyses and annotations of the Arabidopsis peroxidase gene family.
FEBS letters 1998;433(1-2):98-102.
1998: Pedersen A G; Baldi P; Chauvin Y; Brunak S
DNA structure in human RNA polymerase II promoters.
Journal of molecular biology 1998;281(4):663-73.
1998: Kreegipuu A; Blom N; Brunak S; Järv J
Statistical analysis of protein kinase specificity determinants.
FEBS letters 1998;430(1-2):45-50.
1998: Hansen J E; Lund O; Nilsson J; Rapacki K; Brunak S
O-GLYCBASE Version 3.0: a revised database of O-glycosylated proteins.
Nucleic acids research 1998;26(1):387-9.
1998: Blom N; Kreegipuu A; Brunak S
PhosphoBase: a database of phosphorylation sites.
Nucleic acids research 1998;26(1):382-6.
1998: Baldi P; Chauvin Y; Brunak S; Gorodkin J; Pedersen A G
Computational applications of DNA structural scales.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1998;6():35-42.
1997: Lund O; Frimand K; Gorodkin J; Bohr H; Bohr J; Hansen J; Brunak S
Protein distance constraints predicted by neural networks and probability density functions.
Protein engineering 1997;10(11):1241-8.
1997: Nielsen H; Engelbrecht J; Brunak S; von Heijne G
A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.
International journal of neural systems 1997;8(5-6):581-99.
1997: Tolstrup N; Rouzé P; Brunak S
A branch point consensus from Arabidopsis found by non-circular analysis allows for better prediction of acceptor sites.
Nucleic acids research 1997;25(15):3159-63.
1997: Knudsen S; Brunak S
Kissing loops hide premature termination codons in pre-mRNA of selenoprotein genes and in genes containing programmed ribosomal frameshifts.
RNA (New York, N.Y.) 1997;3(7):697-701.
1997: Bohr J; Bohr H; Brunak S
Protein folding and wring resonances.
Biophysical chemistry 1997;63(2-3):97-105.
1997: Nielsen H; Engelbrecht J; Brunak S; von Heijne G
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.
Protein engineering 1997;10(1):1-6.
1997: Hansen J E; Lund O; Rapacki K; Brunak S
O-GLYCBASE version 2.0: a revised database of O-glycosylated proteins.
Nucleic acids research 1997;25(1):278-82.
1997: Bohr H; Brunak S; Bohr J
Coherent topological phenomena in protein folding.
Folding & design 1997;2(3):S15-8.
1997: Bohr H; Brunak S; Bohr J
Molecular wring resonances in chain molecules.
Bioelectromagnetics 1997;18(2):187-9.
1996: Lund O; Hansen J; Brunak S; Bohr J
Relationship between protein structure and geometrical constraints.
Protein science : a publication of the Protein Society 1996;5(11):2217-25.
1996: Blom N; Hansen J; Blaas D; Brunak S
Cleavage site analysis in picornaviral polyproteins: discovering cellular targets by neural networks.
Protein science : a publication of the Protein Society 1996;5(11):2203-16.
1996: Baldi P; Brunak S; Chauvin Y; Krogh A
Naturally occurring nucleosome positioning signals in human exons and introns.
Journal of molecular biology 1996;263(4):503-10.
1996: Reese M G; Lund O; Bohr J; Bohr H; Hansen J E; Brunak S
Distance distributions in proteins: a six-parameter representation.
Protein engineering 1996;9(9):733-40.
1996: Hebsgaard S M; Korning P G; Tolstrup N; Engelbrecht J; Rouzé P; Brunak S
Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information.
Nucleic acids research 1996;24(17):3439-52.
1996: Brunak S; Engelbrecht J
Protein structure and the sequential structure of mRNA: alpha-helix and beta-sheet signals at the nucleotide level.
Proteins 1996;25(2):237-52.
1996: Hansen J E; Lund O; Nielsen J O; Brunak S; Hansen J E
Prediction of the secondary structure of HIV-1 gp120.
Proteins 1996;25(1):1-11.
1996: Nielsen H; Engelbrecht J; von Heijne G; Brunak S
Defining a similarity threshold for a functional protein sequence pattern: the signal peptide cleavage site.
Proteins 1996;24(2):165-77.
1996: Korning P G; Hebsgaard S M; Rouze P; Brunak S
Cleaning the GenBank Arabidopsis thaliana data set.
Nucleic acids research 1996;24(2):316-20.
1996: Hansen J E; Lund O; Nielsen J O; Hansen J E; Brunak S
O-GLYCBASE: a revised database of O-glycosylated proteins.
Nucleic acids research 1996;24(1):248-52.
1996: Pedersen A G; Baldi P; Brunak S; Chauvin Y
Characterization of prokaryotic and eukaryotic promoters using hidden Markov models.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1996;4():182-91.
1995: Larsen N I; Engelbrecht J; Brunak S
Analysis of eukaryotic promoter sequences reveals a systematically occurring CT-signal.
Nucleic acids research 1995;23(7):1223-30.
1995: Baldi P; Brunak S; Chauvin Y; Engelbrecht J; Krogh A
Periodic sequence patterns in human exons.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1995;3():30-8.
1994: Tolstrup N; Toftgård J; Engelbrecht J; Brunak S
Neural network model of the genetic code is strongly correlated to the GES scale of amino acid transfer free energies.
Journal of molecular biology 1994;243(5):816-20.
1993: Bohr J; Bohr H; Brunak S; Cotterill R M; Fredholm H; Lautrup B; Petersen S B
Protein structures from distance inequalities.
Journal of molecular biology 1993;231(3):861-9.
1992: Engelbrecht J; Knudsen S; Brunak S
G+C-rich tract in 5' end of human introns.
Journal of molecular biology 1992;227(1):108-13.
1992: Lukashin A V; Engelbrecht J; Brunak S
Multiple alignment using simulated annealing: branch point definition in human mRNA splicing.
Nucleic acids research 1992;20(10):2511-6.
1991: Brunak S; Engelbrecht J; Knudsen S
Prediction of human mRNA donor and acceptor sites from the DNA sequence.
Journal of molecular biology 1991;220(1):49-65.
1990: Brunak S; Engelbrecht J; Knudsen S
Neural network detects errors in the assignment of mRNA splice sites.
Nucleic acids research 1990;18(16):4797-801.
1990: Brunak S; Engelbrecht J; Knudsen S
Cleaning up gene databases.
Nature 1990;343(6254):123.
1990: Andreassen H; Bohr H; Bohr J; Brunak S; Bugge T; Cotterill R M; Jacobsen C; Kusk P; Lautrup B; Petersen S B
Analysis of the secondary structure of the human immunodeficiency virus (HIV) proteins p17, gp120, and gp41 by computer modeling based on neural network methods.
Journal of acquired immune deficiency syndromes 1990;3(6):615-22.
1988: Bohr H; Bohr J; Brunak S; Cotterill R M; Lautrup B; Nørskov L; Olsen O H; Petersen S B
Protein secondary structure and homology by neural networks. The alpha-helices in rhodopsin.
FEBS letters 1988;241(1-2):223-8.

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