|
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
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 |
|
|
