Søren Brunak - Publications

Affiliations: 
Systems Biology Technical University of Denmark, Kongens Lyngby, Denmark 
Website:
http://www.cbs.dtu.dk/staff/show-staff.php?id=514

251 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Jørgensen IF, Russo F, Jensen AB, Westergaard D, Lademann M, Hu JX, Brunak S, Belling K. Comorbidity landscape of the Danish patient population affected by chromosome abnormalities. Genetics in Medicine : Official Journal of the American College of Medical Genetics. PMID 31019277 DOI: 10.1038/s41436-019-0519-9  0.56
2019 Njølstad PR, Andreassen OA, Brunak S, Børglum AD, Dillner J, Esko T, Franks PW, Freimer N, Groop L, Heimer H, Hougaard DM, Hovig E, Hveem K, Jalanko A, Kaprio J, et al. Roadmap for a precision-medicine initiative in the Nordic region. Nature Genetics. PMID 30988515 DOI: 10.1038/s41588-019-0391-1  0.6
2019 Westergaard D, Moseley P, Sørup FKH, Baldi P, Brunak S. Population-wide analysis of differences in disease progression patterns in men and women. Nature Communications. 10: 666. PMID 30737381 DOI: 10.1038/s41467-019-08475-9  0.56
2019 Burgdorf KS, Trabjerg BB, Pedersen MG, Nissen J, Banasik K, Pedersen OB, Sørensen E, Nielsen KR, Larsen MH, Erikstrup C, Bruun-Rasmussen P, Westergaard D, Thørner LW, Hjalgrim H, Paarup HM, ... Brunak S, et al. Large-scale study of Toxoplasma and Cytomegalovirus shows an association between infection and serious psychiatric disorders. Brain, Behavior, and Immunity. PMID 30685531 DOI: 10.1016/j.bbi.2019.01.026  0.6
2018 Hu JX, Helleberg M, Jensen AB, Brunak S, Lundgren J. A large-cohort, longitudinal study determines pre-cancer disease routes across different cancer types. Cancer Research. PMID 30591553 DOI: 10.1158/0008-5472.CAN-18-1677  0.4
2018 Pedersen HK, Forslund SK, Gudmundsdottir V, Petersen AØ, Hildebrand F, Hyötyläinen T, Nielsen T, Hansen T, Bork P, Ehrlich SD, Brunak S, Oresic M, Pedersen O, Nielsen HB. A computational framework to integrate high-throughput '-omics' datasets for the identification of potential mechanistic links. Nature Protocols. PMID 30382244 DOI: 10.1038/s41596-018-0064-z  0.92
2018 Jensen AB, Sørensen TI, Pedersen O, Jess T, Brunak S, Allin KH. Increase in clinically recorded type 2 diabetes after colectomy. Elife. 7. PMID 30373718 DOI: 10.7554/eLife.37420  0.4
2018 Teare HJA, de Masi F, Banasik K, Barnett A, Herrgard S, Jablonka B, Postma JWM, McDonald TJ, Forgie I, Chmura PJ, Rydzka EK, Gupta R, Brunak S, Pearson E, Kaye J. The governance structure for data access in the DIRECT consortium: an innovative medicines initiative (IMI) project. Life Sciences, Society and Policy. 14: 20. PMID 30182269 DOI: 10.1186/s40504-018-0083-0  0.56
2018 Tsafou K, Katschnig AM, Radic-Sarikas B, Mutz CN, Iljin K, Schwentner R, Kauer MO, Mühlbacher K, Aryee DNT, Westergaard D, Haapa-Paananen S, Fey V, Superti-Furga G, Toretsky J, Brunak S, et al. Identifying the druggable interactome of EWS-FLI1 reveals MCL-1 dependent differential sensitivities of Ewing sarcoma cells to apoptosis inducers. Oncotarget. 9: 31018-31031. PMID 30123424 DOI: 10.18632/oncotarget.25760  0.56
2018 Oprea TI, Bologa CG, Brunak S, Campbell A, Gan GN, Gaulton A, Gomez SM, Guha R, Hersey A, Holmes J, Jadhav A, Jensen LJ, Johnson GL, Karlson A, Leach AR, et al. Unexplored therapeutic opportunities in the human genome. Nature Reviews. Drug Discovery. PMID 29567993 DOI: 10.1038/nrd.2018.52  0.92
2018 Jensen KH, Izarzugaza JMG, Juncker AS, Hansen RB, Hansen TF, Timshel P, Blondal T, Jensen TS, Rygaard-Hjalsted E, Mouritzen P, Thorsen M, Wernersson R, Nielsen HB, Jakobsen A, Brunak S, et al. Analysis of a gene panel for targeted sequencing of colorectal cancer samples. Oncotarget. 9: 9043-9060. PMID 29507673 DOI: 10.18632/oncotarget.24138  0.8
2018 Oprea TI, Bologa CG, Brunak S, Campbell A, Gan GN, Gaulton A, Gomez SM, Guha R, Hersey A, Holmes J, Jadhav A, Jensen LJ, Johnson GL, Karlson A, Leach AR, et al. Unexplored therapeutic opportunities in the human genome. Nature Reviews. Drug Discovery. PMID 29472638 DOI: 10.1038/nrd.2018.14  0.92
2018 Westergaard D, Stærfeldt HH, Tønsberg C, Jensen LJ, Brunak S. A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts. Plos Computational Biology. 14: e1005962. PMID 29447159 DOI: 10.1371/journal.pcbi.1005962  0.92
2018 Gudmundsdottir V, Pedersen HK, Allebrandt KV, Brorsson C, van Leeuwen N, Banasik K, Mahajan A, Groves CJ, van de Bunt M, Dawed AY, Fritsche A, Staiger H, Simonis-Bik AMC, Deelen J, Kramer MHH, ... ... Brunak S, et al. Integrative network analysis highlights biological processes underlying GLP-1 stimulated insulin secretion: A DIRECT study. Plos One. 13: e0189886. PMID 29293525 DOI: 10.1371/journal.pone.0189886  0.56
2017 Ellesøe SG, Workman CT, Bouvagnet P, Loffredo CA, McBride KL, Hinton RB, van Engelen K, Gertsen EC, Mulder BJM, Postma AV, Anderson RH, Hjortdal VE, Brunak S, Larsen LA. Familial co-occurrence of congenital heart defects follows distinct patterns. European Heart Journal. PMID 29106500 DOI: 10.1093/eurheartj/ehx314  0.4
2017 Russo F, Di Bella S, Vannini F, Berti G, Scoyni F, Cook HV, Santos A, Nigita G, Bonnici V, Laganà A, Geraci F, Pulvirenti A, Giugno R, De Masi F, Belling K, ... ... Brunak SR, et al. miRandola 2017: a curated knowledge base of non-invasive biomarkers. Nucleic Acids Research. PMID 29036351 DOI: 10.1093/nar/gkx854  0.92
2017 Molnos S, Wahl S, Haid M, Eekhoff EMW, Pool R, Floegel A, Deelen J, Much D, Prehn C, Breier M, Draisma HH, van Leeuwen N, Simonis-Bik AMC, Jonsson A, Willemsen G, ... ... Brunak S, et al. Metabolite ratios as potential biomarkers for type 2 diabetes: a DIRECT study. Diabetologia. PMID 28936587 DOI: 10.1007/s00125-017-4436-7  0.56
2017 Maretty L, Jensen JM, Petersen B, Sibbesen JA, Liu S, Villesen P, Skov L, Belling K, Theil Have C, Izarzugaza JMG, Grosjean M, Bork-Jensen J, Grove J, Als TD, Huang S, ... ... Brunak S, et al. Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. Nature. PMID 28746312 DOI: 10.1038/nature23264  0.56
2017 Pedersen HK, Gudmundsdottir V, Brunak S. Pancreatic Islet Protein Complexes and Their Dysregulation in Type 2 Diabetes. Frontiers in Genetics. 8: 43. PMID 28473845 DOI: 10.3389/fgene.2017.00043  0.32
2017 Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Pedersen HK, Arumugam M, Kristiansen K, Voigt AY, Vestergaard H, Hercog R, ... ... Brunak S, et al. Corrigendum: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature. 545: 116. PMID 28470190 DOI: 10.1038/nature22318  0.92
2017 Russo F, Belling K, Jensen AB, Scoyni F, Brunak S, Pellegrini M. MicroRNAs, Regulatory Networks, and Comorbidities: Decoding Complex Systems. Methods in Molecular Biology (Clifton, N.J.). 1580: 281-295. PMID 28439840 DOI: 10.1007/978-1-4939-6866-4_19  0.4
2017 Belling K, Russo F, Jensen AB, Dalgaard MD, Westergaard D, Rajpert-De Meyts E, Skakkebæk NE, Juul A, Brunak S. Klinefelter syndrome comorbidities linked to increased X chromosome gene dosage and altered protein interactome activity. Human Molecular Genetics. PMID 28369266 DOI: 10.1093/hmg/ddx014  0.56
2017 Francavilla C, Lupia M, Tsafou K, Villa A, Kowalczyk K, Rakownikow Jersie-Christensen R, Bertalot G, Confalonieri S, Brunak S, Jensen LJ, Cavallaro U, Olsen JV. Phosphoproteomics of Primary Cells Reveals Druggable Kinase Signatures in Ovarian Cancer. Cell Reports. 18: 3242-3256. PMID 28355574 DOI: 10.1016/j.celrep.2017.03.015  0.92
2017 Kirk IK, Weinhold N, Belling K, Skakkebæk NE, Jensen TS, Leffers H, Juul A, Brunak S. Chromosome-wise Protein Interaction Patterns and Their Impact on Functional Implications of Large-Scale Genomic Aberrations. Cell Systems. PMID 28215527 DOI: 10.1016/j.cels.2017.01.001  0.8
2016 Pedersen HK, Gudmundsdottir V, Pedersen MK, Brorsson C, Brunak S, Gupta R. Ranking factors involved in diabetes remission after bariatric surgery using machine-learning integrating clinical and genomic biomarkers. Npj Genomic Medicine. 1: 16035. PMID 29263820 DOI: 10.1038/npjgenmed.2016.35  0.56
2016 Nguyen DT, Mathias S, Bologa C, Brunak S, Fernandez N, Gaulton A, Hersey A, Holmes J, Jensen LJ, Karlsson A, Liu G, Ma'ayan A, Mandava G, Mani S, Mehta S, et al. Pharos: Collating protein information to shed light on the druggable genome. Nucleic Acids Research. PMID 27903890 DOI: 10.1093/nar/gkw1072  0.92
2016 Beck MK, Westergaard D, Jensen AB, Groop L, Brunak S. TEMPORAL ORDER OF DISEASE PAIRS AFFECTS SUBSEQUENT DISEASE TRAJECTORIES: THE CASE OF DIABETES AND SLEEP APNEA. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 22: 380-389. PMID 27896991  0.56
2016 Li T, Wernersson R, Hansen RB, Horn H, Mercer J, Slodkowicz G, Workman CT, Rigina O, Rapacki K, Stærfeldt HH, Brunak S, Jensen TS, Lage K. A scored human protein-protein interaction network to catalyze genomic interpretation. Nature Methods. PMID 27892958 DOI: 10.1038/nmeth.4083  0.8
2016 Beck MK, Jensen AB, Nielsen AB, Perner A, Moseley PL, Brunak S. Diagnosis trajectories of prior multi-morbidity predict sepsis mortality. Scientific Reports. 6: 36624. PMID 27812043 DOI: 10.1038/srep36624  0.4
2016 Malaspinas AS, Westaway MC, Muller C, Sousa VC, Lao O, Alves I, Bergström A, Athanasiadis G, Cheng JY, Crawford JE, Heupink TH, Macholdt E, Peischl S, Rasmussen S, Schiffels S, ... ... Brunak S, et al. A genomic history of Aboriginal Australia. Nature. PMID 27654914 DOI: 10.1038/nature18299  0.92
2016 Plichta DR, Juncker AS, Bertalan M, Rettedal E, Gautier L, Varela E, Manichanh C, Fouqueray C, Levenez F, Nielsen T, Doré J, Machado AM, de Evgrafov MC, Hansen T, Jørgensen T, ... ... Brunak S, et al. Transcriptional interactions suggest niche segregation among microorganisms in the human gut. Nature Microbiology. 1: 16152. PMID 27564131 DOI: 10.1038/nmicrobiol.2016.152  0.92
2016 Hu JX, Thomas CE, Brunak S. Network biology concepts in complex disease comorbidities. Nature Reviews. Genetics. PMID 27498692 DOI: 10.1038/nrg.2016.87  0.92
2016 Pedersen HK, Gudmundsdottir V, Nielsen HB, Hyotylainen T, Nielsen T, Jensen BA, Forslund K, Hildebrand F, Prifti E, Falony G, Le Chatelier E, Levenez F, Doré J, Mattila I, Plichta DR, ... ... Brunak S, et al. Human gut microbes impact host serum metabolome and insulin sensitivity. Nature. PMID 27409811 DOI: 10.1038/nature18646  0.92
2016 Ellinghaus D, Jostins L, Spain SL, Cortes A, Bethune J, Han B, Park YR, Raychaudhuri S, Pouget JG, Hübenthal M, Folseraas T, Wang Y, Esko T, Metspalu A, Westra HJ, ... ... Brunak S, et al. Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci. Nature Genetics. PMID 26974007 DOI: 10.1038/ng.3528  0.92
2016 Ellesøe SG, Jensen AB, Ängquist LH, Hjortdal VE, Larsen LA, Brunak S. How Suitable Are Registry Data for Recurrence Risk Calculations? Validation of Diagnoses on 1,593 Families With Congenital Heart Disease. World Journal For Pediatric & Congenital Heart Surgery. 7: 169-77. PMID 26957399 DOI: 10.1177/2150135115615786  0.4
2016 Kringelum J, Kjaerulff SK, Brunak S, Lund O, Oprea TI, Taboureau O. ChemProt-3.0: a global chemical biology diseases mapping. Database : the Journal of Biological Databases and Curation. 2016. PMID 26876982 DOI: 10.1093/database/bav123  0.4
2016 Mollerup S, Friis-Nielsen J, Vinner L, Hansen TA, Richter SR, Fridholm H, Herrera JA, Lund O, Brunak S, Izarzugaza JM, Mourier T, Nielsen LP, Hansen AJ. Propionibacterium acnes - disease causing agent or common contaminant? Detection in diverse patient samples by next generation sequencing. Journal of Clinical Microbiology. PMID 26818667 DOI: 10.1128/JCM.02723-15  0.92
2015 Ellesøe SG, Johansen MM, Bjerre JV, Hjortdal VE, Brunak S, Larsen LA. Familial Atrial Septal Defect and Sudden Cardiac Death: Identification of a Novel NKX2-5 Mutation and a Review of the Literature. Congenital Heart Disease. PMID 26679770 DOI: 10.1111/chd.12317  0.92
2015 Jensen AB, Ajslev TA, Brunak S, Sørensen TI. Long-term risk of cardiovascular and cerebrovascular disease after removal of the colonic microbiota by colectomy: a cohort study based on the Danish National Patient Register from 1996 to 2014. Bmj Open. 5: e008702. PMID 26671951 DOI: 10.1136/bmjopen-2015-008702  0.4
2015 Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Krogh Pedersen H, Arumugam M, Kristiansen K, Yvonne Voigt A, Vestergaard H, Hercog R, ... ... Brunak S, et al. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature. PMID 26633628 DOI: 10.1038/nature15766  0.92
2015 Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Krogh Pedersen H, Arumugam M, Kristiansen K, Yvonne Voigt A, Vestergaard H, Hercog R, ... ... Brunak S, et al. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature. PMID 26618873 DOI: 10.1038/nature15766  0.92
2015 Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, ... ... Brunak S, et al. Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Research. PMID 26538599 DOI: 10.1093/nar/gkv1116  0.92
2015 Rasmussen S, Allentoft ME, Nielsen K, Orlando L, Sikora M, Sjögren KG, Pedersen AG, Schubert M, Van Dam A, Kapel CM, Nielsen HB, Brunak S, Avetisyan P, Epimakhov A, Khalyapin MV, et al. Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago. Cell. 163: 571-82. PMID 26496604 DOI: 10.1016/j.cell.2015.10.009  0.36
2015 Vinner L, Mourier T, Friis-Nielsen J, Gniadecki R, Dybkaer K, Rosenberg J, Langhoff JL, Cruz DF, Fonager J, Izarzugaza JM, Gupta R, Sicheritz-Ponten T, Brunak S, Willerslev E, Nielsen LP, et al. Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing. Scientific Reports. 5: 13201. PMID 26285800 DOI: 10.1038/srep13201  0.92
2015 Allentoft ME, Sikora M, Sjögren KG, Rasmussen S, Rasmussen M, Stenderup J, Damgaard PB, Schroeder H, Ahlström T, Vinner L, Malaspinas AS, Margaryan A, Higham T, Chivall D, Lynnerup N, ... ... Brunak S, et al. Population genomics of Bronze Age Eurasia. Nature. 522: 167-72. PMID 26062507 DOI: 10.1038/nature14507  0.92
2015 Warrer P, Jensen PB, Aagaard L, Jensen LJ, Brunak S, Krag MH, Rossing P, Almdal T, Andersen HU, Hansen EH. Identification of possible adverse drug reactions in clinical notes: The case of glucose-lowering medicines. Journal of Research in Pharmacy Practice. 4: 64-72. PMID 25984543 DOI: 10.4103/2279-042X.155753  0.92
2015 Rasmussen HB, Bjerre D, Linnet K, Jürgens G, Dalhoff K, Stefansson H, Hankemeier T, Kaddurah-Daouk R, Taboureau O, Brunak S, Houmann T, Jeppesen P, Pagsberg AK, Plessen K, Dyrborg J, et al. Individualization of treatments with drugs metabolized by CES1: combining genetics and metabolomics. Pharmacogenomics. 16: 649-65. PMID 25896426 DOI: 10.2217/pgs.15.7  0.92
2015 Rondas D, Gudmundsdottir V, D'Hertog W, Crèvecoeur I, Waelkens E, Brunak S, Mathieu C, Overbergh L. A proteomic study of the regulatory role for STAT-1 in cytokine-induced beta-cell death. Proteomics. Clinical Applications. PMID 25712914 DOI: 10.1002/prca.201400124  0.92
2015 Kjartansdóttir KR, Friis-Nielsen J, Asplund M, Mollerup S, Mourier T, Jensen RH, Hansen TA, Rey-Iglesia A, Richter SR, Alquezar-Planas DE, Olsen PV, Vinner L, Fridholm H, Sicheritz-Pontén T, Nielsen LP, ... Brunak S, et al. Traces of ATCV-1 associated with laboratory component contamination. Proceedings of the National Academy of Sciences of the United States of America. 112: E925-6. PMID 25654983 DOI: 10.1073/pnas.1423756112  0.92
2015 Besenbacher S, Liu S, Izarzugaza JM, Grove J, Belling K, Bork-Jensen J, Huang S, Als TD, Li S, Yadav R, Rubio-García A, Lescai F, Demontis D, Rao J, Ye W, ... ... Brunak S, et al. Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios. Nature Communications. 6: 5969. PMID 25597990 DOI: 10.1038/ncomms6969  0.92
2015 Thomsen R, Nielsen LM, Holm NB, Rasmussen HB, Linnet K. Synthetic cannabimimetic agents metabolized by carboxylesterases. Drug Testing and Analysis. 7: 565-76. PMID 25346527 DOI: 10.1002/dta.1731  0.92
2015 WesoÅ‚owska-Andersen A, Borst L, Dalgaard MD, Yadav R, Rasmussen KK, Wehner PS, Rasmussen M, Ørntoft TF, Nordentoft I, Koehler R, Bartram CR, Schrappe M, Sicheritz-Ponten T, Gautier L, Marquart H, ... ... Brunak S, et al. Genomic profiling of thousands of candidate polymorphisms predicts risk of relapse in 778 Danish and German childhood acute lymphoblastic leukemia patients. Leukemia. 29: 297-303. PMID 24990611 DOI: 10.1038/leu.2014.205  0.92
2014 Eriksson R, Aagaard L, Jensen LJ, Borisova L, Hørlück D, Brunak S, Hansen EH. Discrepancies in listed adverse drug reactions in pharmaceutical product information supplied by the regulatory authorities in Denmark and the USA. Pharmacology Research & Perspectives. 2: e00038. PMID 25505588 DOI: 10.1002/prp2.38  0.92
2014 Gustafsson M, Nestor CE, Zhang H, Barabási AL, Baranzini S, Brunak S, Chung KF, Federoff HJ, Gavin AC, Meehan RR, Picotti P, Pujana MÀ, Rajewsky N, Smith KG, Sterk PJ, et al. Modules, networks and systems medicine for understanding disease and aiding diagnosis. Genome Medicine. 6: 82. PMID 25473422 DOI: 10.1186/s13073-014-0082-6  0.92
2014 Malaspinas AS, Lao O, Schroeder H, Rasmussen M, Raghavan M, Moltke I, Campos PF, Sagredo FS, Rasmussen S, Gonçalves VF, Albrechtsen A, Allentoft ME, Johnson PL, Li M, Reis S, ... ... Brunak S, et al. Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil. Current Biology : Cb. 24: R1035-7. PMID 25455029 DOI: 10.1016/j.cub.2014.09.078  0.92
2014 Roitmann E, Eriksson R, Brunak S. Patient stratification and identification of adverse event correlations in the space of 1190 drug related adverse events. Frontiers in Physiology. 5: 332. PMID 25249979 DOI: 10.3389/fphys.2014.00332  0.92
2014 Re A, Workman CT, Waldron L, Quattrone A, Brunak S. Lineage-specific interface proteins match up the cell cycle and differentiation in embryo stem cells. Stem Cell Research. 13: 316-28. PMID 25173649 DOI: 10.1016/j.scr.2014.07.008  0.92
2014 Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, ... ... Brunak S, et al. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nature Biotechnology. 32: 822-8. PMID 24997787 DOI: 10.1038/nbt.2939  0.92
2014 Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, Arumugam M, Kultima JR, Prifti E, Nielsen T, Juncker AS, Manichanh C, Chen B, Zhang W, Levenez F, ... ... Brunak S, et al. An integrated catalog of reference genes in the human gut microbiome. Nature Biotechnology. 32: 834-41. PMID 24997786 DOI: 10.1038/nbt.2942  0.92
2014 Jensen AB, Moseley PL, Oprea TI, Ellesøe SG, Eriksson R, Schmock H, Jensen PB, Jensen LJ, Brunak S. Temporal disease trajectories condensed from population-wide registry data covering 6.2 million patients. Nature Communications. 5: 4022. PMID 24959948 DOI: 10.1038/ncomms5022  0.92
2014 Lundby A, Rossin EJ, Steffensen AB, Acha MR, Newton-Cheh C, Pfeufer A, Lynch SN, Olesen SP, Brunak S, Ellinor PT, Jukema JW, Trompet S, Ford I, Macfarlane PW, et al. Annotation of loci from genome-wide association studies using tissue-specific quantitative interaction proteomics. Nature Methods. 11: 868-74. PMID 24952909 DOI: 10.1038/nmeth.2997  0.92
2014 Koivula RW, Heggie A, Barnett A, Cederberg H, Hansen TH, Koopman AD, RidderstrÃ¥le M, Rutters F, Vestergaard H, Gupta R, HerrgÃ¥rd S, Heymans MW, Perry MH, Rauh S, Siloaho M, ... ... Brunak S, et al. Discovery of biomarkers for glycaemic deterioration before and after the onset of type 2 diabetes: rationale and design of the epidemiological studies within the IMI DIRECT Consortium. Diabetologia. 57: 1132-42. PMID 24695864 DOI: 10.1007/s00125-014-3216-x  0.92
2014 Audouze K, Tromelin A, Le Bon AM, Belloir C, Petersen RK, Kristiansen K, Brunak S, Taboureau O. Identification of odorant-receptor interactions by global mapping of the human odorome. Plos One. 9: e93037. PMID 24695519 DOI: 10.1371/journal.pone.0093037  0.92
2014 Eriksson R, Werge T, Jensen LJ, Brunak S. Dose-specific adverse drug reaction identification in electronic patient records: temporal data mining in an inpatient psychiatric population. Drug Safety. 37: 237-47. PMID 24634163 DOI: 10.1007/s40264-014-0145-z  0.92
2014 Wohlfahrt-Veje C, Audouze K, Brunak S, Antignac JP, le Bizec B, Juul A, Skakkebæk NE, Main KM. Polychlorinated dibenzo-p-dioxins, furans, and biphenyls (PCDDs/PCDFs and PCBs) in breast milk and early childhood growth and IGF1. Reproduction (Cambridge, England). 147: 391-9. PMID 24586095 DOI: 10.1530/REP-13-0422  0.92
2014 Geertz-Hansen HM, Blom N, Feist AM, Brunak S, Petersen TN. Cofactory: sequence-based prediction of cofactor specificity of Rossmann folds. Proteins. 82: 1819-28. PMID 24523134 DOI: 10.1002/prot.24536  0.92
2014 Rasmussen M, Anzick SL, Waters MR, Skoglund P, DeGiorgio M, Stafford TW, Rasmussen S, Moltke I, Albrechtsen A, Doyle SM, Poznik GD, Gudmundsdottir V, Yadav R, Malaspinas AS, White SS, ... ... Brunak S, et al. The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature. 506: 225-9. PMID 24522598 DOI: 10.1038/nature13025  0.92
2014 Krysiak-Baltyn K, Nordahl Petersen T, Audouze K, Jørgensen N, Angquist L, Brunak S. Compass: a hybrid method for clinical and biobank data mining. Journal of Biomedical Informatics. 47: 160-70. PMID 24513869 DOI: 10.1016/j.jbi.2013.10.007  0.92
2014 Raghavan M, Skoglund P, Graf KE, Metspalu M, Albrechtsen A, Moltke I, Rasmussen S, Stafford TW, Orlando L, Metspalu E, Karmin M, Tambets K, Rootsi S, Mägi R, Campos PF, ... ... Brunak S, et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature. 505: 87-91. PMID 24256729 DOI: 10.1038/nature12736  0.92
2014 Kouskoumvekaki I, Shublaq N, Brunak S. Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics. Briefings in Bioinformatics. 15: 942-52. PMID 23908249 DOI: 10.1093/bib/bbt055  0.92
2013 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, ... ... Brunak S, et al. Whole-exome sequencing of 2,000 Danish individuals and the role of rare coding variants in type 2 diabetes. American Journal of Human Genetics. 93: 1072-86. PMID 24290377 DOI: 10.1016/j.ajhg.2013.11.005  0.92
2013 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, et al. Bacterial natural transformation by highly fragmented and damaged DNA. Proceedings of the National Academy of Sciences of the United States of America. 110: 19860-5. PMID 24248361 DOI: 10.1073/pnas.1315278110  0.92
2013 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, et al. Metagenomic species profiling using universal phylogenetic marker genes. Nature Methods. 10: 1196-9. PMID 24141494 DOI: 10.1038/nmeth.2693  0.92
2013 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, et al. A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk. Cell. 155: 70-80. PMID 24074861 DOI: 10.1016/j.cell.2013.08.030  0.92
2013 Audouze K, Brunak S, Grandjean P. A computational approach to chemical etiologies of diabetes. Scientific Reports. 3: 2712. PMID 24048418 DOI: 10.1038/srep02712  0.92
2013 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, ... ... Brunak S, et al. Richness of human gut microbiome correlates with metabolic markers. Nature. 500: 541-6. PMID 23985870 DOI: 10.1038/nature12506  0.92
2013 Spisák S, Solymosi N, Ittzés P, Bodor A, Kondor D, Vattay G, Barták BK, Sipos F, Galamb O, Tulassay Z, Szállási Z, Rasmussen S, Sicheritz-Ponten T, Brunak S, Molnár B, et al. Complete genes may pass from food to human blood. Plos One. 8: e69805. PMID 23936105 DOI: 10.1371/journal.pone.0069805  0.92
2013 Johansen MB, Izarzugaza JM, Brunak S, Petersen TN, Gupta R. Prediction of disease causing non-synonymous SNPs by the Artificial Neural Network Predictor NetDiseaseSNP. Plos One. 8: e68370. PMID 23935863 DOI: 10.1371/journal.pone.0068370  0.92
2013 Börnigen D, Pers TH, Thorrez L, Huttenhower C, Moreau Y, Brunak S. Concordance of gene expression in human protein complexes reveals tissue specificity and pathology. Nucleic Acids Research. 41: e171. PMID 23921638 DOI: 10.1093/nar/gkt661  0.92
2013 Cases M, Furlong LI, Albanell J, Altman RB, Bellazzi R, Boyer S, Brand A, Brookes AJ, Brunak S, Clark TW, Gea J, Ghazal P, Graf N, Guigó R, Klein TE, et al. Improving data and knowledge management to better integrate health care and research. Journal of Internal Medicine. 274: 321-8. PMID 23808970 DOI: 10.1111/joim.12105  0.92
2013 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, ... ... Brunak S, et al. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature. 499: 74-8. PMID 23803765 DOI: 10.1038/nature12323  0.92
2013 Belling KC, Tanaka M, Dalgaard MD, Nielsen JE, Nielsen HB, Brunak S, Almstrup K, Leffers H. Transcriptome profiling of mice testes following low dose irradiation. Reproductive Biology and Endocrinology : Rb&E. 11: 50. PMID 23714422 DOI: 10.1186/1477-7827-11-50  0.92
2013 Eriksson R, Jensen PB, Frankild S, Jensen LJ, Brunak S. Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text. Journal of the American Medical Informatics Association : Jamia. 20: 947-53. PMID 23703825 DOI: 10.1136/amiajnl-2013-001708  0.92
2013 Pers TH, Dworzy?ski P, Thomas CE, Lage K, Brunak S. MetaRanker 2.0: a web server for prioritization of genetic variation data. Nucleic Acids Research. 41: W104-8. PMID 23703204 DOI: 10.1093/nar/gkt387  0.92
2013 Steentoft C, Vakhrushev SY, Joshi HJ, Kong Y, Vester-Christensen MB, Schjoldager KT, Lavrsen K, Dabelsteen S, Pedersen NB, Marcos-Silva L, Gupta R, Bennett EP, Mandel U, Brunak S, Wandall HH, et al. Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology. The Embo Journal. 32: 1478-88. PMID 23584533 DOI: 10.1038/emboj.2013.79  0.92
2013 Tinti M, Kiemer L, Costa S, Miller ML, Sacco F, Olsen JV, Carducci M, Paoluzi S, Langone F, Workman CT, Blom N, Machida K, Thompson CM, Schutkowski M, Brunak S, et al. The SH2 domain interaction landscape. Cell Reports. 3: 1293-305. PMID 23545499 DOI: 10.1016/j.celrep.2013.03.001  0.92
2013 Edsgärd D, Dalgaard MD, Weinhold N, Wesolowska-Andersen A, Rajpert-De Meyts E, Ottesen AM, Juul A, Skakkebæk NE, Skøt Jensen T, Gupta R, Leffers H, Brunak S. Genome-wide assessment of the association of rare and common copy number variations to testicular germ cell cancer. Frontiers in Endocrinology. 4: 2. PMID 23372565 DOI: 10.3389/fendo.2013.00002  0.92
2013 Jensen PB, Jensen LJ, Brunak S. Reply to 'Mining electronic health records: an additional perspective'. Nature Reviews. Genetics. 14: 75. PMID 23247438 DOI: 10.1038/nrg3208-c2  0.92
2013 Kim Kjærulff S, Wich L, Kringelum J, Jacobsen UP, Kouskoumvekaki I, Audouze K, Lund O, Brunak S, Oprea TI, Taboureau O. ChemProt-2.0: visual navigation in a disease chemical biology database. Nucleic Acids Research. 41: D464-9. PMID 23185041 DOI: 10.1093/nar/gks1166  0.92
2012 Stranzl T, Larsen MV, Lund O, Nielsen M, Brunak S. The cancer exome generated by alternative mRNA splicing dilutes predicted HLA class I epitope density. Plos One. 7: e38670. PMID 23049726 DOI: 10.1371/journal.pone.0038670  0.92
2012 Lage K, Greenway SC, Rosenfeld JA, Wakimoto H, Gorham JM, Segrè AV, Roberts AE, Smoot LB, Pu WT, Pereira AC, Mesquita SM, Tommerup N, Brunak S, Ballif BC, Shaffer LG, et al. Genetic and environmental risk factors in congenital heart disease functionally converge in protein networks driving heart development. Proceedings of the National Academy of Sciences of the United States of America. 109: 14035-40. PMID 22904188 DOI: 10.1073/pnas.1210730109  0.92
2012 Thomsen R, Rasmussen HB, Linnet K. Enantioselective determination of methylphenidate and ritalinic acid in whole blood from forensic cases using automated solid-phase extraction and liquid chromatography-tandem mass spectrometry. Journal of Analytical Toxicology. 36: 560-8. PMID 22833645 DOI: 10.1093/jat/bks065  0.92
2012 Jensen PB, Jensen LJ, Brunak S. Mining electronic health records: towards better research applications and clinical care. Nature Reviews. Genetics. 13: 395-405. PMID 22549152 DOI: 10.1038/nrg3208  0.92
2012 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. Association between chemical pattern in breast milk and congenital cryptorchidism: modelling of complex human exposures. International Journal of Andrology. 35: 294-302. PMID 22519522 DOI: 10.1111/j.1365-2605.2012.01268.x  0.92
2012 Rojas AM, Santamaria A, Malik R, Jensen TS, Körner R, Morilla I, de Juan D, Krallinger M, Hansen DA, Hoffmann R, Lees J, Reid A, Yeats C, Wehner A, Elowe S, ... ... Brunak S, et al. Uncovering the molecular machinery of the human spindle--an integration of wet and dry systems biology. Plos One. 7: e31813. PMID 22427808 DOI: 10.1371/journal.pone.0031813  0.92
2012 Beck T, Gollapudi S, Brunak S, Graf N, Lemke HU, Dash D, Buchan I, Díaz C, Sanz F, Brookes AJ. Knowledge engineering for health: a new discipline required to bridge the "ICT gap" between research and healthcare. Human Mutation. 33: 797-802. PMID 22392843 DOI: 10.1002/humu.22066  0.92
2012 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, ... ... Brunak S, et al. A genome-wide association study of men with symptoms of testicular dysgenesis syndrome and its network biology interpretation. Journal of Medical Genetics. 49: 58-65. PMID 22140272 DOI: 10.1136/jmedgenet-2011-100174  0.92
2012 Jørgensen JR, Fransson A, Fjord-Larsen L, Thompson LH, Houchins JP, Andrade N, Torp M, Kalkkinen N, Andersson E, Lindvall O, Ulfendahl M, Brunak S, Johansen TE, Wahlberg LU. Cometin is a novel neurotrophic factor that promotes neurite outgrowth and neuroblast migration in vitro and supports survival of spiral ganglion neurons in vivo. Experimental Neurology. 233: 172-81. PMID 21985865 DOI: 10.1016/j.expneurol.2011.09.027  0.92
2011 Wang K, Wernersson R, Brunak S. The strength of intron donor splice sites in human genes displays a bell-shaped pattern. Bioinformatics (Oxford, England). 27: 3079-84. PMID 21994226 DOI: 10.1093/bioinformatics/btr532  0.92
2011 Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nature Methods. 8: 785-6. PMID 21959131 DOI: 10.1038/nmeth.1701  0.92
2011 Rasmussen M, Guo X, Wang Y, Lohmueller KE, Rasmussen S, Albrechtsen A, Skotte L, Lindgreen S, Metspalu M, Jombart T, Kivisild T, Zhai W, Eriksson A, Manica A, Orlando L, ... ... Brunak S, et al. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (New York, N.Y.). 334: 94-8. PMID 21940856 DOI: 10.1126/science.1211177  0.92
2011 Schjoldager KT, Vester-Christensen MB, Goth CK, Petersen TN, Brunak S, Bennett EP, Levery SB, Clausen H. A systematic study of site-specific GalNAc-type O-glycosylation modulating proprotein convertase processing. The Journal of Biological Chemistry. 286: 40122-32. PMID 21937429 DOI: 10.1074/jbc.M111.287912  0.92
2011 Roque FS, Jensen PB, Schmock H, Dalgaard M, Andreatta M, Hansen T, Søeby K, Bredkjær S, Juul A, Werge T, Jensen LJ, Brunak S. Using electronic patient records to discover disease correlations and stratify patient cohorts. Plos Computational Biology. 7: e1002141. PMID 21901084 DOI: 10.1371/journal.pcbi.1002141  0.92
2011 Jensen MK, Pers TH, Dworzynski P, Girman CJ, Brunak S, Rimm EB. Protein interaction-based genome-wide analysis of incident coronary heart disease. Circulation. Cardiovascular Genetics. 4: 549-56. PMID 21880673 DOI: 10.1161/CIRCGENETICS.111.960393  0.92
2011 Li Q, Eklund AC, Birkbak NJ, Desmedt C, Haibe-Kains B, Sotiriou C, Symmans WF, Pusztai L, Brunak S, Richardson AL, Szallasi Z. Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response. Bmc Bioinformatics. 12: 310. PMID 21798043 DOI: 10.1186/1471-2105-12-310  0.92
2011 Berchtold LA, Størling ZM, Ortis F, Lage K, Bang-Berthelsen C, Bergholdt R, Hald J, Brorsson CA, Eizirik DL, Pociot F, Brunak S, Størling J. Huntingtin-interacting protein 14 is a type 1 diabetes candidate protein regulating insulin secretion and beta-cell apoptosis. Proceedings of the National Academy of Sciences of the United States of America. 108: E681-8. PMID 21705657 DOI: 10.1073/pnas.1104384108  0.92
2011 Edsgärd D, Scheel M, Hansen NT, Ralfkiaer U, Jensen TS, Skakkebaek NE, Brunak S, Gupta R, Rajpert-De Meyts E, Ottesen AM. Heterozygous deletion at the RLN1 locus in a family with testicular germ cell cancer identified by integrating copy number variation data with phenome and interactome information. International Journal of Andrology. 34: e122-32. PMID 21696394 DOI: 10.1111/j.1365-2605.2011.01188.x  0.92
2011 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, ... ... Brunak S, et al. Enterotypes of the human gut microbiome. Nature. 473: 174-80. PMID 21508958 DOI: 10.1038/nature09944  0.92
2011 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, ... ... Brunak S, et al. Meta-analysis of heterogeneous data sources for genome-scale identification of risk genes in complex phenotypes. Genetic Epidemiology. 35: 318-32. PMID 21484861 DOI: 10.1002/gepi.20580  0.92
2011 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, et al. Cost-effective multiplexing before capture allows screening of 25 000 clinically relevant SNPs in childhood acute lymphoblastic leukemia. Leukemia. 25: 1001-6. PMID 21415851 DOI: 10.1038/leu.2011.32  0.92
2011 Banasik K, Justesen JM, Hornbak M, Krarup NT, Gjesing AP, Sandholt CH, Jensen TS, Grarup N, Andersson A, Jørgensen T, Witte DR, Sandbæk A, Lauritzen T, Thorens B, Brunak S, et al. Bioinformatics-driven identification and examination of candidate genes for non-alcoholic fatty liver disease. Plos One. 6: e16542. PMID 21339799 DOI: 10.1371/journal.pone.0016542  0.92
2011 Kristensen DM, Skalkam ML, Audouze K, Lesné L, Desdoits-Lethimonier C, Frederiksen H, Brunak S, Skakkebæk NE, Jégou B, Hansen JB, Junker S, Leffers H. Many putative endocrine disruptors inhibit prostaglandin synthesis. Environmental Health Perspectives. 119: 534-41. PMID 21081300 DOI: 10.1289/ehp.1002635  0.92
2011 Kristensen DM, Hass U, Lesné L, Lottrup G, Jacobsen PR, Desdoits-Lethimonier C, Boberg J, Petersen JH, Toppari J, Jensen TK, Brunak S, Skakkebaek NE, Nellemann C, Main KM, Jégou B, et al. Intrauterine exposure to mild analgesics is a risk factor for development of male reproductive disorders in human and rat. Human Reproduction (Oxford, England). 26: 235-44. PMID 21059752 DOI: 10.1093/humrep/deq323  0.92
2011 Taboureau O, Nielsen SK, Audouze K, Weinhold N, Edsgärd D, Roque FS, Kouskoumvekaki I, Bora A, Curpan R, Jensen TS, Brunak S, Oprea TI. ChemProt: a disease chemical biology database. Nucleic Acids Research. 39: D367-72. PMID 20935044 DOI: 10.1093/nar/gkq906  0.92
2010 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, ... ... Brunak S, et al. Dissecting spatio-temporal protein networks driving human heart development and related disorders. Molecular Systems Biology. 6: 381. PMID 20571530 DOI: 10.1038/msb.2010.36  0.92
2010 Audouze K, Juncker AS, Roque FJ, Krysiak-Baltyn K, Weinhold N, Taboureau O, Jensen TS, Brunak S. Deciphering diseases and biological targets for environmental chemicals using toxicogenomics networks. Plos Computational Biology. 6: e1000788. PMID 20502671 DOI: 10.1371/journal.pcbi.1000788  0.92
2010 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, ... ... Brunak S, et al. ImmunoGrid: towards agent-based simulations of the human immune system at a natural scale. Philosophical Transactions. Series a, Mathematical, Physical, and Engineering Sciences. 368: 2799-815. PMID 20439274 DOI: 10.1098/rsta.2010.0067  0.92
2010 Blicher T, Gupta R, Wesolowska A, Jensen LJ, Brunak S. Protein annotation in the era of personal genomics. Current Opinion in Structural Biology. 20: 335-41. PMID 20403684 DOI: 10.1016/j.sbi.2010.03.008  0.92
2010 Brorsson C, Tue Hansen N, Bergholdt R, Brunak S, Pociot F. The type 1 diabetes - HLA susceptibility interactome--identification of HLA genotype-specific disease genes for type 1 diabetes. Plos One. 5: e9576. PMID 20221424 DOI: 10.1371/journal.pone.0009576  0.92
2010 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, ... ... Brunak S, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 464: 59-65. PMID 20203603 DOI: 10.1038/nature08821  0.92
2010 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 MT, Wang Y, Raghavan M, ... ... Brunak S, et al. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature. 463: 757-62. PMID 20148029 DOI: 10.1038/nature08835  0.92
2010 Kristensen DM, Nielsen JE, Kalisz M, Dalgaard MD, Audouze K, Larsen ME, Jacobsen GK, Horn T, Brunak S, Skakkebaek NE, Leffers H. OCT4 and downstream factors are expressed in human somatic urogenital epithelia and in culture of epididymal spheres. Molecular Human Reproduction. 16: 835-45. PMID 20123703 DOI: 10.1093/molehr/gaq008  0.92
2010 Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Science Signaling. 3: ra3. PMID 20068231 DOI: 10.1126/scisignal.2000475  0.92
2010 Gauthier NP, Jensen LJ, Wernersson R, Brunak S, Jensen TS. Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results. Nucleic Acids Research. 38: D699-702. PMID 19934261 DOI: 10.1093/nar/gkp1044  0.92
2010 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. Country-specific chemical signatures of persistent environmental compounds in breast milk. International Journal of Andrology. 33: 270-8. PMID 19780864 DOI: 10.1111/j.1365-2605.2009.00996.x  0.92
2009 Juncker AS, Larsen MV, Weinhold N, Nielsen M, Brunak S, Lund O. Systematic characterisation of cellular localisation and expression profiles of proteins containing MHC ligands. Plos One. 4: e7448. PMID 19826487 DOI: 10.1371/journal.pone.0007448  0.92
2009 Bergholdt R, Brorsson C, Lage K, Nielsen JH, Brunak S, Pociot F. Expression profiling of human genetic and protein interaction networks in type 1 diabetes. Plos One. 4: e6250. PMID 19609442 DOI: 10.1371/journal.pone.0006250  0.92
2009 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. The type 2 diabetes associated minor allele of rs2237895 KCNQ1 associates with reduced insulin release following an oral glucose load. Plos One. 4: e5872. PMID 19516902 DOI: 10.1371/journal.pone.0005872  0.92
2009 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, et al. Analysis of gene expression profiles of microdissected cell populations indicates that testicular carcinoma in situ is an arrested gonocyte. Cancer Research. 69: 5241-50. PMID 19491264 DOI: 10.1158/0008-5472.CAN-08-4554  0.92
2009 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, ... ... Brunak S, et al. ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization. Briefings in Bioinformatics. 10: 330-40. PMID 19383844 DOI: 10.1093/bib/bbp014  0.92
2009 Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Brunak S, Butte A, Califano A, Celis J, Cufer T, Ferrell J, Galas D, Gallahan D, Gatenby R, et al. Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008). Molecular Oncology. 3: 9-17. PMID 19383362 DOI: 10.1016/j.molonc.2008.11.003  0.92
2009 Hansen NT, Brunak S, Altman RB. Generating genome-scale candidate gene lists for pharmacogenomics. Clinical Pharmacology and Therapeutics. 86: 183-9. PMID 19369935 DOI: 10.1038/clpt.2009.42  0.92
2009 Juncker AS, Jensen LJ, Pierleoni A, Bernsel A, Tress ML, Bork P, von Heijne G, Valencia A, Ouzounis CA, Casadio R, Brunak S. Sequence-based feature prediction and annotation of proteins. Genome Biology. 10: 206. PMID 19226438 DOI: 10.1186/gb-2009-10-2-206  0.92
2009 Brorsson C, Hansen NT, 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. 11: 60-6. PMID 19143816 DOI: 10.1111/j.1463-1326.2008.01004.x  0.92
2009 Wang K, Ussery DW, Brunak S. Analysis and prediction of gene splice sites in four Aspergillus genomes. Fungal Genetics and Biology : Fg & B. 46: S14-8. PMID 18948220 DOI: 10.1016/j.fgb.2008.09.010  0.92
2008 Lage K, Hansen NT, Karlberg EO, Eklund AC, Roque FS, Donahoe PK, Szallasi Z, Jensen TS, Brunak S. 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. 105: 20870-5. PMID 19104045 DOI: 10.1073/pnas.0810772105  0.92
2008 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, ... ... Brunak S, et al. Linear motif atlas for phosphorylation-dependent signaling. Science Signaling. 1: ra2. PMID 18765831 DOI: 10.1126/scisignal.1159433  0.92
2008 Jensen LJ, de Lichtenberg U, Jensen TS, Brunak S, Bork P. Circular reasoning rather than cyclic expression. Genome Biology. 9: 403. PMID 18598377 DOI: 10.1186/gb-2008-9-6-403  0.92
2008 Thorsen K, Sørensen KD, Brems-Eskildsen AS, Modin C, Gaustadnes M, Hein AM, Kruhøffer M, Laurberg S, Borre M, Wang K, Brunak S, Krainer AR, Tørring N, Dyrskjøt L, Andersen CL, et al. Alternative splicing in colon, bladder, and prostate cancer identified by exon array analysis. Molecular & Cellular Proteomics : McP. 7: 1214-24. PMID 18353764 DOI: 10.1074/mcp.M700590-MCP200  0.92
2008 Li Q, Jørgensen FS, Oprea T, Brunak S, Taboureau O. hERG classification model based on a combination of support vector machine method and GRIND descriptors. Molecular Pharmaceutics. 5: 117-27. PMID 18197627 DOI: 10.1021/mp700124e  0.92
2008 Spicker JS, Brunak S, Frederiksen KS, Toft H. Integration of clinical chemistry, expression, and metabolite data leads to better toxicological class separation. Toxicological Sciences : An Official Journal of the Society of Toxicology. 102: 444-54. PMID 18178960 DOI: 10.1093/toxsci/kfn001  0.92
2008 Gauthier NP, Larsen ME, Wernersson R, de Lichtenberg U, Jensen LJ, Brunak S, Jensen TS. Cyclebase.org--a comprehensive multi-organism online database of cell-cycle experiments. Nucleic Acids Research. 36: D854-9. PMID 17940094 DOI: 10.1093/nar/gkm729  0.92
2008 Miller ML, Hanke S, Hinsby AM, Friis C, Brunak S, Mann M, Blom N. Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2. Molecular & Cellular Proteomics : McP. 7: 181-92. PMID 17938406 DOI: 10.1074/mcp.M700241-MCP200  0.92
2007 Lundegaard C, Lund O, Kesmir C, Brunak S, Nielsen M. Modeling the adaptive immune system: predictions and simulations. Bioinformatics (Oxford, England). 23: 3265-75. PMID 18045832 DOI: 10.1093/bioinformatics/btm471  0.92
2007 Bergholdt R, Størling ZM, Lage K, Karlberg EO, Olason PI, Aalund M, Nerup J, Brunak S, Workman CT, Pociot F. Integrative analysis for finding genes and networks involved in diabetes and other complex diseases. Genome Biology. 8: R253. PMID 18045462 DOI: 10.1186/gb-2007-8-11-r253  0.92
2007 de Lichtenberg U, Jensen TS, Brunak S, Bork P, Jensen LJ. Evolution of cell cycle control: same molecular machines, different regulation. Cell Cycle (Georgetown, Tex.). 6: 1819-25. PMID 17671420  0.92
2007 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, ... ... Brunak S, et al. SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation. Bioinformatics (Oxford, England). 23: i387-91. PMID 17646321 DOI: 10.1093/bioinformatics/btm192  0.92
2007 Spicker JS, Pedersen HT, Nielsen HB, Brunak S. Analysis of cell death inducing compounds. Archives of Toxicology. 81: 803-11. PMID 17503021 DOI: 10.1007/s00204-007-0207-4  0.92
2007 Thorn M, Wang M, Kløverpris H, Schmidt EG, Fomsgaard A, Wenandy L, Berntsen A, Brunak S, Buus S, Claesson MH. Identification of a new hTERT-derived HLA-A*0201 restricted, naturally processed CTL epitope. Cancer Immunology, Immunotherapy : Cii. 56: 1755-63. PMID 17464507 DOI: 10.1007/s00262-007-0319-y  0.92
2007 Emanuelsson O, Brunak S, von Heijne G, Nielsen H. Locating proteins in the cell using TargetP, SignalP and related tools. Nature Protocols. 2: 953-71. PMID 17446895 DOI: 10.1038/nprot.2007.131  0.92
2007 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, ... ... Brunak S, et al. Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags. Genome Biology. 8: R45. PMID 17407547 DOI: 10.1186/gb-2007-8-4-r45  0.92
2007 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, López G, Sadowski MI, ... ... Brunak S, et al. The implications of alternative splicing in the ENCODE protein complement. Proceedings of the National Academy of Sciences of the United States of America. 104: 5495-500. PMID 17372197 DOI: 10.1073/pnas.0700800104  0.92
2007 Lage K, Karlberg EO, Størling ZM, Olason PI, Pedersen AG, Rigina O, Hinsby AM, Tümer Z, Pociot F, Tommerup N, Moreau Y, Brunak S. A human phenome-interactome network of protein complexes implicated in genetic disorders. Nature Biotechnology. 25: 309-16. PMID 17344885 DOI: 10.1038/nbt1295  0.92
2006 Rapin N, Kesmir C, Frankild S, Nielsen M, Lundegaard C, Brunak S, Lund O. Modelling the human immune system by combining bioinformatics and systems biology approaches. Journal of Biological Physics. 32: 335-53. PMID 19669470 DOI: 10.1007/s10867-006-9019-7  0.92
2006 Hansen NT, Kouskoumvekaki I, Jørgensen FS, Brunak S, Jónsdóttir SO. Prediction of pH-dependent aqueous solubility of druglike molecules. Journal of Chemical Information and Modeling. 46: 2601-9. PMID 17125200 DOI: 10.1021/ci600292q  0.92
2006 Regenberg B, Grotkjaer T, Winther O, Fausbøll A, Akesson M, Bro C, Hansen LK, Brunak S, Nielsen J. Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae. Genome Biology. 7: R107. PMID 17105650 DOI: 10.1186/gb-2006-7-11-r107  0.92
2006 Jensen LJ, Jensen TS, de Lichtenberg U, Brunak S, Bork P. Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature. 443: 594-7. PMID 17006448 DOI: 10.1038/nature05186  0.92
2006 Johansen MB, Kiemer L, Brunak S. Analysis and prediction of mammalian protein glycation. Glycobiology. 16: 844-53. PMID 16762979 DOI: 10.1093/glycob/cwl009  0.92
2006 Neshich G, Bourne PE, Brunak S. ISMB 2006. Plos Computational Biology. 2: e11. PMID 16758006 DOI: 10.1371/journal.pcbi.0020011  0.92
2006 Hinsby AM, Kiemer L, Karlberg EO, Lage K, Fausbøll A, Juncker AS, Andersen JS, Mann M, Brunak S. A wiring of the human nucleolus. Molecular Cell. 22: 285-95. PMID 16630896 DOI: 10.1016/j.molcel.2006.03.012  0.92
2005 de Lichtenberg U, Wernersson R, Jensen TS, Nielsen HB, Fausbøll A, Schmidt P, Hansen FB, Knudsen S, Brunak S. New weakly expressed cell cycle-regulated genes in yeast. Yeast (Chichester, England). 22: 1191-201. PMID 16278933 DOI: 10.1002/yea.1302  0.92
2005 Bendtsen JD, Kiemer L, Fausbøll A, Brunak S. Non-classical protein secretion in bacteria. Bmc Microbiology. 5: 58. PMID 16212653 DOI: 10.1186/1471-2180-5-58  0.92
2005 Larsen MV, Lundegaard C, Lamberth K, Buus S, Brunak S, Lund O, Nielsen M. 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. 35: 2295-303. PMID 15997466 DOI: 10.1002/eji.200425811  0.92
2005 Bendtsen JD, Nielsen H, Widdick D, Palmer T, Brunak S. Prediction of twin-arginine signal peptides. Bmc Bioinformatics. 6: 167. PMID 15992409 DOI: 10.1186/1471-2105-6-167  0.92
2005 Wernersson R, Schierup MH, Jørgensen FG, Gorodkin J, Panitz F, Staerfeldt HH, Christensen OF, Mailund T, Hornshøj H, Klein A, Wang J, Liu B, Hu S, Dong W, Li W, ... ... Brunak S, et al. Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing. Bmc Genomics. 6: 70. PMID 15885146 DOI: 10.1186/1471-2164-6-70  0.92
2005 Jónsdóttir SO, Jørgensen FS, Brunak S. Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates. Bioinformatics (Oxford, England). 21: 2145-60. PMID 15713739 DOI: 10.1093/bioinformatics/bti314  0.92
2005 de Lichtenberg U, Jensen LJ, Brunak S, Bork P. Dynamic complex formation during the yeast cell cycle. Science (New York, N.Y.). 307: 724-7. PMID 15692050 DOI: 10.1126/science.1105103  0.92
2005 de Lichtenberg U, Jensen LJ, Fausbøll A, Jensen TS, Bork P, Brunak S. Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics (Oxford, England). 21: 1164-71. PMID 15513999 DOI: 10.1093/bioinformatics/bti093  0.92
2005 Julenius K, Mølgaard A, Gupta R, Brunak S. Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites Glycobiology. 15: 153-164. PMID 15385431 DOI: 10.1093/glycob/cwh151  0.92
2004 La Cour T, Kiemer L, Mølgaard A, Gupta R, Skriver K, Brunak S. Analysis and prediction of leucine-rich nuclear export signals Protein Engineering, Design and Selection. 17: 527-536. PMID 15314210 DOI: 10.1093/protein/gzh062  0.92
2004 Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0. Journal of Molecular Biology. 340: 783-95. PMID 15223320 DOI: 10.1016/j.jmb.2004.05.028  0.92
2004 Kiemer L, Lund O, Brunak S, Blom N. Coronavirus 3CLpro proteinase cleavage sites: Possible relevance to SARS virus pathology Bmc Bioinformatics. 5. PMID 15180906 DOI: 10.1186/1471-2105-5-72  0.92
2004 Bovin LF, Rieneck K, Workman C, Nielsen H, Sørensen SF, Skjødt H, Florescu A, Brunak S, Bendtzen K. Blood cell gene expression profiling in rheumatoid arthritis. Discriminative genes and effect of rheumatoid factor. Immunology Letters. 93: 217-26. PMID 15158620 DOI: 10.1016/j.imlet.2004.03.018  0.92
2004 Bendtsen JD, Jensen LJ, Blom N, Von Heijne G, Brunak S. Feature-based prediction of non-classical and leaderless protein secretion. Protein Engineering, Design & Selection : Peds. 17: 349-56. PMID 15115854 DOI: 10.1093/protein/gzh037  0.92
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. 63: 395-400. PMID 15104671 DOI: 10.1111/j.0001-2815.2004.00221.x  0.92
2004 Duckert P, Brunak S, Blom N. Prediction of proprotein convertase cleavage sites Protein Engineering, Design and Selection. 17: 107-112. PMID 14985543 DOI: 10.1093/protein/gzh013  0.92
2004 Lund O, Nielsen M, Kesmir C, Petersen AG, Lundegaard C, Worning P, Sylvester-Hvid C, Lamberth K, Røder G, Justesen S, Buus S, Brunak S. Definition of supertypes for HLA molecules using clustering of specificity matrices Immunogenetics. 55: 797-810. PMID 14963618 DOI: 10.1007/s00251-004-0647-4  0.92
2004 Nielsen M, Lundegaard C, Worning P, Sylvester Hvid C, Lamberth K, Buus S, Brunak S, Lund O. Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach Bioinformatics. 20: 1388-1397. PMID 14962912 DOI: 10.1093/bioinformatics/bth100  0.92
2004 Eden E, Brunak S. Analysis and recognition of 5′ UTR intron splice sites in human pre-mRNA Nucleic Acids Research. 32: 1131-1142. PMID 14960723 DOI: 10.1093/nar/gkh273  0.92
2004 Lundegaard C, Nielsen M, Lamberth K, Worning P, Sylvester-Hvid C, Buus S, Brunak S, Lund O. MHC class I epitope binding prediction trained on small data sets Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3239: 217-225.  0.92
2004 Andersen CAF, Brunak S. Representation of Protein-Sequence Information by Amino Acid Subalphabets Ai Magazine. 25: 97-104.  0.92
2003 Christensen JK, Lamberth K, Nielsen M, Lundegaard C, Worning P, Lauemøller SL, Buus S, Brunak S, Lund O. Selecting Informative Data for Developing Peptide-MHC Binding Predictors Using a Query by Committee Approach Neural Computation. 15: 2931-2942. PMID 14629874 DOI: 10.1162/089976603322518803  0.92
2003 Buus S, Lauemøller SL, 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. 62: 378-384. PMID 14617044 DOI: 10.1034/j.1399-0039.2003.00112.x  0.92
2003 Jensen LJ, Ussery DW, Brunak S. Functionality of system components: conservation of protein function in protein feature space. Genome Research. 13: 2444-9. PMID 14559779 DOI: 10.1101/gr.1190803  0.92
2003 Corbet S, Nielsen HV, Vinner L, Lauemoller S, Therrien D, Tang S, Kronborg G, Mathiesen L, Chaplin P, Brunak S, Buus S, Fomsgaard A. Optimization and immune recognition of multiple novel conserved HLA-A2, human immunodeficiency virus type 1-specific CTL epitopes Journal of General Virology. 84: 2409-2421. PMID 12917462 DOI: 10.1099/vir.0.19152-0  0.92
2003 Juncker AS, Willenbrock H, Von Heijne G, Brunak S, Nielsen H, Krogh A. Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Science : a Publication of the Protein Society. 12: 1652-62. PMID 12876315 DOI: 10.1110/ps.0303703  0.92
2003 Saxová P, Buus S, Brunak S, Keşmir C. Predicting proteasomal cleavage sites: A comparison of available methods International Immunology. 15: 781-787. PMID 12807816  0.92
2003 de Lichtenberg U, Jensen TS, Jensen LJ, Brunak S. Protein feature based identification of cell cycle regulated proteins in yeast. Journal of Molecular Biology. 329: 663-74. PMID 12787668 DOI: 10.1016/S0022-2836(03)00490-X  0.92
2003 Nielsen M, Lundegaard C, Worning P, Lauemøller SL, Lamberth K, Buus S, Brunak S, Lund O. Reliable prediction of T-cell epitopes using neural networks with novel sequence representations Protein Science. 12: 1007-1017. PMID 12717023 DOI: 10.1110/ps.0239403  0.92
2003 Jensen LJ, Gupta R, Staerfeldt HH, Brunak S. Prediction of human protein function according to Gene Ontology categories. Bioinformatics (Oxford, England). 19: 635-42. PMID 12651722 DOI: 10.1093/bioinformatics/btg036  0.92
2003 la Cour T, Gupta R, Rapacki K, Skriver K, Poulsen FM, Brunak S. NESbase version 1.0: a database of nuclear export signals. Nucleic Acids Research. 31: 393-6. PMID 12520031 DOI: 10.1093/nar/gkg101  0.92
2003 Lundegaard C, Petersen TN, Nielsen M, Bohr H, Bohr J, Brunak S, Gippert C, Lund O. Prediction of protein secondary structure at high accuracy using a combination of many neural networks Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2666: 117-122.  0.92
2002 Jensen LJ, Skovgaard M, Brunak S. Prediction of novel archaeal enzymes from sequence-derived features. Protein Science : a Publication of the Protein Society. 11: 2894-8. PMID 12441387 DOI: 10.1110/ps.0225102  0.92
2002 Brunak S, Danchin A, Hattori M, Nakamura H, Shinozaki K, Matise T, Preuss D. Nucleotide sequence database policies [1] Science. 298: 1333. PMID 12436968  0.92
2002 Workman C, Jensen LJ, Jarmer H, Berka R, Gautier L, Nielser HB, Saxild HH, Nielsen C, Brunak S, Knudsen S. A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biology. 3: research0048. PMID 12225587  0.92
2002 Peleg O, Brunak S, Trifonov EN, Nevo E, Bolshoy A. RNA secondary structure and sequence conservation in C1 region of human immunodeficiency virus type 1 env gene Aids Research and Human Retroviruses. 18: 867-878. PMID 12201910 DOI: 10.1089/08892220260190353  0.92
2002 Spicker JS, Wikman F, Lu ML, Cordon-Cardo C, Workman C, Ørntoft TF, Brunak S, Knudsen S. Neural network predicts sequence of TP53 gene based on DNA chip Bioinformatics. 18: 1133-1134. PMID 12176837  0.92
2002 Yusim K, Kesmir C, Gaschen B, Addo MM, Altfeld M, Brunak S, Chigaev A, Detours V, Korber BT. 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. 76: 8757-8768. PMID 12163596 DOI: 10.1128/JVI.76.17.8757-8768.2002  0.92
2002 Ussery D, Soumpasis DM, Brunak S, Staerfeldt HH, Worning P, Krogh A. Bias of purine stretches in sequenced chromosomes. Computers & Chemistry. 26: 531-41. PMID 12144181 DOI: 10.1016/S0097-8485(02)00013-X  0.92
2002 Jensen LJ, Gupta R, Blom N, Devos D, Tamames J, Kesmir C, Nielsen H, Staerfeldt HH, Rapacki K, Workman C, Andersen CA, Knudsen S, Krogh A, Valencia A, Brunak S. Prediction of human protein function from post-translational modifications and localization features. Journal of Molecular Biology. 319: 1257-65. PMID 12079362 DOI: 10.1016/S0022-2836(02)00379-0  0.92
2002 Gupta R, Jensen LJ, Brunak S. Orphan protein function and its relation to glycosylation. Ernst Schering Research Foundation Workshop. 276-94. PMID 12061006  0.92
2002 Keşmir C, Nussbaum AK, Schild H, Detours V, Brunak S. Prediction of proteasome cleavage motifs by neural networks Protein Engineering. 15: 287-296. PMID 11983929  0.92
2002 Gupta R, Brunak S. Prediction of glycosylation across the human proteome and the correlation to protein function Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 310-322. PMID 11928486  0.92
2002 Andersen CA, Palmer AG, Brunak S, Rost B. Continuum secondary structure captures protein flexibility. Structure (London, England : 1993). 10: 175-84. PMID 11839303 DOI: 10.1016/S0969-2126(02)00700-1  0.92
2002 Skovgaard M, Jensen LJ, Friis C, Stærfeldt HH, Worning P, Brunak S, Ussery D. The Atlas visualization of genomewide information Methods in Microbiology. 33: 49-63.  0.92
2001 Andersen CA, Bohr H, Brunak S. Protein secondary structure: category assignment and predictability. Febs Letters. 507: 6-10. PMID 11682049 DOI: 10.1016/S0014-5793(01)02910-6  0.92
2001 Lauemøller SL, Holm A, Hilden J, Brunak S, Holst Nissen M, Stryhn A, Stergaard Pedersen L, Buus S. Quantitative predictions of peptide binding to MHC class I molecules using specificity matrices and anchor-stratified calibrations Tissue Antigens. 57: 405-414. PMID 11556965 DOI: 10.1034/j.1399-0039.2001.057005405.x  0.92
2001 Jarmer H, Larsen TS, Krogh A, Saxild HH, Brunak S, Knudsen S. Sigma A recognition sites in the Bacillus subtilis genome. Microbiology (Reading, England). 147: 2417-24. PMID 11535782  0.92
2001 Skovgaard M, Jensen LJ, Brunak S, Ussery D, Krogh A. On the total number of genes and their length distribution in complete microbial genomes. Trends in Genetics : Tig. 17: 425-8. PMID 11485798 DOI: 10.1016/S0168-9525(01)02372-1  0.92
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 and Chemistry. 25: 301-307. PMID 11339412 DOI: 10.1016/S0097-8485(00)00103-0  0.92
2001 Baisnée PF, Baldi P, Brunak S, Pedersen AG. Flexibility of the genetic code with respect to DNA structure. Bioinformatics (Oxford, England). 17: 237-48. PMID 11294789  0.92
2001 Petersen TR, Buus S, Brunak S, Nissen MH, Sherman LA, Claesson MH. Identification and design of p53-derived HLA-A2-binding peptides with increased CTL immunogenicity. Scandinavian Journal of Immunology. 53: 357-64. PMID 11285115 DOI: 10.1046/j.1365-3083.2001.00887.x  0.92
2001 Ussery D, Larsen TS, Wilkes KT, Friis C, Worning P, Krogh A, Brunak S. Genome organisation and chromatin structure in Escherichia coli. Biochimie. 83: 201-12. PMID 11278070 DOI: 10.1016/S0300-9084(00)01225-6  0.92
2000 Lauemøller SL, Kesmir C, Corbet SL, Fomsgaard A, Holm A, Claesson MH, Brunak S, Buus S. Identifying cytotoxic T cell epitopes from genomic and proteomic information: "The human MHC project" Reviews in Immunogenetics. 2: 477-491. PMID 12361091  0.92
2000 Frimurer TM, Bywater R, Nærum L, Lauritsen LN, Brunak S. Improving the Odds in Discriminating "Drug-like" from "Non Drug-like" Compounds Journal of Chemical Information and Computer Sciences. 40: 1315-1324. PMID 11128089  0.92
2000 Baldi P, Pollastri G, Andersen CA, 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. 8: 25-36. PMID 10977063  0.92
2000 Petersen TN, Lundegaard C, Nielsen M, Bohr H, Bohr J, Brunak S, Gippert GP, Lund O. Prediction of protein secondary structure at 80% accuracy Proteins: Structure, Function and Genetics. 41: 17-20. PMID 10944389 DOI: 10.1002/1097-0134(20001001)41:1<17::AID-PROT40>3.0.CO;2-F  0.92
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. 300: 1005-1016. PMID 10891285 DOI: 10.1006/jmbi.2000.3903  0.92
2000 Baldi P, Brunak S, Chauvin Y, Andersen CA, Nielsen H. Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics (Oxford, England). 16: 412-24. PMID 10871264  0.92
2000 Pedersen AG, Jensen LJ, Brunak S, Staerfeldt HH, Ussery DW. A DNA structural atlas for Escherichia coli. Journal of Molecular Biology. 299: 907-30. PMID 10843847 DOI: 10.1006/jmbi.2000.3787  0.92
2000 Worning P, Jensen LJ, Nelson KE, Brunak S, Ussery DW. Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima. Nucleic Acids Research. 28: 706-9. PMID 10637321  0.92
2000 Corbet S, Müller-Trutwin MC, 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. 74: 529-534. PMID 10590144  0.92
1999 Gorodkin J, Lund O, Andersen CA, 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. 95-105. PMID 10786291  0.92
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). 15: 937-46. PMID 10743560  0.92
1999 Baldi P, Brunak S, Chauvin Y, Pedersen AG. Structural basis for triplet repeat disorders: A computational analysis Bioinformatics. 15: 918-929. PMID 10743558  0.92
1999 Blom N, Gammeltoft S, Brunak S. Sequence and structure-based prediction of eukaryotic protein phosphorylation sites Journal of Molecular Biology. 294: 1351-1362. PMID 10600390 DOI: 10.1006/jmbi.1999.3310  0.92
1999 Gupta R, Jung E, Gooley AA, Williams KL, Brunak S, Hansen J. Scanning the available Dictyostelium discoideum proteome for O-linked GlcNAc glycosylation sites using neural networks Glycobiology. 9: 1009-1022. PMID 10521537 DOI: 10.1093/glycob/9.10.1009  0.92
1999 Gorodkin J, Stærfeldt HH, Lund O, Brunak S. MatrixPlot: Visualizing sequence constraints Bioinformatics. 15: 769-770. PMID 10498780 DOI: 10.1093/bioinformatics/15.9.769  0.92
1999 Pedersen AG, Baldi P, Chauvin Y, Brunak S. The biology of eukaryotic promoter prediction - A review Computers and Chemistry. 23: 191-207. PMID 10404615  0.92
1999 Nielsen H, Brunak S, Von Heijne G. Machine learning approaches for the prediction of signal peptides and other protein sorting signals Protein Engineering. 12: 3-9. PMID 10065704  0.92
1999 Gupta R, Birch H, Rapacki K, Brunak S, Hansen JE. O-GLYCBASE version 4.0: A revised database of O-glycosylated proteins Nucleic Acids Research. 27: 370-372. PMID 9847232 DOI: 10.1093/nar/27.1.370  0.92
1999 Kreegipuu A, Blom N, Brunak S. PhosphoBase, a database of phosphorylation sites: Release 2.0 Nucleic Acids Research. 27: 237-239. PMID 9847189 DOI: 10.1093/nar/27.1.237  0.92
1999 Baldi P, Borodovsky M, Brunak S, Burge C, Fickett J, Henikoff S, Koonin E, Sali A, Sander C, Stormo G. The Second International Conference on Bioinformatics: Sequence, Structure and Function, Atlanta, Georgia, November 11-14 1999: Editorial Bioinformatics. 15: 865-866.  0.92
1998 Baldi P, Chauvin Y, Brunak S, Gorodkin J, Pedersen AG. Computational applications of DNA structural scales. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 6: 35-42. PMID 9783207  0.92
1998 Østergaard L, Pedersen AG, Jespersen HM, Brunak S, Welinder KG. Computational analyses and annotations of the Arabidopsis peroxidase gene family Febs Letters. 433: 98-102. PMID 9738941 DOI: 10.1016/S0014-5793(98)00849-7  0.92
1998 Pedersen AG, Baldi P, Chauvin Y, Brunak S. DNA structure in human RNA polymerase II promoters Journal of Molecular Biology. 281: 663-673. PMID 9710538 DOI: 10.1006/jmbi.1998.1972  0.92
1998 Kreegipuu A, Blom N, Brunak S, Järv J. Statistical analysis of protein kinase specificity determinants Febs Letters. 430: 45-50. PMID 9678592 DOI: 10.1016/S0014-5793(98)00503-1  0.92
1998 Hansen JE, Lund O, Tolstrup N, Gooley AA, Williams KL, Brunak S. NetOglyc: Prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility Glycoconjugate Journal. 15: 115-130. PMID 9557871 DOI: 10.1023/A:1006960004440  0.92
1998 Hansen JE, Lund O, Nilsson J, Rapacki K, Brunak S. O-GLYCBASE version 3.0: A revised database of O-glycosylated proteins Nucleic Acids Research. 26: 387-389. PMID 9399880 DOI: 10.1093/nar/26.1.387  0.92
1998 Blom N, Kreegipuu A, Brunak S. PhosphoBase: A database of phosphorylation sites Nucleic Acids Research. 26: 382-386. PMID 9399879 DOI: 10.1093/nar/26.1.382  0.92
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. 8: 581-599. PMID 10065837  0.92
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. 10: 1241-1248. PMID 9514112  0.92
1997 Gorodkin J, Heyer LJ, Brunak S, Stormo GD. Displaying the information contents of structural RNA alignments: The structure logos Computer Applications in the Biosciences. 13: 583-586. PMID 9475985  0.92
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. 25: 3159-3163. PMID 9224618 DOI: 10.1093/nar/25.15.3159  0.92
1997 Bohr H, Brunak S, Bohr J. Coherent topological phenomena in protein folding Folding and Design. 2: S15-S18. PMID 9218961  0.92
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. 3: 697-701. PMID 9214653  0.92
1997 Claros MG, Brunak S, Heijne GV. Prediction of N-terminal protein sorting signals Current Opinion in Structural Biology. 7: 394-398. PMID 9204282 DOI: 10.1016/S0959-440X(97)80057-7  0.92
1997 Bohr H, Brunak S, Bohr J. Molecular Wring Resonances in Chain Molecules Bioelectromagnetics. 18: 187-189. PMID 9084871  0.92
1997 Hansen JE, Lund O, Rapacki K, Brunak S. O-GLYCBASE version 2.0: A revised database of O-glycosylated proteins Nucleic Acids Research. 25: 278-282. PMID 9016554 DOI: 10.1093/nar/25.1.278  0.92
1997 Bohr J, Bohr H, Brunak S. Protein folding and wring resonances Biophysical Chemistry. 63: 97-105. DOI: 10.1016/S0301-4622(96)02249-1  0.92
1997 Bohr H, Brunak S. Distance-based approaches to protein structure determination III (Copenhagen, Denmark, 5-8 November 1996) - Introductory overview Folding and Design. 2: S1-S2.  0.92
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