Publications

2010 (11)

2009 (62)

2008 (71)

2007 (73)

2006 (46)

2005 (50)

2004 and before (289)

Books (23)

2010

• 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, 2010
  
  
• 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
  
  
• 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
  
  
• Amplification of LAPTM4B and YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer
  Li Y, Zou L, Li Q, Haibe-Kains B, Tian R, Li Y, Desmedt C, Sotiriou C, Szallasi Z, Iglehart JD, Richardson AL, Wang ZC, Nat Med, 2010
  PubMed
  
  
• Efficacy of Neoadjuvant Cisplatin in Triple-Negative Breast Cancer
  Silver DP, Richardson AL, Eklund AC, Wang ZC, Szallasi Z, Li Q, Juul N, Leong CO, Calogrias D, Buraimoh A, Fatima A, Gelman RS, Ryan PD, Tung NM, De Nicolo A, Ganesan S, Miron A, Colin C, Sgroi DC, Ellisen LW, Winer EP, Garber JE, J Clin Oncol, 2010
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• The Thousandth Genome – A Cautionary Tale
  Lagesen K, Ussery DW, Wassenaar TM, Microbiology 156:603-609, 2010
  
  
• Lactobacillus acidophilus induces a slow but more sustained chemokine and cytokine response in naive foetal enterocytes compared to commensal Escherichia coli
  Zeuthen LH, Fink LN, Metzdorff SB, Kristensen MB, Licht TR, Nellemann C, Frokiaer H, BMC Immunol Jan 19;11(1):2, 2010
  Relevant URL
  
  
• Genomic Analysis of Two-Component Signal Transduction Proteins in Basidiomycetes
  Lavín JL, Ramírez L, Ussery DW, Pisabarro AG, Oguiza JA, Journal of Molecular Microbiology and Biotechnology, 18:63-73 in the press, 2010
  
  
• Differences in two-component signal transduction proteins among the genus Brucella: implications for host preference and pathogenesis
  Lavín JL, Binnewies TT, Pisabarro AG, Ussery DW, García-Lobo JM, Oguiza JA, Veterinary Microbiology, in the press, 2010
  
  
• Comparative Genomics of Green Sulfur Bacteria
  Davenport C, Ussery DW, Tümmler B, Photosynthesis Research, 103: in the press, 2010
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• On the Origins of a Vibrio species
  Vesth T, Wassenaar TM, Hallin PF, Snipen L, Lagesen K, , Ussery DW, Microbial Ecology, 59:1-13, 2010
  
  

2009

• Studies on Monitoring and Tracking Genetic Resources
  Garrity GM, Thompson LM, Ussery DW, Paskin N, Baker D, Desmeth P, Schindel DE, Ong PS, Convention on Biological Diversity (21 January, 2009)[UNEP/CBD/ABS/GTLE/2/INF/4], 2009
  
  
• Dietary fibers as immunoregulatory compounds in health and disease
  Wismar R, Brix S, Frøkiær H, Lærke HN, Ann NY Acad Sci, 2009
  
  
• CD4+ T cell activation is differentially modulated by bacteria-primed dendritic cells, but generally downregulated by n-3 polyunsaturated fatty acids
  Brix S, Lund P, Kjaer TMR, Straarup EM, Hellgren LI, Frøkiær H, Immunology DOI: 10.1111/j.1365-2567.2009.03163.x, 2009
  
  
• Pseudomonas aeruginosa quorum-sensing signal molecules interfere with dendritic cell-induced T-cell proliferation
  Skindersoe ME, Zeuthen LH, Brix S, Fink LN, Lazenby J, Whittall C, Williams P, Diggle SP, Froekiaer H, Cooley M, Givskov M, FEMS Immunol Med Microbiol. 55(3):335-45. Epub 2009 Jan 28, 2009
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• Probiotic yogurt in the elderly with intestinal bacterial overgrowth: endotoxaemia and innate immune functions
  Schiffrin EJ, Parlesak A, Bode C, Bode JC, van\'t Hof MA, Grathwohl D, Guigoz Y, Br J Nutr. 101(7):961-6., 2009
  PubMed
  
  
• Phosphatidylcholine reverses ethanol-induced increase in transepithelial endotoxin permeability and abolishes transepithelial leukocyte activation
  Mitzscherling K, Volynets V, Parlesak A, Alcohol Clin Exp Res. 33(3):557-62, 2009
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• 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. 4(6):e5872, 2009
  
  
• An online survival analysis tool to rapidly assess the effect of 22,277 genes on breast cancer prognosis using microarray data of 1,809 patients
  Györffy B, Lanczky A, Eklund AC, Denkert C, Budczies J, Li Q, Szallasi Z, Breast Cancer Res Treat, 2009
  PubMed
  
  
• The 2008 update of the Aspergillus nidulans genome annotation: a community effort
  Wortman JR, Gilsenan JM, Joardar V, Deegan J, Clutterbuck J, Andersen MR, Archer D, Bencina M, Braus G, Coutinho P, von Döhren H, Doonan J, Driessen AJ, Durek P, Espeso E, Fekete E, Flipphi M, Estrada CG, Geysens S, Goldman G, de Groot PW, Hansen K, Harris SD, Heinekamp T, Helmstaedt K, Henrissat B, Hofmann G, Homan T, Horio T, Horiuchi H, James S, Jones M, Karaffa L, Karányi Z, Kato M, Keller N, Kelly DE, Kiel JA, Kim JM, van der Klei IJ, Klis FM, Kovalchuk A, Krasevec N, Kubicek CP, Liu B, Maccabe A, Meyer V, Mirabito P, Miskei M, Mos M, Mullins J, Nelson DR, Nielsen J, Oakley BR, Osmani SA, Pakula T, Paszewski A, Paulsen I, Pilsyk S, Pócsi I, Punt PJ, Ram AF, Ren Q, Robellet X, Robson G, Seiboth B, van Solingen P, Specht T, Sun J, Taheri-Talesh N, Takeshita N, Ussery D, vanKuyk PA, Visser H, van de Vondervoort PJ, de Vries RP, Walton J, Xiang X, Xiong Y, Zeng AP, Brandt BW, Cornell MJ, van den Hondel CA, Visser J, Oliver SG, Turner G, Fungal Genetics and Biology, 45:S2-S13,, 2009
  
  
• Studies on Monitoring and Tracking Genetic Resources: An Executive Summary
  Garrity GM, Thompson LM, Ussery DW, Paskin N, Baker D, Desmeth P, Schindel DE, Ong PS, Standards in Genomic Sciences, 1:78-86, 2009
  
  
• The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding
  Zhang H, Lund O, Nielsen M, Bioinformatics 15;25(10):1293-9, 2009
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• Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information
  Buslje CM, Santos J, Delfino JM, Nielsen M, Bioinformatics1;25(9):1125-31, 2009
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• Stretches of alternating pyrimidine/ purines and purines are respectively linked with pathogenicity and growth temperature in prokaryotes
  Bohlin J, Hardy SP, Ussery DW, BMC Genomics, 10:346, 2009
  PubMed Relevant URL
  
  
• Phytanic acid: An overlooked bioactive fatty acid in dairy products?
  Lars I Hellgren, Annals of the New York Academy of Science, in press, 2009
  
  
• Validation of Cyanoacrylate Method for Collection of Stratum Corneum in Human Skin for Lipid Analysis
  Jungersted JM, Hellgren LI, Drachmann T, Jemec GBE, Agner T, Skin Pharmacology and Physiology (2010) 23:62-67, 2009
  Relevant URL
  
  
• Lipid assymetry in plant plasma membranes: phosphate deficiency-induced phospholipid replacement is restricted to the cytosolic leaflet
  Tjällström H, Hellgren LI, Wieslander Å & Sandelius AS, FASEB Journal doi: 10.1096/fj.09-139410, 2009
  
  
• Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization
  Aron C Eklund; Pia Friis; Rasmus Wernersson; Zoltan Szallasi, Nucleic Acids Research doi: 10.1093/nar/gkp1116, 2009
  Relevant URL
  
  
• Transcriptomic variation in a coral reveals pathways of clonal organisation
  Line K Bay, Bjørn Nielsen H, Hanne Jarmer, Francois Seneca, Madeleine J H van Oppe, Marine Genomics, 2009
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• Induction of regulatory T cells by probiotics: potential for treatment of allergy?
  Fink LN, Clinical & Experimental Allergy, (40) 5–8., 10.1111/j.1365-2222.2009.03408.x, 2009
  
  
• Mutational mapping and modeling of the binding site for (S)-citalopram in the human serotonin transporter
  Andersen J, Olsen L, Hansen KB, Taboureau O, Jorgensen FS, Jorgensen AM, Bang-Andersen B, Egebjerg J, Stromgaard K, Kristensen AS, J. Biol Chem, 2009
  
  
• Some putative prebiotics increase the severity of Salmonella enterica serovar Typhimurium infection in mice
  Petersen A, Heegaard PMH, Pedersen AL, Andersen JB, Sørensen RB, Frøkiær H, Lahtinen SJ, Ouwehand AC, Poulsen M & Licht TR, BMC Microbiology, 2009
  
  
• The Immune Epitope Database 2.0
  Vita R, Zarebski L, Greenbaum JA, Emami H, Hoof I, Salimi N, Damle R, Sette A, Peters B, Nucleic Acids Res. 2009 Nov 11, 2009
  
  
• Genomic taxonomy of vibrios
  Thompson CC, Vicente AC, Souza RC, Vasconcelos AT, Vesth T, Alves N Jr, Ussery DW, Iida T, Thompson FL, BMC Evol Biol, 9:258, 2009
  PubMed Relevant URL
  
  
• Analysis of genomic signatures in prokaryotes using multinomial regression and hierarchical clustering
  Bohlin J, Skjerve E, Ussery DW, BMC Genomics, 10:487, 2009
  Relevant URL
  
  
• Systematic Characterization of Cellular Localization and Expression Profiles of Proteins Containing MHC Ligands
  Juncker AS, Larsen MV, Weinhold N, Nielsen M, Brunak S, Lund O, /PLoS ONE/ ; 4(10): e7448. doi:10.1371/journal.pone.0007448, 2009
  
  
• GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes
  Hallin PF, Stærfeldt HH, Rotenberg E, Binnewies TT, Benham CJ, , Ussery DW, Standards in Genomic Sciences, 1:204-215, 2009
  Relevant URL
  
  
• Higher variability in the number of sexual partners in males can contribute to a higher prevalence of sexually transmitted diseases in females
  Gouveia-Oliveira R, Pedersen AG, Journal of Theoretical Biology, 261:100-106, 2009
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• Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus PAL5
  Bertalan M, Albano R, Padua V, Rouws L, Rojas C, Hemerly A, Teixeira K, Schwab S, Araujo J, Oliveira A, Franca L, Magalhaes V, Alqueres S, Cardoso A, Almeida W, Loureiro MM, Nogueira E, Cidade D, Oliveira D, Simao T, Macedo J, Valadao A, Dreschsel M, Freitas F, Vidal M, Guedes H, Rodrigues E, Meneses C, Brioso P, Pozzer L, BMC Genomics 10:450doi:10.1186/1471-2164-10-450, 2009
  
  
• An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction.
  Nielsen M, Lund O, BMC bioinformatics, 2009
  
  
• Impaired uptake and/or utilisation of leucine is suppressed by the SPT15-300 allele of the TATA binding protein gene.
  Baerends RJ, Qiu JL, Rasmussen S, Nielsen HB, Brandt A, Appl Environ Microbiol, 2009
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• Transcriptional landscape estimation from tiling array data using a model of signal shift and drift.
  Nicolas P, Leduc A, Robin S, Rasmussen S, Jarmer H, Bessières P, Bioinformatics 25: 2341-7, 2009
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• The transcriptionally active regions in the genome of Bacillus subtilis
  Rasmussen S, Nielsen HB, Jarmer H, Mol Micro 73: 1043-57, 2009
  PubMed
  
  
• Microbial comparative pan-genomics using binomial mixture models
  Snipen L, Almøy T, Ussery DW, BMC Genomics. ;10:385, 2009
  PubMed
  
  
• An in silico study of the molecular basis of B-RAF activation and conformational stability
  Fratev FF, Jónsdóttir SÓ, BMC Structural Biology, 9:47, 2009
  PubMed Link to publication
  
  
• Expression profiling of human genetic and protein interaction networks in type 1 diabetes
  Bergholdt R, Brorsson C, Lage K, Nielsen JH, Brunak S, Pociot F, PLoS One;4(7):e6250, 2009
  PubMed
  
  
• Proteome analysis demonstrates profound alterations in human dendritic cell nature by TX527, an analogue of vitamin D
  Ferreira GB, van Etten E, Lage K, Hansen DA, Moreau Y, Workman CT, Waer M, Verstuyf A, Waelkens E, Overbergh L, Mathieu C, Proteomics;9(14):3752-64, 2009
  PubMed
  
  
• The validation and assessment of machine learning: a game of prediction from high-dimensional data
  Pers TH, Albrechtsen A, Holst C, Sørensen TI, Gerds TA, PLoS One;4(8):e6287, 2009
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• A generic method for assignment of reliability scores applied to solvent accessibility predictions
  Petersen B, Petersen TN, Andersen P, Nielsen M, Lundegaard C, BMC Struct Biol.;9(1):51, 2009
  PubMed
  
  
• InterMap3D: predicting and visualizing co-evolving protein residues
  Gouveia-Oliveira R, Roque FS, Wernersson R, Sicheritz-Ponten T, Sackett PW, Mølgaard A, Pedersen AG, Bioinformatics, 2009
  PubMed PDF
  
  
• Evolution of the leukotoxin promoter in genus Mannheimia
  Larsen J, Pedersen AG, Davies R, Kuhnert P, Frey J, Christensen H, Bisgaard M, Olsen J, BMC Evolutionary Biology, 2009
  PubMed PDF
  
  
• Controlled indole-3-acetaldoxime production through ethanol-induced expression of CYP79B2
  Mikkelsen MD, Fuller VL, Hansen BG, Nafisi M, Olsen CE, Nielsen HB, Halkier BA, Planta;229(6):1209-17, 2009
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• Microarray analysis reveals transcriptional plasticity in the reef building coral Acropora millepora
  Bay LK, Ulstrup KE, Nielsen HB, Jarmer H, Goffard N, Willis BL, Miller DJ, van Oppen MJH, Molecular Ecology; doi: 10.1111/j.1365-294X.2009.04257.x, 2009
  
  
• Genome-wide gene expression profiling of SCID mice with T-cell-mediated Colitis
  Brudzewsky D, Pedersen AE, Claesson MH, Gad M, Kristensen NN, Lage K, Jensen T, Tommerup N, Larsen LA, Knudsen S, Tümer Z, Scand J Immunol;69(5):437-46, 2009
  PubMed
  
  
• Evaluation of microarray preprocessing algorithms based on concordance with rt-PCR in clinical samples
  Gyorffy B, Molnar B, Lage H, Szallasi Z, Eklund AC, PLoS ONE;4(5):e5645, 2009
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• Chromosomal instability determines taxane response
  Swanton C, Nicke B, Schuett M, Eklund AC, Ng C, Li Q, Hardcastle T, Lee A, Roy R, East P, Kschischo M, Endesfelder D, Wylie P, Kim SN, Chen JG, Howell M, Ried T, Habermann JK, Auer G, Brenton JD, Szallasi Z, Downward J, Proc Natl Acad Sci U S A;106(21):8671-6, 2009
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• Macrophages and Adipocytes in Human Obesity: Adipose Tissue Gene Expression and Insulin Sensitivity during Calorie Restriction and Weight Stabilization
  Capel F, Klimcáková E, Viguerie N, Roussel B, Vítková M, Kováciková M, Polák J, Kovácová Z, Galitzky J, Maoret JJ, Hanácek J, Pers TH, Bouloumié A, Stich V, Langin D, Diabetes (in press), 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
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• 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
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• Genetic Tools and Algorithms for Gene Discovery in Major Congenital Anomalies
  Donahoe PK, Noonan KM, Lage K, Birth defects research. Part A, Clinical and molecular teratology, 2009 Jan;85(1):6-12, 2009
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• Expression analyses of human cleft palate tissue suggest a role for osteopontin and immune related factors in palatal development
  Jakobsen LP, Borup R, Vestergaard J, Larsen LA, Lage K, Maroun LL, Kjaer I, Niemann CU, Andersen M, Knudsen MA, Møllgård K, Tommerup N, Experimental and Molecular;41(2):77-85, 2009
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• Kinase-specific prediction of protein phosphorylation sites.
  Miller ML, Blom N, Methods in Molecular Biology, 2009;527:299-310, 2009
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• High-affinity human leucocyte antigen class I binding variola-derived peptides induce CD4+ T cell responses more than 30 years post-vaccinia virus vaccination
  Wang M, Tang ST, Lund O, Dziegiel MH, Buus S, Claesson MH, Clinical and Experimental Immunology, 2009 Mar;155(3):441-6., 2009
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• Transepithelial activation of human leukocytes by probiotics and commensal bacteria: role of Enterobacteriaceae-type endotoxin
  Baeuerlein A, Ackermann S, Parlesak A, Microbiol Immunol. 53(4):241-50, 2009
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• 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
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• Fatness-associated FTO gene variant increases mortality independent of fatness--in cohorts of Danish men
  Zimmermann E, Kring SI, Berentzen TL, Holst C, Pers TH, Hansen T, Pedersen O, Sørensen TI, Jess T, PLoS ONE. 2009;4(2):e4428, 2009
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• Molecular basis of inactive B-RAF(WT) and B-RAF(V600E) ligand inhibition, selectivity and conformational stability: an in silico study.
  Fratev F, Jónsdóttir SO, Mihaylova E, Pajeva I, Molecular Pharmaceutics, 2009 Jan-Feb;6(1):144-57, 2009
  PubMed
  
  
• Classification of cytochrome P450 1A2 inhibitors and noninhibitors by machine learning techniques.
  Vasanthanathan P, Taboureau O, Oostenbrink C, Vermeulen NP, Olsen L, Jørgensen FS, Drug metabolism and disposition: the biological fate of chemicals, March ;37(3):658-64. Epub 2008 Dec 4, 2009
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• Virtual screening and prediction of site of metabolism for cytochrome P450 1A2 ligands.
  Vasanthanathan P, Hritz J, Taboureau O, Olsen L, Jørgensen FS, Vermeulen NP, Oostenbrink C, Journal of Chemical information and Modeling, January ;49(1):43-52, 2009
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• Location of the antidepressant binding site in the serotonin transporter: Importance of SER438 in recognition of citalopram and tricyclic antidepressants.
  Andersen J, Taboureau O, Hansen KB, Olsen L, Egebjerg J, Strømgaard K, Kristensen AS, Journal of Biological Chemistry, Feb 12., 2009
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• The proteome of seed development in the model legume Lotus japonicus.
  Dam S, Laursen BS, Ornfelt JH, Jochimsen B, Stærfeldt HH, Friis C, Nielsen K, Goffard N, Besenbacher S, Krusell L, Sato S, Tabata S, Thogersen IB, Enghild JJ, Stougaard J, Plant Physiology, 2009, 7 January, 2009
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• Pan-specific MHC class I predictors: A benchmark of HLA class I pan-specific prediction methods
  Zhang H, Lundegaard C, Nielsen M, Bioinformatics 61(1):1-13, 2009
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• NetMHCpan, a method for MHC class I binding prediction beyond humans.
  Hoof I, Peters B, Sidney J, Pedersen LE, Sette A, Lund O, Buus S, Nielsen M, Immunogenetics 61(1):1-13, 2009
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2008

• Concordance of exon array and real-time PCR assessment of gene expression following cancer cell cytotoxic drug exposure
  Lee AJ, East P, Pepper S, Nicke B, Szallasi Z, Eklund AC, Downward J, Swanton C, Cell Cycle. 15;7(24):3947-8. Epub 2008 Dec 17, 2008
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• Acetone-water complexes at MRCI level using localized orbitals: n ->pi* and pi ->pi* electronic transitions
  Hoyau S, Ben Amor N, Borini S, Evangelisti S, Maynau D, CHEMICAL PHYSICS LETTERS, Vol.: 451, Issue: 1-3, Pages: 141-146, Published: JAN 14 2008, 2008
  
  
• The effects of fish oil and high or low linoleic acid intake on fatty acid composition of human peripheral blood mononuclear cells
  Damsgaard CT, Frokiaer H, Lauritzen L, BRITISH JOURNAL OF NUTRITION, Vol.: 99, Issue: 1, Pages: 147-154, Published: JAN 2008, 2008
  
  
• Fish oil in combination with high or low intakes of linoleic acid lowers plasma triacylglycerols but does not affect other cardiovascular risk markers in healthy men
  Damsgaard CT, Frokiaer H, Andersen AD, Lauritzen L, JOURNAL OF NUTRITION, Vol.: 138, Issue: 6, Pages: 1061-1066, Published: JUN 2008, 2008
  
  
• Occurrence of multiple infections with different Borrelia burgdorferi genospecies in Danish Ixodes ricinus nymphs
  Vennestrøm J, Egholm H, Jensen PM, Parasitology International, 2008 Mar;57(1):32-7. Epub 2007 Aug 1, 2008
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• 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
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• Protein abundance profiling of the Escherichia coli cytosol
  Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D, BMC Genomics, 2008 Feb 27;9:102, 2008
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• The minimum information about a genome sequence (MIGS) specification
  Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A, Nature Biotechnology, 2008 May;26(5):541-7, 2008
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• Identification of glycosaminoglycan binding regions in the Plasmodium falciparum encoded placental sequestration ligand, VAR2CSA
  Resende M, Nielsen MA, Dahlbäck M, Ditlev SB, Andersen P, Sander AF, Ndam NT, Theander TG, Salanti A, Malaria Journal, 2008 Jun 6;7:104, 2008
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• Whole-genome pyrosequencing of an epidemic multidrug-resistant Acinetobacter baumannii strain belonging to the European clone II group
  Iacono M, Villa L, Fortini D, Bordoni R, Imperi F, Bonnal RJ, Sicheritz-Ponten T, De Bellis G, Visca P, Cassone A, Carattoli A, Antimicrobial agents and chemotherapy, 2008 Jul;52(7):2616-25. Epub 2008 Apr 14, 2008
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• Dietary soya saponins increase gut permeability and play a key role in the onset of soyabean-induced enteritis in Atlantic salmon ( Salmo salar L.)
  Knudsen D, Jutfelt F, Sundh H, Sundell K, Koppe W, Frøkiaer H, The British Journal of Nutrition, 2008 Jul;100(1):120-9. Epub 2008 Jan 2, 2008
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• Arabidopsis mitogen-activated protein kinase kinases MKK1 and MKK2 have overlapping functions in defense signaling mediated by MEKK1, MPK4, and MKS1
  Qiu JL, Zhou L, Yun BW, Nielsen HB, Fiil BK, Petersen K, Mackinlay J, Loake GJ, Mundy J, Morris PC, Plant Physiology, 2008 Sep;148(1):212-22. Epub 2008 Jul 3, 2008
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• Functional genomic analysis of drug sensitivity pathways to guide adjuvant strategies in breast cancer
  Swanton C, Szallasi Z, Brenton JD, Downward J, Breas Cancer Research, 2008;10(5):214. Epub 2008 Oct 31, 2008
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• 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
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• NetPhosBac - A predictor for Ser/Thr phosphorylation sites in bacterial proteins.
  Miller ML, Soufi B, Jers C, Blom N, Macek B, Mijakovic I, Proteomics. 2008 Dec 3, 2008
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• MHC-I-restricted epitopes conserved among variola and other related orthopoxviruses are recognized by T cells 30 years after vaccination
  Tang ST, Wang M, Lamberth K, Harndahl M, Dziegiel MH, Claesson MH, Buus S, Lund O, Arch Virol. 2008;153(10):1833-44, 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
  
  
• Bioavailability of omega-3 long-chain polyunsaturated fatty acids from foods
  Mu H, Supplement to AgroFood industry hi-tech, 19 (4), 24-26, 2008
  
  
• Butter blend containing fish oil does not affect cholesterol absorption in a single meal study in humans
  Overgaard J, Porsgaard T, Guo Z, Lauritzen L, Mu H, Molecular Nutrition and Food Research, 52:1140-1146., 2008
  PubMed
  
  
• Comparison of 3 ad libitum diets for weight-loss maintenance, risk of cardiovascular disease, and diabetes: A 6-mo randomized, controlled trial
  Due A, Larsen TM, Mu H, Hermansen K, Stender S, Astrup A, Am. J. Clin. Nutr., 88:1232-1241, 2008
  PubMed
  
  
• Staphylokokkens ømme punkt.
  Jarmer HO, Dynamo, November 2008, 2008
  
  
• Classification of Cytochrome P450 1A2 Inhibitors and Non-Inhibitors by Machine Learning Techniques
  Vasanthanathan P, Taboureau O, Oostenbrink C, Vermeulen NPE, Olsen L, Jorgensen FS, Drug, Metabolism and Disposition (DMD), December 4, 2008; doi: 10.1124/dmd.108.023507, 2008
  PubMed
  
  
• Phospholipase C-catalyzed sphingomyelin hydrolysis in a membrane reactor for ceramide production
  Zhang L, Liang S, Hellgren LI, Jonsson GE, Xu X, Journal of Membrane Science, 2008
  
  
• A pathway-specific microarray analysis highlights the complex and co-ordinated transcriptional networks of the developing grain of field-grown barley
  Hansen M, Friis C, Bowra S, Holm PB, Vincze E, Journal of Experimental Botany, doi:10.1093/jxb/ern270, 2008
  PubMed Relevant URL
  
  
• Linear motif atlas for phosphorylation-dependent signaling.
  Miller ML, Jensen LJ, Diella F, Jørgensen C, Tinti M, Li L, Hsiung M, Parker SA, Bordeaux J, Sicheritz-Ponten T, Olhovsky M, Pasculescu A, Alexander J, Knapp S, Blom N, Bork P, Li S, Cesareni G, Pawson T, Turk BE, Yaffe MB, Brunak S, Linding R, Science Signaling, 2008 Sep 2;1(35):ra2, 2008
  PubMed
  
  
• Fedtsyrebalance påvirker livsstilssygdomme og allergi
  Hellgren LI, Brix S, FoodDTU, nr. 44, maj (2008)., 2008
  
  
• Allergen specific responses in cord and adult blood are differentially modulated in the presence of endotoxins
  Eiwegger T, Mayer E, Brix S, Schabussova I, Dehlink E, Bohle B, Barkholt V, Szépfalusi Z, Clin Exp Allergy, ePub Sep (2008) DOI: 10.1111/j.1365-2222.2008.03080.x, 2008
  
  
• The peptide-binding specificity of HLA-A*3001 demonstrates membership of the HLA-A3 supertype
  Lamberth K, Røder G, Harndahl M, Nielsen M, Lundegaard C, Schafer- Nielsen C, Lund O, Buus S, Immunogenetics. 2008 Sep 4. [Epub ahead of print], 2008
  PubMed
  
  
• Adjuvant auricular electroacupuncture and autogenic training in rheumatoid arthritis: a randomized controlled trial. Auricular acupuncture and autogenic training in rheumatoid arthritis.
  Bernateck M, Becker M, Schwake C, Hoy L, Passie T, Parlesak A, Fischer MJ, Fink M, Karst M, Forsch Komplementmed. 2008 Aug;15(4):187-93., 2008
  PubMed
  
  
• Towards a richer description of our complete collection of genomes and metagenomes: the ’Minimum Information about a Genome Sequence’ (MIGS) specification
  Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuolii SV, Ashburner M, Axelrod N, Baldauf S, Boore SBJ, Cochrane G, Cole J, Dawyndt P, Vos PD, dePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister A, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Moxon R, Nelson K, Parkhill J, Proctor L, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery DW, Vaughan B, Ward N, Whetzel T, Wilson G, Wipat A, Nature Biotechnology, 26:541-547, (2008), 2008
  PubMed
  
  
• Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes
  Bohlin J, Skjerve E, Ussery DW, BMC Genomics, 49:104 (2008). doi:10.1371/journal.pcbi.1000057, 2008
  PubMed BMC Genomics link
  
  
• Transcriptomics and adaptive genomics of the asymptomatic bacteria Escherichia coli strain 83972
  Hancock V, Seshasayee AS, Ussery DW, Luscombe NM, Klemm P, Mol Genet Genomics, 279:523-534, (2008)., 2008
  PubMed
  
  
• Investigations of oligonucleotide usage variance within and between prokaryotes
  Bohlin J, Skjerve E, Ussery D, PLoS Computational Biology, 4:e1000057 (2008), 2008
  PubMed PLoS Computational Biology link
  
  
• Toward a Standards-Compliant Genomic and Metagenomic Publication Record
  Garrity GM, Field D, Kyrpides N, Hirschman L, Sansone SA, Angiuoli S, Cole JR, Glöckner FO, Kolker E, Kowalchuk G, Moran MA, Ussery D, White O, OMICS - A Journal of Integrative Biology, 12:157-160, (2008), 2008
  PubMed
  
  
• Protein-induced changes during the maturation process of human dendritic cells: A 2-D DIGE approach
  Ferreira GB, Overbergh L, Etten EV, Lage K, D’Hertog W, Hansen DA, Maris M, Moreau Y, Workman CT, Waelkens E, Mathieu C, Proteomics Clinical Applications, Volume 2 Issue 9, Pages 1349 - 1360, 2008
  
  
• MHC motif viewer
  Rapin N, Hoof I, Lund O, Nielsen M, Immunogenetics. 2008 Sep 3. [Epub ahead of print], 2008
  PubMed
  
  
• Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq.
  Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT, Hinton JC, Vogel J, PLoS Genet. 2008 Aug 22;4(8):e1000163, 2008
  PubMed
  
  
• The complete genome sequence and analysis of the human pathogen Campylobacter lari
  Miller WG, Wang G, Binnewies TT, Parker CT, Foodborne Pathog Dis. 2008 Aug;5(4):371-86, 2008
  PubMed
  
  
• Molecular analysis of the emergence of pandemic Vibrio parahaemolyticus
  Boyd EF, Cohen AL, Naughton LM, Ussery DW, Binnewies TT, Stine OC, Parent MA, BMC Microbiol. 2008 Jun 30;8:110, 2008
  PubMed
  
  
• The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571
  Lee KB, De Backer P, Aono T, Liu CT, Suzuki S, Suzuki T, Kaneko T, Yamada M, Tabata S, Kupfer DM, Najar FZ, Wiley GB, Roe B, Binnewies TT, Ussery DW, D’Haeze WD, Herder JD, Gevers D, Vereecke D, Holsters M, Oyaizu H, BMC Genomics. 2008 Jun 4;9:271., 2008
  PubMed
  
  
• Detection of anoxia-reponsive genes in cultured cells of the rainbow trout Oncorhynchus mykiss (Walbaum), using an optimized, genome-wide oligoarray
  Olohan LA, Li W, Wulff T, Jarmer HO, Gracey AY, Cossins AR, Journal of Fish Biology. 2008. 72, 2170-2186, 2008
  
  
• Arabidopsis MAP Kinase Kinases MKK1 and MKK2 have overlapping functions in defense signalling mediated by MEKK1, MPK4 and MKS1.
  Qiu J, Nielsen HB, Fiil BK, Petersen K, MacKinlay J, Loake G, Mundy J, Morris PC, Plant Physiol. 2008 Jul 3, 2008
  PubMed Relevant URL
  
  
• Arabidopsis MAP Kinase 4 regulates gene expression via transcription factor release in the nucleus
  Qiu J, Fiil BK, Petersen K, Nielsen HB, Botanga CJ, Thorgrimsen S, Lichota J, Brodersen P, Grasser KD, Mattsson O, Glazebrook J, Mundy J, Petersen M, The EMBO Journal 2008 (16):2214-21, 2008
  PubMed Relevant URL
  
  
• Influence of dietary fatty acids on endocannabinoid and N-acylethanolamine levels in rat brain, liver and small intestine
  Artmann A, Petersen G, Hellgren LI, Boberg J, Skonberg C, Nellemann C, Hansen SH, Hansen HS, Biochim. Biophys. Acta 1781: 200-212., 2008
  PubMed
  
  
• Lipids and skin barrier function--a clinical perspective
  Jungersted JM, Hellgren LI, Jemec GB, Agner T, Contact Dermatitis 58: 255-262., 2008
  PubMed
  
  
• Kinetic study of sphingomyelin hydrolysis for ceramide production.
  Zhang L, Hellgren LI, Xu X, Journal of Molecular Catalysis B: Enzymatic 51: 93-99., 2008
  
  
• Prediction of fat oxidation capacity using 1H-NMR and LC-MS lipid metabolomic data
  Pers TH, Martin FP, Verdich C, Holst C, Johansen JV, Astrup A, Polak J, Martinez JA, Rezzi S, Blaak EE, Saris WHM, Kochhar S, Macdonald IA, Sørensen TIA, Ramadan Z, Chemometrics and Intelligent Laboratory Systems 93, 34–42, 2008
  
  
• Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: a three factor design
  Fazio A, Jewett MC, Daran-Lapujade P, Mustacchi R, Usaite R, Pronk JT, Workman CT, Nielsen J, BMC Genomics 2008, 9:341, 2008
  
  
• GLI1 is involved in cell cycle regulation and proliferation of NT2 embryonal carcinoma stem cells
  Vestergaard J, Lind-Thomsen A, Pedersen MW, Jarmer HO, Bak M, Hasholt L, Tommerup N, Tümer Z, Larsen LA, DNA Cell Biol. 2008 May;27(5):251-6., 2008
  PubMed
  
  
• Global features of the Alcanivorax borkumensis SK2 genome
  Reva ON, Hallin PF, Willenbrock H, Sicheritz-Ponten T, Tummler B, Ussery DW, Environ Microbiol. 2008 Mar;10(3):614-25 and Mol Genet Genomics, 279:523-534, (2008), 2008
  PubMed
  
  
• The genome BLASTatlas-a GeneWiz extension for visualization ofwhole-genome homology
  Hallin PF, Binnewies TT, Ussery DW, Mol Biosyst 4:363-71 (2008), 2008
  PubMed
  
  
• Dendritic Cells from Peyer\'s Patches and Mesenteric Lymph Nodes Differ from Spleen Dendritic Cells in their Response to Commensal Gut Bacteria
  Fink LN, Frøkiær H, Scand J Immunol. 2008 Jun 19., 2008
  PubMed
  
  
• Toll-like receptor 2 and nucleotide-binding oligomerization domain-2 play divergent roles in the recognition of gut-derived lactobacilli and bifidobacteria in dendritic cells
  Zeuthen LH, Fink LN, Frøkiær H, Immunology. 2008 Vol. 124 (4):489-503, 2008
  PubMed
  
  
• Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan
  Nielsen M, Lundegaard C, Blicher T, Peters B, Sette A, Justesen S, Buus S, Lund O, PLoS Comput Biol. 2008 Jul 4;4(7):e1000107, 2008
  PubMed
  
  
• Immune epitope database analysis resource (IEDB-AR)
  Zhang Q, Wang P, Kim Y, Haste-Andersen P, Beaver J, Bourne PE, Bui HH, Buus S, Frankild S, Greenbaum J, Lund O, Lundegaard C, Nielsen M, Ponomarenko J, Sette A, Zhu Z, Peters B, Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W513-8. Epub 2008 May 31., 2008
  PubMed
  
  
• NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11
  Lundegaard C, Lamberth K, Harndahl M, Buus S, Lund O, Nielsen M, Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W509-12. Epub 2008 May 7., 2008
  PubMed
  
  
• Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers
  Lundegaard C, Lund O, Nielsen M, Bioinformatics. 2008 Jun 1;24(11):1397-8. Epub 2008 Apr 14, 2008
  PubMed
  
  
• Prediction of pH-dependent solubility of Histone Deacetylase (HDAC)inhibitors
  Kouskoumvekaki I, Hansen NT, Björkling F, Vadlamudi SM, Jónsdóttir SÓ, SAR and QSAR in Environmental Research, 19, 167-177, 2008, 2008
  PubMed
  
  
• Humans with chimpanzee-like major histocompatibility complex-specificities control HIV-1 infection
  Hoof I, Kesmir C, Lund O, Nielsen M, AIDS, 11;22(11):1299-303, 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
  
  
• Structural Insight into Epitopes in the Pregnancy-Associated Malaria Protein VAR2CSA
  Andersen P, Nielsen MA, Resende M, Rask TS, Dahlbäck M, Theander T, Lund O, Salanti A, PLoS Pathog. 2008 Feb 15;4(2):e42, 2008
  PubMed
  
  
• Amino acid similarity accounts for T cell cross-reactivity and for \\\'holes\\\' in the T cell repertoire
  Frankild S, de Boer RJ, Lund O, Nielsen M, Kesmir C, PLoS ONE. 2008 Mar 19;3(3):e1831, 2008
  PubMed
  
  
• Broadly Immunogenic HLA Class I Supertype-Restricted Elite CTL Epitopes Recognized in a Diverse Population Infected with Different HIV-1 Subtypes
  Pérez CL, Larsen MV, Gustafsson R, Norström MM, Atlas A, Nixon DF, Nielsen M, Lund O, Karlsson AC, J Immunol.,2008 Apr 1;180(7):5092-100, 2008
  PubMed
  
  
• Obesity - a social and physical risk
  Parlesak A, Krömker D, J Dtsch Dermatol Ges;6(6):442-9, 2008
  PubMed
  
  
• Correction of technical bias in clinical microarray data improves concordance with known biological information
  Eklund AC, Szallasi Z, Genome Biol., 4;9(2):R26, 2008
  PubMed Web
  
  
• Phylogenetic relationships between Sarcocystis species from reindeer and other Sarcocystidae deduced from ssu rRNA gene sequences
  Dahlgren SS, Gouveia-Oliveira R, Gjerde B, Vet Parasitol,25;151(1):27-35, 2008
  PubMed
  
  
• hERG Classification Model Based on a Combination of Support Vector Machine Method and GRIND Descriptors
  Li Q, Jørgensen FS, Oprea T, Brunak S, Taboureau O, Mol Pharm,4;5(1):117-127, 2008
  PubMed
  
  
• Identification of biomarkers for genotyping Aspergilli using non-linear methods for clustering and classification
  Kouskoumvekaki I, Yang Z, Jonsdottir SO, Olsson L, Panagiotou G, BMC Bioinformatics,28;9(1):59, 2008
  PubMed
  
  
• Is nutrient intake a gender-specific cause for enhanced susceptibility to alcohol-induced liver disease in women?
  Wagnerberger S, Schäfer C, Schwarz E, Bode C, Parlesak A, Alcohol Alcohol.;43(1):9-14, 2008
  PubMed
  
  
• Effect of gender on lipid-induced insulin resistance in obese subjects
  Vistisen B, Hellgren LI, Vadset T, Scheede-Bergdahl C, Helge JW, Dela F, Stallknecht B, Eur J Endocrinol., 158(1):61-8, 2008
  PubMed
  
  
• Epithelial cells prime the immune response to an array of gut-derived commensals towards a tolerogenic phenotype through distinct actions of thymic stromal lymphopoietin and transforming growth factor-beta
  Zeuthen LH, Fink LN, Frokiaer H, Immunology. 2008 Feb;123(2):197-208, 2008
  PubMed
  
  

2007

• Sequence conservation of subdominant HLA-A2-binding CTL epitopes in HIV-1 clinical isolates and CD8+ T-lymphocyte cross-recognition may explain the immune reaction in infected individuals
  Thorn M, Tang ST, Therrien D, Kløverpris H, Vinner L, Kronborg G, Gerstoft J, Corbet S, Fomsgaard A, APMIS;115(6):757-68, 2007
  PubMed
  
  
• Inhibition of type I and type III interferons by a secreted glycoprotein from Yaba-like disease virus
  Huang J, Smirnov SV, Lewis-Antes A, Balan M, Li W, Tang ST, Silke GV, Pütz MM, Smith GL, Kotenko SV, Proc Natl Acad Sci U S A;104(23):9822-7, 2007
  PubMed
  
  
• Characterization of near full-length genomes of HIV type 1 strains in Denmark: basis for a universal therapeutic vaccine
  Andresen BS, Vinner L, Tang ST, Bragstad K, Kronborg G, Gerstoft J, Corbet S, Fomsgaard A, AIDS Res Hum Retroviruses;23(11):1442-8, 2007
  PubMed
  
  
• Proteome-analysis of gut bacteria-matured dendritic cells
  Brix S, Kragh M, Sondergaard JN, Bjerkan L, Jacobsen S, Frokiaer H, Annals of Nutrition and Metabolism, 51:383-383 Suppl. 1 (2007), 2007
  
  
• The potential of gut bacteria-matured DCs to activate CD4+T cells highly depends on the lipid composition of the T cell membrane.
  Brix S, Lund P, Kjaer TMR, Straarup EM, Hellgren LI, Frokiaer H, Annals of Nutrition and Metabolism, 51:65-65 Suppl. 1 (2007), 2007
  
  
• Identification of putative noncoding RNA genes in the Burkholderia cenocepacia J2315 genome
  Coenye T, Drevinek P, Mahenthiralingam E, Shah SA, Gill RT, Vandamme P, Ussery DW, FEMS Microbiol Lett 276:83-92,(2007)., 2007
  PubMed
  
  
• Comparative genomic analysis of two-component regulatory proteins in Pseudomonas syringae
  Lavin JL, Kiil K, Resano O, Ussery DW, Oguiza JA, BMC Genomics, 8:397 (Sept. 2007), 2007
  PubMed Link to article
  
  
• Synthesis of structured phospholipids by immobilized phospholipase A2 catalyzed acidolysis
  Vikbjerg A, Mu H, Xu X, J. Biotechnol., 128:545-554, 2007
  PubMed
  
  
• Oxidative stability of liposomes composed of DHA-containing phospholipids
  Vikbjerg A, Andersen TL, Jørgensen K, Mu H, Xu X, J. Am. Oil Chem. Soc. 84:631-637, 2007
  
  
• Increased lipids in non-lipogenic tissues are indicators of the severity of type 2 diabetes in mice
  Campbell JA, Hansen HS, Mu H, Mølgaard P, Prostaglandins, Leukotrienes and Essential Fatty Acids, 76: 9-18., 2007
  PubMed
  
  
• Food matrices affect the bioavailability of (n-3) polyunsaturated fatty acids in a single meal study in humans
  Schram LB, Nielsen CJ, Porsgaard T, Nielsen NS, Holm R, Mu H, Food Res. Inter. 40:1062-1068., 2007
  
  
• Butter blend containing fish oil improves the level of n-3 fatty acids in biological tissues of hamster
  Porsgaard T, Overgaard J, Krogh AL, Jensen MB, Guo Z, Mu H, J. Agric. Food Chem., 55, 7615 -7619, 2007
  PubMed
  
  
• The Complete Genome Sequence and Analysis of the EpsilonproteobacteriumArcobacter butzleri
  Miller WG, Parker CT, Rubenfield M, Mendz GL, Wosten MM, Ussery DW, Stolz JF, Binnewies TT, Hallin PF, Wang G, Malek JA, Rogosin A, Stanker LH, Mandrell RE, PLoS ONE. 2007 Dec 26;2(12):e1358., 2007
  PubMed
  
  
• Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray
  Willenbrock H, Hallin PF, Wassenaar TM, Ussery DW, Genome Biol 8:R267 (2007), 2007
  PubMed
  
  
• Antisense-mediated suppression of C-hordein biosynthesis in the barley grain results in correlated changes in the transcriptome, protein profile, and amino acid composition
  Hansen M, Lange M, Friis C, Dionisio G, Holm PB, Vincze E, Journal of Experimental Botany 2007 58(14):3987-3995; doi:10.1093/jxb/erm254, 2007
  PubMed
  
  
• Modeling the adaptive immune system: predictions and simulations
  Lundegaard C, Lund O, Kesmir C, Brunak S, Nielsen M, Bioinformatics, 23:3265-75, 2007
  PubMed
  
  
• Forsg med ny online eksamensform i \\
  Wernersson R, DTU Avisen, 2007
  
  
• Computational Analysis and Modeling of Bacterial Pathogenesis
  Binnewies TT, PhD thesis, 2007
  
  
• Kemoinformatik: Lær computeren at finde nye lægemidler
  Kouskoumvekaki I, Hansen NT, Jónsdóttir SÓ, Dansk Kemi, 88(8),23-25, 2007
  
  
• Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction
  Larsen MV, Lundegaard C, Lamberth K, Buus S, Lund O, Nielsen M, BMC Bioinformatics,31;8:424, 2007
  PubMed
  
  
• Integrative analysis for finding genes and networks involved in diabetes and other complex diseases
  Bergholdt R, Størling ZM, Lage K, Karlberg EO, Olason PI, Aalund M, Nerup J, Brunak S, Workman CT, Pociot F, Genome Biol., 28;8(11):R253, 2007
  PubMed
  
  
• Proteomics analysis of cytokine-induced dysfunction and death in insulin-producing INS-1E cells: new insights into the pathways involved
  Hertog W, Overbergh L, Lage K, Ferreira GB, Maris M, Gysemans C, Flamez D, Cardozo AK, Van den Bergh G, Schoofs L, Arckens L, Moreau Y, Hansen DA, Eizirik DL, Waelkens E, Mathieu C, Mol Cell Proteomics.;6(12):2180-99, 2007
  PubMed
  
  
• Kamp med og mod bakterier
  Jarmer H, DTU-avisen, 27 April, nr. 5, 2007
  
  
• Det er ikke bare et fedt
  Hellgren LI, Dansk Kemi, 88:14-6, 2007
  
  
• Immobilization of phospholipase C for the production of ceramide from sphingomyelin hydrolysis
  Zhang L, Hellgren LI, Xu XB, J American Oil Chem Soc, 84:237-47, 2007
  
  
• The source of dietary fatty acids alter the activity of secretory sphingomyelinase in the rat
  Drachmann T, Mathiassen JH, Pedersen MH, Hellgren LI, European Journal of Lipid Science and Technology, 109:1003-9, 2007
  
  
• Locating proteins in the cell using TargetP, SignalP and related tools
  Emanuelsson O, Brunak S, von Heijne G, Nielsen H, Nature Protoc. 2, 953-971, 2007
  
  
• Identification of a new hTERT-derived HLA-A*0201 restricted, naturally processed CTL epitope
  Thorn M, Wang M, Kloverpris H, Schmidt EG, Fomsgaard A, Wenandy L, Berntsen A, Brunak S, Buus S, Claesson MH, Cancer Immunol, 2007
  
  
• Evolution of cell cycle control: same molecular machines, different regulation
  de Lichtenberg U, Jensen TS, Brunak S, Bork P, Jensen LJ, Cell Cycle,1;6(15):1819-25, 2007
  PubMed
  
  
• Dynamics of Escherichia coli Chromosome Segregation during Multifork Replication
  Nielsen HJ, Youngren B, Hansen FG, Austin S, J Bacteriol., 189(23):8660-6, 2007
  PubMed
  
  
• DNA and origin region segregation are not affected by the transition from rod to sphere after inhibition of Escherichia coli MreB by A22
  Karczmarek A, Martínez-Arteaga R, Alexeeva S, Hansen FG, Vicente M, Nanninga N, den Blaauwen T, Mol Microbiol., 65(1):51-63, 2007
  PubMed
  
  
• Structure and Content of the Entamoeba histolytica Genome
  Clark CG, Alsmark UCM, Tazreiter M, Saito Y, Nakano, Ali V, Marion S, Weber C, Mukherjee C, Bruchhaus I, Tannich E, Leippe M, Sicheritz-Ponten T, Foster PG, Samuelson J, Noël CJ, Hirt RP, Embley TM, Gilchrist CA, Mann BJ, Singh U, Ackers JP, Bhattacharya S, Bhattacharya S, Lohia A, Guillén N, Duchêne M, Nozaki T, Hall N, Advances in Parasitology, 65, 51-190, 2007
  PubMed
  
  
• Trichomonas vaginalis surface proteins: a view from the genome
  Hirt RP, Noel CJ, Sicheritz-Ponten T, Tachezy J, Fiori PL, Trends Parasitol., 23(11):540-7, 2007
  PubMed
  
  
• Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2
  Miller ML, Hanke S, Hinsby AM, Friis C, Brunak S, Mann M, Blom N, Mol Cell Proteomics (in press), 2007
  PubMed
  
  
• Conjugated primary bile salts reduce permeability of endotoxin through intestinal epithelial cells and synergize with phosphatidylcholine in suppression of inflammatory cytokine production
  Parlesak A, Schaeckeler S, Moser L, Bode C, Crit Care Med., 35(10):2367-74, 2007
  PubMed
  
  
• Human antigen-presenting cells respond differently to gut-derived probiotic bacteria but mediate similar strain-dependent NK and T cell activation
  Fink LN, Zeuthen LH, Ferlazzo G, Frøkiær H, FEMS Immunol Med Microbiol. 6;51(3):535-546, 2007
  PubMed
  
  
• Distinct gut-derived lactic acid bacteria elicit divergent dendritic cell-mediated NK cell responses
  Fink LN, Zeuthen LH, Christensen HR, Morandi B, Frøkiær H, Ferlazzo G, Int Immunol., 19(12):1319-1327, 2007
  PubMed
  
  
• HLA Alleles Associated with Slow Progression to AIDS Truly Prefer to Present HIV-1 p24
  Borghans JA, Molgaard A, de Boer RJ, Kesmir C, PLoS ONE. Sep 19;2(9):e920, 2007
  PubMed
  
  
• Branchio-Oto-Renal Syndrome: Detection of EYA1 and SIX1 mutations in five out of six Danish families by combining linkage, sequencing and MLPA analyses
  Sanggaard KM, Kjaer KW, Eiberg H, Rendtorff ND, Johnsen T, Gimsing S, Dyrmose J, Nielsen KO, Lage K, Tranebjærg L, Eur J Hum Genet. Jul 18, 2007
  PubMed
  
  
• Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina
  Arvas MM, Kivioja T, Mitchell A, Saloheimo M, Ussery DW, Penttila M, Oliver S, BMC Genomics 3:325, 2007
  PubMed
  
  
• Dice & DNA
  Wernersson R, BioScience Education e-journal, (in press), 2007
  
  
• Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method
  Nielsen M, Lundegaard C, Lund O, BMC Bioinformatics. Jul 4;8(1):238, 2007
  PubMed
  
  
• Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis
  Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, Wortman JR, Bidwell SL, Alsmark UC, Besteiro S, Sicheritz-Ponten T, Noel CJ, Dacks JB, Foster PG, Simillion C, Van de Peer Y, Miranda-Saavedra D, Barton GJ, Westrop GD, Müller S, Dessi D, Fiori PL, Ren Q, Paulsen I, Zhang H, Bastida-Corcuera FD, Simoes-Barbosa A, Brown MT, Hayes RD, Mukherjee M, Okumura CY, Schneider R, Smith AJ, Vanacova S, Villalvazo M, Haas BJ, Pertea M, Feldblyum TV, Utterback TR, Shu CL, Osoegawa K, de Jong PJ, Hrdy I, Horvathova L, Zubacova Z, Dolezal P, Malik SB, Logsdon JM Jr, Henze K, Gupta A, Wang CC, Dunne RL, Upcroft JA, Upcroft P, White O, Salzberg SL, Tang P, Chiu CH, Lee YS, Embley TM, Coombs GH, Mottram JC, Tachezy J, Fraser-Liggett CM, Johnson PJ, Science. Jan 12;315(5809):207-12, 2007
  PubMed
  
  
• State-Wide Molecular and Epidemiological Study on the Nosocomial Transmission of HCV in Hemodialysis Patients in Brazil
  Carneiro MAS, Teles SA, Lampe E, Espirito-Santo MP, Gouveia-Oliveira R, Reis NRS, Yoshida CFT, Martins MBR, J Med Virol. Sep;79(9):1325-33, 2007
  
  
• Finding Coevolving Amino acid Residues using Row and Column Weighing of Mutual Information and Multi-Dimensional Amino acid Representation
  Gouveia-Oliveira R, Pedersen AG, Algorithms in Molecular Biology, 3;2(1):12, 2007
  PubMed PDF
  
  
• NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence
  Nielsen M, Lundegaard C, Blicher T, Lamberth K, Harndahl M, Justesen S, Roder G, Peters B, Sette A, Lund O, Buus S, PLoS ONE. Aug 29;2(8):e796, 2007
  PubMed
  
  
• Structure-function analysis of the ER oxidoreductase TMX3 reveals inter-domain stabilization of the N-terminal redox-active domain
  Haugstetter J, Maurer MA, Blicher T, Pagac M, Wider G, Ellgaard L, J Biol Chem. Sep 18, 2007
  PubMed
  
  
• The essential YycFG two-component system controls cell wall metabolism in Bacillus subtilis
  Bisicchia P,Noone D,Lioliou E,Howell A,Quigley S,Jensen T,Jarmer H,Devine KM, Mol Microbiol. Jul;65(1):180-200, 2007
  PubMed
  
  
• CycleBase.org - a comprehensive multi-organism online database of cell-cycle experiments
  Gauthier NP, Jensen TS, de Lichtenberg U, Wernersson R, Larsen ME, Brunak S, Nucleic Acids Res. (in press), 2007
  Web
  
  
• Probe Selection for DNA Microarrays using OligoWiz
  Wernersson R, Juncker AS, Nielsen HB, Nature Protocols, vol. 2, no. 11, p. 2677-91, 2007
  PubMed
  
  
• SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation
  Panitz F, Stengaard H, Hornshøj H, Gorodkin J, Hedegaard J, Cirera S, Thomsen B, Madsen LB, Høj A, Vingborg RK, Zahn B, Wang X, Wang X, Wernersson R, Jørgensen CB, Scheibye-Knudsen K, Arvin T, Lumholdt S, Sawera M, Green T, Nielsen BJ, Havgaard JH, Brunak S, Fredholm M, Bendixen C, Bioinformatics. 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
  
  
• MaxAlign: maximizing usable data in an alignment
  Gouveia-Oliveira R, Sackett PW, Pedersen AG, BMC Bioinformatics. Aug 28;8(1):312, 2007
  PubMed PDF
  
  
• Functional Associations by Response Overlap (FARO), a functional genomics approach matching gene expression phenotypes
  Nielsen HB, Mundy J, Willenbrock H, PLoS ONE. Aug 1;2:e676, 2007
  PubMed
  
  
• Analysis of cell death inducing compounds
  Spicker JS, Pedersen HT, Nielsen HB, Brunak S, Archives of Toxicology, DOI 10.1007/s00204-007-0207-4, 2007
  
  
• Evidence for Vertical Inheritance and Loss of the Leukotoxin Operon in Genus Mannheimia
  Larsen J, Pedersen AG, Christensen H, Bisgaard M, Angen Ø, Ahrens P, Olsen JE, J. Mol. Evol., 64(4):423-37, 2007
  PubMed
  
  
• Monitoring novel metabolic pathways using metabolomics and machine learning: induction of the phosphoketolase pathway in Aspergillus nidulans cultivations
  Panagiotou G, Kouskoumvekaki I, Jónsdóttir SÓ, Olsson L, Metabolomics,3,503-516, 2007
  
  
• A high-quality catalog of the Drosophila melanogaster proteome
  Brunner E, Ahrens CH, Mohanty S, Baetschmann H, Loevenich S, Potthast F, Deutsch EW, Panse C, de Lichtenberg U, Rinner O, Lee H, Pedrioli PG, Malmstrom J, Koehler K, Schrimpf S, Krijgsveld J, Kregenow F, Heck AJ, Hafen E, Schlapbach R, Aebersold R, Nat Biotechnol, 25(5):576-83, 2007
  PubMed
  
  
• The implications of alternative splicing in the ENCODE protein complement
  Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PI, Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA, Lopez G, Sadowski MI, Watson JD, Fariselli P, Rossi I, Nagy A, Wang K, Storling Z, Orsini M, Assenov Y, Blankenburg H, Huthmacher C, Ramirez F, Schlicker A, Denoued F, Jones P, Kerrien S, Orchard S, Antonarakis SE, Reymond A, Birney E, Brunak S, Casadio R, Guigo R, Harrow J, Hermjakob H, Jones DT, Lengauer T, Orengo CA, Patthy L, Thornton JM, Tramontano A, Valencia A, Proc Natl Acad Sci U S A (in press), 2007
  PubMed
  
  
• Sequence Characteristics Required for Cooperative Binding and Efficient inVivo Titration of the Replication Initiator Protein DnaA in E. coli
  Hansen FG, Christensen BB, Atlung T, J Mol Biol., 367 (4), 942-52, 2007
  PubMed
  
  
• Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88
  Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, Turner G, de Vries RP, Albang R, Albermann K, Andersen MR, Bendtsen JD, Benen JA, van den Berg M, Breestraat S, Caddick MX, Contreras R, Cornell M, Coutinho PM, Danchin EG, Debets AJ, Dekker P, van Dijck PW, van Dijk A, Dijkhuizen L, Driessen AJ, d\'Enfert C, Geysens S, Goosen C, Groot GS, de Groot PW, Guillemette T, Henrissat B, Herweijer M, van den Hombergh JP, van den Hondel CA, van der Heijden RT, van der Kaaij RM, Klis FM, Kools HJ, Kubicek CP, van Kuyk PA, Lauber J, Lu X, van der Maarel MJ, Meulenberg R, Menke H, Mortimer MA, Nielsen J, Oliver SG, Olsthoorn M, Pal K, van Peij NN, Ram AF, Rinas U, Roubos JA, Sagt CM, Schmoll M, Sun J, Ussery D, Varga J, Vervecken W, van de Vondervoort PJ, Wedler H, Wosten HA, Zeng AP, van Ooyen AJ, Visser J, Stam H, Nat Biotechnol., 25 (2), 221-31, 2007
  PubMed
  
  
• Prediction of highly expressed genes in microbes based on chromatin accessibility
  Willenbrock H, Ussery DW, BMC Mol Biol., 8 (1), 11, 2007
  PubMed Link to BMC Molecular Biology file
  
  
• The importance of virulence prediction and gene networks in microbial risk assessment
  Wassenaar GM, Gamieldien J, Shatkin JA, Luber P, Moyer N, Carpenter T, Ussery DW, Human and Ecological Risk Assessment, 13, 1-15, 2007
  
  
• RNAmmer: consistent and rapid annotation of ribosomal RNA genes
  Lagesen K, Hallin P, Rødland EA, Stærfeldt HH, Rognes T, Ussery DW, Nucleic Acids Research 35:3100-3108,(2007)., 2007
  PubMed
  
  
• Genome-wide analysis of the Arabidopsis leaf transcriptome reveals interaction of phosphate and sugar metabolism
  Muller R, Morant M, Jarmer H, Nilsson L, Nielsen TH, Plant Physiol., 143 (1), 156-71, 2007
  PubMed
  
  
• Midbrain expression of Delta-like 1 homologue is regulated by GDNF and is associated with dopaminergic differentiation
  Christophersen NS, Gronborg M, Petersen TN, Fjord-Larsen L, Jorgensen JR, Juliusson B, Blom N, Rosenblad C, Brundin P, Exp Neurol., (in press), 2007
  PubMed
  
  
• Prediction of protein phosphorylation sites in yeast
  Ingrell CR, Miller ML, Jensen ON, Blom N, Bioinformatics, 1;23(7):895-7, 2007
  PubMed
  
  
• Human pregnancy-associated malaria-specific B cells target polymorphic, conformational epitopes in VAR2CSA
  Barfod L, Bernasconi NL, Dahlback M, Jarrossay D, Andersen PH, Salanti A, Ofori MF, Turner L, Resende M, Nielsen MA, Theander TG, Sallusto F, Lanzavecchia A, Hviid L, Mol Microbiol., 63 (2), 335-47, 2007
  PubMed
  
  
• Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools
  Greenbaum JA, Andersen PH, Blythe M, Bui HH, Cachau RE, Crowe J, Davies M, Kolaskar AS, Lund O, Morrison S, Mumey B, Ofran Y, Pellequer JL, Pinilla C, Ponomarenko JV, Raghava GP, van Regenmortel MH, Roggen EL, Sette A, Schlessinger A, Sollner J, Zand M, Peters B, J. Mol. Recognit. (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
  
  
• Identification of a novel Mannheimia granulomatis lineage from pathological lesions in roe deer (Capreolus capreolus)
  Bojesen AM, Larsen J, Pedersen AG, Mörner T, Mattson R, Bisgaard M, J. Wildlife Dis., 43(3), 345-352, 2007
  PubMed PDF Publication download
  
  
• Improving comparability between microarray probe signals by thermodynamic intensity correction
  Bruun GM, Wernersson R, Juncker AS, Willenbrock H, Nielsen HB, Nucleic Acids Research, doi:10.1093/nar/gkl1098, 2007
  PubMed Web
  
  
• Investigating Signs of Recent Evolution in the Pool of Pro-viral DNA during Years of Successful HAART
  Mens H, Pedersen AG, Jørgensen LB, Hue S, Gerstoft J, Katzenstein TL, AIDS Res. Hum. Retroviruses, 23 (1), 107-115, 2007
  PubMed Publication download
  
  

2006

• Kan kosten påvirke vores risiko for at udvikle allergi?
  Brix S, Frokiaer H, Miljø og Sundhed, Indenrigs- og Sundhedsministeriets Miljømedicinske Forskningscenter, 31: 5-9 (2006)., 2006
  
  
• A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers
  Carter SL, Eklund AC, Kohane IS, Harris LN, Szallasi Z, Nat Genet 38(9):1043-8, 2006
  PubMed
  
  
• Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae
  Regenberg B, Grotkjr T, Winther O, Fausbll A, Akesson M, Bro C, Hansen LK, Brunak S, Nielsen J, Genome Biol. 7, R107, 2006
  
  
• The Escherichia coli chromosome is organized with the left and right chromosome arms in separate cell halves
  Nielsen HJ, Ottesen JR, Youngren B, Austin SJ, Hansen FG, Mol Microbiol., 62(2):331-8, 2006
  PubMed
  
  
• Progressive segregation of the Escherichia coli chromosome
  Nielsen HJ, Li Y, Youngren B, Hansen FG, Austin S, Mol Microbiol., 61(2):383-93, 2006
  PubMed
  
  
• Insights into the quality of DnaA boxes and their cooperativity
  Hansen FG, Christensen BB, Nielsen CB, Atlung T, J Mol Biol., 6;355(1):85-95, 2006
  PubMed
  
  
• Lactic acid bacteria inducing a weak interleukin-12 and tumor necrosis factor alpha response in human dendritic cells inhibit strongly stimulating lactic acid bacteria but act synergistically with gram-negative bacteria
  Zeuthen LH, Christensen HR, Frøkiaer H, Clin Vaccine Immunol.,13(3):365-75, 2006
  PubMed
  
  
• Crystal structures of two peptide-HLA-B*1501 complexes; structural characterization of the HLA-B62 supertype
  Roder G, Blicher T, Justesen S, Johannesen B, Kristensen O, Kastrup J, Buus S, Gajhede M, Acta Crystallogr D Biol Crystallogr. Nov;62(Pt 11):1300-10, 2006
  
  
• FeatureMap3D - a tool to map protein features and sequence conservation onto homologous structures in the PDB
  Wernersson R, Rapacki K, Staerfeldt HH, Sackett PW, Mølgaard A, Nucleic Acids Res. Jul 1;34(Web Server issue):W84-8, 2006
  PubMed Web
  
  
• Virtual Ribosome - a comprehensive DNA translation tool with support for integration of sequence feature annotation
  Wernersson R, Nucleic Acids Res. Jul 1;34(Web Server issue):W385-8, 2006
  PubMed Web
  
  
• Mesoscopic Simulations of Biological Membranes
  Smit B, Kranenburg K, Sperotto MM, Venturoli M, Lect. Notes Phys. 704, 259-286, 2006
  
  
• Modelling of proteins in membranes
  Sperotto MM, May S, Baumgaertner A, Chem. Phys. Lipids, 141, 2-29, 2006
  PubMed
  
  
• Mesoscopic Models of Biological Membranes
  Venturoli M, Sperotto MM, Kranenburg M, Smit B, Physics Reports, 437: 1-54, 2006
  
  
• TAP-Independent MHC Class I Presentation
  Larsen MV, Nielsen M, Weinzierl A, Lund O, Curr Immunol Rev, 2, 233-245, 2006
  
  
• Opening the pan-genomics box
  Read T, Ussery DW, Current Opinion in Microbiology, 9:496-498, 2006
  
  
• Design of a 7 Genomes Escherichia coli Microarray for Comparative Genomic Profiling
  Willenbrock H, Petersen A, Sekse C, Kiil K, Wasteson Y, Ussery DW, Journal of Bacteriology, 188:7713-7721, 2006
  PubMed
  
  
• Leaner and Meaner Genomes in Escherichia coli
  Ussery DW, GenomeBiology, 7:237, 2006
  PubMed
  
  
• An environmental signature for 323 microbial genomes based on codon adaptation indices
  Willenbrock H, Friis C, Juncker AS, Ussery DW, Genome Biology, 7, R114, 2006
  PubMed
  
  
• Metabolic network driven analysis of genome-wide transcription data from Aspergillus nidulans
  David H, Hofmann G, Oliveira AP, Jarmer H, Nielsen J, Genome Biol., 7 (11): R108, 2006
  PubMed
  
  
• Modelling the human immune system by combining bioinformatics and systems biology approaches
  Rapin N, Kesmir C, Frankild S et al, Journal of Biological Physics, 32 (3-4), 335-353, 2006
  
  
• A community resource benchmarking predictions of peptide binding to MHC-I molecules
  Peters B, Bui HH, Frankild S, Nielson M, Lundegaard C, Kostem E, Basch D, Lamberth K, Harndahl M, Fleri W, Wilson SS, Sidney J, Lund O, Buus S, Sette A, PLoS Comput Biol., 2 (6):e65, 2006
  PubMed
  
  
• The validity of predicted T-cell epitopes
  Lundegaard C, Nielsen M, Lund O, Trends Biotechnol., 24 (12), 537-8, 2006
  PubMed
  
  
• CTL epitopes for influenza A including the H5N1 bird flu; genome-, pathogen-, and HLA-wide screening
  Wang M, Lamberth K, Harndahl M, Roder G, Stryhn A, Larsen MV, Nielsen M, Lundegaard C, Tang ST, Dziegiel MH, Rosenkvist J, Pedersen AE, Buus S, Claesson MH, Lund O, Vaccine (in press), 2006
  PubMed
  
  
• 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
  
  
• Prediction of residues in discontinuous B-cell epitopes using protein 3D structures
  Andersen PH, Nielsen M, Lund O, Protein Sci., 15 (11), 2558-67, 2006
  PubMed
  
  
• Analysis and prediction of mammalian protein glycation
  Johansen MB, Kiemer L, Brunak S, Glycobiology vol. 16 no. 9, 844-853, 2006
  PubMed
  
  
• An overabundance of phase 0 introns immediately after the start codon in eukaryotic genes
  Nielsen H, Wernersson R, BMC Genomics 7, 256, 2006
  PubMed Web
  
  
• Arabidopsis MAP kinase 4 regulates salicylic acid- and jasmonic acid/ethylene-dependent responses via EDS1 and PAD4
  Brodersen P, Petersen M, Nielsen HB, Zhu S, Newman MA, Shokat KM, Rietz S, Parker J, Mundy J, Plant J., 47 (4), 532-46, 2006
  PubMed
  
  
• Transcription analysis using high-density micro-arrays of Aspergillus nidulans wild-type and creA mutant during growth on glucose or ethanol
  Mogensen J, Nielsen HB, Hofmann G, Nielsen J, Fungal Genet Biol., 43 (8), 593-603, 2006
  PubMed
  
  
• Epitope mapping and topographic analysis of VAR2CSA DBL3X involved in P. falciparum placental sequestration
  Dahlbäck M, Rask TS, Andersen PH, Nielsen MA, Ndam NT, Resende M, Turner L, Deloron P, Lund O, Pedersen AG, Hviid L, Theander TG, Salanti A, PLoS Pathogens, 2 (11):e124, 2006
  PubMed PDF
  
  
• Protein Evolution is Faster Outside the Cell
  Julenius K, Pedersen AG, Mol. Biol. Evol., 23 (11), 2039-2048, 2006
  PubMed PDF
  
  
• The genomic code: inferring Vibrionaceae niche specialization
  Reen FJ, Almagro-Moreno S, Ussery D et al, Nature Reviews Microbiology 4, 697-704, 2006
  PubMed
  
  
• Distinct developmental defense activations in barley embryos identified by transcriptome profiling
  Nielsen ME, Lok F, Nielsen HB, Plant molecular biology, 61, 589-601, 2006
  PubMed
  
  
• Identification of Tn5397-like and Tn916-like transposons and diversity of the tetracycline resistance gene tet(M) in enterococci from humans, pigs and poultry
  Agersø Y, Pedersen AG, Aarestrup FM, Journal of Antimicrobial Chemotherapy, 57, 832-839, 2006
  PubMed PDF
  
  
• Transcriptome analysis of FSH and FSH variant stimulation in granulosa cells from IVM patients reveals novel regulated genes
  Perlman S, Bouquin T, van den Hazel B, Jensen TH, Schambye HT, Knudsen S, Okkels JS, Mol Hum Reprod, 12, 135-44, 2006
  PubMed
  
  
• The more the merrier: comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast
  Marguerat S, Jensen TS, de Lichtenberg U, Wilhelm BT, Jensen LJ, Bahler J, Yeast, 23, 261-77, 2006
  PubMed
  
  
• Improved method for predicting linear B-cell epitopes
  Larsen JE, Lund O, Nielsen M, Immunome Res, 2: 2, 2006
  PubMed
  
  
• A Wiring of the Human Nucleolus
  Hinsby AM, Kiemer L, Karlberg EO, Lage K, Fausboll A, Juncker AS, Andersen JS, Mann M, Brunak S, Molecular Cell, 22, 285-295, 2006
  PubMed
  
  
• Structural features of fungal genomes
  Wanchanthuek P, Hallin PF, Gouveia-Oliveira R, Ussery DW, Topics in Current Genetics, 15, 47-77, 2006
  
  
• Ten years of bacterial genome sequencing: comparative-genomics-based discoveries
  Binnewies TT, Motro Y, Hallin PF, Lund O, Dunn D, La T, Hampson DJ, Bellgard M, Wassenaar TM, Ussery DW, Functional and Integrative Genomics, 6, [Epub ahead of print], 2006
  PubMed
  
  
• The TNFalpha receptor TNFRSF1A and genes encoding the amiloride-sensitive sodium channel ENaC as modulators in cystic fibrosis
  Stanke F, Becker T, Cuppens H, Kumar V, Cassiman JJ, Jansen S, Radojkovic D, Siebert B, Yarden J, Ussery DW, Wienker TF, Tummler B, Hum Genet, 119(3):331-43, 2006
  PubMed
  
  
• Genome update: purine strand bias in 280 bacterial genomes
  Champ PC, Binnewies TT, Nielsen N, Zinman G, Kiil K, Wu H, Bohlin J, Ussery DW, Microbiology, 152(Pt 3): 579-83, 2006
  PubMed
  
  
• Identification of novel genes regulated in the developing human ventral mesencephalon
  Jorgensen JR, Juliusson B, Henriksen KF, Hansen C, Knudsen S, Petersen TN, Blom N, Seiger A, Wahlberg LU, Experimental neurology, 198(2):427-37, 2006
  PubMed
  
  
• Crosstalk
  Mundy J, Nielsen HB, Brodersen P, Trends plant Sci, 11, 63-64, 2006
  PubMed
  
  
• Origin of Replication in Circular Prokaryotic Chromosomes
  Worning P, Jensen LJ, Hallin PF, Stærfeldt HH, Ussery DW, Environ Microbiol, 8, 353-61, 2006
  PubMed
  
  

2005

• Interactions between milk proteins and the immune system: modulation of nonspecific and antigen-specific immune responses
  Brix S, ISBN: 87-991021-0-2, 2005
  
  
• Effect of prior dietary exposure to cow’s milk protein on antigen-specific and nonspecific cellular proliferation in mice
  Brix S, Magyar OH, Barkholt V, Frøkiær H, J Dairy Res, 72:217-225 (2005), 2005
  
  
• Milk-derived GM3 and GD3 differentially inhibit dendritic cell maturation and effector functionalities
  Brønnum H, Seested T, Hellgren LI, Brix S, Frøkiær H, Scand J Immunol, 61:551-557 (2005), 2005
  
  
• Effect of maternal dietary cow’s milk on the immune response to beta-lactoglobulin in the offspring: A four generation study in mice
  Brix S, Christensen HR, Barkholt V, Frøkiær H, Int Arch Allergy Immunol, 136:250-259 (2005), 2005
  
  
• Maternal transfer of oral tolerance to ingested soy proteins
  Christensen HR, Brix S, Frokiaer H, Immunology, 116:61-61 Suppl. 1 Dec (2005), 2005
  
  
• The 3\' region of human papillomavirus type 16 early mRNAs decrease expression
  Vinther J, Rosenstierne MW, Kristiansen K, Norrild B, BMC Infect Dis.,14;5:83, 2005
  PubMed
  
  
• Genome Update: Protein secretion systems in 225 bacterial genomes
  Binnewies TT, Bendtsen JD, Hallin PF, Nielsen N, Wassenaar TM, Pedersen MB, Klemm P, Ussery DW, Microbiology., 151(Pt 4):1013-6, 2005
  PubMed
  
  
• Simulation studies of protein-induced bilayer deformations, and lipid-induced protein tilting, on a mesoscopic model for lipid bilayers with embedded proteins
  Venturoli M, Smit B, Sperotto MM, Biophys. J. 88: 1778-1798, 2005
  PubMed
  
  
• Selection of proteins for human MHC class II presentation
  Jiang L, Lund O, Tan JQ, Cell Mol Immunol, 2, 49-56, 2005
  PubMed
  
  
• Extracytoplasmic function sigma factors in Pseudomona syringae
  Oguiza JA, Kiil K, Ussery DW, Trends Microbiology, 13(12):565-8, 2005
  PubMed
  
  
• Genome opdate: Protein secretion systems in 225 bacterial genomes
  Bennewies TT, Bendtsen JD, Hallin PF, Nielsen N, Wassenaar TM, Pedersen MB, Klemm P, Ussery DW, Microbiology, 151, 1013-1016, 2005
  PubMed
  
  
• Genome update: Prediction of secreted proteins in 225 bacterial proteomes
  Bendtsen JD, Binnewies TT, Hallin PF, Sicheritz-Pontén T, Ussery DW, Microbiology, 151, 1725-1727, 2005
  PubMed
  
  
• The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota
  Chen LM, Brugger K, Skovgaard M, Redder P, She QX, Torarinsson E, Greve B, Awayez M, Zibat A, Klenk HP, Garrett RA, Bacteriology, 187, 4992-4999, 2005
  PubMed
  
  
• Genome update: Prediction of membrane proteins in prokaryotic genomes
  Bendtsen JD, Binnewies TT, Hallin PF, Ussery DW, Microbiology, 151, 2119-2121, 2005
  PubMed
  
  
• Alcohol-induced surface attachment of Listeria monocytogenes: Which mechanisms lie behind?
  Knudsen B, Jarmer H, Knochel S, Gravesen A, Biotechnology, 118, 158-158, 2005
  
  
• Temporal interactome for the eukaryotic cell cycle by data integration
  Brunak S, Biotechnology, 118, 7-8, 2005
  
  
• Genome update: Sigma factors in 240 bacterial genomes
  Kiil K, Binnewies TT, Sicheritz-Pontén T, Willenbrock H, Hallin PF, Wassenaart TM, Ussery DW, Microbiology-SGM, 151, 3147-3150, 2005
  PubMed
  
  
• Improvement of galactose uptake in Saccharomyces cerevisiae through overexpression of phosphoglucomutase: Example of transcript analysis as a tool in inverse metabolic engineering
  Bro C, Knudsen S, Regenberg B, Olsson L, Nielsen J, Applied and environmental microbiology, 71, 6465-6472, 2005
  PubMed
  
  
• A comparison study: Applying segmentation to array CGH data for downstream analyses
  Willenbrock H, Fridlyand J, Bioinformatics, 21, 4084-4091, 2005
  PubMed
  
  
• Genome update: Distribution of two.component trensduction systems in 250 bacterial genomes
  Kiil K, Ferchaud JB, David C, Binnewies T, Wu H, Sicheritz-Pontén T, Willenbrock H, Ussery DW, Microbiology, 151, 3447-3452, 2005
  PubMed
  
  
• Genetic evolution of HIV in patients remaining on a stable HAART regimen despite insufficient viral suppression
  Kristiansen TB, Pedersen AG, Eugen-Olsen J, Katzenstein TL, Lundgren JD, Scand J Infect Dis, 37, 890-901, 2005
  PubMed PDF
  
  
• Presence of a functional but dispensable Nuclear Export Signal in the HTLV-2 Tax protein
  Chevalier SA, Meertens L, Calattini S, Gessain A, Kiemer L, Mahieux R, Retrovirology, 14, 70, 2005
  PubMed
  
  
• Integrating protein annotation resources through the Distributed Annotation System
  Olason PI, Nucleic Acids research, 33, 468-470, 2005
  PubMed
  
  
• New weakly expressed cell cycle-regulated genes in yeast
  Hansen B, Schmidt P, Fausboll A, de Lichtenberg U, Wernersson R, Skøt Jensen T, Nielsen HB, Knudsen S, Brunak S, Yeast, 22, 1191-201, 2005
  PubMed
  
  
• Non-classical protein secretion in bacteria
  Bendtsen J, Kiemer L, Fausboll A, Brunak S, BMC Microbiol, 5,58, 2005
  PubMed
  
  
• Identification and analysis of 21 novel disease-causing amino acid substitutions in the conserved part of ATP7A
  Moller LB, Bukrinsky JT, Molgaard A, Paulsen M, Lund C, Tumer Z, Larsen S, Horn N, Hum Mutat, 26, 84-93, 2005
  PubMed
  
  
• The design and implementation of the immune epitope database and analysis resource
  Peters B, Sidney J, Bourne P, Bui HH, Buus S, Doh G, Fleri W, Kronenberg M, Kubo R, Lund O, Nemazee D, Ponomarenko JV, Sathiamurthy M, Schoenberger SP, Stewart S, Surko P, Way S, Wilson S, Sette A, Immunogenetics, 57, 326-36, 2005
  PubMed
  
  
• Crystal ball. Systems biology: in the broadest sense of the word
  Ussery DW, de Lichtenberg U, Jensen LJ, Environmental Microbiology, 7, 482-83, 2005
  PubMed
  
  
• A Systems Biology Investigation and Comparison of the Cell Cycle in Eukaryotic Cells
  Jensen TS, Ph.D. thesis, 2005
  
  
• Systems Biology of the Eukaryotic Cell Cycle
  de Lichtenberg U, Ph.D. thesis, 2005
  
  
• Prediction and Analysis of Protein Motifs
  Kiemer L, Ph.D. thesis, 2005
  
  
• An integrative approach to CTL epitope prediction: A combined algorithm integrating MHC class I binding, TAP transport
  Larsen MV, Lundegaard C, Lamberth K, Buus S, Brunak S, Lund O, Nielsen M, Eur J Immunol,35, 2295-2303, 2005
  PubMed
  
  
• Limited Inter- and Intra-patient Sequence Diversity of the Genetic Lineage A human metapneumovirus fusion gene
  Winther TN, Madsen CD, Pedersen AG, von Linstow ML, Eugen-Olsen J, Hogh B, Virus Genes, 31, 89-97, 2005
  PubMed PDF
  
  
• Characterization of rotavirus strains in a Danish population: high frequency of mixed infections and diversity within the VP4 gene of P [8] strains
  Fischer TK, Eugen-Olsen J, Pedersen AG, Molbak K, Bottiger B, Rostgaard K, Nielsen NM, J Clin Microbiol, 43, 1099-104, 2005
  PubMed PDF
  
  
• OligoWiz 2.0 - Integrating sequence feature annotation into the design of microarray probes
  Wernersson R, Nielsen HB, Nucleic Acids, 33, 611-5, 2005
  PubMed
  
  
• The MAP kinase substrate MKS1 is a regulator of plant defense responses
  Andreasson E, Jenkins T, Brodersen P, Thorgrimsen S, Petersen NH, Zhu S, Qiu JL, Micheelsen P, Rocher A, Petersen M, Newman MA, Nielsen HB, Hirt H, Somssich I, Mattsson O, Mundy J, EMBO Journal, 24, 2579-89, 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
  
  
• FeatureExtract--extraction of sequence annotation made easy
  Wernersson R, Nucleic Acids Res, 33(Web Server issue), W567-9, 2005
  PubMed
  
  
• Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing
  Wernersson R, Schierup MH, Jorgensen FG, Gorodkin J, Panitz F, Staerfeldt HH, Christensen OF, Mailund T, Hornshoj H, Klein A, Wang J, Liu B, Hu S, Dong W, Li W, Wong GK, Yu J, Wang J, Bendixen C, Fredholm M, Brunak S, Yang H, Bolund L, BMC Genomics, 6, 70, 2005
  PubMed
  
  
• Implementation of a gene expression index cal-culation method based on the PDNN model
  Nielsen HB, Gautier L, Knudsen S, Bioinformatics, 1;21, 687-8, 2005
  PubMed
  
  
• Comparison of computational methods for the identification of cell cycle-regulated genes
  de Lichtenberg U, Jensen LJ, Fausboll A, Jensen TS, Bork P, Brunak S, Bioinformatics, 1;21, 1164-71, 2005
  PubMed
  
  
• The genome of the protist parasite Entamoeba histolytica
  Loftus B, Anderson I, Davies R, Alsmark UC, Samuelson J, Amedeo P, Roncaglia P, Berriman M, Hirt RP, Mann BJ, Nozaki T, Suh B, Pop M, Duchene M, Ackers J, Tannich E, Leippe M, Hofer M, Bruchhaus I, Willhoeft U, Bhattacharya A, Chillingworth T, Churcher C, Hance Z, Harris B, Harris D, Jagels K, Moule S, Mungall K, Ormond D, Squares R, Whitehead S, Quail MA, Rabbinowitsch E, Norbertczak H, Price C, Wang Z, Guillen N, Gilchrist C, Stroup SE, Bhattacharya S, Lohia A, Foster PG, Sicheritz-Pontén T, Weber C, Singh U, Mukherjee C, El-Sayed NM, Petri WA Jr, Clark CG, Embley TM, Barrell B, Fraser CM, Hall N, Nature, 24;433, 865-8, 2005
  PubMed
  
  
• The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage
  Nielsen M, Lundegaard C, Lund O, Kesmir C, Immunogenetics, 57, 33-41, 2005
  PubMed
  
  
• The Immune Epitope Database and Analysis Resource: From Vision to Blueprint
  Peters B, Sidney J, Bourne P, Bui HH, Buus S, Doh G, Fleri W, Kronenberg M, Kubo R, Lund O, Nemazee D, Ponomarenko JV, Sathiamurthy M, Schoenberger S, Stewart S, Surko P, Way S, Wilson S, Sette A, PLoS Biol, 3, 91, 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
  
  
• Genome Update: proteome comparisons
  Binnewies TT, Hallin PF, Staerfeldt HH, Ussery DW, Microbiology, 151, 1-4, 2005
  PubMed
  
  
• Genome update: 2D clustering of bacterial genomes
  Willenbrock H, Binnewies TT, Hallin PF, Ussery DW, Microbiology, 151, 333-6, 2005
  PubMed
  
  
• Genome update: base skews in 200+ bacterial chromosomes
  Hallin PF, Nielsen N, Devine KM, Binnewies TT, Willenbrock H, Ussery DW, Microbiology, 151, 633-7, 2005
  PubMed
  
  
• Lid L11 of the glutamine amidotransferase domain of CTP synthase mediates allosteric GTP activation of glutaminase activity
  Willemoës M, Mølgaard A, Johansson E, Martinussen J, FEBS Journal, 272, 856-64, 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

• Det vi spiser påvirker vores immunforsvar – men hvordan?
  Christensen HR, Kjaer TMR, Brix S, Frokiaer H, Dansk Kemi, 84:26-27 (2004), 2004
  
  
• Immune response in mice to ingested soya protein: antibody production, oral tolerance and maternal transfer
  Christensen HR, Brix S, Frøkiær H, British J Nutr, 91:725-732 (2004), 2004
  
  
• Lipopolysaccharide contamination of beta-lactoglobulin affects the immune response against intraperitoneally and orally administrated antigen
  Brix S, Kjær TMR, Barkholt V, Frøkiær H, Int Arch Allergy Immunol, 135:216-220 (2004), 2004
  
  
• Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins
  Diella F, Cameron S, Gemünd C, Linding R, Via A, Kuster B, Sicheritz-Pontén T, Blom N, Gibson TJ, BMC Bioinformatics. Jun 22;5:79, 2004
  PubMed
  
  
• DNA bendability and Nucleosome positioning in transcriptional regulation
  Dlakic M, Brunak S, Ussery DW, DNA Conformation in Transcription, chapter 14, 2004
  
  
• Transcriptional profiling of extracellular amino acid in Saccharomyces cerevisiae and the role of St1p and Stp2p
  Eckert-Boulet N, Nielsen PS, Friis C, dos Santos MM, Nielsen J, Kielland-Brandt MC, Regenberg B, Yeast, 21, 634-48, 2004
  PubMed
  
  
• Biological Sequence Analysis of Archeal Genomes
  Skovgaard M, Ph.D. thesis, 2004
  
  
• Analysis and Prediction of Translocation Signals in Eukaryotes and Prokaryotes
  Bendtsen JD, Ph.D. thesis, 2004
  
  
• Integrative Approaches to the Analysis of Microarrays Expression Data: Application to High-density nucleotide Arrays
  Gautier L, Ph.D. thesis, 2004
  
  
• Distribution and characterization of staphylococcal interspersed repeat units (SIRUs) and potential use for strain differentiation
  Hardy KJ, Ussery DW, Oppenheim BA, Hawkey PM, Microbiology, 150, 4045-52, 2004
  PubMed
  
  
• Structure-function analysis of the human sialyltransferase ST3Gal I: role of n-glycosylation and a novel conserved sialylmotif
  Jeanneau C, Chazalet V, Auge C, Soumpasis DM, Harduin-Lepers A, Delannoy P, Imberty A, Breton C, J Biol Chem, 2;279, 13461-8, 2004
  PubMed
  
  
• QSPR models for various physical properties of carbohydrates based on molecular mechanics and quantum chemical calculations
  Dyekjaer JD, Jonsdottir SO, Carbohydr Res, 22;339, 269-80, 2004
  PubMed
  
  
• ShcA regulates neurite outgrowth stimulated by neural cell adhesion molecule but not by fibroblast growth factor 2: evidence for a distinct fibroblast growth factor receptor response to neural cell adhesion molecule activation
  Hinsby AM, Lundfald L, Ditlevsen DK, Korshunova I, Juhl L, Meakin SO, Berezin V, Bock E, J Neurochem, 91, 694-703, 2004
  PubMed
  
  
• Definition of supertypes for HLA molecules using clustering of specificity matrices
  Lund O, Nielsen M, Kesmir C, Pedersen AG, Lundegaard C, Worning P, Sylvester-Hvid C, Lamberth K, Roder G, Justesen S, Buus S, Brunak S, Immunogenetics, 55, 797-810, 2004
  PubMed PDF
  
  
• Genome update: correlation of bacterial genomic properties
  Hallin PF, Coenye T, Binnewies TT, Jarmer H, Staerfeldt HH, Ussery DW, Microbiology, 150, 3899-903, 2004
  PubMed
  
  
• Identification of a core set of genes that signifies pathways underlying cardiac hypertrophy
  Strøm CC, Kruhøffer M, Knudsen S, Stensgaard-Hansen F, Jonassen TE, Ørntoft TF, Haunsø S, Sheikh SP, Comparative and Functional Genomics 5, 459-470, 2004
  
  
• 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
  
  
• Genome Update: DNA repeats in bacterial genomes
  Ussery DW, Binnewies TT, Gouveia-Oliveira R, Jarmer H, Hallin PF, Microbiology 150, 3519-21, 2004
  PubMed
  
  
• Genome Update: alignment
  Ussery DW, Jensen MS, Poulsen TR, Hallin PF, Microbiology 150, 2491-3, 2004
  PubMed
  
  
• NetAcet: prediction of N-terminal acetylation sites
  Kiemer L, Bendtsen JB, Blom N, Bioinformatics, 1;21, 1269-70, 2004
  PubMed
  
  
• Chromatin architecture and gene expression in Escherichia coli
  Willenbrock H, Ussery DW, Genome Biology, 5, 252, 2004
  PubMed
  
  
• Genome update: chromosome atlases
  Hallin PF, Binnewies TT, Ussery DW, Microbiology, 150, 3091-3, 2004
  PubMed
  
  
• Complete DNA sequence of the linear mitochondrial genome of the pathogenic yeast Candida parapsilosis
  Nosek J, Novotna M, Hlavatovicova Z, Ussery DW, Fajkus J, Tomaska L, Molecular Genetics Genomics, 272, 173-80, 2004
  PubMed
  
  
• Genome update: promoter profiles
  Ussery DW, Tindbaek N, Hallin PF, Microbiology, 150, 2791-3, 2004
  PubMed
  
  
• Genome update: alignment of bacterial chromosomes
  Ussery DW, Jensen MS, Poulsen TR, Hallin PF, Microbiology, 150, 2491-3, 2004
  PubMed
  
  
• Genome Update: annotation quality in sequenced microbial genomes
  Ussery DW, Hallin PF, Microbiology, 150, 2015-7, 2004
  PubMed
  
  
• CBS genome atlas database: a dynamic storage for bioinformatic results and sequence data
  Hallin PF, Ussery DW, Bioinformatics, 12;20, 3682-6, 2004
  PubMed
  
  
• MHC Class I Epitope Binding Prediction Trained on Small Data Sets
  Lundegaard C, Nielsen M, Lamberth K, Worning P, Sylvester-Hvid C, Søren Buus, Brunak S, Lund O, Lecture Notes in Computer Science, vol 3239, proceeding of ICARIS 2004, 217-225, 2004
  Abstract from Springer-Verlag
  
  
• Arabidopsis VARIEGATED 3encodes a chloroplasttargeted, zinc-finger protein required for chloroplast and palisade cell development
  Næsted H, Holm A, Jenkins T, Bjørn Nielsen H, Harris CA, Beale MH, Andersen M, Mant A, Scheller H, Camara B, Mattsson O, Mundy J, Journal of Cell Science, 117, 4807-4818, 2004
  PubMed
  
  
• Implementation of a gene expression index calculatation method based on the PDNN model
  Bjørn Nielsen H, Gautier L, Knudsen S, Bioinformatics, 1;21, 687-8, 2004
  PubMed
  
  
• Analysis and prediction of leucine-rich nuclear export signals
  La Cour T, Kiemer L, Mølgaard A, Gupta R, Skriver K, Brunak S, Protein Engineering Design and Selection, 17, 527-36, 2004
  PubMed
  
  
• Predicting protein structure classes from function predictions
  Sommer I, Rahnenfuhrer J, Domingues FS, de Lichtenberg U, Lengauer T, Bioinformatics, 20,770-6, 2004
  PubMed
  
  
• Feature-based prediction of non-classical and leaderless protein secretion
  Bendtsen JD, Jensen LJ, Blom N, Von Heijne G, Brunak S, Protein 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
  
  
• Genome Update: tRNAs in sequenced microbial genomes
  Ussery DW, Hallin PF, Lagesen K, Wassenaar TM, Microbiology, 150, 1603-6, 2004
  PubMed
  
  
• Genome update: rRNAs in sequenced microbial genomes
  Ussery DW, Hallin PF, Lagesen K, Coenye T, Microbiology, 150, 1113-5, 2004
  PubMed
  
  
• TXTGate: profiling gene groups with text-based information
  Glenisson P, Coessens B, Van Vooren S, Mathys J, Moreau Y, De Moor B, Genome Biology, 5, 43, 2004
  PubMed
  
  
• Comprehensive analysis of the base composition around the transcription start site in Metazoa
  Aerts S, Thijs G, Dabrowski M, Moreau Y, De Moor B, BMC Genomics, 1;5, 34, 2004
  PubMed
  
  
• Prediction of immunophenotype, treatment response, and relapse in childhood acute lymphoblastic leukemia using DNA microarrays
  Willenbrock H, Juncker AS, Schmiegelow K, Knudsen S, Ryder LP, Leukemia, 18, 1270-7, 2004
  PubMed
  
  
• The transcriptional activation program of human neutrophils in skin lesions supports their important role in wound healing
  Theilgaard-Monch K, Knudsen S, Follin P, Borregaard N, Journal of Immunology, 172, 7684-93, 2004
  PubMed
  
  
• Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence
  Blom N, Sicheritz-Ponten T, Gupta R, Gammeltoft S, Brunak S, Proteomics, 4, 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
  
  
• Crystal packing in two pH-dependent crystal forms of rhamnogalacturonan acetylesterase
  Mølgaard A, Larsen S, Acta Crystallogr D Biol Crystallogr, 60, 472-8, 2004
  PubMed
  
  
• Using literature and data to learn Bayesian networks as clinical models of ovarian tumors
  Antal P, Fannes G, Timmerman D, Moreau Y, De Moor B, Artificial intelligence in medicine, 30, 257-81, 2004
  PubMed
  
  
• A first glimpse into the pattern and scale of gene transfer in Apicomplexa
  Huang J, Mullapudi N, Sicheritz-Ponten T, Kissinger JC, International Journal of Parasitology, 34, 265-74, 2004
  PubMed
  
  
• Genome Update: AT content in sequenced prokaryotic genomes
  Ussery DW, Hallin PF, Microbiology, 150, 749-52, 2004
  PubMed
  
  
• Development of in vitro transposon assisted signal sequence trapping and its use in screening Bacillus halodurans C125 and Sulfolobus solfataricus P2 gene libraries
  Becker F, Schnorr K, Wilting R, Tolstrup N, Bendtsen JD, Olsen PB, Journal of Microbiological Methods, 57, 123-33, 2004
  PubMed
  
  
• Structure-function analysis of the human sialyltransferase ST3Gal I
  Jeanneau C, Chazalet V, Auge C, Soumpasis DM, Harduin-Lepers A, Delannoy P, Imberty A, Breton C, Journal of Biological Chemistry, 279, 13461-8, 2004
  PubMed
  
  
• Genome Update: length distributions of sequenced prokaryotic genomes
  Ussery DW, Hallin PF, Microbiology, 150, 513-16, 2004
  PubMed
  
  
• Heterozygote advantage fails to explain the high degree of polymorphism of the MHC
  De Boer RJ, Borghans JA, Van Boven M, Kesmir C, Weissing FJ, Immunogenetics, 55, 725-31, 2004
  PubMed
  
  
• affy--analysis of Affymetrix GeneChip data at the probe level
  Gautier L, Cope L, Bolstad BM, Irizarry RA, Bioinformatics, 20, 307-315, 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
  
  
• Genome Update: 161 prokaryotic genomes sequenced, and counting
  Ussery DW, Microbiology, 150, 261-263, 2004
  PubMed
  
  
• Prediction of proprotein convertase cleavage sites
  Duckert P, Brunak S, Blom N, Protein Engineering, Design & Selection, 17, 107-112, 2004
  
  
• Global regulation of virulence and the stress response by CsrA in the highly adapted human gastric pathogen Helicobacter pylori
  Barnard FM, Loughlin MF, Fainberg HP, Messenger MP, Ussery DW, Williams P, Jenks PJ, Molecular Microbiology, 51,15-32, 2004
  PubMed
  
  

2003

• Pedersen SB, Bovetto L, Fritsche R, Barkholt V, Frøkiaer H
  Immunostimulatory potential of beta-lactoglobulin preparations: Effects caused by endotoxin contamination, J Allergy Clin Immunol, 112:1216-1222 (2003), 2003
  
  
• Analysis of Gene Expression and Regulatory Networks
  Friis C, Ph.D. thesis, 2003
  
  
• Microarray Data Analysis
  Nielsen HB, Ph.D. thesis, 2003
  
  
• Characterization of incompletely typed rotavirus strains from Guinea-Bissau: identification of G8 and G9 types and a high frequency of mixed infections
  Fischer TK, Page NA, Griffin DD, Eugen-Olsen J, Pedersen AG, Valentiner-Branth P, Mølbak K, Sommerfelt H, Nielsen NM, Virology, 311, 125-33, 2003
  PubMed PDF
  
  
• Modeling of the phase equilibria of polystyrene in methylcyclohexane with semi-empirical quantum mechanical methods I
  Wilczura-Wachnik H, Jonsdottir SO, J Mol Model, 9, 108-13, 2003
  PubMed
  
  
• EasyGene - – a prokaryotic gene finder that ranks ORFs by statistical significance
  Larsen TS, Krogh A, BMC Bioinformatics, 3;4, 21, 2003
  PubMed
  
  
• Bioinformatic analysis of functional differences between the immunoproteasome and the constitutive proteasome
  Kesmir C, van Noort V, de Boer RJ, Hogeweg P, Immunogenetics, 55, 437-49, 2003
  PubMed
  
  
• MUTAGEN: Multi-User Tool for Annotating GENomes
  Brugger K, Redder P, Skovgaard M, Bioinformatics, 19, 2480-1, 2003
  PubMed
  
  
• The sigma54 regulon (sigmulon) of Pseudomonas putida
  Cases I, Ussery DW, de Lorenzo V, Environmental Microbiology, 5, 1281-93, 2003
  PubMed
  
  
• Selecting Informative Data for Developing Peptide-MHC Binding Predictors Using a Query by Committee Approach
  Christensen JK, Lamberth K, Nielsen M, Lundegaard C, Worning P, Lauemøller SL, Buus S, Brunak S, Lund O, Neural Computation, 15, 2931-42, 2003
  PubMed
  
  
• The Plasmid Genome Database
  Molbak L, Tett A, Ussery DW, Wall K, Turner S, Bailey M, Field D, Microbiology, 149, 3043-3045, 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
  
  
• Genomic characteristics of the Campylobacter fetus sap island
  Zheng-Chao Tu, Ussery DW, Pride DT, Blaser MJ, Genome Letters, 2, 34-40, 2003
  Genome Letters website
  
  
• GenePublisher: Automated analysis of DNA microarray data
  Knudsen S, Workman C, Sicheritz-Ponten T, Friis C, Nucleic Acids Res, 31, 3471-76, 2003
  PubMed
  
  
• Sequence analysis of three mitochondrial DNA molecules reveals interesting differences among Saccharomyces yeasts
  Langkjær RB, Casaregola S, Ussery DW, Gaillardin C, Piskur J, Nucleic Acids Res, 31, 3081-91, 2003
  PubMed
  
  
• Strand misalignments lead to quasipalindrome correction
  van Noort V, Worning P, Ussery DW, Rosche WA, Sinden RR, Trends Genet, 19, 365-9, 2003
  PubMed
  
  
• Optimization and immune recognition of multiple novel conserved HLA-A2, human immunodeficiency virus type 1-specific CTL epitopes
  Corbet S, Nielsen HV, Vinner L, Lauemøller S, Therrien D, Tang ST, Kronborg G, Mathiesen L, Chaplin P, Brunak S, Buus S, Fomsgaard A, J Gen Virol, 84, 2409-2421, 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
  
  
• Plasmodium falciparum merozoite surface protein 1
  Hoessli DC, Poincelet M, Gupta R, Ilangumaran S, Nasir-ud-Din, Eur J Biochem., 270, 366-75, 2003
  PubMed
  
  
• RevTrans: multiple alignment of coding DNA from aligned amino acid sequences
  Wernersson R, Pedersen AG, Nucleic Acids Res., 31, 3537-9, 2003
  PubMed PDF
  
  
• Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays
  Nielsen HB, Wernersson R, Knudsen S, Nucleic Acids Res.,31, 3491-6, 2003
  PubMed
  
  
• Classification of Dukes´ B and C colorectal cancers using expression arrays
  Frederiksen CM, Knudsen S, Laurberg S, Ørntoft TF, Journal of Cancer Research and Clinical Oncology, 129,263-271, 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
  
  
• RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box
  Petersen L, Larsen TS, Ussery DW, On SL, Krogh A, J Mol Biol., 326, 1361-72, 2003
  PubMed
  
  
• Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome
  Jensen LJ, Skovgaard M, Sicheritz-Ponten T, Jørgensen MK, Lundegaard C, Pedersen CC, Petersen N, Ussery D, BMC Genomics, 4, 12, 2003
  PubMed
  
  
• Reliable prediction of T-cell epitopes using neural networks with novel sequence representations
  Nielsen M, Lundegaard C, Worning P, Lauemøller SL, Lamberth K, Buus S, Brunak S, Lund O, Protein 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

• Genmanipuleret virus angriber kræftceller
  Hansen DA, Larsen DH, Jakobsen RK, Information, 08-26 - s. 6, 2002
  bibliotek.dk
  
  
• Web-based Tools for Vaccine Design
  Lund O, Nielsen M, Kesmir C, Christensen JK, Lundegaard C, Worning P, Brunak S, HIV Molecular Immunology, pp. 45-51, 2002
  
  
• Prediction of protein function from sequence derived protein features
  Jensen LJ, Ph.D. thesis, 2002
  
  
• Gene and motif finding in prokaryotic DNA using hidden Markov models
  Larsen TS, Ph.D. thesis, 2002
  
  
• Phylogenetic and Functional Analysis of the Bacteriophage P1 Single-Stranded DNA-Binding Protein
  Bendtsen JD, Nilsson AS, Lehnherr H, Journal of Virology, 76, 9695-9701, 2002
  PubMed
  
  
• Comparative Genomics of Pseudomonas aeruginosa PAO1 and Pseudomonas putida KT2440: Orthologs, Codon Usage, REP Elements and Oligonucleotide Motif Signatures
  Weinel C, Ussery DW, Ohlsson H, Sicheritz-Ponten T, Kiewitz C, Tümmler B, Genome Letters, 1, 175-187, 2002
  Genome Letters website
  
  
• Hyperstructures, genome analysis and I-cells
  Amar P, Ballet P, Barlovatz-Meimon G, Benecke A, Bernot G, Bouligand Y, Bourguine P, Delaplace F, Delosme JM, Demarty M, Fishov I, Fourmentin-Guilbert J, Fralick J, Giavitto JL, Gleyse B, Godin C, Incitti R, Kepes F, Lange C, Le Sceller L, Loutellier C, Michel O, Molina F, Monnier C, Natowicz R, Norris V, Orange N, Pollard H, Raine D, Ripoll P, Rouviere-Yaniv J, Saier M Jr, Soler P, Tambourin P, Thellier M, Tracqui P, Ussery D, Vincent JC, Vannier JP, Wiggins P, Zemirline A, vActa Biotheor, 50, 357-73, 2002
  PubMed
  
  
• Roles of PucR, GlnR, and TnrA in regulating expression of the Bacillus subtilis ure P3 promoter
  Brandenburg JL, Wray LV Jr, Beier L, Jarmer H, Saxild HH, Fisher SH, J Bacteriol, 184, 6060-4, 2002
  PubMed
  
  
• 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
  
  
• DNA Microarray analysis of fim mutations in Escherichia coli
  Schembri MA, Ussery D, Workman C, Hasman H, Klemm P, Molecular Genetics and Genomics, 267, 721-729, 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
  
  
• Mean-field approaches to independent component analysis
  Højen-Sørensen PA, Winther O, Hansen LK, Neural Comput., 14, 889-918, 2002
  
  
• Avoiding cross hybridization by choosing nonredundant targets on cDNA arrays
  Nielsen HB, Knudsen S, Bioinformatics, 18, 321-322, 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
  
  
• Gene expression analysis and gene regulation: from DNA microarrays to comparative genomics
  Workman C, Ph.D. thesis, 2002
  
  
• Inheritance and organisation of the mitochondiral genome differ between two Saccharomyces
  Petersen RF, Langkjær RB, Hvidfeldt J, Gartner J, Palmen W, Ussery DW, Piskur J, J. Mol. Biol., 318, 627-636, 2002
  PubMed
  
  
• Continuum secondary structure captures protein flexibility
  Anderson CAF, Palmer AG, Brunak S, Structure, 10,175-184, 2002
  PubMed
  
  
• Visualisation and Significance of DNA Structural Motifs in the Campylobacter jejuni genome
  Petersen L, On SLW, Ussery D, Genome Letters, 1, 16-25, 2002
  
  
• Transcription Analysis of the Bacillus subtilis PucR Regulon and Identification of a cis-Acting Sequence Required PucR-Regulated Expression of Genes Involved in Purine Catabolism
  Beier L, Nygaard P, Jarmer H, Saxild HH, J. Bacteriol.,184, 3232-3241, 2002
  PubMed
  
  
• Transcriptome analysis documents induced competence of Bacillus subtilis during nitrogen limiting conditions
  Jarmer H, Berka R, Knudsen S, Saxild HH, FEMS Microbiology letters, 206, 197-200, 2002
  PubMed
  
  
• The genome sequence of Schizosaccharomyces pombe
  Wood V, Gwilliam R, Rajandream M-A, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, Baker S, Basham D, Bowman S, Brooks K, Brown D, Brown S, Chillingworth T, Churcher C, Collins M, Connor R, Cronin A, Davis P, Feltwell T, Fraser A, Gentles S, Goble A, Hamlin N, Harris D, Hidalgo J, Hodgson G, Holroyd S, Hornsby T, Howarth S, Huckle EJ, Hunt S, Jagels K, James K, Jones L, Jones M, Leather S, McDonald S, McLean J, Moule S, Mungall K, Murphy L, Niblett D, Odell C, Oliver K, O'Neil S, Pearson D, Quail MA, Rabbinowitsch E, Rutherford K, Rutter S, Saunders D, Seeger K, Sharp S, Skelton J, Simmonds M, Squares R, Squares S, Stevens K, Taylor K, Taylor RG, Walsh S, Warren T, Whitehead S, Woodward J, Volckaert G, Aert R, Robben J, Grymonprez B, Weltjens I, Vanstreels E, Rieger M, Schäfer M, Muller-Auer S, Gabel C, Fuchs M, Fritzc C, Holzer E, Moestl D, Hilbert H, Borzym K, Langer I, Beck A, Lehrach H, Reinhardt R, Pohl TM, Eger P, Zimmermann W, Wedler H, Wambutt R, Purnelle B, Goffeau A, Cadieu E, Dréano S, Gloux S, Lelaure V, Mottier S, Galibert F, Aves SJ, Xiang Z, Hunt C, Moore K, Hurst SM, Lucas M, Rochet M, Gaillardin C, Tallada VA, Garzon A, Thode G, Daga RR, Cruzado L, Jimenez J, Sanchez M, del Rey F, Dominguez A, Revuelta JL, Moreno S, Armstrong J, Forsburg S, Cerrutti L, Lowe T, McCombie WR, Paulsen I, Potashkin J, Shpakovski GV, Ussery D, Barrell BG, Nurse P, Nature, 415, 871-880, 2002
  PubMed
  
  
• Evaluation of potential regulatory elements identified as DNase I hypersensitive sites in the CFTR gene
  Phylactides M, Rowntree R, Nuthall H, Ussery D, Wheeler A, Harris A, Eur. J. Biochem, 269, 553-559, 2002
  PubMed
  
  
• Variety identification of wheat using mass spectrometry with neural networks and the influence of mass spectra processing prior to neural network analysis
  Aagaard Sørensen H, Sperotto MM, Petersen M, Kesmir C, Radzikowski L, Jacobsen S, Søndergaard I, Rapid Comm. Mass Spectrom., 16, 1232-1237, 2002
  PubMed
  
  
• Reproducibility of transcriptome analyses using oligonucleotide microarrays: an interlaboratory comparison of chemostat cultures of Saccharomyces cerevisiae
  Piper M, Daran-Lapujade P, Bro C, Regenberg B, Knudsen S, Nielsen J, Pronk J, Journal of Biological Chemistry, 277, 37001-37008, 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

• Evolutionary and immunological implications of contemporary HIV-1 variation
  Korber B, Gaschen B, Yusim K, Thakallapally R, Kesmir C, Detours V, Br. Med Bull., 58, 19-42, (review), 2001
  
  
• Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes
  Krogh A, Larsson B, von Heijne G, Sonnhammer ELL, J. Mol. Biol., 305, 567-580, 2001
  
  
• A phylogenomic approach to microbial evolution
  Sicheritz-Pontén T, Andersson SGE, Nucleic Acids Res., 29, 545-552, 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
  
  
• Protein secondary structure: category assignment and predictability
  Andersen CAF, Bohr H, Brunak S, FEBS Letters, 507, 6-1, 2001
  
  
• 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
  
  
• 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
  
  
• 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
  
  
• 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
  
  
• Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18
  Parkhill J, Dougan G, James KD, Thomson NR, Pickard D, Wain J, Churcher C, Mungall KL, Bentley SD, Holden MT, Sebaihia M, Baker S, Basham D, Brooks K, Chillingworth T, Connerton P, Cronin A, Davis P, Davies RM, Dowd L, White N, Farrar J, Feltwell T, Hamlin N, Haque A, Hien TT, Holroyd S, Jagels K, Krogh A, Larsen TS, Leather S, Moule S, O\'Gaora P, Parry C, Quail M, Rutherford K, Simmonds M, Skelton J, Stevens K, Whitehead S, Barrell BG, Nature, 413, 848-852, 2001
  
  
• 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
  
  
• 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
  
  
• Proceedings of ISMB
  Brunak S, Krogh A (eds.), Bioinformatics, 17, 2001
  
  
• Identification of gene expression patterns in superficial and invasive human bladder cancer
  Thykjaer T, Workman C, Kruhoffer M, Demtroder K, Wolf H, Andersen LD, Frederiksen CM, Knudsen S, Ørntoft TF, Cancer Res., 61,2492-2499, 2001
  
  
• Definition of the Bacillus subtilis PurR operator sequence using genetic and bioinformatic tools and expansion of the PurR regulon with glyA, guaC, pbuG, xpt-pbuX, yqhZ-folD and pbuO
  Saxild HH, Bruntedt K, Nielsen KI, Jarmer H, Nygaard P, J. Bacteriol., 183, 6175-6183, 2001
  
  
• Enrichment of regulatory signals in conserved non-coding genomic sequence
  Levy S, Hannenhalli S, Workman C, Bioinformatics, 17, 871-877, 2001
  
  
• On the estimation of number of events required for saturation mutagenesis of large genomes
  Phogat SK, Gupta R, Burma PK, Sen K, Pental D, Curr. Sci., 80, 823-824, 2001
  
  
• ISMB2001 - Proceedings for the Ninth international Conference on Intelligent Systems for Molecular Biology
  Brunak S, Gallison F, Gribskov M, Krogh A, Pedersen AG, Rouze P, Stormo G, Tramontano A (eds.), Bioinformatics, 17, Suppl. 1, 2001
  TOC
  
  
• Prediction of glycosylation sites in proteomes: from post-translational modifications to protein function
  Gupta R, Ph.D. thesis, 2001
  
  
• Protein Structure and the Diversity of Hydrogen Bonds
  Andersen CAF, Ph.D. thesis, 2001
  
  
• The Stealth Creationists
  Ussery DW, Skeptic, 8, 72-74, 2001
  
  
• Orphan protein function and its relation to glycosylation
  Gupta R, Jensen LJ, Brunak S, Ernst Schering Research Foundation Proceedings, 38, Chapter 13, Springer-Verlag, 2001
  
  

2000

• Kan mælkeproteiner styrke vores immunforsvar?
  Brix S, Barkholt V, Frokiaer H, Mælkeritidende, 13/14:364-366 (2000)., 2000
  
  
• Caleosins: Ca2+-binding proteins associated with lipid bodies
  Næsted H, Frandsen GI, Jauh G, Hernandez-Pinzon I, Nielsen HB, Murphy DJ, Rogers JC, Mundy J, Plant Molecular Biology (2000) 44: 463–476, 2000
  PubMed Relevant URL
  
  
• Promiscuous and specific phospholipid binding by domains in ZAC, a membrane-associated Arabidopsis protein with an ARF GAP zinc finger and a C2 domain
  Jensen RB, Lykke-Andersen K, Frandsen GI, Nielsen HB, Haseloff J, Jespersen HM, Mundy J, Skriver K, Plant Mol Biol (2000) Dec;44(6):799, 2000
  PubMed Relevant URL
  
  
• In vivo protection of nigral dopamine neurons by lentiviral gene transfer of the novel GDNF-family member neublastin/artemin
  Rosenblad C, Gronborg M, Hansen C, Blom N, Meyer M, Johansen J, Dago L, Kirik D, Patel UA, Lundberg C, Trono D, Bjorklund A, Johansen TE, Mol Cell Neurosci, 15, 199-214 (Erratum in: Mol Cell Neurosci 2001, 18, 332-3), 2000
  PubMed
  
  
• Identifying cytotoxic T cell epitopes from genomic and proteomic information: "The human MHC project"
  Lauemøller SL, Kesmir C, Corbet SL, Fomsgaard A, Holm A, Claesson MH, Brunak S, Buus S, Rev. 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
  
  
• 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
  
  
• 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
  
  
• Using database matches with HMMgene for automated gene detection in Drosophila
  Krogh A, Genome Res., 10, 523-528, 2000
  
  
• Arabidopsis MAP Kinase 4 Negatively Regulates Systemic Acquired Resistance
  Petersen M, Brodersen P, Naested H, Andreasson E, Lindhart U, Johansen B, Nielsen HB, Lacy M, Austin MJ, Parker JE, Sharma SB, Klessig DF, Martienssen R, Mattsson O, Jensen AB, Mundy J, Cell,103, 1111-1120, 2000
  
  
• Efficient Identification and Analysis of Substructures in Proteins Using the Kappa-Tau Framework: Left Turns and Helix c-cap Motifs
  Soumpasis DM, Strahm MC, J. Biomol. Struc. Dyn., 17, 965-979, 2000
  
  
• Visualization of pathogenicity regions in bacteria
  Friis C, Jensen LJ, Ussery DW, Genetica, 108, 47-51, 2000
  
  
• 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 PDF
  
  
• Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation
  Jensen LJ, Knudsen S, Bioinformatics 16, 326-333, 2000
  
  
• The frequency of mutators in populations of Escherichia coli
  Boe L, Danielsen M, Knudsen S, Petersen JB, Maymann J, Jensen PR, Mutat. Res., 448, 47-55, 2000
  
  
• A Classification of Possible Routes of Darwinian Evolution
  Thornhill RH, Ussery DW, J. Theor. Biol., 203, 111-116, 2000
  
  
• 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
  
  
• 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
  
  
• 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
  
  
• Improving the odds in discriminating "drug-like" from "non drug-like" compounds
  Frimurer TM, Bywater R, Nærum L, Nørskov Lauritsen L, Brunak S, J. Chem. Inf. Comp. Sci., 40, 1315-1324, 2000
  
  

1999

• From sequence to sorting: Prediction of signal peptides
  Nielsen H, PhD thesis, 1999
  
  
• Fagre Nye Robotter
  Schou T, Dagbladet Information, 5 March, 1999
  
  
• ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites
  Emanuelsson O, Nielsen H, von Heijne G, Protein Science., 8, 978-984, 1999
  
  
• A mathematical model on germinal center kinetics and termination
  Kesmir C, De Boer RJ, J. Immunol., 163(5), 2463-2469, 1999
  
  
• Identification of wheat varieties using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry and an artificial neural network
  Bloch HA, Kesmir C, Petersen M, Jacobsen S, Sondergaard II, Rapid Commun Mass Spectrom., 13, 1535-1539, 1999
  
  
• No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution
  Workman C, Krogh A, Nucleic Acids Res., 27, 4816-4822, 1999
  
  
• Competition between Sec- and TAT-dependent protein translocation in Escherichia coli
  Cristóbal S, de Gier J-W, Nielsen H, von Heijne G, EMBO Journal, 18, 2982-2990, 1999
  
  
• Sequence and structure-based prediction of eukaryotic protein phosphorylation sites
  Blom N, Gammeltoft S, Brunak S, J. Mol. Biol., 294, 1351-1362, 1999
  
  
• Three views of microbial genomes
  Jensen LJ, Friis C, Ussery DW, Res. Microbiol., 150, 773-777, 1999
  
  
• Structural Basis for Triplet Repeat Disorders: A Computational Analysis
  Baldi P, Brunak S, Chauvin Y, Pedersen AG, Bioinformatics, 15, 918-929, 1999
  PubMed PDF
  
  
• The biology of eukaryotic promoter prediction - a review
  Pedersen AG, Baldi P, Chauvin Y, Brunak S, Comp Chem, 23, 191-207, 1999
  PubMed PDF
  
  
• Modeling regulatory networks with weight matrices
  Weaver D, Workman C, Stormo GD, Proceedings of The Pacific Symposium on Biocomputing (PSB'99), 112-123, 1999
  
  
• 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
  
  
• Characterization of enzymatically induced aggregation of Casein icelles in natural concentration by in situ static light scattering and ultra low shear viscosimetry
  Lehner D, Worning P, Fritz G, Ogendal L, Bauer R, Glatter O, J. Colloid Interface Sci., 213, 445-456, 1999
  
  
• Measures on Hidden Markov Models
  Lyngsø RB, Pedersen CNS, Nielsen H, BRICS Report Series, RS-99-6, February, 1999
  
  
• Scanning the available Dictyostelium discoideum proteome for O-linked GlcNAc glycosylation sites using neural networks
  Gupta R, Jung E, Gooley AA, Williams KL, Brunak S, Hansen J, Glycobiology, 9, 1009-1022, 1999
  
  
• MatrixPlot: visualizing sequence constraints
  Gorodkin J, Stærfeldt HH, Lund O, Brunak S, Bioinformatics, 15 769-770, 1999
  
  
• Nosocomial HIV-transmission in an outpatient clinic detected by epidemiological and phylogenetic analyses
  Katzenstein TL, Jørgensen LB, Permin H, Hansen J, Nielsen C, Machuca R, Gerstoft J, AIDS, 13, 1737-1744, 1999
  
  
• 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
  
  
• Metrics and Similarity Measures for Hidden Markov Models
  Lyngsø RB, Pedersen CNS, Nielsen H, Proceedings of the seventh international conference on Intelligent Systems for Molecular Biology (ISMB '99), AAAI Press, 178-186, 1999
  
  
• Promoter 2.0: for the Recognition of PolII Promoter Sequences and
  Knudsen S, Bioinformatics, 15, 356-361, 1999
  
  
• Hidden neural networks
  Krogh A, Riis SK, Neural Comput., 11, 541-563, 1999
  
  
• Environmental Influences on DNA Curvature
  Ussery DW, Higgins CF, Bolshoy A, J. Biomol. Struct. Dyn., 16, 811-824, 1999
  
  
• 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
  
  
• 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
  
  
• A Biochemist's Response to the Biochemical Challenge to Evolution
  Ussery DW, Bios, 70, 40-45, 1999
  
  
• PhosphoBase, a database of phosphorylation sites: release 2.0
  Kreegipuu A, Blom N, Brunak S, Nucleic Acids Res., 27, 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 PDF
  
  
• Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
  Cole ST et al (Krogh A), Nature, 393, 537-544, 1998
  
  
• The effect of the lacY gene on the induction of IPTG inducible promoters, studied in Eschericia coli and Pseudomonas fluorescens
  Hansen LH, Knudsen S, Sorensen SJ, Curr. Microbiol., 36, 341-347, 1998
  
  
• 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 PDF
  
  
• DNA: Structure and Function
  Sinden RR, Pearson CE, Potaman VN, Ussery DW, in R.D. Verma (ed.), ``Advances in Genome Biology'', 5, 1-141, 1998
  
  
• Gene finding: putting the parts together
  Krogh A, in M.J. Bishop (ed.), ``Guide to Human Genome Computing'', Academic Press, 261-274, 1998
  
  
• An Introduction to Hidden Markov Models for Biological Sequences
  Krogh A, in S.L. Salzberg, D.B. Searls and S. Kasif (eds.), ``Computational Methods in Molecular Biology'', Elsevier, 45-63, 1998
  
  
• Prediction of signal peptides and signal anchors by a hidden Markov model
  Nielsen H, Krogh A, Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB98), 122-130, 1998
  
  
• A hidden Markov model for predicting transmembrane helices in protein sequences
  Sonnhammer ELL, von Heijne G, Krogh A, Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB98), 175-182, 1998
  
  
• 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 PDF
  
  
• Statistical analysis of protein kinase specificity determinants
  Kreegipuu A, Blom N, Brunak S, Järv J, FEBS Letters, 430, 45-50, 1998
  
  
• Comparisons of DNA mediated immunization procedures to surface glycoproteins of Human Immunodeficiency Virus type 1 and Hepatitis B virus
  Fomsgaard A, Vedel Nielsen H, Johansson K, Nielsen C, Machuca R, Bruun L, Hansen J, Buus S, APMIS, 106, 636-646, 1998
  
  
• Improved humoral and cellular immune responses against the gp120 V3 loop of HIV-1 following genetic immunization with a chimeric DNA vaccine encoding the V3 inserted into the Hepatitis B surface antigen (HBsAg)
  Fomsgaard A, Vedel Nielsen H, Johansson K, Nielsen C, Machuca R, Bruun L, Hansen J, Buus S, Scand. J. Immunol., 47, 289-295, 1998
  
  
• PhosphoBase: a database of phosphorylation sites
  Blom N, Kreegipuu A, Brunak S, Nucleic Acids Res., 26, 384-386, 1998
  
  
• 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
  
  
• 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
  
  

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
  
  
• 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
  
  
• Finding the most significant common sequences and structure motifs in a set of RNA sequences
  Gorodkin J, Heyer LJ, Stormo GD, Nucleic Acids Res., 25, 3724-3732, 1997
  
  
• 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
  
  
• Hidden neural networks: a framework for HMM/NN hybrids
  Riis SK, Krogh A, Proceedings of ICASSP '97, 4, IEEE, New York, 3233-3236, 1997
  
  
• Hierarchical organization of aggregated protein molecules
  Bohr H, Kühle A, Sørensen AH, Bohr J, Zeitschrift f. Physik D, 40, 513-515, 1997
  
  
• The implication of topology for protein structure and aggregation
  Bohr J, Bohr H, Zeitschrift f. Physik D, 40, 186-189, 1997
  
  
• Towards a classification of protein folds
  Bohr H, Lindgård PA, Phys. Rev. E, 56, 4497, 1997
  
  
• Packing of protein structures in clusters with magic numbers
  Lindgård PA, Bohr H, Zeitschrift f. Physik D, 40, 236-239, 1997
  
  
• Density functional and neural network analysis of hydration effects and spectroscopic and structural correlations in small peptides and amino acids
  Bohr H, Jalkanen K, Suhai S, in Theoretical and Computational Methods in Genome Research, S. Suhaí (ed.), Plenum Press, N.Y., 255-278, 1997
  
  
• An update of the DEF database of protein fold class predictions
  Reczko M, Karras D, Bohr H, Nucleic Acids Res., 25, 235, 1997
  
  
• 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
  
  
• Coherent topological phenomena in protein folding
  Bohr H, Brunak S, Bohr J, Folding & Design, 2, 15-18, 1997
  
  
• Enhancement of the nucleosomal pattern in sequences of lower complexity
  Bolshoy A, Shapiro K, Trifonov EN, Ioshikhes I, Nucleic Acids Res., 25, 3248-3254, 1997
  
  
• 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
  
  
• Prediction of N-terminal protein sorting signals
  Claros MG, Brunak S, von Heijne G, Curr. Opin. Struct. Biol., 7, 394-398, 1997
  
  
• Relation between phylogeny of African green monkey CD4 genes and their respective Simian Immunodeficiency Virus genes
  Fomsgaard A, Muller-Trutwin M, Diop O, Hansen J, Mathiot C, Barre-Sinoussi F, Allen JS, J. Med. Primatol., 26, 120-128, 1997
  
  
• Kissing loops hide premature termination codons in pre-mRNA of selenoprotein genes and in genes containing programmed ribosomal frameshifts
  Knudsen S, Brunak S, RNA, 3, 697-701, 1997
  
  
• Finding Common Sequence and Structure Motifs in a Set of RNA Sequences
  Gorodkin J, Heyer LJ, Stormo G, Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology (ISMB97), 120-123, 1997
  
  
• Two Methods for Improving Performance of a HMM and their Application for Gene Finding
  Krogh A, Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology (ISMB97), 179-186, 1997
  
  
• Neural Network Prediction of Translation Initiation Sites in Eukaryotes: Perspectives for EST and Genome analysis
  Pedersen AG, Nielsen H, Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology (ISMB97), 226-233, 1997
  PubMed PDF
  
  
• 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
  
  
• Molecular Wring Resonances in Chain Molecules
  Bohr H, Brunak S, Bohr J, Bioelectromagnetics, 18, 187-189, 1997
  
  
• Protein Folding and Wring Resonances
  Bohr J, Bohr H, Brunak S, Biophys. Chem., 63, 97-105, 1997
  
  
• Non-linear backpropagation: doing back-propagation without derivatives of the activation function
  Hertz JA, Krogh A, Lautrup B, Lehmann T, IEEE Transactions on Neural Networks, 8, 1321-1327, 1997
  
  
• 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
  
  
• 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

• 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
  
  
• Relationship between protein structure and geometrical constraints
  Lund O, Hansen J, Brunak S, Bohr J, Protein Sci., 5, 2217-2225, 1996
  
  
• Magic numbers in protein structures
  Lindgård PA, Bohr H, Phys. Rev. Lett., 77, 779-782, 1996
  
  
• 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
  
  
• 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 PDF
  
  
• 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
  
  
• 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
  
  
• 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
  
  
• 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
  
  
• Update on protein structure prediction: results of the 1995 IRBM workshop
  Hubbard T, Tramontano A, Hansen J, Vinals C, Fjellstrom O, Ribas de Pouplana L, the rest of the workshop team, Folding and Design, 1, R55-R63, (Review), 1996
  
  
• The gntP Gene of Escherichia coli Involved in Gluconate Uptake
  Klemm P, Tong S, Nielsen H, Conway T, J. of Bacteriol, 178, 61-67, 1996
  
  
• Cleaning the GenBank Arabidopsis thaliana data set
  Korning PG, Hebsgaard SM, Rouzé P, Brunak S, Nucleic Acids Res., 24, 316-320, 1996
  
  

1995

• Prediction of hypervariable CDR-H3 loop structures in antibodies
  Reczko M, Martin ACR, Bohr H, Suhai S, Protein Eng., 8, 389-395, 1995
  
  
• Increased adhesion as a mechanism of antibody-dependent and antibody-independent complement-mediated enhancement of human immunodeficiency virus infection
  Lund O, Hansen J, Sørensen AM, Mosekilde E, Nielsen JO, Hansen J-ES, J. Virol., 69, 1995
  
  
• Receptor Function of CD4 Structures from African Green Monkey and Pig-Tail Macaque for Simian Immunodeficiency Virus, SIVsm, SIVagm, and Human Immunodeficiency Virus Type-1
  Fomsgaard A, Johnson PR, Nielsen C, Novembre FJ, Hansen J, Goldstein S, Hirsch VM, Viral Immunol., 8, 121-133, 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
  
  
• Pruning of a large network by optimal brain damage and surgeon: An example from biological sequence analysis
  Tolstrup N, Int. J. Neural Sys., 6, 31-42, 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
  
  
• How many protein fold classes are to be found?
  Lindgård PA, Bohr H, in Protein folds -- a distance-based approach, H Bohr and S Brunak (eds.), 98-102, CRC Press, 1995
  
  
• Investigations of Escherichia coli promoter sequences with artificial neural networks: New signals discovered upstream of the transcriptional startpoint
  Pedersen AG, Engelbrecht J, Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology (ISMB95), AAAI Press, 292-299, 1995
  PubMed PDF
  
  
• 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
  
  
• Analysis of Eukaryotic Promoter Sequences reveals a systematically occurring CT-signal
  Larsen NI, Engelbrecht J, Brunak S, Nucleic Acids Res., 23, 1223-1230, 1995
  
  
• 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
  
  

1994

• Structure and geometry of proteins and membranes: a physical view
  Bohr H, 100 pp. Lecture notes for College in biophysics: experimental and theoretical aspects of biomolecules, International Center for Theoretical Physics, Trieste, Italien, 26/9 - 14/10, 1994
  
  
• Glycosylation and protein conformation
  Clausen H, Hansen JE, Lund O, Rapacki K, Clausen H, Mosekilde E, Nielsen JO, Hansen JES, in Protein structure by distance analysis, H. Bohr and S. Brunak (eds.), 247-254, IOS Press & Ohmsha, 1994
  
  
• Recurrent networks for protein distance matrix prediction
  Bohr H, Reczko M, in Protein structure by distance analysis, H. Bohr and S. Brunak (eds.), 87-97, IOS Press & Ohmsha, 1994
  
  
• Growth of domains in distance geometry through protein folding
  Bohr H, Wang J, Wolynes P, in Protein Structure by Distance Analysis, eds. H. Bohr and S. Brunak, 98-109, IOS Press & Ohmsha, 1994
  
  
• Viscous trees and Voronoi structure formation in expanding systems
  Bohr J, Brunak S, Nørretranders T, Europhysics Lett., 25, 245-251, 1994
  
  
• Neural network model of the genetic code is strongly correlated to the GES scale of amino acid transfer free energies
  Tolstrup N, Toftgaard J, Engelbrecht J, Brunak S, J. Mol. Biol., 243, 816-820, (Cover illustration), 1994
  
  
• Correlation between protein secondary structure and the mRNA nucleotide sequence
  Brunak S, Engelbrecht J, Kesmir C, in ``Protein Structure by Distance Analysis'', H. Bohr and S. Brunak (eds.), 327-334, IOS Press, Amsterdam, 1994
  
  
• The DEF data base of sequence based protein fold class predictions
  Reczko M, Bohr H, Nucleic Acids Res., 22, 3616-3619, 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

• Predictive Recognition of Signal Peptides Using Artificial Neural Networks
  Nielsen H, M.Sc. thesis, 1993
  
  
• Protein structures from distance inequalities
  Bohr J, Bohr H, Brunak S, Cotterill RMJ, Fredholm H, Lautrup B, Petersen SB, J. Mol. Biol., 231, 861-869, 1993
  
  
• Computational Biosequence Analysis by Neural Networks
  Brunak S, Engelbrecht J, Proceedings of the "Workshop on Physics and Computation, PhysComp 92", October 2-4, 1992, Dallas, Texas, 111-115, IEEE Computer Society Press, 1993
  
  
• Doing sequence analysis by inspecting the order in which neural networks learn
  Brunak S, Proceedings of ``Computation of Biomolecular Structures - Achievements, Problems and Perspectives'', March 5-10, 1990, eds: D.M. Soumpasis & T.M. Jovin, 43-54, Springer Verlag, Berlin, 1993
  
  

1992

• Multiple Alignment Using Simulated Annealing: Branch Point Definition in Human mRNA Splicing
  Lukashin AV, Engelbrecht J, Brunak S, Nucleic Acids Res. 20, 2511-2516, 1992
  
  
• G/C rich tract in 5' end of human introns
  Engelbrecht J, Knudsen S, Brunak S, J. Mol. Biol., 227, 108-113, 1992
  
  

1991

• Neural networks applied to protein structure
  Bohr H, Bohr J, Brunak S, Cotterill RMJ, Fredholm H, Lautrup B, Petersen SB, in ``Advances in Biomolecular Simulations'', AIP Conference proceedings 239, 293-310, 1991
  
  
• Non-linearities in training sets identified by inspecting the order in which neural networks learn
  Brunak S, in ``Neural Networks: from Biology to High Energy Physics'', Proceedings of the workshop held in Elba International Physics Center - Italy, June 5-14, 1991, eds. O. Benhar, C. Bosio, P. del Giudice and E. Tabet, 277-288, ETS Editrice, 1991
  
  
• Neural networks applied to the study of protein sequences and protein structures
  Fredholm H, Bohr H, Bohr J, Brunak S, Cotterill RMJ, Lautrup B, Petersen SB, Site-Directed Mutagenesis and Protein Engineering, ed. M.R. El-Gewely, Elsevier Science Publishers B.V., pages 41-46, 1991
  
  
• Prediction of human mRNA donor and acceptor sites from the DNA sequence
  Brunak S, Engelbrecht J, Knudsen S, J. Mol. Biol., 220, 49-65, 1991
  
  

1990

• Training neural networks to analyse biological sequences
  Petersen SB, Bohr H, Bohr J, Brunak S, Cotterill RMJ, Fredholm H, Lautrup B, Trends Biotechnol., 11, 304-308, 1990
  
  
• Neural Network Detects Errors in the assignment of pre-mRNA splice sites
  Brunak S, Engelbrecht J, Knudsen S, Nucleic Acids Res., 18, 4797-4801, 1990
  
  
• Cleaning up gene databases
  Brunak S, Engelbrecht J, Knudsen S, Nature, 343, 123, 1990
  
  
• A novel approach to prediction of the 3-dimensional structures of protein backbones by neural networks
  Bohr H, Bohr J, Brunak S, Cotterill RMJ, Fredholm H, Lautrup B, Petersen SB, FEBS Letters, 261, 43-46, 1990
  
  
• Analysis of the secondary structure of the human immunodeficiency virus (HIV) proteins p17, gp120 and gp41 by computer modelling based on neural network methods
  Adreassen H, Bohr H, Bohr J, Brunak S, Bugge T, Cotterill RMJ, Jacobsen C, Kusk P, Lautrup B, Petersen SB, Særmark T, Ulrich K, Journal of AIDS, 3, 615-622, 1990
  
  

1989

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

1988

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

Books

• Methods for building quantitative structure-activity relationship (QSAR) descriptors and predictive models for computer-aided design of antimicrobial peptides
  Taboureau O, Methods Mol Biol. 618:77-86, 2010
  PubMed
  
  
• Genome comparison of bacterial pathogens
  Wassenaar TM, Bohlin J, Binnewies TT, Ussery DW, chapter 1 in Genome Dynamics, volume 6 - Microbial Pathogenomics, (Karger AG publishers, Basel), 2009
  
  
• Tools for comparison of bacterial genomes
  Wassenaar TM, Binnewies TT, Hallin PF, Ussery DW, Microbiology of Hydrocarbons, Oils, Lipids, and Derived Compounds, (Springer-Verlag, Heidelberg, Germany), 2009
  
  
• The genus Burkholderia: analysis of 56 genomic sequences
  Ussery DW, Kiil K, Lagesen K, Sicheritz-Ponten T, Bohlin J, Wassenaar TM, Microbial Pathogenomics,Karger AG publishers, Basel, 2009
  PubMed
  
  
• COMPUTING FOR COMPARATIVE GENOMICS: Bioinformatics for Microbiologists
  Ussery DW, Borini S, Wassenaar TM, Springer, Series: Computational Biology , Vol. 8, 2008
  Springer, to be published in autumn 2008
  
  
• Genome Diversity of Pseudomonas aeruginosa
  Klockgether J, Würdemann D, Wiehlmann L, Binnewies TT, Ussery DW, Tümmler B, Chapter 2 in Pseudomonas: Genomics and Molecular Biology, (Edited by: Pierre Cornelis, Caister Academic Press, 2008), 2008
  Link to publisher
  
  
• Comparative Genomics of Pseudomonas
  Kiil K, Binnewies TT, Willenbrock H, Hansen SK, Yang L, Jelsbak L, Ussery DW, Friis C, Chapter 1 in Pseudomonas: Model Organism, Pathogen, Cell Factory, (Edited by: B. H. A. Rehm, Wiley-VCH, 2008), 2008
  Link to publisher
  
  
• Signal peptides and protein localization prediction
  Nielsen H, Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, M.J. Dunn, L.B. Jorde, P.F.R. Little, S. Subramaniam (eds.), Wiley, 2005
  
  
• Immunological Bioinformatics
  Lund O, Nielsen M, Lundegaard C, Kesmir C, Brunak S, MIT Press, 312 pages, 2005
  Details
  
  
• A Biologist's Guide to Analysis of DNA Microarray Data, 2nd edition
  Knudsen S, John Wiley & Sons, New York, 2004
  Details
  
  
• DNA Structure: A-, B-, and Z-DNA Families
  Ussery D, The Encyclopedia of Life Sciences, (Macmillan Publishers, London), 2002
  
  
• A Biologist's Guide to Analysis of DNA Microarray Data, 1st edition
  Knudsen S, John Wiley & Sons, New York, 2002
  Details
  
  
• Genome Sequence Databases
  Ussery DW, Brunak S, Encyclopedia of Genetics, S. Brenner and J.H. Miller (eds.), Academic Press, 2001
  
  
• DNA Denaturation
  Ussery DW, Encyclopedia of Genetics, S. Brenner and J.H. Miller (eds.), Academic Press, 2001
  
  
• Bidirectional Dynamics for Protein Secondary Structure Prediction
  Baldi P, Brunak S, Frasconi P, Pollastri G, Soda G, Sequence Learning - Paradigms, Algorithms, and Applications, R. Sun and C. Lee Giles (eds.), 80-104, Springer Verlag, 2001
  
  
• Bioinformatics: The Machine Learning Approach, 2nd edition
  Baldi P, Brunak S, MIT Press, 360 pages, 2001
  Details
  
  
• Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
  Durbin R, Eddy S, Krogh A, Mitchison GJ, Cambridge University Press, 350 pages, 1998
  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
  
  

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2008 (71)

2007 (73)

2006 (46)

2005 (50)

2004 and before (289)

Books (23)