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2014 (10) 2013 (10) 2012 (13) 2011 (9) 2010 (18) 2009 (5) 2008 and before (51) Books (1)


    Multiparametric bioinformatics distinguish the CD4/CD8 ratio as a suitable laboratory predictor of combined T cell pathogenesis in HIV infection.
    Buggert M, Frederiksen J, Noyan K, Svärd J, Barqasho B, Sönnerborg A, Lund O, Nowak P, Karlsson AC
    Journal of Immunology 2014 Mar 1;192(5):2099-108., 2014
    Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica.
    Leekitcharoenphon P, Nielsen EM, Kaas RS, Lund O, Aarestrup FM
    PLoS One. 2014 Feb 4;9(2):e87991., 2014
    Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli.
    Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, Aarestrup FM
    Journal of Clinical Microbiology. 2014 May;52(5):1501-10, 2014
    In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing
    Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O, Villa L, Møller Aarestrup F, Hasman H
    Antimicrobial Agents and Chemotherapy. 2014 Jul;58(7):3895-903., 2014
    Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.
    Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto JM, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Doré J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Léonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sørensen S, Tap J, Tims S, Ussery DW, Yamada T; MetaHIT Consortium, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD Nat Biotechnol
    Nature Biotechnology. 2014 Jul 6., 2014
    T-bet and Eomes Are Differentially Linked to the Exhausted Phenotype of CD8+ T Cells in HIV Infection
    Buggert M, Tauriainen J, Yamamoto T, Frederiksen J, Ivarsson MA, Michaëlsson J, Lund O, Hejdeman B, Jansson M, Sönnerborg A, Koup RA, Betts MR, Karlsson AC
    PLoS Pathogens 2014 Jul 17;10(7):e1004251, 2014
    NetFCM: A semi-automated web-based method for flow cytometry data analysis
    Frederiksen J, Buggert M, Karlsson AC, Lund O
    Cytometry A. 2014 Jul 18., 2014
    Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms.
    Kaas RS, Leekitcharoenphon P, Aarestrup FM, Lund O
    PLoS One. 2014 Aug 11;9(8):e104984, 2014
    MR1-restricted MAIT cells display ligand discrimination and pathogen selectivity through distinct T cell receptor usage
    Gold MC, McLaren JE, Reistetter JA, Smyk-Pearson S, Ladell K, Swarbrick GM, Yu YY, Hansen TH, Lund O, Nielsen M, Gerritsen B, Kesmir C, Miles JJ, Lewinsohn DA, Price DA, Lewinsohn DM
    Journal of Experimental Medicine. 2014 Jul 28;211(8):1601-10., 2014
    Benchmarking of Methods for Genomic Taxonomy.
    Larsen MV, Cosentino S, Lukjancenko O, Saputra D, Rasmussen S, Hasman H, Sicheritz-Pontén T, Aarestrup FM, Ussery DW, Lund O
    Journal of Clinical Microbiology. 2014 May;52(5):1529-39., 2014


    Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing.
    Zankari E, Hasman H, Kaas RS, Seyfarth AM, Agersø Y, Lund O, Larsen MV, Aarestrup FM
    Journal of Antimicrobial Chemotherapy. 2013 Apr;68(4):771-7., 2013
    PathogenFinder--distinguishing friend from foe using bacterial whole genome sequence data
    Cosentino S, Voldby Larsen M, Møller Aarestrup F, Lund O
    PLoS One. 2013 Oct 28;8(10):e77302., 2013
    Low-bandwidth and non-compute intensive remote identification of microbes from raw sequencing reads.
    Gautier L, Lund O
    PLoS One. 2013 Dec 31;8(12):e83784, 2013
    Targeting of conserved gag-epitopes in early HIV infection is associated with lower plasma viral load and slower CD4(+) T cell depletion.
    Perez CL, Milush JM, Buggert M, Eriksson EM, Larsen MV, Liegler T, Hartogensis W, Bacchetti P, Lund O, Hecht FM, Nixon DF, Karlsson AC
    AIDS Research and Human Retroviruses 29(3):602-12 doi:10.1089/AID.2012.0171, 2013
    Rapid whole genome sequencing for the detection and characterization of microorganisms directly from clinical samples.
    Hasman H, Saputra D, Sicheritz-Ponten T, Lund O, Svendsen CA, Frimodt-Møller N, Aarestrup FM
    Journal of Clinical Microbiology. 52(1):139-46 doi:10.1128/JCM.02452-13, 2013
    Evaluation of peptide selection approaches for epitope-based vaccine design
    Schubert B, Lund O, Nielsen M
    Tissue Antigens, 82: 243–251. doi: 10.1111/tan.12199, 2013
    Relevant URL
    NetMHCIIpan-3.0, a common pan-specific MHC class II prediction method including all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ
    Karosiene E, Rasmussen M, Blicher T, Lund O, Buus S, Nielsen M
    Immunogenetics 65(10):711-24 doi:10.1007/s00251-013-0720-y, 2013
    MHCcluster, a method for functional clustering of MHC molecules
    Thomsen MCF, Lundegaard C, Buus S, Lund O, Nielsen M
    Immunogenetics 65(9):655-65 doi:10.1007/s00251-013-0714-9, 2013
    Relevant URL
    SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments
    Jessen L, Hoof I, Lund O, Nielsen M
    Nucleic Acids Research 2013; doi: 10.1093/nar/gkt497, 2013
    Relevant URL
    Bioinformatics Identification of Antigenic Peptide: Predicting the Specificity of Major MHC Class I and II Pathway Players
    Lund O, Karosiene E, Lundegaard C, Larsen MV, Nielsen M
    Methods in Molecular Biology . 960:247-60 doi:10.1007/978-1-62703-218-6_19, 2013


    Multilocus sequence typing of total-genome-sequenced bacteria.
    Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Sicheritz-Pontén T, Ussery DW, Aarestrup FM, Lund O
    Journal of Clinical Microbiology 2012 Apr;50(4):1355-61., 2012
    Identification of a novel UTY-encoded minor histocompatibility antigen.
    Mortensen BK, Rasmussen AH, Larsen ME, Larsen MV, Lund O, Braendstrup P, Harndahl M, Rasmussen M, Buus S, Stryhn A, Vindeløv L
    Scandinavian Journal of Immunology . 2012 Aug;76(2):141-50., 2012
    Structural analysis of B-cell epitopes in antibody:protein complexes.
    Kringelum JV, Nielsen M, Padkjær SB, Lund O
    Molecular Immunology 2013 Jan;53(1-2):24-34, 2012
    Characterization of HIV-specific CD4+ T cell responses against peptides selected with broad population and pathogen coverage.
    Buggert M, Norström MM, Czarnecki C, Tupin E, Luo M, Gyllensten K, Sönnerborg A, Lundegaard C, Lund O, Nielsen M, Karlsson AC
    PLoS One. 2012;7(7):e39874, 2012
    The cancer exome generated by alternative mRNA splicing dilutes predicted HLA class I epitope density.
    Stranzl T, Larsen MV, Lund O, Nielsen M, Brunak S
    PLoS One. 2012;7(9):e38670, 2012
    Integrating genome-based informatics to modernize global disease monitoring, information sharing, and response.
    Aarestrup FM, Brown EW, Detter C, Gerner-Smidt P, Gilmour MW, Harmsen D, Hendriksen RS, Hewson R, Heymann DL, Johansson K, Ijaz K, Keim PS, Koopmans M, Kroneman A, Lo Fo Wong D, Lund O, Palm D, Sawanpanyalert P, Sobel J, Schlundt J
    Emerging Infectious Diseases. 2012 Nov;18(11):e1., 2012
    Reliable B cell epitope predictions: impacts of method development and improved benchmarking.
    Kringelum JV, Lundegaard C, Lund O, Nielsen M
    PLoS Comput Biol. 2012 Dec;8(12):e1002829., 2012
    Mycobacterium leprae virulence-associated peptides are indicators of exposure to M. leprae in Brazil, Ethiopia and Nepal.
    Bobosha K, Tang ST, van der Ploeg-van Schip JJ, Bekele Y, Martins MV, Lund O, Franken KL, Khadge S, Pontes MA, Gonçalves Hde S, Hussien J, Thapa P, Kunwar CB, Hagge DA, Aseffa A, Pessolani MC, Pereira GM, Ottenhoff TH, Geluk A
    Mem. Inst. Oswaldo Cruz:112-23 pii:S0074-02762012000900018, 2012
    Identification of acquired antimicrobial resistance genes
    Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, Aarestrup FM, Larsen MV
    Journal of Antimicrobial Chemotherapy. 67(11):2640-4 doi:10.1093/jac/dks261, 2012
    ChemProt-2.0: visual navigation in a disease chemical biology database
    Kim Kjærulff S, Wich L, Kringelum J, Jacobsen UP, Kouskoumvekaki I, Audouze K, Lund O, Brunak S, Oprea TI, Taboureau O
    Nucleic Acids Research. 41:D464-9 doi:10.1093/nar/gks1166, 2012
    Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach
    Andreatta M, Lund O, Nielsen M
    Bioinformatics 29(1):8-14 doi:10.1093/bioinformatics/bts621, 2012
    Relevant URL
    Immune epitope database analysis resource
    Kim Y, Ponomarenko J, Zhu Z, Tamang D, Wang P, Greenbaum J, Lundegaard C, Sette A, Lund O, Bourne PE, Nielsen M, Peters B
    PubMed, 2012
    Relevant URL
    Predictions versus high- throughput experiments in T-cell epitope discovery: competition or synergy?
    Lundegaard C, Lund O, Nielsen M
    Expert Rev. Vaccines 11(1), 43–54 (2012), 2012


    Immune system simulation online.
    Rapin N, Lund O, Castiglione F
    Bioinformatics. 2011 Jul 15;27(14):2013-4., 2011
    Human leukocyte antigen (HLA) class I restricted epitope discovery in yellow fever and dengue viruses: importance of HLA binding strength
    Lund O, Nascimento EJ, Maciel M Jr, Nielsen M, Larsen MV, Lundegaard C, Harndahl M, Lamberth K, Buus S, Salmon J, August TJ, Marques ET Jr
    PLoS One. 2011;6(10):e26494, 2011
    Porcine major histocompatibility complex (MHC) class I molecules and analysis of their peptide-binding specificities.
    Pedersen LE, Golde WT, Lund O, Nielsen M, Buus S
    Immunogenetics, 2011
    Machine learning competition in immunology - Prediction of HLA class I binding peptides
    Zhang GL6, Ansari HR, Bradley P, Cawley GC, Hertz T, Hu X, Jojic N, Kim Y, Kohlbacher O, Lund O, Lundegaard C, Magaret CA, Nielsen M, Papadopoulos H, Raghava GP, Tal VS, Xue LC, Yanover C, Zhu S, Rock MT, Crowe JE Jr, Panayiotou C, Polycarpou MM, Duch W, Brusic V
    J Immunol Methods., 2011
    NNAlign: A Web-Based Prediction Method Allowing Non-Expert End-User Discovery of Sequence Motifs in Quantitative Peptide Data
    Andreatta M, Schafer-Nielsen C, Lund O, Buus S, Nielsen M
    PLoS ONE 6(11): e26781. doi:10.1371/journal.pone.0026781, 2011
    An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia
    Rasmussen M, Guo X, Wang Y, Lohmueller KE, Rasmussen S, Albrechtsen A, Skotte L, Lindgren S, Metspalu M, Jombart T, Kivisild T, Zhai W, Eriksson A, Manica A, Orlando L, De La Vega F, Tridico S, Metspalu E, Nielsen K, Ávila-Arcos MA, Moreno-Mayar JV, Muller C, Dortch J, Gilbert MTP, Lund O, Wesolowska A, Karmin M, Weinert LA, Wang B, Li J, Tai S, Xiao F, Hanihara T, van Driem G, Jha AR, Ricaut FX, de Knijf P, Migliano AB, Gallego-Romero I, Kristiansen K, Lambert DM, Brunak S, Forster P, Brinkmann B, Nehlich O, Bunce M, Richards M, Gupta R, Bustamante CD, Krogh A, Foley RA, Lahr MM, Balloux F, Sichertitz-Pontén T, Villems R, Nielsen R, Jun W, Willerslev E
    Science 334(6052):94-8 doi:10.1126/science.1211177, 2011
    NetMHCcons: a consensus method for the major histocompatibility complex class I predictions
    Karosiene E, Lundegaard C, Lund O, Nielsen M
    Immunogenetics, 2011
    Relevant URL
    Genome-Based In Silico Identification of New Mycobacterium tuberculosis Antigens Activating Polyfunctional CD8+ T Cells in Human Tuberculosis
    Tang ST, van Meijgaarden KE, Caccamo N, Guggino G, Klein MR, van Weeren P, Kazi F, Stryhn A, Zaigler A, Sahin U, Buus S, Dieli F, Lund O, Ottenhoff TH
    The Journal of Immunology. 186(2):1068-80 doi:10.4049/jimmunol.1002212, 2011
    Bistability in autoimmune diseases
    Rapin N, Mosekilde E, Lund O
    Autoimmunity 44(4):256-60 doi:10.3109/08916934.2010.523233, 2011


    ImmunoGrid: towards agent-based simulations of the human immune system at a natural scale
    Halling-Brown M, Pappalardo F, Rapin N, Zhang P, Alemani D, Emerson A, Castiglione F, Duroux P, Pennisi M, Miotto O, Churchill D, Rossi E, Moss DS, Sansom CE, Bernaschi M, Lefranc MP, Brunak S, Lund O, Motta S, Lollini PL, Murgo A, Palladini A, Basford KE, Brusic V, Shepherd AJ
    Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences 368(1920):2799-815 doi:10.1098/rsta.2010.0067, 2010
    HLA class I binding 9mer peptides from influenza A virus induce CD4 T cell responses
    Wang M, Larsen MV, Nielsen M, Harndahl M, Justesen S, Dziegiel MH, Buus S, Tang ST, Lund O, Claesson MH
    PLoS ONE 5(5):e10533 doi:10.1371/journal.pone.0010533, 2010
    Plasmodium falciparum population dynamics in a cohort of pregnant women in Senegal
    Guitard J, Andersen P, Ermont C, Gnidehou S, Fievet N, Lund O, Deloron P, Ndam NT
    Malar. J. 9:165 doi:10.1186/1475-2875-9-165, 2010
    Identification of CD8+ T cell epitopes in the West Nile virus polyprotein by reverse-immunology using NetCTL
    Larsen MV, Lelic A, Parsons R, Nielsen M, Hoof I, Lamberth K, Loeb MB, Buus S, Bramson J, Lund O
    PLoS ONE 5(9):e12697 doi:10.1371/journal.pone.0012697, 2010
    MULTIPRED2: a computational system for large-scale identification of peptides predicted to bind to HLA supertypes and alleles
    Zhang GL, Deluca DS, Keskin DB, Chitkushev L, Zlateva T, Lund O, Reinherz EL, Brusic V
    Journal of Immunological Methods 374:53-61 doi:10.1016/j.jim.2010.11.009, 2010
    In Silico Prediction of Human Pathogenicity in the γ-Proteobacteria
    Andreatta M, Nielsen M, Møller Aarestrup F, Lund O
    PLoS ONE 5(10):e13680 doi:10.1371/journal.pone.0013680, 2010
    Read article
    Peptide binding predictions for HLA DR, DP and DQ molecules
    Wang P, Sidney J, Kim Y, Sette A, Lund O, Nielsen M, Peters B
    BMC Bioinformatics 11:568 doi:10.1186/1471-2105-11-568, 2010
    NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure
    Nielsen M, Justesen S, Lund O, Lundegaard C, Buus S
    Immunome Res 6:9 doi:10.1186/1745-7580-6-9, 2010
    State of the art and challenges in sequence based T-cell epitope prediction
    Lundegaard C, Hoof I, Lund O, Nielsen M
    Immunome Res:S3 doi:10.1186/1745-7580-6-S2-S3, 2010
    Insight into Antigenic Diversity of VAR2CSA-DBL5å Domain from Multiple Plasmodium falciparum Placental Isolates
    Gnidehou S, Jessen L, Gangnard S, Ermont C, Triqui C, Quiviger M, Guitard J, Lund O, Deloron P, Ndam NT
    PLoS ONE 5(10) doi:10.1371/journal.pone.0013105, 2010
    CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles
    Nielsen M, Lundegaard C, Lund O, Petersen TN
    Nucleic Acids Research. 38:W576-81 doi:10.1093/nar/gkq535, 2010
    Major histocompatibility complex class I binding predictions as a tool in epitope discovery
    Lundegaard C, Lund O, Buus S, Nielsen M
    Immunology 130(3):309-18 doi:10.1111/j.1365-2567.2010.03300.x, 2010
    MHC Class II epitope predictive algorithms
    Nielsen M, Lund O, Buus S, Lundegaard C
    Immunology 130(3):319-28 doi:10.1111/j.1365-2567.2010.03268.x, 2010
    Computational Immunology Meets Bioinformatics: The Use of Prediction Tools for Molecular Binding in the Simulation of the Immune System
    Rapin N, Lund O, Bernaschi M, Castiglione F
    PLoS ONE 5(4):e9862 doi:10.1371/journal.pone.0009862, 2010
    Read article
    The Degree of Predicted Minor Histocompatibility Antigen Mismatch Correlates with Poorer Clinical Outcome of Non-myeloablative Allogeneic Hematopoietic Cell Transplantation
    Larsen ME, Kornblit B, Larsen MV, Masmas TN, Nielsen M, Thiim M, Garred P, Stryhn A, Lund O, Buus S, Vindelov L
    Biol. Blood Marrow Transplant. 16(10):1370-81 doi:10.1016/j.bbmt.2010.03.022, 2010
    Interdisciplinary Analysis of HIV-Specific CD8+ T Cell Responses against Variant Epitopes Reveals Restricted TCR Promiscuity
    Hoof I, Pérez CL, Buggert M, Gustafsson RK, Nielsen M, Lund O, Karlsson AC
    The Journal of Immunology. 184(9):5383-91 doi:10.4049/jimmunol.0903516, 2010
    Limitations of Ab Initio Predictions of Peptide Binding to MHC Class II Molecules
    Zhang H, Wang P, Papangelopoulos N, Xu Y, Sette A, Bourne PE, Lund O, Ponomarenko J, Nielsen M, Peters B
    PLoS ONE 5(2):e9272 doi:10.1371/journal.pone.0009272, 2010
    The MHC motif viewer: a visualization tool for MHC binding motifs
    Rapin N, Hoof I, Lund O, Nielsen M
    Curr Protoc Immunol:Unit 18.17 doi:10.1002/0471142735.im1817s88, 2010


    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 25(10):1293-9 doi:10.1093/bioinformatics/btp137, 2009
    Systematic Characterization of Cellular Localization and Expression Profiles of Proteins Containing MHC Ligands
    Juncker AS, Larsen MV, Weinhold N, Nielsen M, Brunak S, Lund O
    /PLoS ONE/ ; 4(10): e7448. doi:10.1371/journal.pone.0007448, 2009
    An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction.
    Nielsen M, Lund O
    BMC bioinformatics, 2009
    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
    Clin. Exp. Immunol. 155(3):441-6 doi:10.1111/j.1365-2249.2008.03856.x, 2009
    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 doi:10.1007/s00251-008-0341-z, 2009


    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. 153(10):1833-44 doi:10.1007/s00705-008-0194-7, 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 60(11):633-43 doi:10.1007/s00251-008-0317-z, 2008
    MHC motif viewer
    Rapin N, Hoof I, Lund O, Nielsen M
    Immunogenetics 60(12):759-65 doi:10.1007/s00251-008-0330-2, 2008
    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. 4(7):e1000107 doi:10.1371/journal.pcbi.1000107, 2008
    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. 36:W513-8 doi:10.1093/nar/gkn254, 2008
    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. 36:W509-12 doi:10.1093/nar/gkn202, 2008
    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 24(11):1397-8 doi:10.1093/bioinformatics/btn128, 2008
    Humans with chimpanzee-like major histocompatibility complex-specificities control HIV-1 infection
    Hoof I, Kesmir C, Lund O, Nielsen M
    AIDS 22(11):1299-303 doi:10.1097/QAD.0b013e328302f39f, 2008
    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. 4(2):e42 doi:10.1371/journal.ppat.0040042, 2008
    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 3(3):e1831 doi:10.1371/journal.pone.0001831, 2008
    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
    The Journal of Immunology. 180(7):5092-100, 2008


    Modeling the adaptive immune system: predictions and simulations
    Lundegaard C, Lund O, Kesmir C, Brunak S, Nielsen M
    Bioinformatics 23(24):3265-75, 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 8:424, 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 8:238, 2007
    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 2(8):e796, 2007
    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. 20(2):75-82, 2007


    TAP-Independent MHC Class I Presentation
    Larsen MV, Nielsen M, Weinzierl A, Lund O
    Curr Immunol Rev, 2, 233-245, 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
    The validity of predicted T-cell epitopes
    Lundegaard C, Nielsen M, Lund O
    Trends Biotechnol. 24(12):537-8, 2006
    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 25(15):2823-31, 2006
    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
    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 Pathog. 2(11):e124, 2006
    Improved method for predicting linear B-cell epitopes
    Larsen JE, Lund O, Nielsen M
    Immunome Res 2:2, 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


    Selection of proteins for human MHC class II presentation
    Jiang L, Lund O, Tan JQ
    Cell. Mol. Immunol. 2(1):49-56, 2005
    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(5):326-36, 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(8):2295-303, 2005
    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
    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(3):e91, 2005


    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(12):797-810, 2004
    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
    Coronavirus 3CLpro proteinase cleavage sites: possible relevance to SARS virus pathology
    Kiemer L, Lund O, Brunak S, Blom N
    BMC Bioinformatics 5:72, 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(5):395-400, 2004
    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 20(9):1388-97, 2004


    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 Comput 15(12):2931-42, 2003
    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 Sci. 12(5):1007-17, 2003


    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 secondary structure at 80% accuracy
    Petersen TN, Lundegaard C, Nielsen M, Bohr H, Brunak S, Gippert GP, Lund O
    Proteins 41(1):17-20, 2000


    MatrixPlot: visualizing sequence constraints
    Gorodkin J, Stærfeldt HH, Lund O, Brunak S
    Bioinformatics 15(9):769-70, 1999
    Using Sequence Motifs for Enhanced Neural Network Prediction of Protein Distance Constraints
    Gorodkin J, Lund O, Andersen CA, Brunak S
    Proc Int Conf Intell Syst Mol Biol:95-105, 1999


    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(1):387-9, 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
    Glycoconj. J. 15(2):115-30, 1998


    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(11):1241-8, 1997
    O-glycbase version 2.0 - A revised database of O-glycosylated proteins
    Hansen JE, Lund O, Rapacki K, Brunak S
    Nucleic Acids Res. 25(1):278-82, 1997


    Relationship between protein structure and geometrical constraints
    Lund O, Hansen J, Brunak S, Bohr J
    Protein Sci. 5(11):2217-25, 1996
    Distance distributions in proteins: A six parameter representation
    Reese MG, Lund O, Bohr J, Bohr H, Hansen JE, Brunak S
    Protein Eng. 9(9):733-40, 1996
    Prediction of the secondary structure of HIV-1 gp120
    Hansen JE, Lund O, Nielsen JO, Brunak S, Hansen J-ES
    Proteins 25(1):1-11, 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


    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(4):2393-400, 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.:801-13, 1995


    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


    Immunological Bioinformatics
    Lund O, Nielsen M, Lundegaard C, Kesmir C, Brunak S
    MIT Press, 312 pages, 2005

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