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2013 (3) 2012 (2) 2011 (3) 2010 (8) 2009 (2) 2008 (5) 2007 and before (18) Books (1)

2013

    MHCcluster, a method for functional clustering of MHC molecules
    Thomsen M, Lundegaard C, Buus S, Lund O, Nielsen M
    Immunogenetics 65(9):655-65 doi:10.1007/s00251-013-0714-9, 2013
    PubMed
    Relevant URL
    In silico peptide-binding predictions of passerine MHC class I reveal similarities across distantly related species, suggesting convergence on the level of protein function
    Follin E, Karlsson M, Lundegaard C, Nielsen M, Wallin S, Paulsson K, Westerdahl H
    Immunogenetics 65(4):299-311 doi:10.1007/s00251-012-0676-3, 2013
    PubMed
    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 Mol. Biol. 960:247-60 doi:10.1007/978-1-62703-218-6_19, 2013
    PubMed

2012

    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

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
    Human Leukocyte Antigen (HLA) Class I Restricted Epitope Discovery in Yellow Fewer and Dengue Viruses: Importance of HLA Binding Strength.
    Lund O4, Nascimento EJM, Maciel M Jr, Nielsen M, Larsen MV, Lundegaard C, Harndahl M, Lamberth K, Buus S, Salmon J, August TJ, Marques Jr ETA
    PLoS ONE 6(10): e26494. doi:10.1371/journal.pone.0026494, 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

2010

    NetTurnP - Neural Network Prediction of Beta-turns by Use of Evolutionary Information and Predicted Protein Sequence Features
    Petersen B, Lundegaard C, Petersen TN
    PLoS ONE 5(11):e15079 doi:10.1371/journal.pone.0015079, 2010
    PubMed
    NetTurnP
    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
    PubMed
    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
    PubMed
    Mice, men and MHC supertypes
    Lundegaard C
    Expert Rev Vaccines 9(7):713-8 doi:10.1586/erv.10.76, 2010
    PubMed
    CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles
    Nielsen M, Lundegaard C, Lund O, Petersen TN
    Nucleic Acids Res. 38:W576-81 doi:10.1093/nar/gkq535, 2010
    PubMed
    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
    PubMed
    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
    PubMed
    NetCTLpan: pan-specific MHC class I pathway epitope predictions
    Stranzl T, Larsen MV, Lundegaard C, Nielsen M
    Immunogenetics 62(6):357-68 doi:10.1007/s00251-010-0441-4, 2010
    PubMed
    Read abstract

2009

    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. 9:51 doi:10.1186/1472-6807-9-51, 2009
    PubMed
    Pan-specific MHC class I predictors: A benchmark of HLA class I pan-specific prediction methods
    Zhang H, Lundegaard C, Nielsen M
    Bioinformatics 25(1):83-9 doi:10.1093/bioinformatics/btn579, 2009
    PubMed

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
    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. 4(7):e1000107 doi:10.1371/journal.pcbi.1000107, 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. 36:W513-8 doi:10.1093/nar/gkn254, 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. 36:W509-12 doi:10.1093/nar/gkn202, 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 24(11):1397-8 doi:10.1093/bioinformatics/btn128, 2008
    PubMed

2007

    Modeling the adaptive immune system: predictions and simulations
    Lundegaard C, Lund O, Kesmir C, Brunak S, Nielsen M
    Bioinformatics 23(24):3265-75, 2007
    PubMed
    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
    PubMed
    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
    PubMed
    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
    PubMed

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 25(15):2823-31, 2006
    PubMed

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
    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

2004

    Definition of supertypes for HLA molecules using clustering of specificity matrices
    Lund O, Nielsen M, Kesmir C, Pedersen AG, Lundegaard C, Worning P, Sylvester-Hvid C, Lamberth K, Roder G, Justesen S, Buus S, Brunak S
    Immunogenetics 55(12):797-810, 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
    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
    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 20(9):1388-97, 2004
    PubMed

2003

    Selecting Informative Data for Developing Peptide-MHC Binding Predictors Using a Query by Committee Approach
    Christensen JK, Lamberth K, Nielsen M, Lundegaard C, Worning P, Lauemøller SL, Buus S, Brunak S, Lund O
    Neural Comput 15(12):2931-42, 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(1):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 Sci. 12(5):1007-17, 2003
    PubMed

2002

    Web-based Tools for Vaccine Design
    Lund O, Nielsen M, Kesmir C, Christensen JK, Lundegaard C, Worning P, Brunak S
    HIV Molecular Immunology, pp. 45-51, 2002

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(1):17-20, 2000
    PubMed


Books

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

2013 (3) 2012 (2) 2011 (3) 2010 (8) 2009 (2) 2008 (5) 2007 and before (18) Books (1)