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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
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ATAF1 transcription factor directly regulates abscisic acid biosynthetic gene NCED3 in Arabidopsis thaliana.
Jensen MK, Lindemose S, Masi Fd, Reimer JJ, Nielsen M, Perera V, Workman CT, Turck F, Grant MR, Mundy J, Petersen M, Skriver K
FEBS Open Bio. 2013, 2013 |
PubMed
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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. 2013 Jul 31., 2013 |
PubMed
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MHCcluster, a method for functional clustering of MHC molecules
Thomsen M, Lundegaard C, Buus S, Lund O, Nielsen M
Immunogenetics., 2013 |
PubMed
Relevant URL
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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
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MISTIC: mutual information server to infer coevolution
Simonetti FL, Teppa E, Chernomoretz A, Nielsen M, Buslje CM
Nucl. Acids Res. (2013), 2013 |
Relevant URL
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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. 2013 Jan 29, 2013 |
PubMed
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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. 2013, 2013 |
PubMed
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2012
Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach
Andreatta M, Lund O, Nielsen M
Bioinformatics. 2012 Oct 24. [Epub ahead of print], 2012 |
PubMed
Relevant URL
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Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction
Teppa E, Wilkins AD, Nielsen M, Marino Buslje C
BMC Bioinformatics. 2012 Sep 14;13(1):235. [Epub ahead of print], 2012 |
PubMed
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Identification of peptides from foot-and-mouth disease virus structural proteins bound by class I swine leukocyte antigen (SLA) alleles, SLA-1*0401 and SLA-2*0401
Pedersen LE, Harndahl M, Nielsen M, Patch JR, Jungersen G, Buus S, Golde WT
Anim Genet. 2012 Sep 18. doi: 10.1111/j.1365-2052.2012.02400.x. [Epub ahead of print], 2012 |
PubMed
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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
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Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion
Thomsen MCF, Nielsen M
Oxford Journals, 2012 |
Relevant URL
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Peptide-MHC class I stability is a better predictor than peptide affinity of CTL immunogenicity
Harndahl M, Rasmussen M, Roder G, Pedersen ID, Sørensen M, Nielsen M, Buus S
Wiley, 2012 |
Relevant URL
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Designing bovine T cell vaccines via reverse immunology
Nene V, Svitek N, Toye P, Golde WT, Barlow J, Harndahl M, Buus S, Nielsen M
Science Direct, 2012 |
Relevant URL
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Characterizing the binding motifs of 11 common human HLA-DP and HLA-DQ molecules using NNAlign
Andreatta M, Nielsen M
Immunology (publication ahead of print), 2012 |
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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 |
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2011
Induction of foot-and-mouth disease virus (FMDV) specific cytotoxic T cell killing by vaccination.
Patch JR, Pedersen LE, Toka FN, Moreas M, Grubman MJ, Nielsen M, Jungersen G, Buus S, Golde WT
Clin Vaccine Immunol.; 18(2):280-8., 2011 |
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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 |
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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 |
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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 |
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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 |
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Designing bovine T-cell vaccines via reverse immunology
Nene T, Svitek N, Toye P, Golde WT, Barlow J, Buus S, Nielsen M
In presss Ticks and Tick-Borne Diseases,, 2011 |
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NetMHCcons: a consensus method for the major histocompatibility complex class I predictions
Karosiene E, Lundegaard C, Lund O, Nielsen M
Immunogenetics, 2011 |
Relevant URL
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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, May 7, 2010 |
PubMed
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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, September 14, 2010 |
PubMed
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Structural Properties of MHC Class II Ligands, Implications for the Prediction of MHC Class II Epitopes
Jørgensen KW, Buus S, Nielsen M
PLoS One, 2010 |
Read article
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Induction of foot-and-mouth disease virus (FMDV) specific cytotoxic T cell killing by vaccination
Patch JR, Pedersen LE, Toka FN, Moreas M, Grubman MJ, Nielsen M, Jungersen G, Buus S, Golde WT
Clinical and Vaccine Immunology, December 22, 2010 |
PubMed
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In Silico Prediction of Human Pathogenicity in the γ-Proteobacteria
Andreatta M, Nielsen M, Møller Aarestrup F, Lund O
PLoS One, October 27, 2010 |
PubMed
Read article
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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, November 22, 2010 |
PubMed
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HLArestrictor-a tool for patient-specific predictions of HLA restriction elements and optimal epitopes within peptides
Erup Larsen M, Kloverpris H, Stryhn A, Koofhethile CK, Sims S, Ndung\'u T, Goulder P, Buus S, Nielsen M
Immunogenetics, Nov 16, 2010 |
PubMed
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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 Research, Nov 13, 2010 |
PubMed
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State of the art and challenges in sequence based T-cell epitope prediction
Lundegaard C, Hoof I, Lund O, Nielsen M
Immunome Research, Nov 3, 2010 |
PubMed
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Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic Residue Identification
Buslje CM, Teppa E, Doménico TD, Delfino JM, Nielsen M
PloS Computational Biology, 2010 |
PubMed
Read article
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CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles
Nielsen M, Lundegaard C, Lund O, Petersen TN
Nucleic Acids Research, 2010 |
PubMed
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Major histocompatibility complex class I binding predictions as a tool in epitope discovery
Lundegaard C, Lund O, Buus S, Nielsen M
Immunology, 2010 |
PubMed
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MHC Class II epitope predictive algorithms
Nielsen M, Lund O, Buus S, Lundegaard C
Immunology, 2010 |
PubMed
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NetCTLpan: pan-specific MHC class I pathway epitope predictions
Stranzl T, Larsen MV, Lundegaard C, Nielsen M
Immunogenetics, 2010 |
PubMed
Read abstract
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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, 2010 |
PubMed
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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
J Immunol, 2010 |
PubMed
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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. 17;5(2):e9272, 2010 |
PubMed
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The MHC motif viewer: a visualization tool for MHC binding motifs
Rapin N, Hoof I, Lund O, Nielsen M
Curr Protoc Immunol.Chapter 18:Unit18.17, 2010 |
PubMed
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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 |
PubMed
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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 |
PubMed
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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 |
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An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction.
Nielsen M, Lund O
BMC bioinformatics, 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
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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 |
PubMed
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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 |
PubMed
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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
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MHC motif viewer
Rapin N, Hoof I, Lund O, Nielsen M
Immunogenetics. 2008 Sep 3. [Epub ahead of print], 2008 |
PubMed
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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
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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
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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
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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
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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
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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
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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
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2007
Modeling the adaptive immune system: predictions and simulations
Lundegaard C, Lund O, Kesmir C, Brunak S, Nielsen M
Bioinformatics, 23:3265-75, 2007 |
PubMed
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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
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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
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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
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2006
TAP-Independent MHC Class I Presentation
Larsen MV, Nielsen M, Weinzierl A, Lund O
Curr Immunol Rev, 2, 233-245, 2006 |
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The validity of predicted T-cell epitopes
Lundegaard C, Nielsen M, Lund O
Trends Biotechnol., 24 (12), 537-8, 2006 |
PubMed
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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
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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
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Improved method for predicting linear B-cell epitopes
Larsen JE, Lund O, Nielsen M
Immunome Res, 2: 2, 2006 |
PubMed
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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
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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
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2004
Definition of supertypes for HLA molecules using clustering of specificity matrices
Lund O, Nielsen M, Kesmir C, Pedersen AG, Lundegaard C, Worning P, Sylvester-Hvid C, Lamberth K, Roder G, Justesen S, Buus S, Brunak S
Immunogenetics, 55, 797-810, 2004 |
PubMed
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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
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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
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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
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2003
Selecting Informative Data for Developing Peptide-MHC Binding Predictors Using a Query by Committee Approach
Christensen JK, Lamberth K, Nielsen M, Lundegaard C, Worning P, Lauemøller SL, Buus S, Brunak S, Lund O
Neural Computation, 15, 2931-42, 2003 |
PubMed
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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
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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 |
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2000
Prediction of protein secondary structure at 80% accuracy
Petersen TN, Lundegaard C, Nielsen M, Bohr H, Brunak S, Gippert GP, Lund O
Proteins, 41, 17-20, 2000 |
PubMed
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Books
Immunological Bioinformatics
Lund O, Nielsen M, Lundegaard C, Kesmir C, Brunak S
MIT Press, 312 pages, 2005 |
Details
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This file was last modified Friday 31st 2013f May 2013 08:37:15 GMT |
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