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2013
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
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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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
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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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
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, November 30, 2010 |
PubMed
NetTurnP
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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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Mice, men and MHC supertypes
Lundegaard C
Expert Rev Vaccines, 2010 |
PubMed
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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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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(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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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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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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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
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
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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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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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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
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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 3rd of September 2010 09:03:29 GMT |
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