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Ole Lund

Research Profile

Chemicals & Drugs

Phenomena

Protein Binding

Genes & Molecular Sequences

Amino Acid Sequences

Concepts & Ideas

Occupations

Computational Biology

Activities & Behaviors

Procedures

Anatomy

T-Lymphocytes, Cytotoxic

Co-author Network

Publications

TOP 3
Ea Zankari; Yvonne Agersø; Henrik Hasman; Rolf Sommer Kaas; Mette Voldby Larsen; Ole Lund; Anne Mette Seyfarth; Frank M Aarestrup
Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing.
Ole Lund; Claus Lundegaard; Edita Karosiene; Mette Voldby Larsen; Morten Nielsen
Bioinformatics identification of antigenic peptide: predicting the specificity of major MHC class I and II pathway players.
Sonny Kim Kjærulff; Irene Kouskoumvekaki; Jens Kringelum; Ole Lund; Tudor I Oprea; Karine Audouze; Søren Brunak; Ulrik P Jacobsen; Louis Wich; Olivier Taboureau
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All Publications

2013: Ea Zankari; Yvonne Agersø; Henrik Hasman; Rolf Sommer Kaas; Mette Voldby Larsen; Ole Lund; Anne Mette Seyfarth; Frank M Aarestrup
Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing.
The Journal of antimicrobial chemotherapy 2013;68(4):771-7.
2013: Ole Lund; Claus Lundegaard; Edita Karosiene; Mette Voldby Larsen; Morten Nielsen
Bioinformatics identification of antigenic peptide: predicting the specificity of major MHC class I and II pathway players.
Methods in molecular biology (Clifton, N.J.) 2013;960():247-60.
2013: Sonny Kim Kjærulff; Irene Kouskoumvekaki; Jens Kringelum; Ole Lund; Tudor I Oprea; Karine Audouze; Søren Brunak; Ulrik P Jacobsen; Louis Wich; Olivier Taboureau
ChemProt-2.0: visual navigation in a disease chemical biology database.
Nucleic acids research 2013;41(Database issue):D464-9.
2013: Massimo Andreatta; Ole Lund; Morten Nielsen
Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach.
Bioinformatics (Oxford, England) 2013;29(1):8-14.
2013: Jens Vindahl Kringelum; Morten Nielsen; Søren Berg Padkjær; Ole Lund
Structural analysis of B-cell epitopes in antibody:protein complexes.
Molecular immunology 2013;53(1-2):24-34.
2012: Ea Zankari; Ole Lund; Simon Rasmussen; Martin Vestergaard; Frank M Aarestrup; Salvatore Cosentino; Henrik Hasman; Mette Voldby Larsen
Identification of acquired antimicrobial resistance genes.
The Journal of antimicrobial chemotherapy 2012;67(11):2640-4.
2012: B K Mortensen; A H Rasmussen; M Rasmussen; Anette Stryhn; P Braendstrup; Soren Buus; Mikkel Harndahl; M E Larsen; M V Larsen; Ole Lund; L Vindeløv
Identification of a novel UTY-encoded minor histocompatibility antigen.
Scandinavian journal of immunology 2012;76(2):141-50.
2012: Yohan Kim; Ole Lund; Claus Lundegaard; Morten Nielsen; Julia V Ponomarenko; Alessandro Sette; Dorjee Tamang; Peng Wang; Zhanyang Zhu; Philip Bourne; Jason Greenbaum; Bjoern Peters
Immune epitope database analysis resource.
Nucleic acids research 2012;40(Web Server issue):W525-30.
2012: Edita Karosiene; Ole Lund; Claus Lundegaard; Morten Nielsen
NetMHCcons: a consensus method for the major histocompatibility complex class I predictions.
Immunogenetics 2012;64(3):177-86.
2012: Jens Vindahl Kringelum; Ole Lund; Claus Lundegaard; Morten Nielsen
Reliable B cell epitope predictions: impacts of method development and improved benchmarking.
PLoS computational biology 2012;8(12):e1002829.
2012: Thomas Stranzl; Mette V Larsen; Ole Lund; Morten Nielsen; Søren Brunak
The cancer exome generated by alternative mRNA splicing dilutes predicted HLA class I epitope density.
PloS one 2012;7(9):e38670.
2011: Lasse Eggers Pedersen; Michael Rasmussen; William T Golde; Mikkel Harndahl; Kasper Lamberth; Ole Lund; Morten Nielsen; Soren Buus
Porcine major histocompatibility complex (MHC) class I molecules and analysis of their peptide-binding specificities.
Immunogenetics 2011;63(12):821-34.
2011: Nicolas Rapin; Erik Mosekilde; Ole Lund
Bistability in autoimmune diseases.
Autoimmunity 2011;44(4):256-60.
2011: Mingjun Wang; Sheila Tuyet Tang; Anette Stryhn; Sune Justesen; Mette V Larsen; Morten H Dziegiel; David M Lewinsohn; Soren Buus; Ole Lund; Mogens H Claesson
Identification of MHC class II restricted T-cell-mediated reactivity against MHC class I binding Mycobacterium tuberculosis peptides.
Immunology 2011;132(4):482-91.
2011: Sheila Tuyet Tang; Krista E van Meijgaarden; Nadia Caccamo; Giuliana Guggino; Michèl R Klein; Pascale van Weeren; Fatima Kazi; Anette Stryhn; Alexander Zaigler; Ugur Sahin; Søren Buus; Francesco Dieli; Ole Lund; Tom H M Ottenhoff
Genome-based in silico identification of new Mycobacterium tuberculosis antigens activating polyfunctional CD8+ T cells in human tuberculosis.
Journal of immunology (Baltimore, Md. : 1950) 2011;186(2):1068-80.
2011: Massimo Andreatta; Søren Buus; Ole Lund; Claus Schafer-Nielsen; Morten Nielsen
NNAlign: a web-based prediction method allowing non-expert end-user discovery of sequence motifs in quantitative peptide data.
PloS one 2011;6(11):e26781.
2011: Ole Lund; Claus Lundegaard; Milton Jr. Maciel; Thomas J August; Søren Buus; Mikkel Harndahl; Kasper Lamberth; Eduardo J M Nascimento; Morten Nielsen; Jérôme Salmon; Mette Voldby Larsen; Ernesto Marques
Human leukocyte antigen (HLA) class I restricted epitope discovery in yellow fewer and dengue viruses: importance of HLA binding strength.
PloS one 2011;6(10):e26494.
2010: Malene Erup Larsen; Brian Kornblit; Mette Voldby Larsen; Tania Nicole Masmas; Morten Nielsen; Martin Thiim; Peter Garred; Anette Stryhn; Ole Lund; Soren Buus; Lars Vindelov
Degree of predicted minor histocompatibility antigen mismatch correlates with poorer clinical outcomes in nonmyeloablative allogeneic hematopoietic cell transplantation.
Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation 2010;16(10):1370-81.
2010: Morten Nielsen; Claus Lundegaard; Ole Lund; Thomas Nordahl Petersen
CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles.
Nucleic acids research 2010;38(Web Server issue):W576-81.
2010: Claus Lundegaard; Ole Lund; Søren Buus; Morten Nielsen
Major histocompatibility complex class I binding predictions as a tool in epitope discovery.
Immunology 2010;130(3):309-18.
2010: Morten Nielsen; Ole Lund; Søren Buus; Claus Lundegaard
MHC class II epitope predictive algorithms.
Immunology 2010;130(3):319-28.
2010: Mark D Halling-Brown; Francesco Pappalardo; Nicolas Rapin; Ping Zhang; Davide Alemani; Andrew Emerson; Filippo Castiglione; Patrice Duroux; Marzio Pennisi; Olivo Miotto; Daniel Churchill; Elda Rossi; David S Moss; Clare E Sansom; Massimo Bernaschi; Marie-Paule Lefranc; Søren Brunak; Ole Lund; Santo Motta; Pier-Luigi Lollini; Annalisa Murgo; Arianna Palladini; Kaye E Basford; Vladimir Brusic; Adrian J Shepherd
ImmunoGrid: towards agent-based simulations of the human immune system at a natural scale.
Philosophical transactions. Series A, Mathematical, physical, and engineering sciences 2010;368(1920):2799-815.
2010: Nicolas Rapin; Ilka Hoof; Ole Lund; Morten Nielsen
The MHC motif viewer: a visualization tool for MHC binding motifs.
Current protocols in immunology / edited by John E. Coligan ... [et al.] 2010;Chapter 18():Unit 18.17.
2010: Peng Wang; John Sidney; Yohan Kim; Alessandro Sette; Ole Lund; Morten Nielsen; Bjoern Peters
Peptide binding predictions for HLA DR, DP and DQ molecules.
BMC bioinformatics 2010;11():568.
2010: Morten Nielsen; Sune Justesen; Ole Lund; Claus Lundegaard; Soren Buus
NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure.
Immunome research 2010;6():9.
2010: Claus Lundegaard; Ilka Hoof; Ole Lund; Morten Nielsen
State of the art and challenges in sequence based T-cell epitope prediction.
Immunome research 2010;6 Suppl 2():S3.
2010: Massimo Andreatta; Morten Nielsen; Frank Møller Aarestrup; Ole Lund
In silico prediction of human pathogenicity in the γ-proteobacteria.
PloS one 2010;5(10):e13680.
2010: Mette Voldby Larsen; Alina Lelic; Robin Parsons; Morten Nielsen; Ilka Hoof; Kasper Lamberth; Mark B Loeb; Søren Buus; Jonathan Bramson; Ole Lund
Identification of CD8+ T cell epitopes in the West Nile virus polyprotein by reverse-immunology using NetCTL.
PloS one 2010;5(9):e12697.
2010: Mingjun Wang; Mette V Larsen; Morten Nielsen; Mikkel Harndahl; Sune Justesen; Morten H Dziegiel; Soren Buus; Sheila Tuyet Tang; Ole Lund; Mogens H Claesson
HLA class I binding 9mer peptides from influenza A virus induce CD4 T cell responses.
PloS one 2010;5(5):e10533.
2010: Nicolas Rapin; Ole Lund; Massimo Bernaschi; Filippo Castiglione
Computational immunology meets bioinformatics: the use of prediction tools for molecular binding in the simulation of the immune system.
PloS one 2010;5(4):e9862.
2010: Hao Zhang; Peng Wang; Nikitas Papangelopoulos; Ying Xu; Alessandro Sette; Philip E Bourne; Ole Lund; Julia Ponomarenko; Morten Nielsen; Bjoern Peters
Limitations of Ab initio predictions of peptide binding to MHC class II molecules.
PloS one 2010;5(2):e9272.
2009: Hao Zhang; Ole Lund; Morten Nielsen
The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding.
Bioinformatics (Oxford, England) 2009;25(10):1293-9.
2009: Agnieszka S Juncker; Mette V Larsen; Nils Weinhold; Morten Nielsen; Søren Brunak; Ole Lund
Systematic characterisation of cellular localisation and expression profiles of proteins containing MHC ligands.
PloS one 2009;4(10):e7448.
2009: Morten Nielsen; Ole Lund
NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction.
BMC bioinformatics 2009;10():296.
2009: Ilka Hoof; Bjoern Peters; John Sidney; Lasse Eggers Pedersen; Alessandro Sette; Ole Lund; Soren Buus; Morten Nielsen
NetMHCpan, a method for MHC class I binding prediction beyond humans.
Immunogenetics 2009;61(1):1-13.
2008: Nicolas Rapin; Ilka Hoof; Ole Lund; Morten Nielsen
MHC motif viewer.
Immunogenetics 2008;60(12):759-65.
2008: Kasper Lamberth; Gustav Røder; Mikkel Harndahl; Morten Nielsen; Claus Lundegaard; Claus Schafer-Nielsen; Ole Lund; Soren Buus
The peptide-binding specificity of HLA-A*3001 demonstrates membership of the HLA-A3 supertype.
Immunogenetics 2008;60(11):633-43.
2008: Ilka Hoof; Can Keşmir; Ole Lund; Morten Nielsen
Humans with chimpanzee-like major histocompatibility complex-specificities control HIV-1 infection.
AIDS (London, England) 2008;22(11):1299-303.
2008: Qing Zhang; Peng Wang; Yohan Kim; Pernille Haste-Andersen; John Beaver; Philip Bourne; Huynh-Hoa Bui; Soren Buus; Sune Frankild; Jason Greenbaum; Ole Lund; Claus Lundegaard; Morten Nielsen; Julia V Ponomarenko; Alessandro Sette; Zhanyang Zhu; Bjoern Peters
Immune epitope database analysis resource (IEDB-AR).
Nucleic acids research 2008;36(Web Server issue):W513-8.
2008: Claus Lundegaard; Kasper Lamberth; Mikkel Harndahl; Soren Buus; Ole Lund; Morten Nielsen
NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11.
Nucleic acids research 2008;36(Web Server issue):W509-12.
2008: Claus Lundegaard; Ole Lund; Morten Nielsen
Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers.
Bioinformatics (Oxford, England) 2008;24(11):1397-8.
2008: Pernille Andersen; Morten A Nielsen; Mafalda Resende; Thomas S Rask; Madeleine Dahlbäck; Thor G Theander; Ole Lund; Ali Salanti
Structural insight into epitopes in the pregnancy-associated malaria protein VAR2CSA.
PLoS pathogens 2008;4(2):e42.
2008: Sheila Tuyet Tang; M Wang; Kasper Lamberth; Mikkel Harndahl; M H Dziegiel; M H Claesson; Soren Buus; Ole Lund
MHC-I-restricted epitopes conserved among variola and other related orthopoxviruses are recognized by T cells 30 years after vaccination.
Archives of virology 2008;153(10):1833-44.
2008: Morten Nielsen; Claus Lundegaard; Thomas Blicher; Bjoern Peters; Alessandro Sette; Sune Justesen; Soren Buus; Ole Lund
Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan.
PLoS computational biology 2008;4(7):e1000107.
2008: Sune Frankild; Rob J De Boer; Ole Lund; Morten Nielsen; Can Kesmir
Amino acid similarity accounts for T cell cross-reactivity and for "holes" in the T cell repertoire.
PloS one 2008;3(3):e1831.
2007: Claus Lundegaard; Ole Lund; Can Kesmir; Søren Brunak; Morten Nielsen
Modeling the adaptive immune system: predictions and simulations.
Bioinformatics (Oxford, England) 2007;23(24):3265-75.
2007: Mingjun Wang; Kasper Lamberth; Mikkel Harndahl; Gustav Røder; Anette Stryhn; Mette V Larsen; Morten Nielsen; Claus Lundegaard; Sheila Tuyet Tang; Morten Hanefeld Dziegiel; Jørgen Rosenkvist; Anders Elm Pedersen; Soren Buus; Mogens H Claesson; Ole Lund
CTL epitopes for influenza A including the H5N1 bird flu; genome-, pathogen-, and HLA-wide screening.
Vaccine 2007;25(15):2823-31.
2007: Jason A Greenbaum; Pernille Haste Andersen; Martin Blythe; Huynh-Hoa Bui; Raul E Cachau; James Crowe; Matthew Davies; A S Kolaskar; Ole Lund; Sherrie Morrison; Brendan Mumey; Yanay Ofran; Jean-Luc Pellequer; Clemencia Pinilla; Julia V Ponomarenko; Gajendra PS Raghava; Marc H V van Regenmortel; Erwin L Roggen; Alessandro Sette; Avner Schlessinger; johannes söllner; Martin Zand; Bjoern Peters
Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools.
Journal of molecular recognition : JMR 2007;20(2):75-82.
2007: Mette V Larsen; Claus Lundegaard; Kasper Lamberth; Soren Buus; Ole Lund; Morten Nielsen
Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction.
BMC bioinformatics 2007;8():424.
2007: Morten Nielsen; Claus Lundegaard; Thomas Blicher; Kasper Lamberth; Mikkel Harndahl; Sune Justesen; Gustav Røder; Bjoern Peters; Alessandro Sette; Ole Lund; Soren Buus
NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence.
PloS one 2007;2(8):e796.
2007: Morten Nielsen; Claus Lundegaard; Ole Lund
Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method.
BMC bioinformatics 2007;8():238.
2006: Claus Lundegaard; Morten Nielsen; Ole Lund
The validity of predicted T-cell epitopes.
Trends in biotechnology 2006;24(12):537-8.
2006: Madeleine Dahlbäck; Thomas S Rask; Pernille Haste Andersen; Morten A Nielsen; Nicaise T Ndam; Mafalda Resende; Louise Turner; Philippe Deloron; Lars Hviid; Ole Lund; Anders Gorm Pedersen; Thor G Theander; Ali Salanti
Epitope mapping and topographic analysis of VAR2CSA DBL3X involved in P. falciparum placental sequestration.
PLoS pathogens 2006;2(11):e124.
2006: Pernille Haste Andersen; Morten Nielsen; Ole Lund
Prediction of residues in discontinuous B-cell epitopes using protein 3D structures.
Protein science : a publication of the Protein Society 2006;15(11):2558-67.
2006: Nicolas Rapin; Can Kesmir; Sune Frankild; Morten Nielsen; Claus Lundegaard; Søren Brunak; Ole Lund
Modelling the human immune system by combining bioinformatics and systems biology approaches.
Journal of biological physics 2006;32(3-4):335-53.
2006: Tim T Binnewies; Yair Motro; Peter F Hallin; Ole Lund; David Dunn; Tom La; David J Hampson; Matthew Bellgard; Trudy M. Wassenaar; David W Ussery
Ten years of bacterial genome sequencing: comparative-genomics-based discoveries.
Functional & integrative genomics 2006;6(3):165-85.
2006: Bjoern Peters; Huynh-Hoa Bui; Sune Frankild; Morten Nielson; Claus Lundegaard; Emrah Kostem; Derek Basch; Kasper Lamberth; Mikkel Harndahl; Ward Fleri; Stephen S Wilson; John Sidney; Ole Lund; Soren Buus; Alessandro Sette
A community resource benchmarking predictions of peptide binding to MHC-I molecules.
PLoS computational biology 2006;2(6):e65.
2006: Jens Erik Pontoppidan Larsen; Ole Lund; Morten Nielsen
Improved method for predicting linear B-cell epitopes.
Immunome research 2006;2():2.
2005: Mette Voldby Larsen; Claus Lundegaard; Kasper Lamberth; Soren Buus; Søren Brunak; Ole Lund; Morten Nielsen
An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions.
European journal of immunology 2005;35(8):2295-303.
2005: Bjoern Peters; John Sidney; Phil Bourne; Huynh-Hoa Bui; Soren Buus; Grace Doh; Ward Fleri; Mitch Kronenberg; Ralph Kubo; Ole Lund; David Nemazee; Julia V Ponomarenko; Muthuraman Sathiamurthy; Stephen P Schoenberger; Scott Douglas Stewart; Pamela Surko; Scott Way; Steve Wilson; Alessandro Sette
The design and implementation of the immune epitope database and analysis resource.
Immunogenetics 2005;57(5):326-36.
2005: Morten Nielsen; Claus Lundegaard; Ole Lund; Can Keşmir
The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage.
Immunogenetics 2005;57(1-2):33-41.
2005: Bjoern Peters; John Sidney; Phil Bourne; Huynh-Hoa Bui; Soren Buus; Grace Doh; Ward Fleri; Mitch Kronenberg; Ralph Kubo; Ole Lund; David Nemazee; Julia V Ponomarenko; Muthuraman Sathiamurthy; Stephen P Schoenberger; Scott Douglas Stewart; Pamela Surko; Scott Way; Steve Wilson; Alessandro Sette
The immune epitope database and analysis resource: from vision to blueprint.
PLoS biology 2005;3(3):e91.
2004: Morten Nielsen; Claus Lundegaard; Peder Worning; Christina Sylvester Hvid; Kasper Lamberth; Soren Buus; Søren Brunak; Ole Lund
Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach.
Bioinformatics (Oxford, England) 2004;20(9):1388-97.
2004: Lars Kiemer; Ole Lund; Søren Brunak; Nikolaj Blom
Coronavirus 3CLpro proteinase cleavage sites: possible relevance to SARS virus pathology.
BMC bioinformatics 2004;5():72.
2004: Christina Sylvester-Hvid; Morten Nielsen; Kasper Lamberth; Gustav Røder; Sune Justesen; Claus Lundegaard; Peder Worning; H Thomadsen; Ole Lund; Søren Brunak; Soren Buus
SARS CTL vaccine candidates; HLA supertype-, genome-wide scanning and biochemical validation.
Tissue antigens 2004;63(5):395-400.
2004: Ole Lund; Morten Nielsen; Can Kesmir; Anders Gorm Petersen; Claus Lundegaard; Peder Worning; Christina Sylvester-Hvid; Kasper Lamberth; Gustav Røder; Sune Justesen; Soren Buus; Søren Brunak
Definition of supertypes for HLA molecules using clustering of specificity matrices.
Immunogenetics 2004;55(12):797-810.
2003: Jens Kaae Christensen; Kasper Lamberth; Morten Nielsen; Claus Lundegaard; Peder Worning; Sanne Lise Lauemøller; Soren Buus; Søren Brunak; Ole Lund
Selecting informative data for developing peptide-MHC binding predictors using a query by committee approach.
Neural computation 2003;15(12):2931-42.
2003: Morten Nielsen; Claus Lundegaard; Peder Worning; Sanne Lise Lauemøller; Kasper Lamberth; Soren Buus; Søren Brunak; Ole Lund
Reliable prediction of T-cell epitopes using neural networks with novel sequence representations.
Protein science : a publication of the Protein Society 2003;12(5):1007-17.
1999: Jan Gorodkin; Hans-Henrik Staerfeldt; Ole Lund; Søren Brunak
MatrixPlot: visualizing sequence constraints.
Bioinformatics (Oxford, England) 1999;15(9):769-70.
1999: Jan Gorodkin; Ole Lund; C A F Andersen; Søren Brunak
Using sequence motifs for enhanced neural network prediction of protein distance constraints.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1999;():95-105.
1997: Ole Lund; K Frimand; Jan Gorodkin; Henrik Bohr; J Bohr; J Hansen; Søren Brunak
Protein distance constraints predicted by neural networks and probability density functions.
Protein engineering 1997;10(11):1241-8.
1996: Ole Lund; J Hansen; Søren Brunak; J Bohr
Relationship between protein structure and geometrical constraints.
Protein science : a publication of the Protein Society 1996;5(11):2217-25.
1996: M G Reese; Ole Lund; J Bohr; Henrik Bohr; John-Erik Stig Hansen; Søren Brunak
Distance distributions in proteins: a six-parameter representation.
Protein engineering 1996;9(9):733-40.