Ole Lund

Massimo Andreatta, Ole Lund, Morten Nielsen: Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach. Bioinformatics 29(1): 8-14 (2013)

Sonny Kim Kjærulff, Louis Wich, Jens Kringelum, Ulrik Plesner Jacobsen, Irene Kouskoumvekaki, Karine Audouze, Ole Lund, Søren Brunak, Tudor I. Oprea, Olivier Taboureau: ChemProt-2.0: visual navigation in a disease chemical biology database. Nucleic Acids Research 41(Database-Issue): 464-469 (2013)

Yohan Kim, Julia V. Ponomarenko, Zhanyang Zhu, Dorjee Tamang, Peng Wang, Jason Greenbaum, Claus Lundegaard, Alessandro Sette, Ole Lund, Philip E. Bourne, Morten Nielsen, Bjoern Peters: Immune epitope database analysis resource. Nucleic Acids Research 40(Web-Server-Issue): 525-530 (2012)

Nicolas Rapin, Ole Lund, Filippo Castiglione: Immune system simulation online. Bioinformatics 27(14): 2013-2014 (2011)

Peng Wang, John Sidney, Yohan Kim, Alessandro Sette, Ole Lund, Morten Nielsen, Björn Peters: Peptide binding predictions for HLA DR, DP and DQ molecules. BMC Bioinformatics 11: 568 (2010)

Morten Nielsen, Claus Lundegaard, Ole Lund, Thomas Nordahl Petersen: CPHmodels-3.0 - remote homology modeling using structure-guided sequence profiles. Nucleic Acids Research 38(Web-Server-Issue): 576-581 (2010)

Claus Lundegaard, M. Buggert, A. C. Karlsson, Ole Lund, Carina Perez, Morten Nielsen: PopCover: a method for selecting of peptides with optimal population and pathogen coverage. BCB 2010: 658-659

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 25(10): 1293-1299 (2009)

Morten Nielsen, Ole Lund: NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction. BMC Bioinformatics 10: 296 (2009)

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 24(11): 1397-1398 (2008)

Claus Lundegaard, Kasper Lamberth, Mikkel Harndahl, Søren 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 36(Web-Server-Issue): 509-512 (2008)

Qing Zhang, Peng Wang, Yohan Kim, Pernille Haste-Andersen, John E. Beaver, Philip E. Bourne, Huynh-Hoa Bui, Søren Buus, Sune Frankild, Jason Greenbaum, Ole Lund, Claus Lundegaard, Morten Nielsen, Julia V. Ponomarenko, Alessandro Sette, Zhanyang Zhu, Björn Peters: Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Research 36(Web-Server-Issue): 513-518 (2008)

Morten Nielsen, Claus Lundegaard, Thomas Blicher, Bjoern Peters, Alessandro Sette, Sune Justesen, Søren Buus, Ole Lund: Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan. PLoS Computational Biology 4(7) (2008)

Claus Lundegaard, Ole Lund, Can Kesmir, Søren Brunak, Morten Nielsen: Modeling the adaptive immune system: predictions and simulations. Bioinformatics 23(24): 3265-3275 (2007)

Mette V. Larsen, Claus Lundegaard, Kasper Lamberth, Søren Buus, Ole Lund, Morten Nielsen: Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. BMC Bioinformatics 8 (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 8 (2007)

Bjoern Peters, Huynh-Hoa Bui, Sune Frankild, Morten Nielsen, Claus Lundegaard, Emrah Kostem, Derek Basch, Kasper Lamberth, Mikkel Harndahl, Ward Fleri, Stephen S. Wilson, John Sidney, Ole Lund, Søren Buus, Alessandro Sette: A Community Resource Benchmarking Predictions of Peptide Binding to MHC-I Molecules. PLoS Computational Biology 2(6) (2006)

Alessandro Sette, Huynh-Hoa Bui, John Sidney, Philip E. Bourne, Søren Buus, Ward Fleri, R. Kubo, Ole Lund, D. Nemazee, Julia V. Ponomarenko, Muthu Sathiamurthy, Scott Stewart, Scott Way, Stephen S. Wilson, Björn Peters: The Immune Epitope Database and Analysis Resource. PRIB 2006: 126-132

Morten Nielsen, Claus Lundegaard, Peder Worning, Christina Sylvester-Hvid, Kasper Lamberth, Søren Buus, Søren Brunak, Ole Lund: Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. Bioinformatics 20(9): 1388-1397 (2004)

Lars Kiemer, Ole Lund, Søren Brunak, Nikolaj Blom: Coronavirus 3CL^pro proteinase cleavage sites: Possible relevance to SARS virus pathology. BMC Bioinformatics 5: 72 (2004)

Claus Lundegaard, Morten Nielsen, Kasper Lamberth, Peder Worning, Christina Sylvester-Hvid, Søren Buus, Søren Brunak, Ole Lund: MHC Class I Epitope Binding Prediction Trained on Small Data Sets. ICARIS 2004: 217-225

Jens Kaae Christensen, Kasper Lamberth, Morten Nielsen, Claus Lundegaard, Peder Worning, Sanne Lise Lauemøller, Søren Buus, Søren Brunak, Ole Lund: Selecting Informative Data for Developing Peptide-MHC Binding Predictors Using a Query by Committee Approach. Neural Computation 15(12): 2931-2942 (2003)

Claus Lundegaard, Thomas Nordahl Petersen, Morten Nielsen, Henrik Bohr, Jakob Bohr, Søren Brunak, Garry Gippert, Ole Lund: Prediction of Protein Secondary Structure at High Accuracy Using a Combination of Many Neural Networks. Mathematical Methods for Protein Structure Analysis and Design 2003: 117-122

Jan Gorodkin, Hans Henrik Stærfeldt, Ole Lund, Søren Brunak: MatrixPlot: visualizing sequence constraints. Bioinformatics 15(9): 769-770 (1999)

Jan Gorodkin, Ole Lund, Claus A. F. Andersen, Søren Brunak: Using Sequence Motifs for Enhanced Neural Network Prediction of Protein Distance Constraints. ISMB 1999: 95-105

Jan E. Hansen, Ole Lund, Jette Nilsson, Kristoffer Rapacki, Søren Brunak: O-GLYCBASE Version 3.0: a revised database of O-glycosylated proteins. Nucleic Acids Research 26(1): 387-389 (1998)

Jan E. Hansen, Ole Lund, Kristoffer Rapacki, Søren Brunak: O-GLYCBASE version 2.0: a revised database of O-glycosylated proteins. Nucleic Acids Research 25(1): 278-282 (1997)

Jan E. Hansen, Ole Lund, Jens O. Nielsen, John-E. S. Hansen, Søren Brunak: O-GLYCBASE: a revised database of O-glycosylated proteins. Nucleic Acids Research 24(1): 248-252 (1996)

Ole Lund, Erik Mosekilde, Jan E. Hansen: Period doubling route to chaos in a model of HIV infection of the immune system: A comment on the Anderson-May model. Simul. Pr. Theory 1(2): 49-55 (1993)