Period Doubling Route to Chaos in a Model of HIV infection of the Immune System. - Ole Lund; Erik Mosekilde; Jan E. Hansen (EUROSIM, 1992)

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

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

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

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

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

MatrixPlot: visualizing sequence constraints. - Jan Gorodkin; Hans Henrik Stærfeldt; Ole Lund; Søren Brunak (Bioinform., 1999)

Prediction of Protein Secondary Structure at High Accuracy Using a Combination of Many Neural Networks. - Claus Lundegaard; Thomas Nordahl Petersen; Morten Nielsen 001; Henrik Bohr; Jakob Bohr; Søren Brunak; Garry Gippert; Ole Lund (Mathematical Methods for Protein Structure Analysis and Design, 2003)

Selecting Informative Data for Developing Peptide-MHC Binding Predictors Using a Query by Committee Approach. - Jens Kaae Christensen; Kasper Lamberth; Morten Nielsen 001; Claus Lundegaard; Peder Worning; Sanne Lise Lauemøller; Søren Buus; Søren Brunak; Ole Lund (Neural Comput., 2003)

MHC Class I Epitope Binding Prediction Trained on Small Data Sets. - Claus Lundegaard; Morten Nielsen 001; Kasper Lamberth; Peder Worning; Christina Sylvester-Hvid; Søren Buus; Søren Brunak; Ole Lund (ICARIS, 2004)

Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. - Morten Nielsen 001; Claus Lundegaard; Peder Worning; Christina Sylvester-Hvid; Kasper Lamberth; Søren Buus; Søren Brunak; Ole Lund (Bioinform., 2004)

Coronavirus 3CLpro proteinase cleavage sites: Possible relevance to SARS virus pathology. - Lars Kiemer; Ole Lund; Søren Brunak; Nikolaj Blom (BMC Bioinform., 2004)

Immunological bioinformatics. - Ole Lund; Morten Nielsen 001; Claus Lundegaard; Can Kesmir; Søren Brunak (AAAI Press, 2005)

The Immune Epitope Database and Analysis Resource. - 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; et al. (PRIB, 2006)

A Community Resource Benchmarking Predictions of Peptide Binding to MHC-I Molecules. - Bjoern Peters; Huynh-Hoa Bui; Sune Frankild; Morten Nielsen 001; Claus Lundegaard; Emrah Kostem; Derek Basch; Kasper Lamberth; Mikkel Harndahl; Ward Fleri; Stephen S. Wilson; John Sidney; et al. (PLoS Comput. Biol., 2006)

Modeling the adaptive immune system: predictions and simulations. - Claus Lundegaard; Ole Lund; Can Kesmir; Søren Brunak; Morten Nielsen 001 (Bioinform., 2007)

Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. - Mette V. Larsen; Claus Lundegaard; Kasper Lamberth; Søren Buus; Ole Lund; Morten Nielsen 001 (BMC Bioinform., 2007)

Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. - Morten Nielsen 001; Claus Lundegaard; Ole Lund (BMC Bioinform., 2007)

Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers. - Claus Lundegaard; Ole Lund; Morten Nielsen 001 (Bioinform., 2008)

NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11. - Claus Lundegaard; Kasper Lamberth; Mikkel Harndahl; Søren Buus; Ole Lund; Morten Nielsen 001 (Nucleic Acids Res., 2008)

Immune epitope database analysis resource (IEDB-AR). - Qing Zhang; Peng Wang 014; Yohan Kim; Pernille Haste-Andersen; John E. Beaver; Philip E. Bourne; Huynh-Hoa Bui; Søren Buus; Sune Frankild; Jason Greenbaum; Ole Lund; Claus Lundegaard; et al. (Nucleic Acids Res., 2008)

Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan. - Morten Nielsen 001; Claus Lundegaard; Thomas Blicher; Bjoern Peters; Alessandro Sette; Sune Justesen; Søren Buus; Ole Lund (PLoS Comput. Biol., 2008)

The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding. - Hao Zhang; Ole Lund; Morten Nielsen 001 (Bioinform., 2009)

NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction. - Morten Nielsen 001; Ole Lund (BMC Bioinform., 2009)

PopCover: a method for selecting of peptides with optimal population and pathogen coverage. - Claus Lundegaard; M. Buggert; A. C. Karlsson; Ole Lund; Carina Perez; Morten Nielsen 001 (BCB, 2010)

Peptide binding predictions for HLA DR, DP and DQ molecules. - Peng Wang 014; John Sidney; Yohan Kim; Alessandro Sette; Ole Lund; Morten Nielsen 001; Björn Peters (BMC Bioinform., 2010)

CPHmodels-3.0 - remote homology modeling using structure-guided sequence profiles. - Morten Nielsen 001; Claus Lundegaard; Ole Lund; Thomas Nordahl Petersen (Nucleic Acids Res., 2010)

Immune system simulation online. - Nicolas Rapin; Ole Lund; Filippo Castiglione (Bioinform., 2011)

Immune epitope database analysis resource. - Yohan Kim; Julia V. Ponomarenko; Zhanyang Zhu; Dorjee Tamang; Peng Wang 014; Jason Greenbaum; Claus Lundegaard; Alessandro Sette; Ole Lund; Philip E. Bourne; Morten Nielsen 001; Bjoern Peters (Nucleic Acids Res., 2012)

Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking. - Jens Vindahl Kringelum; Claus Lundegaard; Ole Lund; Morten Nielsen 001 (PLoS Comput. Biol., 2012)

Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach. - Massimo Andreatta; Ole Lund; Morten Nielsen 001 (Bioinform., 2013)

SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments. - Leon Eyrich Jessen; Ilka Hoof; Ole Lund; Morten Nielsen 001 (Nucleic Acids Res., 2013)

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

Automated benchmarking of peptide-MHC class I binding predictions. - Thomas Trolle; Imir G. Metushi; Jason A. Greenbaum; Yohan Kim; John Sidney; Ole Lund; Alessandro Sette; Bjoern Peters; Morten Nielsen 001 (Bioinform., 2015)

Reads2Type: a web application for rapid microbial taxonomy identification. - Dhany Saputra; Simon Rasmussen; Mette V. Larsen; Nizar Haddad; Maria Sperotto; Frank Aarestrup; Ole Lund; Thomas Sicheritz-Pontén (BMC Bioinform., 2015)

ChemProt-3.0: a global chemical biology diseases mapping. - Jens Kringelum; Sonny Kim Kjærulff; Søren Brunak; Ole Lund; Tudor I. Oprea; Olivier Taboureau (Database J. Biol. Databases Curation, 2016)

RUCS: rapid identification of PCR primers for unique core sequences. - Martin Christen Frølund Thomsen; Henrik Hasman; Henrik Westh; Hülya Kaya; Ole Lund (Bioinform., 2017)

Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. - Lasse Maretty; Jacob Malte Jensen; Bent Petersen; Jonas Andreas Sibbesen; Siyang Liu 007; Palle Villesen; Laurits Skov; Kirstine Belling; Christian Theil Have; José M. G. Izarzugaza; Marie Grosjean; Jette Bork-Jensen; et al. (Nat., 2017)

Rapid and precise alignment of raw reads against redundant databases with KMA. - Philip T. L. C. Clausen; Frank Aarestrup; Ole Lund (BMC Bioinform., 2018)

Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios. - Maria Luisa Matey-Hernandez; Lasse Maretty; Jacob Malte Jensen; Bent Petersen; Jonas Andreas Sibbesen; Siyang Liu 007; Palle Villesen; Laurits Skov; Kirstine Belling; Christian Theil Have; José M. G. Izarzugaza; Marie Grosjean; et al. (BMC Bioinform., 2018)

The COMPARE Data Hubs. - Clara Amid; Nima Pakseresht; Nicole Silvester; Suran Jayathilaka; Ole Lund; Lukasz D. Dynovski; Bálint Á Pataki; Dávid Visontai; Basil Britto Xavier; Blaise T. F. Alako; Ariane Belka; Jose L. B. Cisneros; et al. (Database J. Biol. Databases Curation, 2019)

Automated download and clean-up of family-specific databases for kmer-based virus identification. - Rosa L. Allesøe; Camilla K. Lemvigh; My V. T. Phan; Philip T. L. C. Clausen; Alfred F. Florensa; Marion Koopmans; Ole Lund; Matthew Cotten (Bioinform., 2021)