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)

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

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)

Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods. - Hao Zhang; Claus Lundegaard; Morten Nielsen 001 (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)

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 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)