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)

Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information. - Cristina Marino Buslje; Javier Santos 002; José María Delfino; Morten Nielsen 001 (Bioinform., 2009)

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)

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)

Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic Residue Identification. - Cristina Marino Buslje; Elin Teppa; Tomás Di Domenico; José María Delfino; Morten Nielsen 001 (PLoS Comput. Biol., 2010)

Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction. - Elin Teppa; Angela D. Wilkins; Morten Nielsen 001; Cristina Marino Buslje (BMC Bioinform., 2012)

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)

Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion. - Martin Christen Frølund Thomsen; Morten Nielsen 001 (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)

MISTIC: mutual information server to infer coevolution. - Franco L. Simonetti; Elin Teppa; Ariel Chernomoretz; Morten Nielsen 001; Cristina Marino Buslje (Nucleic Acids Res., 2013)

The interplay of sequence conservation and T cell immune recognition. - Anne Bresciani; Jason Greenbaum; Cecilia S. Lindestam Arlehamn; Alessandro Sette; Morten Nielsen 001; Bjoern Peters (BCB, 2014)

Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions. - Yohan Kim; John Sidney; Søren Buus; Alessandro Sette; Morten Nielsen 001; Bjoern Peters (BMC Bioinform., 2014)

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)

LYRA, a webserver for lymphocyte receptor structural modeling. - Michael Schantz Klausen; Mads Valdemar Anderson; Martin Closter Jespersen; Morten Nielsen 001; Paolo Marcatili (Nucleic Acids Res., 2015)

Gapped sequence alignment using artificial neural networks: application to the MHC class I system. - Massimo Andreatta; Morten Nielsen 001 (Bioinform., 2016)

An introduction to deep learning on biological sequence data: examples and solutions. - Vanessa Isabell Jurtz; Alexander Rosenberg Johansen; Morten Nielsen 001; José Juan Almagro Armenteros; Henrik Nielsen; Casper Kaae Sønderby; Ole Winther; Søren Kaae Sønderby (Bioinform., 2017)

MIToS.jl: mutual information tools for protein sequence analysis in the Julia language. - Diego J. Zea; Diego Anfossi; Morten Nielsen 001; Cristina Marino Buslje (Bioinform., 2017)

NNAlign: a platform to construct and evaluate artificial neural network models of receptor-ligand interactions. - Morten Nielsen 001; Massimo Andreatta (Nucleic Acids Res., 2017)

GibbsCluster: unsupervised clustering and alignment of peptide sequences. - Massimo Andreatta; Bruno Alvarez; Morten Nielsen 001 (Nucleic Acids Res., 2017)

BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes. - Martin Closter Jespersen; Bjoern Peters; Morten Nielsen 001; Paolo Marcatili (Nucleic Acids Res., 2017)

An automated benchmarking platform for MHC class II binding prediction methods. - Massimo Andreatta; Thomas Trolle; Zhen Yan; Jason A. Greenbaum; Bjoern Peters; Morten Nielsen 001 (Bioinform., 2018)

The SysteMHC Atlas project. - Wenguang Shao; Patrick G. A. Pedrioli; Witold Wolski; Christian Scurtescu; Emanuel Schmid; Juan Antonio Vizcaíno; Mathieu Courcelles; Heiko Schuster; Daniel Kowalewski; Fabio Marino; Cecilia S. Lindestam Arlehamn; Kerrie Vaughan; et al. (Nucleic Acids Res., 2018)

A generic deep convolutional neural network framework for prediction of receptor-ligand interactions - NetPhosPan: application to kinase phosphorylation prediction. - Emilio Fenoy; José M. G. Izarzugaza; Vanessa Isabell Jurtz; Søren Brunak; Morten Nielsen 001 (Bioinform., 2019)

Benchmark datasets of immune receptor-epitope structural complexes. - Swapnil Mahajan; Zhen Yan; Martin Closter Jespersen; Kamilla Kjærgaard Jensen; Paolo Marcatili; Morten Nielsen 001; Alessandro Sette; Bjoern Peters (BMC Bioinform., 2019)

IEDB-AR: immune epitope database - analysis resource in 2019. - Sandeep Kumar Dhanda; Swapnil Mahajan; Sinu Paul; Zhen Yan; Haeuk Kim; Martin Closter Jespersen; Vanessa Isabell Jurtz; Massimo Andreatta; Jason A. Greenbaum; Paolo Marcatili; Alessandro Sette; Morten Nielsen 001; et al. (Nucleic Acids Res., 2019)

NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data. - Birkir Reynisson; Bruno Alvarez; Sinu Paul; Bjoern Peters; Morten Nielsen 001 (Nucleic Acids Res., 2020)

Benchmarking predictions of MHC class I restricted T cell epitopes in a comprehensively studied model system. - Sinu Paul; Nathan P. Croft; Anthony W. Purcell; David C. Tscharke; Alessandro Sette; Morten Nielsen 001; Bjoern Peters (PLoS Comput. Biol., 2020)

Sampling SARS-CoV-2 Proteomes for Predicted CD8 T-Cell Epitopes as a Tool for Understanding Immunogenic Breadth and Rational Vaccine Design. - Jonathan Hare; David Morrison; Morten Nielsen 001 (Frontiers Bioinform., 2021)

A comprehensive analysis of the IEDB MHC class-I automated benchmark. - Raphael Trevizani; Zhen Yan; Jason A. Greenbaum; Alessandro Sette; Morten Nielsen 001; Bjoern Peters (Briefings Bioinform., 2022)

NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning. - Magnus Haraldson Høie; Erik Nicolas Kiehl; Bent Petersen; Morten Nielsen 001; Ole Winther; Henrik Nielsen; Jeppe Hallgren; Paolo Marcatili (Nucleic Acids Res., 2022)

The Cancer Epitope Database and Analysis Resource (CEDAR). - Zeynep Kosaloglu-Yalçin; Nina Blazeska; Randi Vita; Hannah Carter; Morten Nielsen 001; Stephen Schoenberger; Alessandro Sette; Bjoern Peters (Nucleic Acids Res., 2023)

PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins. - Daniel Marrama; William D. Chronister; Luise Westernberg; Randi Vita; Zeynep Kosaloglu-Yalçin; Alessandro Sette; Morten Nielsen 001; Jason A. Greenbaum; Bjoern Peters (BMC Bioinform., 2023)

Vegvisir: Probabilistic Model (VAE) for Viral T-Cell Epitope Prediction. - Lys Sanz Moreta; Ibel Carri; Heli M. Garcia Alvarez; Morten Nielsen 001 (LOD (2), 2024)

The receiver operating characteristic curve accurately assesses imbalanced datasets. - Eve Richardson; Raphael Trevizani; Jason A. Greenbaum; Hannah Carter; Morten Nielsen 001; Bjoern Peters (Patterns, 2024)

A modular protein language modelling approach to immunogenicity prediction. - Hugh O'Brien; Max Salm; Laura T. Morton; Maciej Szukszto; Felix O'farrell; Charlotte Boulton; Laurence King; Supreet Kaur Bola; Pablo D. Becker; Andrew Craig; Morten Nielsen 001; Yardena Samuels; et al. (PLoS Comput. Biol., 2024)