Morten Nielsen

51 papers Journal 45Unranked 5
YearRankTypeTitle / Venue / Authors
2025 J jnl
On the impact of local protein structure features on prediction of major histocompatibility complex class I and II antigen presentation.
Briefings Bioinform.
Yat-tsai Richie Wan, Morten Nielsen
2024 J jnl
A modular protein language modelling approach to immunogenicity prediction.
PLoS Comput. Biol.
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, Yardena Samuels, Charles Swanton, Marc R. Mansour, Sine Reker Hadrup, Sergio A. Quezada
2024 J jnl
The receiver operating characteristic curve accurately assesses imbalanced datasets.
Patterns
Eve Richardson, Raphael Trevizani, Jason A. Greenbaum, Hannah Carter, Morten Nielsen, Bjoern Peters
2024 — conf
Vegvisir: Probabilistic Model (VAE) for Viral T-Cell Epitope Prediction.
LOD (2)
Lys Sanz Moreta, Ibel Carri, Heli M. Garcia Alvarez, Morten Nielsen
2023 J jnl
PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins.
BMC Bioinform.
Daniel Marrama, William D. Chronister, Luise Westernberg, Randi Vita, Zeynep Kosaloglu-Yalçin, Alessandro Sette, Morten Nielsen, Jason A. Greenbaum, Bjoern Peters
2023 J jnl
The Cancer Epitope Database and Analysis Resource (CEDAR).
Nucleic Acids Res.
Zeynep Kosaloglu-Yalçin, Nina Blazeska, Randi Vita, Hannah Carter, Morten Nielsen, Stephen Schoenberger, Alessandro Sette, Bjoern Peters
2022 J jnl
A comprehensive analysis of the IEDB MHC class-I automated benchmark.
Briefings Bioinform.
Raphael Trevizani, Zhen Yan, Jason A. Greenbaum, Alessandro Sette, Morten Nielsen, Bjoern Peters
2022 J jnl
NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning.
Nucleic Acids Res.
Magnus Haraldson Høie, Erik Nicolas Kiehl, Bent Petersen, Morten Nielsen, Ole Winther, Henrik Nielsen, Jeppe Hallgren, Paolo Marcatili
2021 J jnl
Sampling SARS-CoV-2 Proteomes for Predicted CD8 T-Cell Epitopes as a Tool for Understanding Immunogenic Breadth and Rational Vaccine Design.
Frontiers Bioinform.
Jonathan Hare, David Morrison, Morten Nielsen
2020 J jnl
Benchmarking predictions of MHC class I restricted T cell epitopes in a comprehensively studied model system.
PLoS Comput. Biol.
Sinu Paul, Nathan P. Croft, Anthony W. Purcell, David C. Tscharke, Alessandro Sette, Morten Nielsen, Bjoern Peters
2020 J jnl
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.
Nucleic Acids Res.
Birkir Reynisson, Bruno Alvarez, Sinu Paul, Bjoern Peters, Morten Nielsen
2019 J jnl
A generic deep convolutional neural network framework for prediction of receptor-ligand interactions - NetPhosPan: application to kinase phosphorylation prediction.
Bioinform.
Emilio Fenoy, José M. G. Izarzugaza, Vanessa Isabell Jurtz, Søren Brunak, Morten Nielsen
2019 J jnl
Benchmark datasets of immune receptor-epitope structural complexes.
BMC Bioinform.
Swapnil Mahajan, Zhen Yan, Martin Closter Jespersen, Kamilla Kjærgaard Jensen, Paolo Marcatili, Morten Nielsen, Alessandro Sette, Bjoern Peters
2019 J jnl
IEDB-AR: immune epitope database - analysis resource in 2019.
Nucleic Acids Res.
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, Bjoern Peters
2018 J jnl
An automated benchmarking platform for MHC class II binding prediction methods.
Bioinform.
Massimo Andreatta, Thomas Trolle, Zhen Yan, Jason A. Greenbaum, Bjoern Peters, Morten Nielsen
2018 J jnl
The SysteMHC Atlas project.
Nucleic Acids Res.
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, Bjoern Peters, Alessandro Sette, Tom H. M. Ottenhoff, Krista E. Meijgaarden, Natalie Nieuwenhuizen, Stefan H. E. Kaufmann, Ralph Schlapbach, John C. Castle, Alexey I. Nesvizhskii, Morten Nielsen, Eric W. Deutsch, David S. Campbell, Robert L. Moritz, Roman A. Zubarev, Anders Jimmy Ytterberg, Anthony W. Purcell, Miguel Marcilla, Alberto Paradela, Qi Wang, Catherine E. Costello, Nicola Ternette, Peter A. van Veelen, Cécile A. C. M. van Els, Albert J. R. Heck, Gustavo A. de Souza, Ludvig Magne Sollid, Arie Admon, Stefan Stevanovic, Hans-Georg Rammensee, Pierre Thibault, Claude Perreault, Michal Bassani-Sternberg, Ruedi Aebersold, Etienne Caron
2017 J jnl
An introduction to deep learning on biological sequence data: examples and solutions.
Bioinform.
Vanessa Isabell Jurtz, Alexander Rosenberg Johansen, Morten Nielsen, José Juan Almagro Armenteros, Henrik Nielsen, Casper Kaae Sønderby, Ole Winther, Søren Kaae Sønderby
2017 J jnl
BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes.
Nucleic Acids Res.
Martin Closter Jespersen, Bjoern Peters, Morten Nielsen, Paolo Marcatili
2017 J jnl
GibbsCluster: unsupervised clustering and alignment of peptide sequences.
Nucleic Acids Res.
Massimo Andreatta, Bruno Alvarez, Morten Nielsen
2017 J jnl
MIToS.jl: mutual information tools for protein sequence analysis in the Julia language.
Bioinform.
Diego J. Zea, Diego Anfossi, Morten Nielsen, Cristina Marino Buslje
2017 J jnl
NNAlign: a platform to construct and evaluate artificial neural network models of receptor-ligand interactions.
Nucleic Acids Res.
Morten Nielsen, Massimo Andreatta
2016 J jnl
Gapped sequence alignment using artificial neural networks: application to the MHC class I system.
Bioinform.
Massimo Andreatta, Morten Nielsen
2015 J jnl
Automated benchmarking of peptide-MHC class I binding predictions.
Bioinform.
Thomas Trolle, Imir G. Metushi, Jason A. Greenbaum, Yohan Kim, John Sidney, Ole Lund, Alessandro Sette, Bjoern Peters, Morten Nielsen
2015 J jnl
LYRA, a webserver for lymphocyte receptor structural modeling.
Nucleic Acids Res.
Michael Schantz Klausen, Mads Valdemar Anderson, Martin Closter Jespersen, Morten Nielsen, Paolo Marcatili
2014 J jnl
Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions.
BMC Bioinform.
Yohan Kim, John Sidney, Søren Buus, Alessandro Sette, Morten Nielsen, Bjoern Peters
2014 — conf
The interplay of sequence conservation and T cell immune recognition.
BCB
Anne Bresciani, Jason Greenbaum, Cecilia S. Lindestam Arlehamn, Alessandro Sette, Morten Nielsen, Bjoern Peters
2013 J jnl
MISTIC: mutual information server to infer coevolution.
Nucleic Acids Res.
Franco L. Simonetti, Elin Teppa, Ariel Chernomoretz, Morten Nielsen, Cristina Marino Buslje
2013 J jnl
Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach.
Bioinform.
Massimo Andreatta, Ole Lund, Morten Nielsen
2012 J jnl
Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction.
BMC Bioinform.
Elin Teppa, Angela D. Wilkins, Morten Nielsen, Cristina Marino Buslje
2012 J jnl
Immune epitope database analysis resource.
Nucleic Acids Res.
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
2012 J jnl
Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking.
PLoS Comput. Biol.
Jens Vindahl Kringelum, Claus Lundegaard, Ole Lund, Morten Nielsen
2010 J jnl
CPHmodels-3.0 - remote homology modeling using structure-guided sequence profiles.
Nucleic Acids Res.
Morten Nielsen, Claus Lundegaard, Ole Lund, Thomas Nordahl Petersen
2010 J jnl
Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic Residue Identification.
PLoS Comput. Biol.
Cristina Marino Buslje, Elin Teppa, Tomás Di Domenico, José María Delfino, Morten Nielsen
2010 J jnl
Peptide binding predictions for HLA DR, DP and DQ molecules.
BMC Bioinform.
Peng Wang, John Sidney, Yohan Kim, Alessandro Sette, Ole Lund, Morten Nielsen, Björn Peters
2010 — conf
PopCover: a method for selecting of peptides with optimal population and pathogen coverage.
BCB
Claus Lundegaard, M. Buggert, A. C. Karlsson, Ole Lund, Carina Perez, Morten Nielsen
2009 J jnl
Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information.
Bioinform.
Cristina Marino Buslje, Javier Santos, José María Delfino, Morten Nielsen
2009 J jnl
Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods.
Bioinform.
Hao Zhang, Claus Lundegaard, Morten Nielsen
2009 J jnl
The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding.
Bioinform.
Hao Zhang, Ole Lund, Morten Nielsen
2008 J jnl
Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers.
Bioinform.
Claus Lundegaard, Ole Lund, Morten Nielsen
2008 J jnl
Immune epitope database analysis resource (IEDB-AR).
Nucleic Acids Res.
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
2008 J jnl
NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11.
Nucleic Acids Res.
Claus Lundegaard, Kasper Lamberth, Mikkel Harndahl, Søren Buus, Ole Lund, Morten Nielsen
2008 J jnl
Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan.
PLoS Comput. Biol.
Morten Nielsen, Claus Lundegaard, Thomas Blicher, Bjoern Peters, Alessandro Sette, Sune Justesen, Søren Buus, Ole Lund
2007 J jnl
Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction.
BMC Bioinform.
Mette V. Larsen, Claus Lundegaard, Kasper Lamberth, Søren Buus, Ole Lund, Morten Nielsen
2007 J jnl
Modeling the adaptive immune system: predictions and simulations.
Bioinform.
Claus Lundegaard, Ole Lund, Can Kesmir, Søren Brunak, Morten Nielsen
2007 J jnl
Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method.
BMC Bioinform.
Morten Nielsen, Claus Lundegaard, Ole Lund
2006 J jnl
A Community Resource Benchmarking Predictions of Peptide Binding to MHC-I Molecules.
PLoS Comput. Biol.
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
2005 — book
Immunological bioinformatics.
Ole Lund, Morten Nielsen, Claus Lundegaard, Can Kesmir, Søren Brunak
2004 J jnl
Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach.
Bioinform.
Morten Nielsen, Claus Lundegaard, Peder Worning, Christina Sylvester-Hvid, Kasper Lamberth, Søren Buus, Søren Brunak, Ole Lund
2004 — conf
MHC Class I Epitope Binding Prediction Trained on Small Data Sets.
ICARIS
Claus Lundegaard, Morten Nielsen, Kasper Lamberth, Peder Worning, Christina Sylvester-Hvid, Søren Buus, Søren Brunak, Ole Lund
2003 — conf
Prediction of Protein Secondary Structure at High Accuracy Using a Combination of Many Neural Networks.
Mathematical Methods for Protein Structure Analysis and Design
Claus Lundegaard, Thomas Nordahl Petersen, Morten Nielsen, Henrik Bohr, Jakob Bohr, Søren Brunak, Garry Gippert, Ole Lund
2003 J jnl
Selecting Informative Data for Developing Peptide-MHC Binding Predictors Using a Query by Committee Approach.
Neural Comput.
Jens Kaae Christensen, Kasper Lamberth, Morten Nielsen, Claus Lundegaard, Peder Worning, Sanne Lise Lauemøller, Søren Buus, Søren Brunak, Ole Lund