Morten Nielsen

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 18

Top Topics

Unsupervised Clustering

Imbalanced Datasets

Top Venues

Nucleic Acids Res.

Briefings Bioinform.

Publications

Eve Richardson, Raphael Trevizani, Jason A. Greenbaum, Hannah Carter, Morten Nielsen, Bjoern Peters
The receiver operating characteristic curve accurately assesses imbalanced datasets. Patterns 5 (6) (2024)
Zeynep Kosaloglu-Yalçin, Nina Blazeska, Randi Vita, Hannah Carter, Morten Nielsen, Stephen Schoenberger, Alessandro Sette, Bjoern Peters
The Cancer Epitope Database and Analysis Resource (CEDAR). Nucleic Acids Res. 51 (D1) (2023)
Daniel Marrama, William D. Chronister, Luise Westernberg, Randi Vita, Zeynep Kosaloglu-Yalçin, Alessandro Sette, Morten Nielsen, Jason A. Greenbaum, Bjoern Peters
PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins. BMC Bioinform. 24 (1) (2023)
Magnus Haraldson Høie, Erik Nicolas Kiehl, Bent Petersen, Morten Nielsen, Ole Winther, Henrik Nielsen, Jeppe Hallgren, Paolo Marcatili
NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning. Nucleic Acids Res. 50 (W1) (2022)
Raphael Trevizani, Zhen Yan, Jason A. Greenbaum, Alessandro Sette, Morten Nielsen, Bjoern Peters
A comprehensive analysis of the IEDB MHC class-I automated benchmark. Briefings Bioinform. 23 (4) (2022)
Sinu Paul, Nathan P. Croft, Anthony W. Purcell, David C. Tscharke, Alessandro Sette, Morten Nielsen, Bjoern Peters
Benchmarking predictions of MHC class I restricted T cell epitopes in a comprehensively studied model system. PLoS Comput. Biol. 16 (5) (2020)
Birkir Reynisson, Bruno Alvarez, Sinu Paul, Bjoern Peters, Morten Nielsen
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. 48 (Webserver-Issue) (2020)
Emilio Fenoy, José M. G. Izarzugaza, Vanessa Isabell Jurtz, Søren Brunak, Morten Nielsen
A generic deep convolutional neural network framework for prediction of receptor-ligand interactions - NetPhosPan: application to kinase phosphorylation prediction. Bioinform. 35 (7) (2019)
Swapnil Mahajan, Zhen Yan, Martin Closter Jespersen, Kamilla Kjærgaard Jensen, Paolo Marcatili, Morten Nielsen, Alessandro Sette, Bjoern Peters
Benchmark datasets of immune receptor-epitope structural complexes. BMC Bioinform. 20 (1) (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, Bjoern Peters
IEDB-AR: immune epitope database - analysis resource in 2019. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
Massimo Andreatta, Thomas Trolle, Zhen Yan, Jason A. Greenbaum, Bjoern Peters, Morten Nielsen
An automated benchmarking platform for MHC class II binding prediction methods. Bioinform. 34 (9) (2018)
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 M. Sollid, Arie Admon, Stefan Stevanovic, Hans-Georg Rammensee, Pierre Thibault, Claude Perreault, Michal Bassani-Sternberg, Ruedi Aebersold, Etienne Caron
The SysteMHC Atlas project. Nucleic Acids Res. 46 (Database-Issue) (2018)
Vanessa Isabell Jurtz, Alexander Rosenberg Johansen, Morten Nielsen, José Juan Almagro Armenteros, Henrik Nielsen, Casper Kaae Sønderby, Ole Winther, Søren Kaae Sønderby
An introduction to deep learning on biological sequence data: examples and solutions. Bioinform. 33 (22) (2017)
Massimo Andreatta, Bruno Alvarez, Morten Nielsen
GibbsCluster: unsupervised clustering and alignment of peptide sequences. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Morten Nielsen, Massimo Andreatta
NNAlign: a platform to construct and evaluate artificial neural network models of receptor-ligand interactions. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Diego J. Zea, Diego Anfossi, Morten Nielsen, Cristina Marino Buslje
MIToS.jl: mutual information tools for protein sequence analysis in the Julia language. Bioinform. 33 (4) (2017)
Martin Closter Jespersen, Bjoern Peters, Morten Nielsen, Paolo Marcatili
BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Massimo Andreatta, Morten Nielsen
Gapped sequence alignment using artificial neural networks: application to the MHC class I system. Bioinform. 32 (4) (2016)
Michael Schantz Klausen, Mads Valdemar Anderson, Martin Closter Jespersen, Morten Nielsen, Paolo Marcatili
LYRA, a webserver for lymphocyte receptor structural modeling. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
Thomas Trolle, Imir G. Metushi, Jason A. Greenbaum, Yohan Kim, John Sidney, Ole Lund, Alessandro Sette, Bjoern Peters, Morten Nielsen
Automated benchmarking of peptide-MHC class I binding predictions. Bioinform. 31 (13) (2015)
Anne Bresciani, Jason Greenbaum, Cecilia S. Lindestam Arlehamn, Alessandro Sette, Morten Nielsen, Bjoern Peters
The interplay of sequence conservation and T cell immune recognition. BCB (2014)
Yohan Kim, John Sidney, Søren Buus, Alessandro Sette, Morten Nielsen, Bjoern Peters
Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions. BMC Bioinform. 15 (2014)
Franco L. Simonetti, Elin Teppa, Ariel Chernomoretz, Morten Nielsen, Cristina Marino Buslje
MISTIC: mutual information server to infer coevolution. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
Massimo Andreatta, Ole Lund, Morten Nielsen
Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach. Bioinform. 29 (1) (2013)
Leon Eyrich Jessen, Ilka Hoof, Ole Lund, Morten Nielsen
: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
Elin Teppa, Angela D. Wilkins, Morten Nielsen, Cristina Marino Buslje
Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction. BMC Bioinform. 13 (2012)
Jens Vindahl Kringelum, Claus Lundegaard, Ole Lund, Morten Nielsen
Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking. PLoS Comput. Biol. 8 (12) (2012)
Martin Christen Frølund Thomsen, Morten Nielsen
: 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. Nucleic Acids Res. 40 (Web-Server-Issue) (2012)
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 Res. 40 (Web-Server-Issue) (2012)
Cristina Marino Buslje, Elin Teppa, Tomás Di Domenico, José María Delfino, Morten Nielsen
Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic Residue Identification. PLoS Comput. Biol. 6 (11) (2010)
Morten Nielsen, Claus Lundegaard, Ole Lund, Thomas Nordahl Petersen
CPHmodels-3.0 - remote homology modeling using structure-guided sequence profiles. Nucleic Acids Res. 38 (Web-Server-Issue) (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)
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 Bioinform. 11 (2010)
Cristina Marino Buslje, Javier Santos, José María Delfino, Morten Nielsen
Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information. Bioinform. 25 (9) (2009)
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. Bioinform. 25 (10) (2009)
Morten Nielsen, Ole Lund
. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction. BMC Bioinform. 10 (2009)
Hao Zhang, Claus Lundegaard, Morten Nielsen
Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods. Bioinform. 25 (1) (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. Bioinform. 24 (11) (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 Res. 36 (Web-Server-Issue) (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 Res. 36 (Web-Server-Issue) (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 Comput. Biol. 4 (7) (2008)
Claus Lundegaard, Ole Lund, Can Kesmir, Søren Brunak, Morten Nielsen
Modeling the adaptive immune system: predictions and simulations. Bioinform. 23 (24) (2007)
Morten Nielsen, Claus Lundegaard, Ole Lund
Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. BMC Bioinform. 8 (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 Bioinform. 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 Comput. Biol. 2 (6) (2006)
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)
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. Bioinform. 20 (9) (2004)
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)
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 Comput. 15 (12) (2003)