Morten Nielsen

Orcid: 0000-0001-7885-4311

Affiliations:
  • Technical University of Denmark, Center for Biological Sequence Analysis, Lyngby, Denmark
  • Universidad Nacional de San Martín, Buenos Aires, Argentina
  • McGill University, Department of Physics, Montreal, QC, Canada (PhD 1999)


According to our database1, Morten Nielsen authored at least 50 papers between 2003 and 2023.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

Legend:

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PhD thesis 
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Links

Online presence:

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Bibliography

2023
PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins.
BMC Bioinform., December, 2023

The Cancer Epitope Database and Analysis Resource (CEDAR).
Nucleic Acids Res., January, 2023

2022
NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning.
Nucleic Acids Res., 2022

A comprehensive analysis of the IEDB MHC class-I automated benchmark.
Briefings Bioinform., 2022

2021
Sampling SARS-CoV-2 Proteomes for Predicted CD8 T-Cell Epitopes as a Tool for Understanding Immunogenic Breadth and Rational Vaccine Design.
Frontiers Bioinform., 2021

2020
Benchmarking predictions of MHC class I restricted T cell epitopes in a comprehensively studied model system.
PLoS Comput. Biol., 2020

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., 2020

2019
IEDB-AR: immune epitope database - analysis resource in 2019.
Nucleic Acids Res., 2019

Benchmark datasets of immune receptor-epitope structural complexes.
BMC Bioinform., 2019

A generic deep convolutional neural network framework for prediction of receptor-ligand interactions - NetPhosPan: application to kinase phosphorylation prediction.
Bioinform., 2019

2018
The SysteMHC Atlas project.
Nucleic Acids Res., 2018

An automated benchmarking platform for MHC class II binding prediction methods.
Bioinform., 2018

2017
BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes.
Nucleic Acids Res., 2017

GibbsCluster: unsupervised clustering and alignment of peptide sequences.
Nucleic Acids Res., 2017

NNAlign: a platform to construct and evaluate artificial neural network models of receptor-ligand interactions.
Nucleic Acids Res., 2017

MIToS.jl: mutual information tools for protein sequence analysis in the Julia language.
Bioinform., 2017

An introduction to deep learning on biological sequence data: examples and solutions.
Bioinform., 2017

2016
Gapped sequence alignment using artificial neural networks: application to the MHC class I system.
Bioinform., 2016

2015
LYRA, a webserver for lymphocyte receptor structural modeling.
Nucleic Acids Res., 2015

Automated benchmarking of peptide-MHC class I binding predictions.
Bioinform., 2015

2014
Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions.
BMC Bioinform., 2014

The interplay of sequence conservation and T cell immune recognition.
Proceedings of the 5th ACM Conference on Bioinformatics, 2014

2013
MISTIC: mutual information server to infer coevolution.
Nucleic Acids Res., 2013

<i>SigniSite</i>: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments.
Nucleic Acids Res., 2013

Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach.
Bioinform., 2013

2012
Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking.
PLoS Comput. Biol., 2012

<i>Seq2Logo</i>: 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., 2012

Immune epitope database analysis resource.
Nucleic Acids Res., 2012

Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction.
BMC Bioinform., 2012

2010
Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic Residue Identification.
PLoS Comput. Biol., 2010

CPHmodels-3.0 - remote homology modeling using structure-guided sequence profiles.
Nucleic Acids Res., 2010

Peptide binding predictions for HLA DR, DP and DQ molecules.
BMC Bioinform., 2010

PopCover: a method for selecting of peptides with optimal population and pathogen coverage.
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010

2009
<i>NN-align</i>. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction.
BMC Bioinform., 2009

The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding.
Bioinform., 2009

Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods.
Bioinform., 2009

Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information.
Bioinform., 2009

2008
Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan.
PLoS Comput. Biol., 2008

Immune epitope database analysis resource (IEDB-AR).
Nucleic Acids Res., 2008

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., 2008

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., 2008

2007
Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method.
BMC Bioinform., 2007

Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction.
BMC Bioinform., 2007

Modeling the adaptive immune system: predictions and simulations.
Bioinform., 2007

2006
A Community Resource Benchmarking Predictions of Peptide Binding to MHC-I Molecules.
PLoS Comput. Biol., 2006

2005
Immunological bioinformatics.
Computational molecular biology, AAAI Press, ISBN: 978-0-262-12280-1, 2005

2004
Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach.
Bioinform., 2004

MHC Class I Epitope Binding Prediction Trained on Small Data Sets.
Proceedings of the Artificial Immune Systems, Third International Conference, 2004

2003
Selecting Informative Data for Developing Peptide-MHC Binding Predictors Using a Query by Committee Approach.
Neural Comput., 2003

Prediction of Protein Secondary Structure at High Accuracy Using a Combination of Many Neural Networks.
Proceedings of the Mathematical Methods for Protein Structure Analysis and Design, 2003


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