List of works - Morten Nielsen

Reliable prediction of T-cell epitopes using neural networks with novel sequence representations

scientific article

Improved method for predicting linear B-cell epitopes

scientific article

NetMHCpan, a method for MHC class I binding prediction beyond humans

scientific article published on 12 November 2008

NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11

scientific article published on 7 May 2008

A generic method for assignment of reliability scores applied to solvent accessibility predictions

scientific article published on 31 July 2009

NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence

scientific article

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

scientific article

NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction

scientific article

Peptide binding predictions for HLA DR, DP and DQ molecules

scientific article

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

scientific article published on 4 July 2007

Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction

scientific article

Prediction of residues in discontinuous B-cell epitopes using protein 3D structures

scientific article published on 25 September 2006

NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data

scientific article published on 4 October 2017

Immune epitope database analysis resource

scientific article

The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage

NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets

scientific article published on March 30, 2016

CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles

scientific article published on 11 June 2010

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

scientific article

Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan

scientific article

A community resource benchmarking predictions of peptide binding to MHC-I molecules

scientific article published on 9 June 2006

Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach

scientific article published on 12 February 2004

An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions

scientific article published in August 2005

Definition of supertypes for HLA molecules using clustering of specificity matrices

scientific article published on 13 February 2004

Reliable B cell epitope predictions: impacts of method development and improved benchmarking

scientific article

MHC class II epitope predictive algorithms.

scientific article

NetMHCIIpan-3.0, a common pan-specific MHC class II prediction method including all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ.

scientific article published on 31 July 2013

Immune epitope database analysis resource (IEDB-AR).

scientific article published on 31 May 2008

NetMHCcons: a consensus method for the major histocompatibility complex class I predictions

scientific article published on 20 October 2011

Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers

scientific article published on 14 April 2008

Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification

scientific article

NetCTLpan: pan-specific MHC class I pathway epitope predictions

scientific article

NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure.

scientific article

MR1-restricted MAIT cells display ligand discrimination and pathogen selectivity through distinct T cell receptor usage

scientific article

Peptide-MHC class I stability is a better predictor than peptide affinity of CTL immunogenicity

scientific article published on June 2012

Structural analysis of B-cell epitopes in antibody:protein complexes

scientific article

Improved methods for predicting peptide binding affinity to MHC class II molecules

scientific article published on 6 January 2018

MISTIC: Mutual information server to infer coevolution

scientific article published on 28 May 2013

CTL epitopes for influenza A including the H5N1 bird flu; genome-, pathogen-, and HLA-wide screening

scientific article published on 29 December 2006

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

scientific article

Major histocompatibility complex class I binding predictions as a tool in epitope discovery.

scientific article published on 26 May 2010

Peptide binding to HLA class I molecules: homogenous, high-throughput screening, and affinity assays

scientific article published on 4 February 2009

Modeling the adaptive immune system: predictions and simulations

scientific article published on 28 November 2007

Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods

scientific article

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

scientific article

Prediction of epitopes using neural network based methods

scientific article published on 31 October 2010

Amino Acid Similarity Accounts for T Cell Cross-Reactivity and for “Holes” in the T Cell Repertoire

scientific article

Automated benchmarking of peptide-MHC class I binding predictions

scientific article published on 25 February 2015

NetMHCstab - predicting stability of peptide-MHC-I complexes; impacts for cytotoxic T lymphocyte epitope discovery

scientific article published in January 2014

Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach

scientific article published on October 24, 2012

Machine learning competition in immunology - Prediction of HLA class I binding peptides

scientific article published on 29 September 2011

List of works by Morten Nielsen

Reliable prediction of T-cell epitopes using neural networks with novel sequence representations

Improved method for predicting linear B-cell epitopes

NetMHCpan, a method for MHC class I binding prediction beyond humans

NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11

A generic method for assignment of reliability scores applied to solvent accessibility predictions

NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence

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

NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction

Peptide binding predictions for HLA DR, DP and DQ molecules

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

Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction

Prediction of residues in discontinuous B-cell epitopes using protein 3D structures

NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data

Immune epitope database analysis resource

The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage

NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets

CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles

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

Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan

A community resource benchmarking predictions of peptide binding to MHC-I molecules

Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach

An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions

Definition of supertypes for HLA molecules using clustering of specificity matrices

Reliable B cell epitope predictions: impacts of method development and improved benchmarking

MHC class II epitope predictive algorithms.

NetMHCIIpan-3.0, a common pan-specific MHC class II prediction method including all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ.

Immune epitope database analysis resource (IEDB-AR).

NetMHCcons: a consensus method for the major histocompatibility complex class I predictions

Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers

Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification

NetCTLpan: pan-specific MHC class I pathway epitope predictions

NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure.

MR1-restricted MAIT cells display ligand discrimination and pathogen selectivity through distinct T cell receptor usage

Peptide-MHC class I stability is a better predictor than peptide affinity of CTL immunogenicity

Structural analysis of B-cell epitopes in antibody:protein complexes

Improved methods for predicting peptide binding affinity to MHC class II molecules

MISTIC: Mutual information server to infer coevolution

CTL epitopes for influenza A including the H5N1 bird flu; genome-, pathogen-, and HLA-wide screening

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

Major histocompatibility complex class I binding predictions as a tool in epitope discovery.

Peptide binding to HLA class I molecules: homogenous, high-throughput screening, and affinity assays

Modeling the adaptive immune system: predictions and simulations

Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods

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

Prediction of epitopes using neural network based methods

Amino Acid Similarity Accounts for T Cell Cross-Reactivity and for “Holes” in the T Cell Repertoire

Automated benchmarking of peptide-MHC class I binding predictions

NetMHCstab - predicting stability of peptide-MHC-I complexes; impacts for cytotoxic T lymphocyte epitope discovery

Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach

Machine learning competition in immunology - Prediction of HLA class I binding peptides