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List of works by Morten Nielsen

A Systematic, Unbiased Mapping of CD8+ and CD4+ T Cell Epitopes in Yellow Fever Vaccinees

scientific article published on 31 August 2020

A combined prediction strategy increases identification of peptides bound with high affinity and stability to porcine MHC class I molecules SLA-1*04:01, SLA-2*04:01, and SLA-3*04:01.

scientific article published on 14 November 2015

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

scientific article

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

scientific article published on 01 April 2019

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

scientific article published on 31 July 2009

A modern approach for epitope prediction: identification of foot-and-mouth disease virus peptides binding bovine leukocyte antigen (BoLA) class I molecules

scientific article published on 24 October 2015

A systematic, unbiased mapping of CD8+ and CD4+ T cell epitopes in Yellow Fever vaccinees

scientific article published on 02 April 2020

APRANK: Computational Prioritization of Antigenic Proteins and Peptides From Complete Pathogen Proteomes

scientific article published on 15 July 2021

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

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

scientific article

An Analysis of Natural T Cell Responses to Predicted Tumor Neoepitopes.

scientific article published on 15 November 2017

An automated benchmarking platform for MHC class II binding prediction methods

scientific article

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

An introduction to Deep learning on biological sequence data - Examples and solutions

scientific article published on 23 August 2017

Antibody Specific B-Cell Epitope Predictions: Leveraging Information From Antibody-Antigen Protein Complexes

scientific article published on 26 February 2019

ArrayPitope: Automated Analysis of Amino Acid Substitutions for Peptide Microarray-Based Antibody Epitope Mapping

scientific article

Automated benchmarking of peptide-MHC class I binding predictions

scientific article published on 25 February 2015

Benchmark datasets of immune receptor-epitope structural complexes

scientific article published on 10 October 2019

Benchmarking predictions of MHC class I restricted T cell epitopes in a comprehensively studied model system

scientific article published on 26 May 2020

Bioinformatics Tools for the Prediction of T-Cell Epitopes

scientific article published on 01 January 2018

Bioinformatics identification of antigenic peptide: predicting the specificity of major MHC class I and II pathway players

scientific article published in January 2013

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

scientific article published on 11 June 2010

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

scientific article published on 29 December 2006

Characterization of Antigenic MHC-Class-I-Restricted T Cell Epitopes in the Glycoprotein of Ebolavirus

scientific article published on 01 November 2019

Characterization of HIV-specific CD4+ T cell responses against peptides selected with broad population and pathogen coverage

scientific article

Characterization of binding specificities of bovine leucocyte class I molecules: impacts for rational epitope discovery

scientific article

Characterizing the binding motifs of 11 common human HLA‐DP and HLA‐DQ molecules using NNAlign ⬇️

scientific article published on July 1, 2012

Computational Tools for the Identification and Interpretation of Sequence Motifs in Immunopeptidomes

Computational Tools for the Identification and Interpretation of Sequence Motifs in Immunopeptidomes.

scientific article published on 12 January 2018

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

scientific article

Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions

scientific article

Defining the HLA class I-associated viral antigen repertoire from HIV-1-infected human cells

scientific article published on 15 October 2015

Definition of supertypes for HLA molecules using clustering of specificity matrices

scientific article published on 13 February 2004

Degree of predicted minor histocompatibility antigen mismatch correlates with poorer clinical outcomes in nonmyeloablative allogeneic hematopoietic cell transplantation

scientific article published on 28 March 2010

Designing bovine T cell vaccines via reverse immunology

scientific article published on 09 January 2012

Different binding motifs of the celiac disease-associated HLA molecules DQ2.5, DQ2.2, and DQ7.5 revealed by relative quantitative proteomics of endogenous peptide repertoires

scientific article

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

scientific article

Ebolavirus comparative genomics

scientific article (publication date: September 2015)

Enhancing Mass Spectrometry-Based MHC-I Peptide Identification Through a Targeted Database Search Approach

scientific article published on 01 January 2019

Epitope Specific Antibodies and T Cell Receptors in the Immune Epitope Database

scientific article published on 20 November 2018

Evaluation of peptide selection approaches for epitope-based vaccine design

scientific article published on October 2013

Expanding specificity of class I restricted CD8+ T cells for viral epitopes following multiple inoculations of swine with a human adenovirus vectored foot-and-mouth disease virus (FMDV) vaccine.

scientific article published on 27 July 2016

Factors Influencing the Prevalence of Resistance-Associated Substitutions in NS5A Protein in Treatment-Naive Patients with Chronic Hepatitis C

scientific article published on 07 April 2020

Footprints of antigen processing boost MHC class II natural ligand binding predictions

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

scientific article

GibbsCluster: unsupervised clustering and alignment of peptide sequences.

scientific article published on 12 April 2017

HLA Class II Specificity Assessed by High-Density Peptide Microarray Interactions

scientific article published on 01 June 2020

HLA class I binding 9mer peptides from influenza A virus induce CD4 T cell responses

scientific article

HLArestrictor--a tool for patient-specific predictions of HLA restriction elements and optimal epitopes within peptides

scientific article published on 16 November 2010

High-throughput sequencing enhanced phage display enables the identification of patient-specific epitope motifs in serum

scientific article published on 6 August 2015

HostPhinder: A Phage Host Prediction Tool

scientific article published on 4 May 2016

Human leukocyte antigen (HLA) class I restricted epitope discovery in yellow fewer and dengue viruses: importance of HLA binding strength

scientific article

IEDB-AR: immune epitope database-analysis resource in 2019

scientific article published on 01 July 2019

Identification and HLA-tetramer-validation of human CD4+ and CD8+ T cell responses against HCMV proteins IE1 and IE2.

scientific article

Identification of CD8+ T cell epitopes in the West Nile virus polyprotein by reverse-immunology using NetCTL.

scientific article

Identification of immediate early gene products of bovine herpes virus 1 (BHV-1) as dominant antigens recognized by CD8 T cells in immune cattle.

scientific article published on 3 July 2017

Identification of peptides from foot-and-mouth disease virus structural proteins bound by class I swine leukocyte antigen (SLA) alleles, SLA-1*0401 and SLA-2*0401.

scientific article

Identification of the cognate peptide-MHC target of T cell receptors using molecular modeling and force field scoring

scientific article

Immune epitope database analysis resource

scientific article

Immune epitope database analysis resource (IEDB-AR).

scientific article published on 31 May 2008

Immunization With the CSF-470 Vaccine Plus BCG and rhGM-CSF Induced in a Cutaneous Melanoma Patient a TCRβ Repertoire Found at Vaccination Site and Tumor Infiltrating Lymphocytes That Persisted in Blood

scientific article published on 18 September 2019

Immunogenicity of HLA Class I and II Double Restricted Influenza A-Derived Peptides

scientific article

Immunopeptidomic Data Integration to Artificial Neural Networks Enhances Protein-Drug Immunogenicity Prediction

scientific article published on 23 June 2020

Improved Prediction of Bovine Leucocyte Antigens (BoLA) Presented Ligands by Use of Mass-Spectrometry-Determined Ligand and in Vitro Binding Data

scientific article

Improved method for predicting linear B-cell epitopes

scientific article

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

scientific article published on 6 January 2018

Improved pan-specific MHC class I peptide-binding predictions using a novel representation of the MHC-binding cleft environment

scientific article published on February 2014

Improved pan-specific prediction of MHC class I peptide binding using a novel receptor clustering data partitioning strategy

scientific article

Improved peptide-MHC class II interaction prediction through integration of eluted ligand and peptide affinity data

scientific article published on 10 June 2019

Improved prediction of HLA antigen presentation hotspots: applications for immunogenicity risk assessment of therapeutic proteins

scientific article published on 03 October 2020

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

scientific article published on 12 February 2004

In Silico Guided Discovery of Novel Class I and II Trypanosoma cruzi Epitopes Recognized by T Cells from Chagas' Disease Patients

scientific article published on 14 February 2020

In silico peptide-binding predictions of passerine MHC class I reveal similarities across distantly related species, suggesting convergence on the level of protein function

scientific article published on 29 January 2013

In silico prediction of human pathogenicity in the γ-proteobacteria ⬇️

scientific article

Induction of foot-and-mouth disease virus-specific cytotoxic T cell killing by vaccination

scientific article

Interdisciplinary analysis of HIV-specific CD8+ T cell responses against variant epitopes reveals restricted TCR promiscuity.

scientific article published on 2 April 2010

LYRA, a webserver for lymphocyte receptor structural modeling

scientific article published on 24 May 2015

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

scientific article

Limitations of Ab initio predictions of peptide binding to MHC class II molecules

scientific article

MHC class II epitope predictive algorithms.

scientific article

MHC motif viewer

scientific article published on 3 September 2008

MHC-I Ligand Discovery Using Targeted Database Searches of Mass Spectrometry Data: Implications for T-Cell Immunotherapies.

scientific article

MHCcluster, a method for functional clustering of MHC molecules

scientific article published on 18 June 2013

MISTIC: Mutual information server to infer coevolution

scientific article published on 28 May 2013

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

scientific article published on 22 October 2016

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

scientific article

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

scientific article published on 29 September 2011

Magnetic ordering in the three-dimensional site-disordered Heisenberg model

article

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

scientific article published on 26 May 2010

MetaPhinder-Identifying Bacteriophage Sequences in Metagenomic Data Sets

scientific article

Metagenomic Analysis of Therapeutic PYO Phage Cocktails from 1997 to 2014.

scientific article published on 3 November 2017

Model of a sub-main transition in phospholipid bilayers.

scientific article published on September 1996

Modeling the adaptive immune system: predictions and simulations

scientific article published on 28 November 2007

Modelling the human immune system by combining bioinformatics and systems biology approaches

scientific article published on 27 October 2006

MuPeXI: prediction of neo-epitopes from tumor sequencing data.

scientific article

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

scientific article

NNAlign: a platform to construct and evaluate artificial neural network models of receptor-ligand interactions.

scientific article published in July 2017

NNAlign: a web-based prediction method allowing non-expert end-user discovery of sequence motifs in quantitative peptide data

scientific article (publication date: 2011)

NNAlign_MA; MHC Peptidome Deconvolution for Accurate MHC Binding Motif Characterization and Improved T-cell Epitope Predictions

scientific article published on 02 October 2019

Neoantigen-specific CD8 T cell responses in the peripheral blood following PD-L1 blockade might predict therapy outcome in metastatic urothelial carcinoma

scientific article published on 11 April 2022

NetAllergen, a random forest model integrating MHC-II presentation propensity for improved allergenicity prediction

scientific article published in 2023

NetCTLpan: pan-specific MHC class I pathway epitope predictions

scientific article

NetH2pan: A Computational Tool to Guide MHC peptide prediction on Murine Tumors

scientific article published on 3 April 2018

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

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

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

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

scientific article published on 20 October 2011

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

scientific article published on 12 November 2008

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

scientific article

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 30 March 2016

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

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

scientific article published on 14 May 2020

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

scientific article published in January 2014

NetTepi: an integrated method for the prediction of T cell epitopes

scientific article published on 27 May 2014

Networks of high mutual information define the structural proximity of catalytic sites: implications for catalytic residue identification.

scientific article

No evidence for the use of DIR, D-D fusions, chromosome 15 open reading frames or VH replacement in the peripheral repertoire was found on application of an improved algorithm, JointML, to 6329 human immunoglobulin H rearrangements

scientific article published in October 2006

Off-lattice model for the phase behavior of lipid-cholesterol bilayers

scientific article published in May 1999

Pan-Specific Prediction of Peptide-MHC Class I Complex Stability, a Correlate of T Cell Immunogenicity

scientific article published on 8 July 2016

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

scientific article

Peptide binding predictions for HLA DR, DP and DQ molecules

scientific article

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

scientific article published on 4 February 2009

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

scientific article published on June 2012

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

PopCover-2.0. Improved Selection of Peptide Sets With Optimal HLA and Pathogen Diversity Coverage

publication published on 17 August 2021

Porcine major histocompatibility complex (MHC) class I molecules and analysis of their peptide-binding specificities

scientific article

Predicted MHC peptide binding promiscuity explains MHC class I 'hotspots' of antigen presentation defined by mass spectrometry eluted ligand data.

scientific article published on 15 February 2018

Prediction and in vitro verification of potential CTL epitopes conserved among PRRSV-2 strains

scientific article

Prediction of Antibody Epitopes

scientific article published on 01 January 2015

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

scientific article

Prediction of epitopes using neural network based methods

scientific article published on 31 October 2010

Prediction of protein secondary structure at 80% accuracy

scientific article published in October 2000

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

scientific article published on 25 September 2006

Predictions versus high-throughput experiments in T-cell epitope discovery: competition or synergy?

scientific article published on January 2012

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

scientific article

Random-lattice models and simulation algorithms for the phase equilibria in two-dimensional condensed systems of particles with coupled internal and translational degrees of freedom

scientific article published in December 1996

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

scientific article

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

scientific article

SARS CTL vaccine candidates; HLA supertype-, genome-wide scanning and biochemical validation

scientific article

Selecting informative data for developing peptide-MHC binding predictors using a query by committee approach.

scientific article

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

Sequence diversity between class I MHC loci of African native and introduced Bos taurus cattle in Theileria parva endemic regions: in silico peptide binding prediction identifies distinct functional clusters

scientific article published on 6 February 2016

SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments

scientific article published on 12 June 2013

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

scientific article published on October 24, 2012

State of the art and challenges in sequence based T-cell epitope prediction

scientific article

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

scientific article

Structural properties of MHC class II ligands, implications for the prediction of MHC class II epitopes

scientific article

Systematic characterisation of cellular localisation and expression profiles of proteins containing MHC ligands

scientific article

T Cell Epitope Predictions

scientific article published on 11 February 2020

T cell receptor fingerprinting enables in-depth characterization of the interactions governing recognition of peptide-MHC complexes

scientific article published on 19 November 2018

T-Cell Receptor Cognate Target Prediction Based on Paired α and β Chain Sequence and Structural CDR Loop Similarities

scientific article published on 28 August 2019

T-cell recognition is shaped by epitope sequence conservation in the host proteome and microbiome

scientific article published on 20 January 2016

TCRpMHCmodels: Structural modelling of TCR-pMHC class I complexes

scientific article published on 10 October 2019

TRAV1-2+ CD8+ T-cells including oligoconal expansions of MAIT cells are enriched in the airways in human tuberculosis.

scientific article published on 5 June 2019

The Immune Epitope Database and Analysis Resource Program 2003-2018: reflections and outlook

scientific article published on 25 November 2019

The Intergenic Recombinant HLA-B∗46:01 Has a Distinctive Peptidome that Includes KIR2DL3 Ligands

scientific article published on May 2017

The Length Distribution of Class I-Restricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC Allele-Specific Binding Preference

scientific article published on 18 January 2016

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

scientific article

The peptide-binding specificity of HLA-A*3001 demonstrates membership of the HLA-A3 supertype

scientific article

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

The validity of predicted T-cell epitopes

scientific article published on 12 October 2006

Towards High-throughput Immunomics for Infectious Diseases: Use of Next-generation Peptide Microarrays for Rapid Discovery and Mapping of Antigenic Determinants

scientific article published on 28 April 2015

Unconventional Peptide Presentation by Major Histocompatibility Complex (MHC) Class I Allele HLA-A*02:01: BREAKING CONFINEMENT.

scientific article

Uncovering the peptide-binding specificities of HLA-C: a general strategy to determine the specificity of any MHC class I molecule

scientific article

Unmasking determinants of specificity in the human kinome.

scientific article published on 16 September 2015

Use of "one-pot, mix-and-read" peptide-MHC class I tetramers and predictive algorithms to improve detection of cytotoxic T lymphocyte responses in cattle.

scientific article

Use of a Regression Model to Study Host-Genomic Determinants of Phage Susceptibility in MRSA.

scientific article

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