Morten Nielsen

ResearcherID Loop profile ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 59

Top Venues

Communications biology

Nature communications

Nucleic acids research

Cancer immunology, immunotherapy : CII

Technical University of Denmark Center for Biological Sequence Analysis

McGill University (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Technical University of Denmark Center for Biological Sequence Analysis Aug 01 2016

Denmark

Professor :: Department of Bio and Health Informatics

Universidad Nacional de San Martín Jul 01 2012

Argentina

Profesor adjunto :: Instituto de Investigaciones Biotecnológicas

Technical University of Denmark Center for Biological Sequence Analysis Jul 01 2004 - Aug 01 2016

Denmark

Associate professor :: Department of Systems Biology

Technical University of Denmark Center for Biological Sequence Analysis Jul 01 2002 - Jul 01 2004

Denmark

Assistance professo :: Department of Systems Biology

Structural Bioinformatics AT A/S. Sep 01 1999 - Jul 01 2002

Denmark

Computational Scientist

Technical University of Denmark Jun 01 1999 - Sep 01 1999

Denmark

Research Assistant :: Department of Chemistry

Education History

McGill University Aug 01 1994 - Jun 01 1999

Canada

PHD :: Department of Physics

University of Copenhagen Aug 01 1990 - Aug 01 1994

Denmark

MSC :: Department of Physics

University of Copenhagen Aug 01 1986 - Aug 01 1990

Denmark

BSC :: Department of physics

Publications

Zhen Yan, Kevin Kim, Haeuk Kim, Brendan Ha, Anaïs Gambiez, Jason Bennett, Marcus Fabiano de Almeida Mendes, Raphael Trevizani, Jarjapu Mahita, Eve Richardson, Daniel Marrama, Nina Blazeska, Zeynep Koşaloğlu-Yalçın, Morten Nielsen, Alessandro Sette, Bjoern Peters, Jason A Greenbaum
Next-generation IEDB tools: a platform for epitope prediction and analysis. Nucleic acids research (2024)
Emilie Egholm Bruun Jensen, Birkir Reynisson, Carolina Barra, Morten Nielsen
New light on the HLA-DR immunopeptidomic landscape. Journal of leukocyte biology (2024)
Yat-Tsai Richie Wan, Zeynep Koşaloğlu-Yalçın, Bjoern Peters, Morten Nielsen
A large-scale study of peptide features defining immunogenicity of cancer neo-epitopes. NAR cancer 6 (1) (2024)
Hanqing Liao, Carolina Barra, Zhicheng Zhou, Xu Peng, Isaac B Woodhouse, Arun Tailor, Robert Parker, Alexia Carré, Persephone Borrow, Michael J Hogan, Wayne Paes, Laurence C Eisenlohr, Roberto Mallone, Morten Nielsen, Nicola Ternette
MARS an improved de novo peptide candidate selection method for non-canonical antigen target discovery in cancer. Nature communications 15 (1) (2024)
Hanqing Liao, Carolina Barra, Zhicheng Zhou, Xu Peng, Isaac B Woodhouse, Arun Tailor, Robert Parker, Alexia Carré, Persephone Borrow, Michael J Hogan, Wayne Paes, Laurence C Eisenlohr, Roberto Mallone, Morten Nielsen, Nicola Ternette
MARS an improved de novo peptide candidate selection method for non-canonical antigen target discovery in cancer. Nature communications 15 (1) (2024)
Hanqing Liao, Carolina Barra, Zhicheng Zhou, Xu Peng, Isaac B Woodhouse, Arun Tailor, Robert Parker, Alexia Carré, Persephone Borrow, Michael J Hogan, Wayne Paes, Laurence C Eisenlohr, Roberto Mallone, Morten Nielsen, Nicola Ternette
MARS an improved de novo peptide candidate selection method for non-canonical antigen target discovery in cancer. Nature communications 15 (1) (2024)
Mathias Fynbo Jensen, Morten Nielsen
Enhancing TCR specificity predictions by combined pan- and peptide-specific training, loss-scaling, and sequence similarity integration. eLife 12 (2024)
Emilie Egholm Bruun Jensen, Birkir Reynisson, Carolina Barra, Morten Nielsen
New light on the HLA-DR immunopeptidomic landscape. Journal of leukocyte biology 115 (5) (2024)
Patricio Yankilevich, Loulieta Nazerai, Shona Caroline Willis, Kjeld Schmiegelow, Daniela De Zio, Morten Nielsen
An analysis pipeline for understanding 6-thioguanine effects on a mouse tumour genome. Cancer immunology, immunotherapy : CII 73 (2) (2024)
Patricio Yankilevich, Loulieta Nazerai, Shona Caroline Willis, Kjeld Schmiegelow, Daniela De Zio, Morten Nielsen
An analysis pipeline for understanding 6-thioguanine effects on a mouse tumour genome. Cancer immunology, immunotherapy : CII 73 (2) (2024)
Mathias Fynbo Jensen, Morten Nielsen
Enhancing TCR specificity predictions by combined pan- and peptide-specific training, loss-scaling, and sequence similarity integration. eLife 12 (2024)
Yat-Tsai Richie Wan, Zeynep Koşaloğlu-Yalçın, Bjoern Peters, Morten Nielsen
A large-scale study of peptide features defining immunogenicity of cancer neo-epitopes. NAR cancer 6 (1) (2024)
Emilie Egholm Bruun Jensen, Birkir Reynisson, Carolina Barra, Morten Nielsen
New light on the HLA-DR immunopeptidomic landscape. Journal of leukocyte biology 115 (5) (2024)
Hanqing Liao, Carolina Barra, Zhicheng Zhou, Xu Peng, Isaac B Woodhouse, Arun Tailor, Robert Parker, Alexia Carré, Persephone Borrow, Michael J Hogan, Wayne Paes, Laurence C Eisenlohr, Roberto Mallone, Morten Nielsen, Nicola Ternette
MARS an improved de novo peptide candidate selection method for non-canonical antigen target discovery in cancer. Nature communications 15 (1) (2024)
Yat-Tsai Richie Wan, Zeynep Koşaloğlu-Yalçın, Bjoern Peters, Morten Nielsen
A large-scale study of peptide features defining immunogenicity of cancer neo-epitopes. NAR cancer 6 (1) (2024)
Mathias Fynbo Jensen, Morten Nielsen
Enhancing TCR specificity predictions by combined pan- and peptide-specific training, loss-scaling, and sequence similarity integration. eLife 12 (2024)
Hanqing Liao, Carolina Barra, Zhicheng Zhou, Xu Peng, Isaac B Woodhouse, Arun Tailor, Robert Parker, Alexia Carré, Persephone Borrow, Michael J Hogan, Wayne Paes, Laurence C Eisenlohr, Roberto Mallone, Morten Nielsen, Nicola Ternette
MARS an improved de novo peptide candidate selection method for non-canonical antigen target discovery in cancer. Nature communications 15 (1) (2024)
Hanqing Liao, Carolina Barra, Zhicheng Zhou, Xu Peng, Isaac B Woodhouse, Arun Tailor, Robert Parker, Alexia Carré, Persephone Borrow, Michael J Hogan, Wayne Paes, Laurence C Eisenlohr, Roberto Mallone, Morten Nielsen, Nicola Ternette
MARS an improved de novo peptide candidate selection method for non-canonical antigen target discovery in cancer. Nature communications 15 (1) (2024)
Mathias Fynbo Jensen, Morten Nielsen
Enhancing TCR specificity predictions by combined pan- and peptide-specific training, loss-scaling, and sequence similarity integration. eLife 12 (2024)
Patricio Yankilevich, Loulieta Nazerai, Shona Caroline Willis, Kjeld Schmiegelow, Daniela De Zio, Morten Nielsen
An analysis pipeline for understanding 6-thioguanine effects on a mouse tumour genome. Cancer immunology, immunotherapy : CII 73 (2) (2024)
Emilie Egholm Bruun Jensen, Birkir Reynisson, Carolina Barra, Morten Nielsen
New light on the HLA-DR immunopeptidomic landscape. Journal of leukocyte biology 115 (5) (2024)
Patricio Yankilevich, Loulieta Nazerai, Shona Caroline Willis, Kjeld Schmiegelow, Daniela De Zio, Morten Nielsen
An analysis pipeline for understanding 6-thioguanine effects on a mouse tumour genome. Cancer immunology, immunotherapy : CII 73 (2) (2024)
Zhen Yan, Kevin Kim, Haeuk Kim, Brendan Ha, Anaïs Gambiez, Jason Bennett, Marcus Fabiano de Almeida Mendes, Raphael Trevizani, Jarjapu Mahita, Eve Richardson, Daniel Marrama, Nina Blazeska, Zeynep Koşaloğlu-Yalçın, Morten Nielsen, Alessandro Sette, Bjoern Peters, Jason A Greenbaum
Next-generation IEDB tools: a platform for epitope prediction and analysis. Nucleic acids research 52 (W1) (2024)
Zhen Yan, Kevin Kim, Haeuk Kim, Brendan Ha, Anaïs Gambiez, Jason Bennett, Marcus Fabiano de Almeida Mendes, Raphael Trevizani, Jarjapu Mahita, Eve Richardson, Daniel Marrama, Nina Blazeska, Zeynep Koşaloğlu-Yalçın, Morten Nielsen, Alessandro Sette, Bjoern Peters, Jason A Greenbaum
Next-generation IEDB tools: a platform for epitope prediction and analysis. Nucleic acids research 52 (W1) (2024)
Patricio Yankilevich, Loulieta Nazerai, Shona Caroline Willis, Kjeld Schmiegelow, Daniela De Zio, Morten Nielsen
An analysis pipeline for understanding 6-thioguanine effects on a mouse tumour genome. Cancer immunology, immunotherapy : CII 73 (2) (2024)
Yuchen Li, Peter Wad Sackett, Morten Nielsen, Carolina Barra
NetAllergen, a random forest model integrating MHC-II presentation propensity for improved allergenicity prediction. Bioinformatics advances 3 (1) (2023)
Jonas Birkelund Nilsson, Saghar Kaabinejadian, Hooman Yari, Bjoern Peters, Carolina Barra, Loren Gragert, William Hildebrand, Morten Nielsen
Machine learning reveals limited contribution of trans-only encoded variants to the HLA-DQ immunopeptidome. Communications biology 6 (1) (2023)
Jonas Birkelund Nilsson, Saghar Kaabinejadian, Hooman Yari, Bjoern Peters, Carolina Barra, Loren Gragert, William Hildebrand, Morten Nielsen
Machine learning reveals limited contribution of trans-only encoded variants to the HLA-DQ immunopeptidome. Communications biology 6 (1) (2023)
Jonas Birkelund Nilsson, Saghar Kaabinejadian, Hooman Yari, Bjoern Peters, Carolina Barra, Loren Gragert, William Hildebrand, Morten Nielsen
Machine learning reveals limited contribution of trans-only encoded variants to the HLA-DQ immunopeptidome. Communications biology 6 (1) (2023)
Jonas Birkelund Nilsson, Saghar Kaabinejadian, Hooman Yari, Bjoern Peters, Carolina Barra, Loren Gragert, William Hildebrand, Morten Nielsen
Machine learning reveals limited contribution of trans-only encoded variants to the HLA-DQ immunopeptidome. Communications biology 6 (1) (2023)
Jonas Birkelund Nilsson, Saghar Kaabinejadian, Hooman Yari, Bjoern Peters, Carolina Barra, Loren Gragert, William Hildebrand, Morten Nielsen
Machine learning reveals limited contribution of trans-only encoded variants to the HLA-DQ immunopeptidome. Communications biology 6 (1) (2023)
Jonas Birkelund Nilsson, Saghar Kaabinejadian, Hooman Yari, Bjoern Peters, Carolina Barra, Loren Gragert, William Hildebrand, Morten Nielsen
Machine learning reveals limited contribution of trans-only encoded variants to the HLA-DQ immunopeptidome. Communications biology 6 (1) (2023)
Jonas Birkelund Nilsson, Saghar Kaabinejadian, Hooman Yari, Michel G D Kester, Peter van Balen, William H Hildebrand, Morten Nielsen
Accurate prediction of HLA class II antigen presentation across all loci using tailored data acquisition and refined machine learning. Science advances 9 (47) (2023)
Jonas Birkelund Nilsson, Saghar Kaabinejadian, Hooman Yari, Bjoern Peters, Carolina Barra, Loren Gragert, William Hildebrand, Morten Nielsen
Machine learning reveals limited contribution of trans-only encoded variants to the HLA-DQ immunopeptidome. Communications biology 6 (1) (2023)
Zeynep Koşaloğlu-Yalçın, Nina Blazeska, Randi Vita, Hannah Carter, Morten Nielsen, Stephen Schoenberger, Alessandro Sette, Bjoern Peters
The Cancer Epitope Database and Analysis Resource (CEDAR). Nucleic acids research (2022)
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 research (2022)
Muhammad Saad Khilji, Pouya Faridi, Erika Pinheiro-Machado, Carolin Hoefner, Tina Dahlby, Ritchlynn Aranha, Soren Buus, Morten Nielsen, Justyna Klusek, Thomas Mandrup-Poulsen, Kirti Pandey, Anthony Wayne Purcell, Michal Tomasz Marzec
Defective Proinsulin Handling Modulates the MHC I Bound Peptidome and Activates the Inflammasome in β-Cells. Biomedicines 10 (4) (2022)
Derek W Wright, William T Harvey, Joseph Hughes, MacGregor Cox, Thomas P Peacock, Rachel Colquhoun, Benjamin C Jackson, Richard J Orton, Morten Nielsen, Nienyun Sharon Hsu, null null, Ewan M Harrison, Thushan I de Silva, Andrew Rambaut, Sharon J Peacock, David L Robertson, Alessandro M Carabelli
Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer. Virus evolution 8 (1) (2022)
Jeppe Sejerø Holm, Samuel A Funt, Annie Borch, Kamilla Kjærgaard Munk, Anne-Mette Bjerregaard, James L Reading, Colleen A Maher, Ashley M Regazzi, Phillip Wong, Hikmat A Al-Ahmadie, Gopakumar V Iyer, Tripti Tamhane, Amalie Kai Bentzen, Nana Overgaard Herschend, Susan De Wolf, Alexandra Snyder, Taha Merghoub, Jedd D Wolchok, Morten Nielsen, Jonathan E Rosenberg, Dean F Bajorin, Sine Reker Hadrup
Neoantigen-specific CD8 T cell responses in the peripheral blood following PD-L1 blockade might predict therapy outcome in metastatic urothelial carcinoma. Nature communications 13 (1) (2022)
Timothy Connelley, Annalisa Nicastri, Tara Sheldrake, Christina Vrettou, Andressa Fisch, Birkir Reynisson, Soren Buus, Adrian Hill, Ivan Morrison, Morten Nielsen, Nicola Ternette
Immunopeptidomic Analysis of BoLA-I and BoLA-DR Presented Peptides from Theileria parva Infected Cells. Vaccines 10 (11) (2022)
Andressa Fisch, Birkir Reynisson, Lindert Benedictus, Annalisa Nicastri, Deepali Vasoya, Ivan Morrison, Soren Buus, Beatriz Rossetti Ferreira, Isabel Kinney Ferreira de Miranda Santos, Nicola Ternette, Tim Connelley, Morten Nielsen
Integral Use of Immunopeptidomics and Immunoinformatics for the Characterization of Antigen Presentation and Rational Identification of BoLA-DR-Presented Peptides and Epitopes. Journal of immunology (Baltimore, Md. : 1950) 206 (10) (2021)
Alessandro Montemurro, Viktoria Schuster, Helle Rus Povlsen, Amalie Kai Bentzen, Vanessa Jurtz, William D Chronister, Austin Crinklaw, Sine R Hadrup, Ole Winther, Bjoern Peters, Leon Eyrich Jessen, Morten Nielsen
NetTCR-2.0 enables accurate prediction of TCR-peptide binding by using paired TCRα and β sequence data. Communications biology 4 (1) (2021)
Sunil Kumar Saini, Ditte Stampe Hersby, Tripti Tamhane, Helle Rus Povlsen, Susana Patricia Amaya Hernandez, Morten Nielsen, Anne Ortved Gang, Sine Reker Hadrup
SARS-CoV-2 genome-wide T cell epitope mapping reveals immunodominance and substantial CD8+ T cell activation in COVID-19 patients. Science immunology 6 (58) (2021)
W Ivan Morrison, Adriana Aguado, Tara A Sheldrake, Nicholas C Palmateer, Olukemi O Ifeonu, Kyle Tretina, Keith Parsons, Emilio Fenoy, Timothy Connelley, Morten Nielsen, Joana C Silva
CD4 T Cell Responses to Theileria parva in Immune Cattle Recognize a Diverse Set of Parasite Antigens Presented on the Surface of Infected Lymphoblasts. Journal of immunology (Baltimore, Md. : 1950) 207 (8) (2021)
Yipeng Ma, Fenglan Liu, Tong Lin, Lei Chen, Aixin Jiang, Geng Tian, Morten Nielsen, Mingjun Wang
Large-Scale Identification of T-Cell Epitopes Derived From Severe Acute Respiratory Syndrome Coronavirus 2 for the Development of Peptide Vaccines Against Coronavirus Disease 2019. The Journal of infectious diseases 224 (6) (2021)
Thomas Osterbye, Morten Nielsen, Nadine L Dudek, Sri H Ramarathinam, Anthony Wayne Purcell, Claus Schafer-Nielsen, Soren Buus
HLA Class II Specificity Assessed by High-Density Peptide Microarray Interactions. Journal of immunology (Baltimore, Md. : 1950) 205 (1) (2020)
Anders Steenholdt Attermann, Carolina Barra, Birkir Reynisson, Heidi Schiøler Schultz, Ulrike Leurs, Kasper Lamberth, Morten Nielsen
Improved prediction of HLA antigen presentation hotspots: Applications for immunogenicity risk assessment of therapeutic proteins. Immunology 162 (2) (2020)
Birkir Reynisson, Carolina Barra, Saghar Kaabinejadian, William H Hildebrand, Bjoern Peters, Morten Nielsen
Improved Prediction of MHC II Antigen Presentation through Integration and Motif Deconvolution of Mass Spectrometry MHC Eluted Ligand Data. Journal of proteome research 19 (6) (2020)
Sinu Paul, Nathan Paul Croft, Anthony Wayne Purcell, David Carl Tscharke, Alessandro Sette, Morten Nielsen, Bjoern Peters
Benchmarking predictions of MHC class I restricted T cell epitopes in a comprehensively studied model system. PLoS computational biology 16 (5) (2020)
Emily B Wong, Marielle C Gold, Erin W Meermeier, Bongiwe Z Xulu, Sharon Khuzwayo, Zuri A Sullivan, Eisa Mahyari, Zoe Rogers, Hénrik Kløverpris, Prabhat K Sharma, Aneta H Worley, Umesh Lalloo, Prinita Baijnath, Anish Ambaram, Leon Naidoo, Moosa Suleman, Rajhmun Madansein, James E McLaren, Kristin Ladell, Kelly L Miners, David A Price, Samuel M Behar, Morten Nielsen, Victoria O Kasprowicz, Alasdair Leslie, William R Bishai, Thumbi Ndung'u, David M Lewinsohn
TRAV1-2+ CD8+ T-cells including oligoconal expansions of MAIT cells are enriched in the airways in human tuberculosis. Communications biology 2 (2019)
Sheridan Martini, Morten Nielsen, Bjoern Peters, Alessandro Sette
The Immune Epitope Database and Analysis Resource Program 2003-2018: reflections and outlook. Immunogenetics 72 (1-2) (2019)
Kamilla Kjaergaard Jensen, Vasileios Rantos, Emma Christine Jappe, Tobias Hegelund Olsen, Martin Closter Jespersen, Vanessa Jurtz, Leon Eyrich Jessen, Esteban Lanzarotti, Swapnil Mahajan, Bjoern Peters, Morten Nielsen, Paolo Marcatili
TCRpMHCmodels: Structural modelling of TCR-pMHC class I complexes. Scientific reports 9 (1) (2019)
Henrike Zschach, Mette V Larsen, Henrik Hasman, Henrik Westh, Morten Nielsen, Ryszard Międzybrodzki, Ewa Jończyk-Matysiak, Beata Weber-Dąbrowska, Andrzej Górski
Use of a Regression Model to Study Host-Genomic Determinants of Phage Susceptibility in MRSA. Antibiotics (Basel, Switzerland) 7 (1) (2018)
Kamilla Kjaergaard Jensen, Massimo Andreatta, Paolo Marcatili, Søren Buus, Jason A Greenbaum, Zhen Yan, Alessandro Sette, Bjoern Peters, Morten Nielsen
Improved methods for predicting peptide binding affinity to MHC class II molecules. Immunology 154 (3) (2018)
Christa I DeVette, Massimo Andreatta, Wilfried Bardet, Steven J Cate, Vanessa I Jurtz, Kenneth W Jackson, Alana L Welm, Morten Nielsen, William H Hildebrand
NetH2pan: A Computational Tool to Guide MHC Peptide Prediction on Murine Tumors. Cancer immunology research 6 (6) (2018)
Emma Christine Jappe, Jens Kringelum, Thomas Trolle, Morten Nielsen
Predicted MHC peptide binding promiscuity explains MHC class I 'hotspots' of antigen presentation defined by mass spectrometry eluted ligand data. Immunology 154 (3) (2018)
Christian Skjødt Hansen, Thomas Østerbye, Paolo Marcatili, Ole Lund, Søren Buus, Morten Nielsen
ArrayPitope: Automated Analysis of Amino Acid Substitutions for Peptide Microarray-Based Antibody Epitope Mapping. PloS one 12 (1) (2017)
Vanessa Jurtz, Sinu Paul, Massimo Andreatta, Paolo Marcatili, Bjoern Peters, Morten Nielsen
NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data. Journal of immunology (Baltimore, Md. : 1950) 199 (9) (2017)
Morten Nielsen, Tim Connelley, Nicola Ternette
Improved Prediction of Bovine Leucocyte Antigens (BoLA) Presented Ligands by Use of Mass-Spectrometry-Determined Ligand and in Vitro Binding Data. Journal of proteome research 17 (1) (2017)

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Publication Activity (10 Years)

Top Topics

Top Venues

Morten Nielsen