DTU Sundhedsteknologi
DTU Bioinformatik
Morten Nielsen

Morten Nielsen

Gruppeleder, Professor

Institut for Sundhedsteknologi

Danmarks Tekniske Universitet

Kemitorvet

Bygning 208, rum 015

2800 Kgs. Lyngby

Tlf.
Tlf.
Fax 45 93 15 85
E-mail morni@dtu.dk
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2019
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A generic deep convolutional neural network framework for prediction of receptor–ligand interactions—NetPhosPan: application to kinase phosphorylation prediction

Fenoy, Emilio ; Gonzalez-Izarzugaza, Jose Maria ; Jurtz, Vanessa ; Brunak, Søren ; Nielsen, Morten
in: Bioinformatics, vol: 35, issue: 7, pages: 1098-1107

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2019     |    DOI: https://doi.org/10.1093/bioinformatics/bty715

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

Jespersen, Martin Closter ; Mahajan, Swapnil ; Peters, Bjoern ; Nielsen, Morten ; Marcatili, Paolo
in: Frontiers in Immunology, vol: 10

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2019     |    DOI: https://doi.org/10.3389/fimmu.2019.00298

 

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

Konda, Prathyusha ; Murphy, J. Patrick ; Nielsen, Morten ; Gujar, Shashi
part of: Immunoproteomics: Methods and protocols, pages: 301-307, 2019, Springer

Type: Book chapter (Peer reviewed)

Status: Published     |    År: 2019     |    DOI: https://doi.org/10.1007/978-1-4939-9597-4_19

 

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

Garde, Christian ; Ramarathinam, Sri H. ; Jappe, Emma Christine ; Nielsen, Morten ; Kringelum, Jens V. ; Trolle, Thomas ; Purcell, Anthony W.
in: Immunogenetics, vol: 71, issue: 7, pages: 445-454

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2019     |    DOI: https://doi.org/10.1007/s00251-019-01122-z

 

NetSurfP-2.0: Improved prediction of protein structural features by integrated deep learning

Klausen, Michael Schantz ; Jespersen, Martin Closter ; Nielsen, Henrik ; Jensen, Kamilla Kjærgaard ; Jurtz, Vanessa Isabell ; Sønderby, Casper Kaae ; Sommer, Morten Otto Alexander ; Winther, Ole ; Nielsen, Morten ; Petersen, Bent ; Marcatili, Paolo
in: Proteins: Structure, Function, and Bioinformatics, vol: 87, issue: 6, pages: 520-527

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2019     |    DOI: https://doi.org/10.1002/prot.25674

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

Wong, Emily B. ; Gold, Marielle C. ; Meermeier, Erin W. ; Xulu, Bongiwe Z. ; Khuzwayo, Sharon ; Sullivan, Zuri A. ; Mahyari, Eisa ; Rogers, Zoe ; Kløverpris, Hénrik ; Sharma, Prabhat K. ; Worley, Aneta H. ; Lalloo, Umesh ; Baijnath, Prinita ; Ambaram, Anish ; Naidoo, Leon ; Suleman, Moosa ; Madansein, Rajhmun ; McLaren, James E. ; Ladell, Kristin ; Miners, Kelly L. ; Price, David A. ; Behar, Samuel M. ; Nielsen, Morten ; Kasprowicz, Victoria O. ; Leslie, Alasdair ; Bishai, William R. ; Ndung'u, Thumbi ; Lewinsohn, David M.
in: Communications Biology, vol: 2

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2019     |    DOI: https://doi.org/10.1038/s42003-019-0442-2

2018
 

An automated benchmarking platform for MHC class II binding prediction methods

Andreatta, Massimo ; Trolle, Thomas ; Yan, Zhen ; Greenbaum, Jason A. ; Peters, Bjoern ; Nielsen, Morten
in: Bioinformatics, vol: 34, issue: 9, pages: 1522-1528

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2018     |    DOI: https://doi.org/10.1093/bioinformatics/btx820

 

Bioinformatics Tools for the Prediction of T-Cell Epitopes

Andreatta, Massimo ; Nielsen, Morten
part of: Methods in Molecular Biology , pages: 269-281, 2018, Springer

Type: Book chapter (Peer reviewed)

Status: Published     |    År: 2018     |    DOI: https://doi.org/10.1007/978-1-4939-7841-0_18

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

Alvarez, Bruno ; Barra, Carolina ; Nielsen, Morten ; Andreatta, Massimo
in: Proteomics, vol: 18, issue: 12

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2018     |    DOI: https://doi.org/10.1002/pmic.201700252

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

Mahajan, Swapnil ; Vita, Randi ; Shackelford, Deborah ; Lane, Jerome ; Schulten, Veronique ; Zarebski, Laura ; Jespersen, Martin Closter ; Marcatili, Paolo ; Nielsen, Morten ; Sette, Alessandro ; Peters, Bjoern
in: Frontiers in Immunology, vol: 9

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2018     |    DOI: https://doi.org/10.3389/fimmu.2018.02688