Group publications

 

Publikationer rss feed

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     |    Year: 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     |    Year: 2019     |    DOI: https://doi.org/10.3389/fimmu.2019.00298

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CD8+ T cells from patients with narcolepsy and healthy controls recognize hypocretin neuron-specific antigens

Pedersen, Natasja Wulff ; Holm, Anja ; Kristensen, Nikolaj Pagh ; Bjerregaard, Anne-Mette ; Bentzen, Amalie Kai ; Marquard, Andrea Marion ; Tamhane, Tripti ; Burgdorf, Kristoffer Sølvsten ; Ullum, Henrik ; Jennum, Poul ; Knudsen, Stine ; Hadrup, Sine Reker ; Kornum, Birgitte Rahbek
in: Nature Communications, vol: 10, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41467-019-08774-1

 

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

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Immunoglobulin G structure and rheumatoid factor epitopes

Maibom-Thomsen, Sheila Lefoli ; Trier, Nicole Hartwig ; Holm, Bettina Eide ; Hansen, Kirsten Beth ; Rasmussen, Morten Ib ; Chailyan, Anna ; Marcatili, Paolo ; Højrup, Peter ; Houen, Gunnar
in: PLOS ONE, vol: 14, issue: 6

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1371/journal.pone.0217624

 

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     |    Year: 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     |    Year: 2019     |    DOI: https://doi.org/10.1002/prot.25674

 

Prediction of neoepitopes from murine sequencing data

Bjerregaard, Anne-Mette ; Pedersen, Thomas Kainamura ; Marquard, Andrea Marion ; Hadrup, Sine Reker
in: Cancer Immunology, Immunotherapy, vol: 68, issue: 1, pages: 159-161

Type: Comment/debate

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1007/s00262-018-2254-5

 

The ABCD database: a repository for chemically defined antibodies

Lima, Wanessa C. ; Gasteiger, Elisabeth ; Marcatili, Paolo ; Duek, Paula ; Bairoch, Amos ; Cosson, Pierre
in: Nucleic acids research

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1093/nar/gkz714

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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     |    Year: 2019     |    DOI: https://doi.org/10.1038/s42003-019-0442-2


https://www.bioinformatics.dtu.dk/research2018/research-groups/immunoinformatics-and-machine-learning1/gruppens-publikationer
16 SEPTEMBER 2019