Photo of Morten Nielsen
  • Kemitorvet, 204, 247

    2800 Kgs. Lyngby

    Denmark

1992 …2022

Research output per year

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Research Output

2020

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

Martini, S., Nielsen, M., Peters, B. & Sette, A., 2020, (Accepted/In press) In : Immunogenetics. 20 p.

Research output: Contribution to journalJournal articleResearchpeer-review

2019

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

Fenoy, E., Gonzalez-Izarzugaza, J. M., Jurtz, V., Brunak, S. & Nielsen, M., 2019, In : Bioinformatics. 35, 7, p. 1098-1107

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
62 Downloads (Pure)

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

Jespersen, M. C., Mahajan, S., Peters, B., Nielsen, M. & Marcatili, P., 2019, In : Frontiers in Immunology. 10, 10 p., 298.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
212 Downloads (Pure)

Benchmark datasets of immune receptor-epitope structural complexes

Mahajan, S., Yan, Z., Jespersen, M. C., Jensen, K. K., Marcatili, P., Nielsen, M., Sette, A. & Peters, B., 2019, In : BMC Bioinformatics. 20, 1, 7 p., 490.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
22 Downloads (Pure)

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

Powlson, J., Wright, D., Zeltina, A., Giza, M., Nielsen, M., Rampling, T., Venkatrakaman, N., Bowden, T. A., Hill, A. V. S. & Ewer, K. J., 2019, In : Cell Reports. 29, 9, p. 2537-2545.e3

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
7 Downloads (Pure)

Dissecting the T cell receptor interactions governing recognition of peptide-MHC complexes

Bentzen, A. K., Such, L., Jensen, K. K., Marquard, A. M., Jessen, L. E., Miller, N. J., Church, C. D., Lyngaa, R. B., Koelle, D. M., Becker, J. C., Linnemann, C., Schumacher, T. N. M., Marcatili, P., Nghiem, P., Nielsen, M. & Hadrup, S. R., 2019, In : European Journal of Immunology. 49, Suppl. 3 SI, p. 1787-1787 O116.

Research output: Contribution to journalConference abstract in journalResearchpeer-review

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

Konda, P., Murphy, J. P., Nielsen, M. & Gujar, S., 2019, Immunoproteomics: Methods and protocols. Fulton, K. M. & Twine, S. M. (eds.). Springer, Vol. 2024. p. 301-307 7 p. (Methods in Molecular Biology).

Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

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

Dhanda, S. K., Mahajan, S., Paul, S., Yan, Z., Kim, H., Jespersen, M. C., Jurtz, V., Andreatta, M., Greenbaum, J. A., Marcatili, P., Sette, A., Nielsen, M. & Peters, B., 2019, In : Nucleic acids research. 47, 1, p. W502-W506

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
32 Downloads (Pure)

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

Aris, M., Bravo, A. I., Garcia Alvarez, H. M., Carri, I., Podaza, E., Blanco, P. A., Rotondaro, C., Bentivegna, S., Nielsen, M., Barrio, M. M. & Mordoh, J., 2019, In : Frontiers in Immunology. 10, 10 p., 2213.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
12 Downloads (Pure)

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

Garde, C., Ramarathinam, S. H., Jappe, E. C., Nielsen, M., Kringelum, J. V., Trolle, T. & Purcell, A. W., 2019, In : Immunogenetics. 71, 7, p. 445-454 10 p.

Research output: Contribution to journalJournal articleResearchpeer-review

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

Klausen, M. S., Jespersen, M. C., Nielsen, H., Jensen, K. K., Jurtz, V. I., Sønderby, C. K., Sommer, M. O. A., Winther, O., Nielsen, M., Petersen, B. & Marcatili, P., 2019, In : Proteins: Structure, Function, and Bioinformatics. 87, 6, p. 520-527 8 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File

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

Alvarez, B., Reynisson, B., Barra, C., Buus, S., Ternette, N., Connelley, T., Andreatta, M. & Nielsen, M., 2019, In : Molecular and Cellular Proteomics. 18, 12, p. 2459-2477

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
21 Downloads (Pure)

T-cell receptor cognate target prediction based on paired α and β chain sequence and structural CDR loop similarities

Lanzarotti, E., Marcatili, P. & Nielsen, M., 2019, In : Frontiers in Immunology. 10, 10 p., 2080.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
11 Downloads (Pure)

TCRpMHCmodels: Structural modelling of TCR-pMHC class I complexes

Jensen, K. K., Rantos, V., Jappe, E. C., Olsen, T. H., Jespersen, M. C., Jurtz, V. I., Jessen, L. E., Lanzarotti, E., Mahajan, S., Peters, B., Nielsen, M. & Marcatili, P., 2019, In : Scientific Reports. 9, 1, 12 p., 14530.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
16 Downloads (Pure)

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

Wong, E. B., Gold, M. C., Meermeier, E. W., Xulu, B. Z., Khuzwayo, S., Sullivan, Z. A., Mahyari, E., Rogers, Z., Kløverpris, H., Sharma, P. K., Worley, A. H., Lalloo, U., Baijnath, P., Ambaram, A., Naidoo, L., Suleman, M., Madansein, R., McLaren, J. E., Ladell, K., Miners, K. L. & 8 others, Price, D. A., Behar, S. M., Nielsen, M., Kasprowicz, V. O., Leslie, A., Bishai, W. R., Ndung'u, T. & Lewinsohn, D. M., 2019, In : Communications Biology. 2, 13 p., 203.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
58 Downloads (Pure)
2018

An automated benchmarking platform for MHC class II binding prediction methods

Andreatta, M., Trolle, T., Yan, Z., Greenbaum, J. A., Peters, B. & Nielsen, M., 2018, In : Bioinformatics. 34, 9, p. 1522-1528 7 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access

Bioinformatics Tools for the Prediction of T-Cell Epitopes

Andreatta, M. & Nielsen, M., 2018, Methods in Molecular Biology . Walker, J. M. (ed.). Springer, Vol. 1785. p. 269-281 13 p. (Methods in Molecular Biology).

Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

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

Alvarez, B., Barra, C., Nielsen, M. & Andreatta, M., 2018, In : Proteomics. 18, 12, 10 p., 1700252.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
75 Downloads (Pure)

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

Mahajan, S., Vita, R., Shackelford, D., Lane, J., Schulten, V., Zarebski, L., Jespersen, M. C., Marcatili, P., Nielsen, M., Sette, A. & Peters, B., 2018, In : Frontiers in Immunology. 9, 10 p., 2688.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
247 Downloads (Pure)

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

Lanzarotti, E., Marcatili, P. & Nielsen, M., 2018, In : Molecular Immunology. 94, p. 91-97 7 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
51 Downloads (Pure)

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

Jensen, K. K., Andreatta, M., Marcatili, P., Buus, S., Greenbaum, J. A., Yan, Z., Sette, A., Peters, B. & Nielsen, M., 2018, In : Immunology. 154, 3, p. 394-406

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
214 Downloads (Pure)

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

Nielsen, M., Connelley, T. & Ternette, N., 2018, In : Journal of Proteome Research. 17, 1, p. 559-567

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
169 Downloads (Pure)

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

DeVette, C. I., Andreatta, M., Bardet, W., Cate, S. J., Jurtz, V. I., Jackson, K. W., Welm, A. L., Nielsen, M. & Hildebrand, W. H., 2018, In : Cancer Immunology Research. 6, 6, p. 636-644 8 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
117 Downloads (Pure)

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

Jappe, E. C., Kringelum, J. V., Trolle, T. & Nielsen, M., 2018, In : Immunology. 154, 3, p. 407-417

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access

Predicting HLA CD4 Immunogenicity in Human Populations

Dhanda, S. K., Karosiene, E., Edwards, L., Grifoni, A., Paul, S., Andreatta, M., Weiskopf, D., Sidney, J., Nielsen, M., Peters, B. & Sette, A., 2018, In : Frontiers in Immunology. 9, 14 p., 1369.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
151 Downloads (Pure)

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

Bentzen, A. K., Such, L., Jensen, K. K., Marquard, A. M., Jessen, L. E., Miller, N. J., Church, C. D., Lyngaa, R. B., Koelle, D. M., Becker, J. C., Linnemann, C., Schumacher, T. N. M., Marcatili, P., Nghiem, P., Nielsen, M. & Hadrup, S. R., 2018, In : Nature Biotechnology. 36, 12, p. 1191-1196

Research output: Contribution to journalLetterResearchpeer-review

Open Access
File
87 Downloads (Pure)

The SysteMHC Atlas project

Shao, W., Pedrioli, P. G. A., Wolski, W., Scurtescu, C., Schmid, E., Vizcaino, J. A., Courcelles, M., Schuster, H., Kowalewski, D., Marino, F., Arlehamn, C. S. L., Vaughan, K., Peters, B., Sette, A., Ottenhoff, T. H. M., Meijgaarden, K. E., Nieuwenhuizen, N., Kaufmann, S. H. E., Schlapbach, R., Castle, J. C. & 26 others, Nesvizhskii, A. I., Nielsen, M., Deutsch, E. W., Campbell, D. S., Moritz, R. L., Zubarev, R. A., Ytterberg, A. J., Purcell, A. W., Marcilla, M., Paradela, A., Wang, Q., Costello, C. E., Ternette, N., van Veelen, P. A., van Els, C. A. C. M., Heck, A. J. R., de Souza, G. A., Sollid, L. M., Admon, A., Stevanovic, S., Rammensee, H-G., Thibault, P., Perreault, C., Bassani-Sternberg, M., Aebersold, R. & Caron, E., 2018, In : Nucleic acids research. 46, D1, p. D1237-D1247

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
178 Downloads (Pure)

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

Zschach, H., Larsen, M. V., Hasman, H., Westh, H., Nielsen, M., Międzybrodzki, R., Jończyk-Matysiak, E., Weber-Dąbrowska, B. & Górski, A., 2018, In : The Journal of Antibiotics. 7, 1, 16 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
309 Downloads (Pure)

Utilizing Computational Machine Learning Tools to Understand Immunogenic Breadth of HIV in the Context of a CD8 T-cell Mediated HIV Response

Hare, J., Dalel, J., Rosenthal, R., Fiore-Gartland, A., Monaco, D., McGowan, E., De Bont, J., Nielsen, M., Hunter, E. & Gilmour, J., 2018, In : Aids Research and Human Retroviruses. 34, Suppl. 1, p. 32-32 OA07.03.

Research output: Contribution to journalConference abstract in journalResearchpeer-review

2017

An Analysis of Natural T Cell Responses to Predicted Tumor Neoepitopes

Bjerregaard, A-M., Nielsen, M., Jurtz, V. I., Barra, C. M., Hadrup, S. R., Szallasi, Z. I. & Eklund, A. C., 2017, In : Frontiers in Immunology. 8, 1566.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
280 Downloads (Pure)

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

Hansen, C. S., Østerbye, T., Marcatili, P., Lund, O., Buus, S. & Nielsen, M., 2017, In : P L o S One. 12, 1, 14 p., e0168453.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
281 Downloads (Pure)

BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes

Jespersen, M. C., Peters, B., Nielsen, M. & Marcatili, P., 2017, In : Nucleic acids research. 45, W1, 6 p., gkx346.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
340 Downloads (Pure)

Breaking confinement: unconventional peptide presentation by major histocompatibility (MHC) class I allele HLA-A*02:01

Remesh, S. G., Andreatta, M., Ying, G., Kaever, T., Nielsen, M., McMurtrey, C. P., Hildebrand, W., Peters, B. & Zajonc, D. M., 2017, In : Journal of Biological Chemistry. 292, 13, p. 5262-5270 jbc.M117.776542.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
92 Downloads (Pure)

Citrullination only infrequently impacts peptide binding to HLA class II MHC

Sidney, J., Becart, S., Zhou, M., Duffy, K., Lindvall, M., Moore, E. C., Moore, E. L., Rao, T., Rao, N., Nielsen, M., Peters, B., Sette, A. & Goldberg, A. C. (ed.), 2017, In : P L o S One. 12, 5, 17 p., e0177140.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
153 Downloads (Pure)

GibbsCluster: unsupervised clustering and alignment of peptide sequences

Andreatta, M., Alvarez, B. & Nielsen, M., 2017, In : Nucleic acids research. 45, W1, p. W458-W463 6 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
153 Downloads (Pure)

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

Hart, J., MacHugh, N. D., Sheldrake, T., Nielsen, M. & Morrison, W. I., 2017, In : Journal of General Virology. 12 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
130 Downloads (Pure)

Machine Learning Reveals a Non-Canonical Mode of Peptide Binding to MHC class II Molecules

Andreatta, M., Jurtz, V. I., Kaever, T., Sette, A., Peters, B. & Nielsen, M., 2017, In : Immunology. p. 255-264

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
155 Downloads (Pure)

Metagenomic Analysis of Therapeutic PYO Phage Cocktails from 1997 to 2014

Villarroel, J., Larsen, M. V., Kilstrup, M. & Nielsen, M., 2017, In : Viruses. 9, 11, 22 p., 328.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
287 Downloads (Pure)

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

Murphy, J. P., Konda, P., Kowalewski, D. J., Schuster, H., Clements, D., Kim, Y., Cohen, A. M., Sharif, T., Nielsen, M., Stevanovic, S., Lee, P. W. & Gujar, S., 2017, In : Journal of Proteome Research. 16, 4, p. 1806-1816 11 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
157 Downloads (Pure)

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

Zea, D. J., Anfossi, D., Nielsen, M. & Marino-Buslje, C., 2017, In : Bioinformatics. 33, 4, 2 p., btw646.

Research output: Contribution to journalJournal articleResearchpeer-review

MuPeXI: prediction of neo-epitopes from tumor sequencing data

Bjerregaard, A-M., Nielsen, M., Hadrup, S. R., Szallasi, Z. I. & Eklund, A. C., 2017, In : Cancer Immunology, Immunotherapy. 66, 9, p. 1123–1130

Research output: Contribution to journalJournal articleResearchpeer-review

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

Jurtz, V. I., Paul, S., Andreatta, M., Marcatili, P., Peters, B. & Nielsen, M., 2017, In : Journal of Immunology. 199, 8, 10 p.

Research output: Contribution to journalJournal articleResearchpeer-review

File
142 Downloads (Pure)

Next-generation ELISA diagnostic assay for Chagas Disease based on the combination of short peptidic epitopes

Mucci, J., Carmona, S. J., Volcovich, R., Altcheh, J., Bracamonte, E., Marco, J. D., Nielsen, M., Buscaglia, C. A. & Aguero, F., 2017, In : P L o S Neglected Tropical Diseases (Online). 11, 10, 19 p., e0005972.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
164 Downloads (Pure)

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

Nielsen, M. & Andreatta, M., 2017, In : Nucleic acids research. 45, W1, p. W344-W349 6 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
208 Downloads (Pure)

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

Welner, S., Nielsen, M., Rasmussen, M., Buus, S., Jungersen, G. & Larsen, L. E., 2017, In : Immunogenetics. 69, 10, p. 689-702

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
159 Downloads (Pure)

Protein features as determinants of wild-type glycoside hydrolase thermostability

Geertz-Hansen, H. M., Kiemer, L., Nielsen, M., Stanchev, K., Blom, N., Brunak, S. & Petersen, T. N., 2017, In : Proteins: Structure, Function, and Bioinformatics. 85, 11, p. 2036-2044

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
141 Downloads (Pure)

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

Hilton, H. G., McMurtrey, C. P., Han, A. S., Djaoud, Z., Guethlein, L. A., Blokhuis, J. H., Pugh, J. L., Goyos, A., Horowitz, A., Buchli, R., Jackson, K. W., Bardet, W., Bushnell, D. A., Robinson, P. J., Mendoza, J. L., Birnbaum, M. E., Nielsen, M., Garcia, K. C., Hildebrand, W. H. & Parham, P., 2017, In : Cell Reports. 19, 7, p. 1394-1405

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
165 Downloads (Pure)
2016

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

Pedersen, L. E., Rasmussen, M., Harndahl, M., Nielsen, M., Buus, S. & Jungersen, G., 2016, In : Immunogenetics. 68, 2, p. 157-165

Research output: Contribution to journalJournal articleResearchpeer-review

A novel approach to probe host-pathogen interactions of bovine digital dermatitis, a model of a complex polymicrobial infection

Marcatili, P., Weiss Nielsen, M., Sicheritz-Pontén, T., Jensen, T. K., Schafer-Nielsen, C., Boye, M., Nielsen, M. & Schou, K. K., 2016, In : BMC Genomics. 17, 1, 13 p., 987.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
271 Downloads (Pure)

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

Ternette, N., Yang, H., Partridge, T., Llano, A., Cedeño, S., Fischer, R., Charles, P. D., Dudek, N. L., Mothe, B., Crespo, M., Fischer, W. M., Korber, B. T. M., Nielsen, M., Borrow, P., Purcell, A. W., Brander, C., Dorrell, L., Kessler, B. M. & Hanke, T., 2016, In : European Journal of Immunology. 46, 1, p. 60-69 10 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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216 Downloads (Pure)