Photo of Morten Nielsen
  • Kemitorvet, 204, 247

    2800 Kgs. Lyngby

    Denmark

1992 …2022

Research output per year

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Research Output

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Journal article
2020

In silico guided discovery of novel class i and ii trypanosoma cruzi epitopes recognized by T cells from chagas' disease patients

Acevedo, G. R., Juiz, N. A., Ziblat, A., Perri, L. P., Girard, M. C., Ossowski, M. S., Fernandez, M., Hernandez, Y., Chadi, R., Wittig, M., Franke, A., Nielsen, M. & Gomez, K. A., 2020, In : Journal of Immunology. 204, 6, p. 1571-1581

Research output: Contribution to journalJournal articleResearchpeer-review

T Cell Epitope Predictions

Peters, B., Nielsen, M. & Sette, A., 2020, In : Annual Review of Immunology. 38, 1, p. 123-145

Research output: Contribution to journalJournal articleResearchpeer-review

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

Martini, S., Nielsen, M., Peters, B. & Sette, A., 2020, In : Immunogenetics. 72, p. 57-76

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
111 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
279 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
66 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
39 Downloads (Pure)

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
76 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
32 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
84 Downloads (Pure)

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
71 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
39 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
53 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
89 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

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
122 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
315 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
95 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
272 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
211 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
172 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
192 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
217 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
344 Downloads (Pure)
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
324 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
345 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
412 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
125 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
193 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
201 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
170 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
203 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
351 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
203 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
192 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
202 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
250 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
195 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
196 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
208 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
327 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
File
255 Downloads (Pure)

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

Pedersen, L. E., Patch, J. R., Kenney, M., Glabman, R. A., Nielsen, M., Jungersen, G., Buus, S. & Golde, W. T., 2016, In : Veterinary Immunology and Immunopathology. 181, p. 59-67 9 p.

Research output: Contribution to journalJournal articleResearchpeer-review

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

Andreatta, M. & Nielsen, M., 2016, In : Bioinformatics. 32, 4, p. 511-517 7 p., btv639.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
383 Downloads (Pure)

HostPhinder: A Phage Host Prediction Tool

Villarroel, J., Kleinheinz, K. A., Jurtz, V. I., Zschach, H., Lund, O., Nielsen, M. & Larsen, M. V., 2016, In : Viruses. 8, 5, 22 p., 116.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
350 Downloads (Pure)