Nielsen, Morten

NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data

Reynisson, B., Alvarez, B., Paul, S., Peters, B., & Nielsen, M. (2020) · Nucleic Acids Research

vaccines and immunoinformatics approachesImmunotherapy and Immune Responses

Cited by 2,361

Robust T Cell Immunity in Convalescent Individuals with Asymptomatic or Mild COVID-19

Sekine, T., Perez-Potti, A., Rivera-Ballesteros, O., Strålin, K., Gorin, J.-B., Olsson, A., Llewellyn-Lacey, S., Kamal, H., Bogdanovic, G., Muschiol, S., et al. (2020) · Cell

SARS-CoV-2 and COVID-19 ResearchT-cell and B-cell Immunology

Cited by 1,788

Reliable B cell epitope predictions: impacts of method development and improved benchmarking

Kringelum, J. V., Lundegaard, C., Lund, O., & Nielsen, M. (2012) · PLoS Computational Biology

vaccines and immunoinformatics approachesMachine Learning in Bioinformatics

Cited by 697

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., et al. (2019) · Nucleic Acids Research

vaccines and immunoinformatics approachesImmunotherapy and Immune Responses

Cited by 427

Structural analysis of B-cell epitopes in antibody: protein complexes

Kringelum, J. V., Nielsen, M., Padkjær, S. B., & Lund, O. (2013) · Molecular Immunology

vaccines and immunoinformatics approachesMonoclonal and Polyclonal Antibodies Research

Cited by 305

BepiPred-3.0: Improved B-cell epitope prediction using protein language models

Clifford, J., Høie, M. H., Nielsen, M., Deleuran, S., Peters, B., & Marcatili, P. (2022) · Protein Science

vaccines and immunoinformatics approachesMachine Learning in Bioinformatics

Cited by 296

BepiPred ‐3.0: Improved B‐cell epitope prediction using protein language models

Clifford, J. N., Høie, M. H., Deleuran, S., Peters, B., Nielsen, M., & Marcatili, P. (2022) · Protein Science

vaccines and immunoinformatics approachesMachine Learning in Bioinformatics

Cited by 296

DiscoTope-3.0: improved B-cell epitope prediction using inverse folding latent representations

Høie, M. H., Gade, F. S., Johansen, J. M., Würtzen, C., Winther, O., Nielsen, M., & Marcatili, P. (2024) · Frontiers in Immunology

vaccines and immunoinformatics approachesProtein Structure and Dynamics

Cited by 151

DiscoTope-3.0 - Improved B-cell epitope prediction using AlphaFold2 modeling and inverse folding latent representations

Høie, M. H., Gade, F. S., Johansen, J. M., Würtzen, C., Winther, O., Nielsen, M., & Marcatili, P. (2023) · Frontiers in Immunology

vaccines and immunoinformatics approachesProtein Structure and Dynamics

Cited by 151

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) · Frontiers in Immunology

vaccines and immunoinformatics approachesMonoclonal and Polyclonal Antibodies Research

Cited by 148

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., et al. (2018) · Frontiers in Immunology

vaccines and immunoinformatics approachesT-cell and B-cell Immunology

Cited by 53

NetMHCphosPan - Pan-specific prediction of MHC class I antigen presentation of phosphorylated ligands

Refsgaard, C. T., Barra, C., Peng, X., Ternette, N., & Nielsen, M. (2021) · ImmunoInformatics

vaccines and immunoinformatics approachesImmunotherapy and Immune Responses

Cited by 12

Molecular characterization of the archaic HLA-B*73:01 allele reveals presentation of a unique peptidome and skewed engagement by KIR2DL2

Ross, P., Hilton, H. G., Lodwick, J., Slezak, T., Guethlein, L. A., McMurtrey, C. P., Han, A. S., Nielsen, M., Yong, D., Dulberger, C. L., et al. (2024) · Journal of Biological Chemistry

vaccines and immunoinformatics approachesImmune Cell Function and Interaction

Cited by 1

Molecular characterization of the archaic HLA-B∗73:01 allele reveals presentation of a unique peptidome and skewed engagement by KIR2DL2

Ross, P., Hilton, H. G., Lodwick, J., Slezak, T., Guethlein, L. A., McMurtrey, C. P., Han, A. S., Nielsen, M., Yong, D., Dulberger, C. L., et al. (2025) · Journal of Biological Chemistry

vaccines and immunoinformatics approachesImmune Cell Function and Interaction

Cited by 1