VACCIMEL, an allogeneic melanoma vaccine, efficiently triggers T cell immune responses against neoantigens and alloantigens, as well as against tumor-associated antigens

Authors: Ibel Carri, Erika Schwab, Juan Carlos Trivino, Erika M. von Euw, Morten Nielsen, José Mordoh, María Marcela Barrio

Source: Frontiers in Immunology, Vol 15 (2025)

Subject Terms: cancer immunotherapy, whole cancer cell vaccine, allogeneic vaccine, VACCIMEL, neoantigen, melanoma, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2024.1496204/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/67177528befd465ebfd7c3018bff6c91

Lessons learned from the IMMREP23 TCR-epitope prediction challenge

Authors: Morten Nielsen, Anne Eugster, Mathias Fynbo Jensen, Manisha Goel, Andreas Tiffeau-Mayer, Aurelien Pelissier, Sebastiaan Valkiers, María Rodríguez Martínez, Barthélémy Meynard-Piganeeau, Victor Greiff, Thierry Mora, Aleksandra M. Walczak, Giancarlo Croce, Dana L Moreno, David Gfeller, Pieter Meysman, Justin Barton

Source: ImmunoInformatics, Vol 16, Iss , Pp 100045- (2024)

Subject Terms: TCR specificity, Benchmark, Prediction, Machine learning, Computer applications to medicine. Medical informatics, R858-859.7

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2667119024000156; https://doaj.org/toc/2667-1190

Access URL: https://doaj.org/article/f6fbb017953840d38d207270376c7d65

Sustainable integration of artificial intelligence and machine learning approaches within the African infectious disease vaccine research and development ecosystem

Authors: Jonathan Hare, Morten Nielsen, Agnes Kiragga, Daniel Ochiel

Source: Frontiers in Pharmacology, Vol 15 (2024)

Subject Terms: machine learning (ML), artiificial intelligence, vaccines, Africa, drug discovery, Therapeutics. Pharmacology, RM1-950

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fphar.2024.1499079/full; https://doaj.org/toc/1663-9812

Access URL: https://doaj.org/article/ce7cc9bef8e341c78b5860030c8a6d89

LTX-315 and adoptive cell therapy using tumor-infiltrating lymphocytes generate tumor specific T cells in patients with metastatic soft tissue sarcoma

Authors: Morten Nielsen, Tine Monberg, Vibeke Sundvold, Benedetta Albieri, Dorrit Hovgaard, Michael Mørk Petersen, Anders Krarup-Hansen, Özcan Met, Ketil Camilio, Trevor Clancy, Richard Stratford, Baldur Sveinbjornsson, Øystein Rekdal, Niels Junker, Inge Marie Svane

Source: OncoImmunology, Vol 13, Iss 1 (2024)

Subject Terms: Adoptive cell therapy, immunotherapy, LTX-315, soft tissue sarcoma, T-cell therapy, tumor infiltrating lymphocytes, Immunologic diseases. Allergy, RC581-607, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://doaj.org/toc/2162-402X

Access URL: https://doaj.org/article/be8b6380d15946d0be5185169cae65f6

A modular protein language modelling approach to immunogenicity prediction.

Authors: Hugh O'Brien, Max Salm, Laura T Morton, Maciej Szukszto, Felix O'Farrell, Charlotte Boulton, Laurence King, Supreet Kaur Bola, Pablo D Becker, Andrew Craig, Morten Nielsen, Yardena Samuels, Charles Swanton, Marc R Mansour, Sine Reker Hadrup, Sergio A Quezada

Source: PLoS Computational Biology, Vol 20, Iss 11, p e1012511 (2024)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

Access URL: https://doaj.org/article/d0648697accf4d3db851dc1ee5b36eb3

MARS an improved de novo peptide candidate selection method for non-canonical antigen target discovery in cancer

Authors: Hanqing Liao, Carolina Barra, Zhicheng Zhou, Xu Peng, Isaac Woodhouse, Arun Tailor, Robert Parker, Alexia Carré, Persephone Borrow, Michael J. Hogan, Wayne Paes, Laurence C. Eisenlohr, Roberto Mallone, Morten Nielsen, Nicola Ternette

Source: Nature Communications, Vol 15, Iss 1, Pp 1-16 (2024)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/cf8a21489fa4434197893cf308fd3b24

PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins

Authors: Daniel Marrama, William D. Chronister, Luise Westernberg, Randi Vita, Zeynep Koşaloğlu-Yalçın, Alessandro Sette, Morten Nielsen, Jason A. Greenbaum, Bjoern Peters

Source: BMC Bioinformatics, Vol 24, Iss 1, Pp 1-14 (2023)

Subject Terms: Peptide matching, T-cell epitopes, Sequence searching, K-mer mapping, BLAST comparison, Benchmarking, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/1b54dfc343104abe9241d35bfc25c6f1

IMPROVE: a feature model to predict neoepitope immunogenicity through broad-scale validation of T-cell recognition

Authors: Annie Borch, Ibel Carri, Birkir Reynisson, Heli M. Garcia Alvarez, Kamilla K. Munk, Alessandro Montemurro, Nikolaj Pagh Kristensen, Siri A. Tvingsholm, Jeppe Sejerø Holm, Christina Heeke, Keith Henry Moss, Ulla Kring Hansen, Anna-Lisa Schaap-Johansen, Frederik Otzen Bagger, Vinicius Araujo Barbosa de Lima, Kristoffer S. Rohrberg, Samuel A. Funt, Marco Donia, Inge Marie Svane, Ulrik Lassen, Carolina Barra, Morten Nielsen, Sine Reker Hadrup

Source: Frontiers in Immunology, Vol 15 (2024)

Subject Terms: neoantigen, neoepitope prediction, machine learning, immunotherapy, immunoinformatics, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2024.1360281/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/0bbbca7628154c30a577b6a43214db8d

Benchmarking data-driven filtering for denoising of TCRpMHC single-cell data

Authors: Alessandro Montemurro, Helle Rus Povlsen, Leon Eyrich Jessen, Morten Nielsen

Source: Scientific Reports, Vol 13, Iss 1, Pp 1-13 (2023)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/c09fb08df37b403b8019257a19c7c5ca

The journey towards complete and accurate prediction of HLA antigen presentation

Authors: Jonas Birkelund Nilsson, Morten Nielsen

Source: ImmunoInformatics, Vol 13, Iss , Pp 100032- (2024)

Subject Terms: Computer applications to medicine. Medical informatics, R858-859.7

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2667119024000028; https://doaj.org/toc/2667-1190

Access URL: https://doaj.org/article/3ffe9e2240b14bb096450bdec7f52983

Enhancing TCR specificity predictions by combined pan- and peptide-specific training, loss-scaling, and sequence similarity integration

Authors: Mathias Fynbo Jensen, Morten Nielsen

Source: eLife, Vol 12 (2024)

Subject Terms: TCR specificity, machine learning, immunology, bioinformatics, Medicine, Science, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://elifesciences.org/articles/93934; https://doaj.org/toc/2050-084X

Access URL: https://doaj.org/article/3decb209a0714510b46e8018fb167246

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

Authors: Magnus Haraldson Høie, Frederik Steensgaard Gade, Julie Maria Johansen, Charlotte Würtzen, Ole Winther, Morten Nielsen, Paolo Marcatili

Source: Frontiers in Immunology, Vol 15 (2024)

Subject Terms: structure-based, B cell epitope prediction, inverse-folding, antibody epitope prediction, ESM-IF1, immunogenicity prediction, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2024.1322712/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/1bdcb6ec1ea745c19c8af6c2886e0985

Machine learning reveals limited contribution of trans-only encoded variants to the HLA-DQ immunopeptidome

Authors: Jonas Birkelund Nilsson, Saghar Kaabinejadian, Hooman Yari, Bjoern Peters, Carolina Barra, Loren Gragert, William Hildebrand, Morten Nielsen

Source: Communications Biology, Vol 6, Iss 1, Pp 1-13 (2023)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/2399-3642

Access URL: https://doaj.org/article/23d9fc25b4d049d9ac606f805ebaabd1

Beyond MHC binding: immunogenicity prediction tools to refine neoantigen selection in cancer patients

Authors: Ibel Carri, Erika Schwab, Enrique Podaza, Heli M. Garcia Alvarez, José Mordoh, Morten Nielsen, María Marcela Barrio

Source: Exploration of Immunology, Vol 3, Iss 2, Pp 82-103 (2023)

Subject Terms: neoantigen, cancer vaccine, melanoma, machine learning, neoepitope prediction, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.explorationpub.com/Journals/ei/Article/100391; https://doaj.org/toc/2768-6655

Access URL: https://doaj.org/article/20a4ab5fe42740d892c2977300cc671e

Thiopurine 6TG treatment increases tumor immunogenicity and response to immune checkpoint blockade

Authors: Loulieta Nazerai, Shona Caroline Willis, Patricio Yankilevich, Luca Di Leo, Francesca Maria Bosisio, Alex Frias, Corine Bertolotto, Jacob Nersting, Maria Thastrup, Soren Buus, Allan Randrup Thomsen, Morten Nielsen, Kristoffer Staal Rohrberg, Kjeld Schmiegelow, Daniela De Zio

Source: OncoImmunology, Vol 12, Iss 1 (2023)

Subject Terms: Thiopurine, 6TG, immune checkpoint inhibitors, melanoma, mouse model, Immunologic diseases. Allergy, RC581-607, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://doaj.org/toc/2162-402X

Access URL: https://doaj.org/article/4dfe4b677ec94c7b9323ef328b78f448

The structure of songbird MHC class I reveals antigen binding that is flexible at the N-terminus and static at the C-terminus

Authors: Sandra Eltschkner, Samantha Mellinger, Soren Buus, Morten Nielsen, Kajsa M. Paulsson, Karin Lindkvist-Petersson, Helena Westerdahl

Source: Frontiers in Immunology, Vol 14 (2023)

Subject Terms: Major Histocompatibility Complex, MHC class I, Passeriformes, X-ray structure, antigen presentation, great reed warbler, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2023.1209059/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/455a33948917410fbe59f17dd030ee1f

Neoantigen-specific CD8 T cell responses in the peripheral blood following PD-L1 blockade might predict therapy outcome in metastatic urothelial carcinoma

Authors: Jeppe Sejerø Holm, Samuel A. Funt, Annie Borch, Kamilla Kjærgaard Munk, Anne-Mette Bjerregaard, James L. Reading, Colleen Maher, Ashley Regazzi, Phillip Wong, Hikmat Al-Ahmadie, Gopa Iyer, Tripti Tamhane, Amalie Kai Bentzen, Nana Overgaard Herschend, Susan De Wolf, Alexandra Snyder, Taha Merghoub, Jedd D. Wolchok, Morten Nielsen, Jonathan E. Rosenberg, Dean F. Bajorin, Sine Reker Hadrup

Source: Nature Communications, Vol 13, Iss 1, Pp 1-17 (2022)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/1e76437c13374a28980b345248e7b551

Improved T cell receptor antigen pairing through data-driven filtering of sequencing information from single cells

Authors: Helle Rus Povlsen, Amalie Kai Bentzen, Mohammad Kadivar, Leon Eyrich Jessen, Sine Reker Hadrup, Morten Nielsen

Source: eLife, Vol 12 (2023)

Subject Terms: single-cell immune profiling, epitope specificity, T cell receptor, sequence similarity, evaluation methods, Medicine, Science, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://elifesciences.org/articles/81810; https://doaj.org/toc/2050-084X

Access URL: https://doaj.org/article/d76db3b2065948f48ebfd0903616482e

Benchmarking solutions to the T-cell receptor epitope prediction problem: IMMREP22 workshop report

Authors: Pieter Meysman, Justin Barton, Barbara Bravi, Liel Cohen-Lavi, Vadim Karnaukhov, Elias Lilleskov, Alessandro Montemurro, Morten Nielsen, Thierry Mora, Paul Pereira, Anna Postovskaya, María Rodríguez Martínez, Jorge Fernandez-de-Cossio-Diaz, Alexandra Vujkovic, Aleksandra M. Walczak, Anna Weber, Rose Yin, Anne Eugster, Virag Sharma

Source: ImmunoInformatics, Vol 9, Iss , Pp 100024- (2023)

Subject Terms: Computer applications to medicine. Medical informatics, R858-859.7

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2667119023000046; https://doaj.org/toc/2667-1190

Access URL: https://doaj.org/article/c337aa296bc14f0e8040baaeb0bebb9e

NetTCR-2.1: Lessons and guidance on how to develop models for TCR specificity predictions

Authors: Alessandro Montemurro, Leon Eyrich Jessen, Morten Nielsen

Source: Frontiers in Immunology, Vol 13 (2022)

Subject Terms: T cell, epitope, deep learning, TCR specificity, neural network, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2022.1055151/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/9f90f8a015f14aeeb8f2f844a59dd11f