Results 71 to 80 of about 4,043 (182)

The gremlin in the works: why T cell receptor researchers need to pay more attention to germline reference sequences

ImmunoInformatics
The rise of T cell receptor (TCR) sequencing technologies is driving both new understandings of the immune system and the development of novel clinical platforms. Such analyses rely on comparing recombined TCR sequences to unrearranged germline reference
James M. Heather, Ayelet Peres, Gur Yaari, William Lees   +3 more
doaj   +1 more source

IMGT-Choreography for immunogenetics and immunoinformatics.

In silico biology, 2004
IMGT, the international ImMunoGeneTics information system (http://imgt.cines.fr), was created in 1989 at Montpellier, France. IMGT is a high quality integrated knowledge resource specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrates, and related proteins of the immune system ...
Lefranc, Marie-Paule, Clément, Olivier, Kaas, Quentin, Duprat, Elodie, Chastellan, Patrick, Coelho, Isabelle, Combres, Kora, Ginestoux, Chantal, Giudicelli, Véronique, Chaume, Denys, Lefranc, Gérard   +10 more
openaire   +5 more sources

Building immune digital twins: An international and transdisciplinary community effort

ImmunoInformatics
Digital twins, initially developed for industrial applications, are set to make significant advancements in medicine and healthcare. They have demonstrated promising potential for drug development and personalised care, especially in cardiovascular ...
Anna Niarakis, Gary An, Luiz Ladeira, Noriko F. Hiroi, Athina Papadopoulou, Francis P. Crawley, Niloofar Nikaein, Laurence Calzone, Eirini Tsirvouli, Hasan Balci, Marina Esteban Medina, Lorenzo Veschini, Ozan Ozisik, Francesco Messina, Malvina Marku, Van Du T. Tran, Arnau Montagud, Nikola Schlosserova, Yashwanth Subbannayya, Martina Kutmon, Michael L. Blinov, Rahuman S Malik Sheriff, Robert Phair, Peter Hunter, Kristin Reiche, Jasmin Fisher, Liesbet Geris, Yaron Ilan, James A. Glazier, Philippe Moingeon, Reinhard Laubenbacher   +30 more
doaj   +1 more source

IApred: A versatile open-source tool for predicting protein antigenicity across diverse pathogens

ImmunoInformatics
Accurate prediction of protein antigenicity is crucial for vaccine development, diagnostic test design, and therapeutic protein engineering. However, existing tools face limitations in accessibility, computational efficiency, and pathogen diversity. Here,
Sebastian Miles, Gonzalo Menafra, Andrés Iriarte, Jose Alejandro Chabalgoity   +3 more
doaj   +1 more source

Where single-cell transcriptomics fails T cells: The misuse of unsupervised clustering for T-cell annotationThis perspective used publicly available data (DOI: 10.5281/zenodo.12569981; ).

ImmunoInformatics
The current state of single-cell transcriptomic interrogation typically consists of using an unsupervised clustering approach followed by expert opinion-based annotation.
Kerry A. Mullan, Sebastiaan Valkiers, Nicky de Vrij, Chen Li, Sara Verbandt, Ting Pu, Pieter Meysman   +6 more
doaj   +1 more source

Comparison of different substitution matrices for distance based T-cell receptor epitope predictions using tcrdist3

ImmunoInformatics
Various methods, differing in complexity, have been developed to predict T-cell receptor epitopes. tcrdist3, which implements an easy-to-interpret distance-based approach, has demonstrated performance comparable to the best feature-based methods. Here, a
Marc Hoffstedt, Hermann Wätzig, Knut Baumann   +2 more
doaj   +1 more source

AnalyzAIRR: A user-friendly guided workflow for AIRR data analysis

ImmunoInformatics
The analysis of bulk adaptive immune receptor repertoires (AIRR) enables the understanding of immune responses in both normal and pathological conditions.
Vanessa Mhanna, Gabriel Pires, Grégoire Bohl-Viallefond, Karim El Soufi, Nicolas Tchitchek, David Klatzmann, Adrien Six, Hang P. Pham, Encarnita Mariotti-Ferrandiz   +8 more
doaj   +1 more source

AMULETY: A Python package to embed adaptive immune receptor sequences

ImmunoInformatics
Large language models have been developed to capture relevant features of adaptive immune receptors, each with unique potential applications. However, the diversity in available models presents challenges in accessibility and usability for downstream ...
Meng Wang, Wengyao Jiang, Yuval Kluger, Steven H. Kleinstein, Gisela Gabernet   +4 more
doaj   +1 more source

Structural insights on the differentiation and reversion of conformational changes in SARS-CoV-2 spike protein models across variants occurring from December, 2019 to November, 2021

ImmunoInformatics
Conformational changes in the SARS-CoV-2 spike protein are critical for understanding viral evolution. In this study, we provide comparative structural and electrostatic analyses across variants, revealing both differentiation and reversion patterns not ...
Marni E. Cueno, Kenichi Imai
doaj   +1 more source

Building immunoglobulin and T cell receptor gene databases for the future

ImmunoInformatics
Genetic databases for immunoglobulin (IG) and T cell receptor (TR) genes have evolved from small catalogs to critical resources underpinning immunogenetic research.
Corey T. Watson, Andrew M. Collins, Mats Ohlin, James M. Heather, Ayelet Peres, William D. Lees, Gur Yaari   +6 more
doaj   +1 more source