Results 71 to 80 of about 4,155 (183)

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

A comparison of clustering models for inference of T cell receptor antigen specificity

ImmunoInformatics
The vast potential sequence diversity of TCRs and their ligands has presented an historic barrier to computational prediction of TCR epitope specificity, a holy grail of quantitative immunology.
Dan Hudson, Alex Lubbock, Mark Basham, Hashem Koohy   +3 more
doaj   +1 more source

Immunoinformatics: Current trends and future directions

Drug Discovery Today, 2009
Immunoinformatics has recently emerged as a critical field for accelerating immunology research. Although still an evolving process, computational models now play instrumental roles, not only in directing the selection of key experiments, but also in the formulation of new testable hypotheses through detailed analysis of complex immunologic data that ...
Tong, Joo Chuan, Ren, Ee Chee
openaire   +2 more sources

SARS-CoV-2-identical protein regions found in mammalian coronaviruses have immunogenic potential and can imply cross-protection

ImmunoInformatics
Coronaviruses are known to infect a wide range of mammals. In humans, coronaviruses have been responsible for causing the common cold. The immune response against common cold coronaviruses appears to elicit a cross-protective response to SARS-CoV-2. This
Luciano Rodrigo Lopes
doaj   +1 more source

Guiding a language-model based protein design method towards MHC Class-I immune-visibility targets in vaccines and therapeutics

ImmunoInformatics
Proteins have an arsenal of medical applications that include disrupting protein interactions, acting as potent vaccines, and replacing genetically deficient proteins.
Hans-Christof Gasser, Diego A. Oyarzún, Ajitha Rajan, Javier Antonio Alfaro   +3 more
doaj   +1 more source

Immunoglobulins: 25 Years of Immunoinformatics and IMGT-ONTOLOGY [PDF]

Biomolecules, 2014
IMGT®, the international ImMunoGeneTics information system® (CNRS and Montpellier University) is the global reference in immunogenetics and immunoinformatics. By its creation in 1989, IMGT® marked the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics.
openaire   +3 more sources