BATMAN: Improved T cell receptor cross-reactivity prediction benchmarked on a comprehensive mutational scan database.

Predicting T cell receptor (TCR) activation is challenging due to the lack of both unbiased benchmarking datasets and computational methods that are sensitive to small mutations to a peptide. To address these challenges, we curated a comprehensive database encompassing complete single amino acid mutational assays of 10,750 TCR-peptide pairs, centered around 14 immunogenic peptides against 66 TCRs. We then present an interpretable Bayesian model, called BATMAN, that can predict the set of peptides that activates a TCR.

Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever.

Infection with Lassa virus (LASV) can cause Lassa fever, a haemorrhagic illness with an estimated fatality rate of 29.7%, but causes no or mild symptoms in many individuals. Here, to investigate whether human genetic variation underlies the heterogeneity of LASV infection, we carried out genome-wide association studies (GWAS) as well as seroprevalence surveys, human leukocyte antigen typing and high-throughput variant functional characterization assays.

copepodTCR: Identification of Antigen-Specific T Cell Receptors with combinatorial peptide pooling.

T cell receptor (TCR) repertoire diversity enables the orchestration of antigen-specific immune responses against the vast space of possible pathogens. Identifying TCR/antigen binding pairs from the large TCR repertoire and antigen space is crucial for biomedical research. Here, we introduce , an open-access tool for the design and interpretation of high-throughput experimental assays to determine TCR specificity.

Association between statin exposure and short-term mortality in patients with high-grade acute-on-chronic liver failure.

Background & Aims: Acute-on-chronic liver failure (ACLF) carries a high short-term mortality for patients with cirrhosis. Prior literature suggests that statin exposure may reduce the likelihood of ACLF events. However, it is unclear if statin exposure is associated with ACLF-related mortality.