This paper analyzes SARS-CoV-2 Spike protein evolution, identifying epitopes and predicting immune escape by correlating structural and sequence data with DMS measurements.

Virus Evolution · Jan 1, 2025Peer-reviewedBiophysics

TRIM7 ubiquitinates SARS-CoV-2 membrane protein to limit apoptosis and viral replication

María González-Orozco, Tseng Hsiang-Chi, Adam Hage, Hongjie Xia, Padmanava Behera, Kazi Sabrina Afreen, Yoatzin Peñaflor-Téllez, María I. Giraldo, Matthew B. Huante, Lucinda Puebla-Clark, Sarah van Tol, Abby E. Odle, Matthew R. Crown, Natália Teruel, Thomas R. Shelite, , Ricardo Rajsbaum

This study identifies TRIM7 as an E3-ubiquitin ligase that ubiquitinates SARS-CoV-2 M protein to inhibit apoptosis and viral replication.

Nature Communications · Nov 30, 2024Peer-reviewedMicrobiology

OMEinfo: Global Geographic Metadata for -omics Experiments

Matthew R. Crown, Matthew Bashton

OMEinfo retrieves and standardizes geographical metadata for -omics experiments, enabling reproducible and consistent analysis of location-based data.

Bioinformatics Advances · Jan 1, 2024Peer-reviewedBioinformatics

ProCogGraph: A Graph-Based Mapping of Cognate Ligand Domain Interactions

Matthew R. Crown, Matthew Bashton

ProCogGraph maps cognate ligand domain interactions using a graph database, improving annotation specificity through ligand assignments.

Bioinformatics Advances · Jan 1, 2024Peer-reviewedBioinformatics

Lycopene Production in Dedicated Novel Chasses for Lignocellulosic Waste Material Utilisation Capable of Sustained Coculture

John Allan, Matthew R. Crown, Matthew Bashton, Gary W. Black

The paper isolates and characterizes strains capable of utilizing lignocellulosic waste for lycopene production, showing their potential in synthetic consortia and genetic modification.

bioRxiv · Oct 10, 2023 · PreprintSynthetic Biology

Viral burdens are associated with age and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection related sampling bias.

Helen R. Fryer, Tanya Golubchik, Matthew D. Hall, Christophe Fraser, Robert Hinch, Luca Ferretti A, Laura Thomson, Anel Nurtay, Lorenzo Pellis, George MacIntyre-Cockett, Amy Trebes, David Buck, Paolo Piazza, Angela Green, Lorne J. Lonie, , Katrina Lythgoe

This study adjusts for sampling bias in SARS-CoV-2 Ct values and finds that viral variant and age affect within-host viral burdens, with variant effects varying by vaccination status.

bioRxiv · Dec 2, 2022 · PreprintGenetics