Scott A. Handley

VICAST: An Integrated Toolkit for Viral Genome Annotation Curation and Low-Frequency Variant Analysis in Passage Studies

VICAST is a toolkit for viral genome annotation and low-frequency variant analysis in passage studies, offering improved speed and accuracy compared to existing tools.

Gut microbe-derived short-chain fatty acids regulate joint inflammation and activation of infiltrating and resident myeloid cells after alphavirus infection

This study shows that gut microbe-derived short-chain fatty acids reduce joint inflammation after alphavirus infection by modulating immune cell activity.

Dengue Virus Surveillance in Nepal Yields the First On-Site Whole Genome Sequences of Isolates from the 2022 Outbreak

The paper reports the first on-site whole genome sequencing of dengue virus isolates from Nepal's 2022 outbreak, identifying DENV1, 2, and 3 and linking them to sequences from India and China.

Host interactions of novel Crassvirales species belonging to multiple families infecting bacterial host, Bacteroides cellulosilyticus WH2

This study isolates and characterizes three novel Crassvirales phages infecting Bacteroides cellulosilyticus WH2, revealing they do not co-evolve with their hosts and share a conserved tail spike protein involved in host interaction.

Hecatomb: An End-to-End Research Platform for Viral Metagenomics

Hecatomb is a bioinformatics platform for viral metagenomics that enables read and contig analysis, integrating reference databases and providing tools for virome discovery.