Scott Cain

This paper demonstrates agentic science on public infrastructure to ensure reproducibility by making all agent actions and workflows publicly accessible.

Apollo 3 is a new manual genome annotation tool that integrates with JBrowse 2, enabling multi-genome editing and synteny visualization.

The paper demonstrates a framework using BRC-Analytics and agentic AI to standardize RNA-seq analysis of fungal pathogens, achieving reproducible results across studies with differing annotations.

The paper introduces BRC-Analytics, a browser-based platform for pathogen genomics, demonstrating its use in analyzing measles virus evolutionary dynamics and revealing asymmetric frame evolution under selective pressures.

The paper introduces FHR, a metadata standard for reference genome data to improve interoperability and data provenance tracking across platforms.

The paper updates the Alliance of Genome Resources' central infrastructure, adding tools and enhancing data management and curation capabilities.

JBrowse 2 is a genome browser with enhanced views for structural variation and synteny, offering modular design and multiple usage options.

JBrowse Jupyter provides a Python interface to JBrowse 2 for interactive genomic visualization within Jupyter notebooks.