Katherine James

This paper introduces a bi-level diversity-optimization framework for selecting representative protein panels, reducing redundancy and improving diversity compared to existing methods.

This paper introduces ro-crate-rs, a Rust library for creating RO-Crates to manage synthetic biology data, enabling FAIR compliance and reproducibility in automated workflows.

The paper identifies genes and regulatory networks involved in shark tooth regeneration using RNAseq, highlighting the role of mycn in dental stem cell proliferation.

This study shows RBMX and RBMXL2 proteins regulate splicing of ultra-long exons by repressing cryptic splice sites, with RBMXL2 rescuing splicing defects in somatic cells.

The paper introduces ssNet, a method to integrate probabilistic functional networks without an external Gold Standard, showing comparable performance using Saccharomyces cerevisiae data.

The paper introduces Virtual Parts Repository 2, a resource for model-driven design of genetic regulatory circuits, providing modular and reusable models and a rule-based abstraction for scalable simulations.

The paper presents the complete genome of Hymenolepis microstoma, revealing chromosome structures capped by centromeres that serve both segregation and protection roles.

The paper shows RBMX prevents non-productive splicing of ultra-long exons, maintaining genome stability by blocking aberrant splice sites in genes like ETAA1.

The paper demonstrates how the SBOL standard can represent multicellular biological systems, enabling better sharing of complex designs across multiple cells.

The paper constructs a confidence-scored protein-protein interaction network for Hymenolepis microstoma using interologs from model organisms, revealing biologically meaningful clusters and potential interactions.

The paper reports the high-quality genome assembly of Pecten maximus, revealing gene duplicates and highlighting Nav1 as a candidate for toxin resistance.