Navami Jain

This paper evaluates variant effect prediction models on viruses, showing that state-of-the-art models underperform on viral proteins compared to alignment-based models, especially in low-sequence regimes.

The paper identifies a Prochlorococcus lineage in oxygen deficient zones that expresses both form I and form II rubiscos, suggesting an adaptation to low oxygen environments.

This study applies a network-based method to identify key genes in BRCA subtypes and chemotherapy response in TNBC, revealing subtype-specific mediators and potential therapeutic targets.

Phanta profiles human gut metagenomes to include viruses directly from short reads, identifying more viral species than assembly-based methods and revealing higher interindividual variability in the virome.