Virag Sharma

TOGA integrates gene annotation and orthology inference across hundreds of genomes, improving ortholog detection and creating large comparative gene resources.

The paper benchmarks 23 TCR-epitope prediction models, finding that using paired-chain alpha-beta and CDR1/2/V/J data improves performance, and simple distance-based methods can be competitive.

The paper identifies convergent loss of TLR5 in four mammalian lineages and shows TLR11 is also absent, suggesting reduced ability to detect extracellular flagellin.

The paper identifies genes controlling limb skeletal proportion differences between mouse and jerboa by comparing transcriptomes of growth cartilages and finding species-specific expression patterns.

The paper uses retapamulin-assisted ribosome profiling to identify alternative translation start sites in E. coli, revealing new proteins and regulatory roles.