Jeb R. Rosen

The paper identifies proteins and regulatory elements associated with vocal learning by analyzing bat neural activity and epigenomic data.

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

A machine learning approach identifies enhancer-phenotype associations across mammals, revealing links to brain size and behavior evolution.

The paper curates TE content in 248 mammalian genomes, finding trends in recent TE accumulation and associations with dietary habits.

The paper identifies bats as a hotspot for horizontal transfer of DNA transposons, finding over 200 putative elements and shared transposons across mammals and reptiles.

The paper presents the first de novo repeat discovery and annotation of a complete human reference genome, identifying novel satellite arrays and characterizing new classes of complex repeats.

The paper presents the genome of Sitophilus oryzae, revealing high transposable element content and host-symbiont metabolic interactions.

PolyA adjudicates competing sequence annotations by computing confidence estimates and identifying optimal alignments with rearrangements.

With a new structural LTR module, RepeatModeler2 recovers 2.9 to 4.7 times more curated TE families near-perfectly than RepeatModeler 1.0.11 in fruit fly, zebrafish, and rice.