Arian F. A. Smit

The paper updates Drosophila melanogaster transposable element (TE) libraries in Dfam 4.0 by integrating new data, resolving redundancies, and improving consensus sequences.

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.

A 240-species placental mammal alignment resolves constraint to single bases, estimating at least 10.7% of the human genome is constrained, with 48.5% of constrained bases unannotated.

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.

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

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 evaluates MSA accuracy for transposable element sequences and finds Refiner outperforms other aligners for high-divergent and fragmented sequences.

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.