Jessica M. Storer

T2T-HG002v1.1, a complete diploid HG002 assembly lacking detectable errors over 99.4% of its length, enables genome-based benchmarking of assemblies, sequencing reads, and phased variant calls.

TEtrimmer automates TE curation by integrating alignment and classification methods, improving intact TE identification across six organisms.

The paper studies NUMTs in great ape T2T genomes, showing they recapitulate species tree topology and are enriched in non-functional regions.

The paper presents haplotype-resolved genomes of six ape species with high accuracy and provides comparative analyses to study evolutionary diversity and gene family evolution.

The paper identifies centromeric transposable elements and epigenetic features in the eastern hoolock gibbon that contribute to karyotypic variation and chromosomal instability.

This study compares manual and automated methods for transposable element annotation in Drosophila melanogaster and Aedes albopictus, finding that automated methods identify more TEs but manual curation provides more detailed classifications.

The paper produces gapless assemblies of ape sex chromosomes for five great apes and a lesser ape, revealing divergence in Y chromosomes and evolutionary dynamics.

The paper investigates Alu-driven DNA transductions in primate genomes and finds no evidence of Alu-mediated transductions in humans, chimpanzees, or rhesus monkeys.

The paper presents the complete sequence of a human Y chromosome, correcting errors in the GRCh38 reference and adding over 30 million base pairs.

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

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.

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