Ying Sims

The paper generates high-quality chromosome-level genomes for three Plasmodium species from natural infections, improving understanding of their biology and evolution.

The paper presents a chromosome-level genome assembly for the European leaf-toed gecko, providing a high-quality reference for studying genome evolution and sex chromosome dynamics.

The paper identifies genomic and transcriptomic changes associated with chromosomal instability and seasonal brain size plasticity in the Eurasian common shrew.

The paper presents 40 new microsporidian genomes, revealing evidence of sexual reproduction and autopolyploidy, with tetraploid genomes organized into diploid compartments.

This study investigates the genomic and genetic factors underlying speciation and pigment pattern diversification in Danio fishes, revealing introgression, functional divergence of specific genes, and evolutionary changes in protein and regulatory sequences.

The paper analyzes genomic diversity loss in whooping cranes despite population recovery, finding 70% genetic diversity loss and increased inbreeding.

This study integrates genomic, transcriptomic, and morphological data from the small-spotted catshark to uncover molecular mechanisms underlying sensory organ evolution in jawed vertebrates.

This paper presents a new chromosome-scale genome assembly of Littorina saxatilis with improved contiguity and completeness, enabling better study of chromosomal inversions and their role in speciation.

The paper presents a chromosome-scale reference genome for the Andean cavefish Trichomycterus rosablanca to study evolutionary mechanisms in cave environments.

The paper generates and analyzes genome assemblies for 24 Antarctic notothenioid fish species to study cold adaptations, identifying genomic changes related to antifreeze proteins and haemoglobin loss.

The paper uses genome assembly and population genomics to show Altai falcons are a distinct species with unique genetic traits.

The paper analyzes genomes of leatherback and green turtles to identify gene family expansions and demographic differences that may influence their ecological adaptations and conservation status.

This paper introduces Asset, a tool to evaluate genome assemblies using long-range data, demonstrating its ability to detect structural misassemblies in human, goat, and fish genomes.

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 summarizes methods and lessons from assembling 16 vertebrate genomes, highlights the importance of long-read sequencing, and introduces the Vertebrate Genomes Project to generate complete reference genomes for all vertebrate species.

This paper presents a chromosome-level genome assembly of Acanthopagrus latus using PacBio and Hi-C technologies, enabling research on sex reversal mechanisms.

The paper presents a high-quality chromosome-level genome assembly of the Black Soldier Fly and identifies genomic features and inbreeding patterns in a lab population.

gEVAL-assisted manual curation of 111 VGP and DToL assemblies averaged 221 interventions per Gb, raising mean scaffold N50 by 40% and cutting scaffold counts by 29%.

The paper reports the high-quality genome assembly of Pecten maximus, revealing gene duplicates and highlighting Nav1 as a candidate for toxin resistance.