James Torrance

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

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.

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

MitoHiFi assembles mitochondrial genomes from PacBio HiFi reads, identifying heteroplasmy variants and excluding nuclear contaminants, and has been used to assemble 374 mitochondrial genomes.

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 presents a pangenome for the barn swallow and identifies genes under selection linked to synanthropy and domestication traits.

The paper evaluates sequencing and assembly methods to create high-quality diploid human genome assemblies, finding that long reads and haplotype sorting improve accuracy and completeness.

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 a high-quality genome and transcriptome of the tufted duck, comparing short and long-read sequencing technologies for transcriptome assembly.

The paper presents a high-quality chromosome-level genome assembly of the reed warbler and identifies two macrochromosomal fusions.

The paper develops a pipeline for mitochondrial genome assembly and identifies errors and novel duplications in reference mitogenomes.

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 generates a high-quality reference genome for the vaquita and analyzes its demographic history, revealing long-term population stability and low genetic diversity.

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

The paper presents full-length de novo genome assemblies for 16 inbred mouse strains, identifying strain-specific haplotypes and novel functional loci, including a large unannotated gene with potential developmental roles.

This paper evaluates GRCh38 and de novo haploid assemblies, finding that GRCh38 remains superior for complex genomic regions and coding sequences despite improvements in newer assemblies.

gEVAL is a web browser for evaluating genome assemblies by comparing them to datasets and highlighting errors and areas for improvement.