Alan Tracey

The paper investigates hatching failure in Alala, the Hawaiian crow, after a near-extinction event, identifying recessive lethal haplotypes as the main cause.

This study investigates gene flow and hybridization in sailfin silversides, finding evidence of both ancient and recent introgression between riverine and lacustrine species in Lake Matano.

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

This study presents chromosome-level genomes for sloths and anteaters, revealing retrocopy formation and domestication as key drivers of xenarthran genome evolution and physiological specializations.

The paper examines sex chromosomes in 14 elasmobranch species, identifying conserved X chromosomes and a shared candidate gene for sex determination.

The paper generates a chromosome-scale genome assembly for Teladorsagia circumcincta and identifies genetic loci associated with drug resistance to improve anthelmintic resistance diagnostics.

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 an improved rat reference genome, mRatBN7.2, which enhances genomic, transcriptomic, and proteomics data mapping and identifies millions of genetic variations across rat strains.

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 high-quality chromosome-level genome assembly for the Rock Ptarmigan, providing a reference for studying its evolution and climate change impacts.

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 presents a haplotype-resolved genome assembly of the Nile rat, revealing unique genomic features relevant to type 2 diabetes and metabolic dysfunctions.

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.

The paper generates the first chromosome-length annotated genomes and transcriptomes of black and mute swans, revealing immune system limitations and plumage-related genetic differences.

The paper generates chromosome-level reference genomes for two C. briggsae strains, improving genomic resources for comparative genomics in the Caenorhabditis genus.

The paper presents a new high-quality genome assembly and annotation for Cryptosporidium parvum IOWA, revealing structural and functional insights into its genome and evolutionary relationships with related species.

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

The paper assembles the chromosomes of Schistosoma mansoni, revealing insights into the evolution of its ZW sex-determination system through gene annotation and synteny analysis.

This study uses single worm whole genome sequencing to show that Strongyloides ratti populations in the UK consist of long-lived asexual lineages with hyperdiverse parasitic genes.

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.

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%.

This study creates a single-cell RNA sequencing atlas of the early intra-mammalian stage of Schistosoma mansoni, identifying gene expression profiles and validating cell markers.

The paper presents a telomere-to-telomere genome assembly of Oscheius tipulae and identifies ancestral chromosomal elements that inform the evolution of rhabditid nematode chromosomes.

The paper uses genomic data from Guinea worm infections in humans and dogs to show they originate from the same population, indicating transmission between species and a population bottleneck.

The paper presents a high-quality, chromosome-scale genome assembly of Haemonchus contortus using long-read sequencing, revealing genetic diversity and transcriptional regulation.

The paper presents the complete genome of Hymenolepis microstoma, revealing chromosome structures capped by centromeres that serve both segregation and protection roles.