David A. Ray

Optimizing genome assembly, chromosome synteny, and genetic variant discovery from Oxford Nanopore sequences of Dermacentor reticulatus ticks

The paper optimizes genome assembly and variant discovery for Dermacentor reticulatus ticks using Oxford Nanopore sequencing, identifying workflow parameters that yield high-quality assemblies and genetic insights.

Evaluating the potential role and contribution of transposable elements to the evolution of microbial multicellularity across the tree of eukaryotes

The paper examines the role of transposable elements in the evolution of multicellularity across protist lineages by analyzing TE composition, diversity, and gene regulation patterns.

Genomic comparisons shed light on the adaptive basis of brain size plasticity and chromosomal instability in the Eurasian common shrew

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

The repetitive genome of the Ixodes ricinus tick reveals transposable elements have driven genome evolution in ticks

The paper generates high-quality genome assemblies for Ixodes ricinus and identifies transposable elements as major drivers of genome evolution in ticks.

Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements

The paper identifies proteins and regulatory elements associated with vocal learning by analyzing bat neural activity and epigenomic data.

Integrating gene annotation with orthology inference at scale

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

Relating enhancer genetic variation across mammals to complex phenotypes using machine learning

A machine learning approach identifies enhancer-phenotype associations across mammals, revealing links to brain size and behavior evolution.

Insights into mammalian TE diversity via the curation of 248 mammalian genome assemblies

The paper curates TE content in 248 mammalian genomes, finding trends in recent TE accumulation and associations with dietary habits.

Evolutionary constraint and innovation across hundreds of placental mammals

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.

Chiropterans are a hotspot for horizontal transfer of DNA transposons in Mammalia

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.

Comparison of genetic variation between rare and common congeners of Dipodomys with estimates of contemporary and historical effective population size

The paper compares genetic variation and effective population size between two Dipodomys species, finding lower diversity and effective population size in the threatened D. elator compared to the common D. ordii.

Unraveling the Myotis Morass: Ultraconserved-Element Analysis Reveals Introgression, Cryptic Diversity, and Taxonomic Trouble in the Most Species-rich Bat Genus

This study uses ultraconserved elements to analyze genetic diversity in New World Myotis bats, revealing introgression, cryptic lineages, and taxonomic challenges.

Six new reference-quality bat genomes illuminate the molecular basis and evolution of bat adaptations

The paper generates six reference-quality bat genomes, identifies genomic adaptations related to echolocation, immunity, and viral tolerance, and reveals regulatory elements contributing to bat traits.

A high-quality genome assembly of the North American Song Sparrow, Melospiza melodia.

The paper presents a high-quality genome assembly of the song sparrow, Melospiza melodia, using Illumina sequencing and provides gene annotations and functional insights.

A high-quality reference genome assembly of the saltwater crocodile, Crocodylus porosus, reveals patterns of selection in Crocodylidae

This paper presents a high-quality genome assembly of the saltwater crocodile and identifies genes under positive selection in crocodilians.

Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling

The paper improves the American alligator genome assembly and identifies estrogen-responsive regions linked to female-biased gene expression in post-temperature-sensitive gonads.