Joanna L. Kelley

The paper examines tissue-specific DNA methylation changes in juvenile mussels across microhabitats, finding significant and gene-related methylation shifts in response to environmental stress.

The paper develops tools to analyze phased genomes of polar fishes, revealing haplotype diversity in antifreeze protein copy numbers while mitigating assembly errors.

The paper investigates how temperature and pressure influenced the evolution of antifreeze proteins (AFPs) in polar and deep sea fishes, showing that AFP III copy number expands under low temperature but decreases with depth.

The paper quantifies genetic diversity across 93 marine species and finds that range size and planktonic dispersal correlate with higher genetic diversity.

The paper evaluates the reliability of phylogenetic inference using primate enamel proteins by simulating sequence fragmentation and comparing results to a reference species tree.

This paper develops a SNP selection pipeline, mPCRselect, to design cost-effective SNP panels for population assignment and individual identification in non-model species.

The paper presents a chromosome-level genome assembly for the gray fox, confirming the loss of PRDM9 functionality in the basal canid lineage.

The paper analyzes repetitive elements across 601 insect species, revealing challenges in repeat annotation and the benefits of long-read sequencing.

This paper presents a high-quality, chromosome-level genome assembly of the brown bear, improving upon previous assemblies and enabling better analysis of evolutionary and medical traits.

This study uses long-read sequencing to generate a high-quality genome assembly for an Antarctic eelpout and identifies genomic adaptations to polar environments.

The paper uses long-read RNA sequencing to analyze isoform expression in brown bears during active and hibernation seasons, finding differential isoform usage in tissues even when genes are not differentially expressed.

The paper assesses the current state of animal genome sequencing, highlighting disparities in taxonomic and geographic representation and assembly quality.

The paper analyzes 601 insect genome assemblies, highlighting taxonomic bias, assembly quality, and the impact of long-read sequencing technologies on contiguity.

The paper highlights the underrepresentation of aquatic insects in genomic research and calls for increased genomic resources to better understand their biology and ecological importance.

The paper presents de novo assemblies of the nuclear and mitochondrial genomes of the meltwater stonefly Lednia tumana, providing foundational resources for studying its evolution and conservation.