Shawn T Sullivan

The paper presents a contiguous de novo genome assembly of sugar beet EL10 using long-read sequencing and scaffolding, showing high congruence with the reference genome and reduced gene copy number variation.

Edison evaluates scaffolding accuracy using edit distance, showing it is more reliable than N50 for assessing genome assembly quality.

The paper develops a platform using proximity-ligation sequencing to reconstruct viral genomes and assign hosts from metagenomic data, showing high accuracy and efficiency.

FALCON-Phase uses long-read sequencing and Hi-C data to create phased diploid genome assemblies, achieving high accuracy in non-human species but lower accuracy in humans.

The paper examines the differential expression of α, β, and γ protocadherin isoforms across differentiation, aging, and cancer using human embryonic stem cells and cancer cell lines.

This study evaluates sequencing technologies and assembly strategies to improve genome completeness in a non-model organism, focusing on resolving dark matter regions like transposable elements and GC-rich areas.

The paper investigates PU degradation by a landfill microbial community using metagenomic analysis, identifying metabolic pathways and enzymes involved in breaking down polyurethanes and xenobiotic additives.

The paper examines the evolutionary divergence of two honey bee mite species, identifying gene families under divergent selection and suggesting species-specific strategies for parasite control.

The paper presents a high-quality phased chromosome-scale genome assembly of a Chinese indigenous pig and identifies genetic differences between this breed and Duroc pigs.

This paper presents the genome of the zebra mussel, Dreissena polymorpha, providing insights into its invasive success and creating a resource for invasive species research.

Hi-C contacts assign assembled contigs to the cell they came from: 50 near-complete genomes among 252 clusters from one human fecal sample, plus plasmid-host links.

This paper presents a de novo mammalian genome assembly for the domestic goat using long-read sequencing, short-read validation, and chromatin interaction mapping, achieving high contiguity and resolving repetitive regions.