Benjamin D. Rosen

The paper introduces Verkko-Fillet, a tool for refining genome assemblies, and applies it to produce a telomere-to-telomere giraffe genome.

This study links geography and mutation profiles in goat species, finding strong correlations between specific mutations and geographic coordinates.

This paper uses genotype imputation to analyze low coverage ancient goat genomes, revealing demographic patterns and genetic consequences of domestication.

This study presents high-quality genome assemblies of five Indian desi cattle breeds, identifying immune-related genetic diversity and rearrangement hotspots.

This paper presents a telomere-to-telomere genome assembly of bighorn sheep, revealing immune gene differences that may explain their susceptibility to respiratory pathogens.

GSOR and MTAO detect widespread cis-regulatory effects on bovine complex traits by linking gene expression with genetic scores and multi-trait associations.

This study constructs a draft pangenome for Indian desi cattle using short-read sequencing, identifying novel sequences that improve genetic variant discovery and mapping accuracy.

This study generates the first banteng reference genome and analyzes 78 resequenced samples to explore its domestication history and genetic structure.

The paper constructs a pangenome for Indian Bos indicus cattle by identifying non-reference sequences, revealing novel genomic content and common insertions with functional implications.

The paper constructs a graph-based sheep pan-genome to identify structural variations and their association with tail phenotypes in domestic and wild sheep.

polishCLR is a Nextflow workflow for polishing PacBio CLR genome assemblies using best practices, improving accuracy through multiple polishing rounds and evaluation tools.

The paper presents a high-quality chromosome-level genome assembly, DNA methylome, and cranial morphology analysis of an Alpine dingo, supporting its status as an archetype for evolutionary studies.

The paper constructs a cattle Genotype-Tissue Expression atlas and identifies genetic regulatory variants linked to gene expression and traits in cattle.

The paper constructs structural variant-based pangenomes from haplotype-resolved bovine assemblies and identifies variants potentially affecting phenotype.

The paper presents a desert dingo genome assembly and compares it to domestic dog genomes, identifying structural variants and physiological differences linked to ecological roles.

The paper presents two high-quality Basenji genome assemblies and compares structural variations across three dog breeds, highlighting the impact of reference genome choice on variant detection.

The paper presents improved pig reference genomes using long-read sequencing, enhancing continuity and accuracy for pig genetics and genomics research.

This study analyzes Y-chromosomal haplotypes in domestic, ancient, and wild goats to reconstruct their population history and phylogeographic patterns.

This study uses trio binning to assemble chromosome-length haplotigs for yak and cattle from an F1 hybrid, achieving high continuity and phasing accuracy.

The paper presents haplotype-resolved cattle genomes to identify structural variants and adaptation traits, finding expanded immune-related gene families and a fatty acid desaturase copy under positive selection in indicine cattle.

The paper presents an annotated genome assembly of the Aedes albopictus C6/36 cell line, revealing genetic features and gene expression patterns relevant to viral propagation.