Timothy P. L. Smith

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

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

The paper constructs a bovine epigenomic atlas to annotate regulatory elements and decode the regulatory syntax of the cattle genome, aiding in fine-mapping GWAS loci for complex traits.

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

The paper analyzes genomic data from Beefalo cattle and finds most lack detectable bison ancestry, challenging the breed association's 3/8 bison requirement.

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 a reference genome assembly for hairy vetch (Vicia villosa) to aid in genetic improvement and genome evolution studies.

The paper improves bovine genome annotation by integrating multi-omics data to identify novel transcripts and gene functions, and constructs a trait similarity network.

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.

This paper presents a high-quality long-read genome assembly of red clover, significantly improving contig count, quality, and accuracy compared to short-read assemblies.

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 performs a global analysis of transcription start sites (TSS) in the ovine reference genome using CAGE sequencing, identifying novel TSS and validating them with bisulfite sequencing.

metaFlye improves metagenome assembly using long-read sequencing, producing more contiguous and accurate assemblies with better reconstruction of 16S RNA genes and novel plasmids/viruses.

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

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.

This paper introduces trio binning, a method for assembling haplotypes from heterozygous genomes using parental short reads, achieving high accuracy in diploid reconstruction.