Alexander S. Leonard

This study identifies a QTL on chromosome 4 associated with circadian feeding rhythmicity in pigs, linking it to genes involved in feeding behavior and energy homeostasis.

The paper identifies crossover events in cattle using haplotype-resolved assemblies and methylation data from long-read sequencing, finding more events in half-siblings than in cousins.

The paper identifies cis-eQTL and reQTL in TB patients during treatment using RNA-seq data and variant imputation, showing changes in cell type proportions and gene expression.

This study identifies lactation-stage specific QTL for milk urea concentration in dairy cattle breeds, highlighting pleiotropic effects and candidate genes.

The paper presents CattleGTEx, a resource characterizing regulatory effects in cattle, resolving GWAS signals and providing insights into adaptive evolution and selection.

The paper performs genome-wide association studies in cattle to identify QTL for stature and mammary gland morphology, finding pleiotropic effects of the Friesian POLLED haplotype on mammary traits.

The paper identifies molecular QTL enriched for structural variants in a cattle long-read sequencing cohort, showing SVs have a significant impact on gene expression and splicing.

PG-SCUnK evaluates pangenome graph representativeness by analyzing single-copy and universal k-mers from source assemblies.

The paper identifies a structural variant upstream of KIT associated with facial depigmentation in white-headed cattle using pangenome analysis and long-read sequencing.

The paper shows RNA sequencing variants in cattle tissues are enriched for eQTL, with 75% of eGenes detected and a 2-fold enrichment compared to DNA sequencing variants.

The paper presents a high-quality wisent genome assembly, identifies a deletion inactivating the THRSP gene, and shows its absence in bison compared to cattle and water buffalo.

This study performs genome-wide association analysis for haemorrhagic bowel syndrome in Swiss Large White pigs but finds no significant genetic variants associated with the disease.

This study uses a pangenome to genotype structural variation in cattle, improving e/sQTL mapping by identifying 92 structural variants as causal for eQTL and 73 for sQTL.

The paper identifies 41k regulatory loci in cattle reproductive tissues linked to male fertility by analyzing gene expression and splicing variation across testis, epididymis, and vas deferens.

The paper quantifies evolutionary constraint on the branch point sequence in 30 species using public variant databases, finding biased variants in 16 species and identifying constrained positions in 14.

This study evaluates how haplotype reference panel size and composition affect variant calling accuracy from low-pass sequencing in cattle, finding that breed-specific panels improve imputation accuracy.

The paper compares three pangenome construction methods, showing their impact on variant representation and analysis in a bovine super-pangenome.

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

The paper constructs a multi-assembly graph from bovine genomes to uncover non-reference sequences, revealing novel transcripts and polymorphic sites.

The paper shows duplication accelerates structural complexity in protein quaternary structures through in silico simulations and analysis of the Protein Data Bank.