Hubert Pausch

A large-effect locus on chromosome 4 underlies circadian feeding rhythmicity in pigs

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.

Identifying crossovers in a cattle pangenome containing haplotype-resolved assemblies from half-siblings

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.

Genetic control of the transcriptional response to active tuberculosis disease and treatment

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.

The genetic architecture of milk urea concentration in dairy cattle differs across the lactation cycle

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

An endogenous retrovirus insertion disrupting bovine ALKBH8 causes a failure-to-thrive syndrome with immunodeficiency associated with juvenile mortality in Brown Swiss cattle

Evidence of inbreeding depression on stature in Brown Swiss cattle

This study identifies inbreeding depression on stature in Brown Swiss cattle and discovers a recessive QTL linked to a splice donor variant in ABCC6.

A novel reusable transcriptome-wide association study workflow used to map key genes linked to important cattle traits

The paper presents a reusable TWAS workflow for cattle to identify gene-trait associations using GWAS and transcriptomic data, improving variant calling and detecting novel associations.

The enhanced multi-tissue atlas of regulatory effects in cattle

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

Across-breed analyses of genome-wide association studies for stature and mammary gland morphology in cattle reveal pleiotropic effects of the Friesian POLLED haplotype

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.

Molecular QTL are enriched for structural variants in a cattle long-read cohort

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: measuring pangenome graph representativeness using Single-Copy and Universal K-mers

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

Genetic analysis of iris pigmentation in Swiss pig breeds identifies a missense KITLG variant as a potential causal factor for pale and heterochromatic irises

A new diagnostic modality for bovine tuberculosis: accurate and robust classification of infected cattle using transcriptomics and machine learning

The paper develops mRNA-based classifiers using RNA-seq and machine learning to accurately distinguish bTB-positive from bTB-negative cattle and other pathogens.

Genome-wide association study and regional heritability mapping of protein efficiency and performance traits in Swiss Large White pigs

This study uses GWAS and RHM to identify genomic regions associated with protein efficiency and performance traits in pigs, highlighting candidate genes and noncoding RNAs.

Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle

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

Integrative genomics sheds light on the immunobiology of tuberculosis in cattle

This study integrates transcriptomic, genomic, and GWAS data to identify genes and eQTLs associated with the PB transcriptome response to M. bovis infection in cattle.

RNA sequencing variants are enriched for eQTL in cattle tissues

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.

Wisent genome assembly uncovers extended runs of homozygosity and a large deletion that inactivates the thyroid hormone responsive gene

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.

Genome-Wide Association Testing for Haemorrhagic Bowel Syndrome in a Swiss Large White Pig Population

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.

Pangenome genotyped structural variation improves molecular phenotype mapping in cattle

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.

Molecular quantitative trait loci in reproductive tissues impact male fertility in cattle

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.

A compendium of genetic regulatory effects across pig tissues

The paper presents PigGTEx, a resource linking genetic variants to transcriptomic phenotypes in pigs, showing pigs' similarity to humans in gene regulation and complex traits.

Exploiting public databases of genomic variation to quantify evolutionary constraint on the branch point sequence in 30 plant and animal species

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.

Structural variants and short tandem repeats impact gene expression and splicing in bovine testis tissue

Size and composition of haplotype reference panels impact the accuracy of imputation from low-pass sequencing in cattle

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.

Comparison of two multi-trait association testing methods and sequence-based fine mapping of six QTL in Swiss Large White pigs

The paper compares two multi-trait association methods and fine-maps six QTL in pigs, finding similar results between methods but highlighting potential missed QTL in multi-trait analyses.

Graph construction method impacts variation representation and analyses in a bovine super-pangenome

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

Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies

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

A 1-bp deletion in bovine QRICH2 causes low sperm count and immotile sperm with multiple morphological abnormalities

The paper identifies a 1-bp deletion in QRICH2 as a recessive cause of low sperm count and immotile sperm with morphological abnormalities in Brown Swiss bulls.

Quantification of the evolutionary constraint on intronic branch point sequences in the bovine and human genome

The paper quantifies evolutionary constraint on intronic branch point sequences in bovine and human genomes, finding strong purifying selection and links to alternative splicing.