Emily L. Clark

A multi-tissue epigenomic atlas links the sheep non-coding genome to domestication and complex traits

SheepEpimap combines 516 histone CUT&Tag, ATAC-seq and RNA-seq datasets from 43 sheep tissues to annotate 2.93 million cis-regulatory elements and 145,407 allele-specific variants for trait interpretation.

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.

Comparative multi-omics of the macrophage response to infection with Mycobacterium tuberculosis complex bacteria reveals pathogen-driven epigenomic reprogramming

This study uses multi-omics approaches to analyze how M. bovis infection reprograms the epigenome of bovine alveolar macrophages, identifying key genes and pathways involved in the host response.

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.

A multi-tissue atlas of genetic regulatory effects in sheep

The paper presents a multi-tissue sheep atlas identifying regulatory variants and their effects on molecular phenotypes, revealing allelic heterogeneity and evolutionary patterns.

Inferring domestic goat demographic history through ancient genome imputation

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

Bighorn sheep T2T genome assembly reveals differences in immune genes: a potential cause of high morbidity due to respiratory pathogens

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

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.

Empowering bioinformatics communities with Nextflow and nf-core

This paper discusses the adoption of Nextflow and nf-core frameworks to standardize bioinformatics pipelines, improving collaboration and interoperability across research communities.

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.

A multi-tissue developmental gene expression atlas towards understanding the biological basis of phenotypes in sheep

The paper constructs a sheep developmental gene expression atlas and identifies key genes associated with economically important traits by analyzing gene expression across developmental stages.

Polyadenylated RNA sequencing analysis helps establish a reliable catalog of circular RNAs - a bovine example.

This study identifies reliable circular RNAs in bovine tissues by comparing total-RNAseq and mRNAseq data, revealing many artificial circRNAs and false entries in existing catalogs.

Cellular heterogeneity of the developing worker honey bee (Apis mellifera) pupa: a single cell transcriptomics analysis

This study uses scRNA-seq to identify cell types and gene signatures in developing worker honey bees, providing a first single-cell atlas of honey bee development.

Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using CAGE sequencing

The paper annotates transcription start sites and enhancers in cattle using CAGE sequencing across multiple tissues and populations to improve genome annotation and inform breeding programs.

Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions

The paper profiles open chromatin in developing pig muscle to identify regulatory regions and provides a resource for genome regulation studies and variant filtering in pig breeding.

The natural adaptation and human selection history of African sheep genomes

The paper analyzes African sheep genomes to identify genetic groups and selection targets related to environmental adaptation and human-driven traits.

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.

The paper identifies widespread transcription initiation at microsatellites across species and develops deep learning models to predict STR-associated transcription and its impact on disease variants.

A putative genomic map for resistance of Bos indicus cattle in Cameroon to bovine tuberculosis

This study investigates genetic variation in bTB resistance in Bos indicus cattle in Cameroon using genomic analysis and heritability studies.

Global analysis of transcription start sites in the new ovine reference genome (Oar rambouillet v1.0)

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.

Gene expression in the cardiovascular system of the domestic sheep (Ovis aries); a new tool to advance our understanding of cardiovascular disease.

This study investigates gene expression in sheep cardiovascular tissues to understand vascular calcification, highlighting gene balance and extracellular matrix roles.

Genomic diversity affects the accuracy of bacterial SNP calling pipelines

This study evaluates SNP calling pipelines' performance on bacterial data, finding that reference genome selection strongly impacts accuracy, with Snippy performing consistently well across diverse genomes.

Genomic analyses underpin the feasibility of concomitant genetic improvement of milk yield and mastitis resistance in dairy sheep

The paper assesses the feasibility of improving milk yield and mastitis resistance in dairy sheep through genomic analysis, finding no significant genetic correlation between the traits.

Elimination of reference mapping bias reveals robust immune related allele-specific expression in cross-bred sheep

This study develops an unbiased pipeline for allele-specific expression analysis in sheep, revealing pervasive and tissue-specific allelic imbalance across genes and SNVs.

A mini-atlas of gene expression for the domestic goat (Capra hircus) reveals transcriptional differences in immune signatures between sheep and goats

The paper creates a gene expression atlas for goats, identifying transcriptional differences in immune signatures compared to sheep.

Comprehensive transcriptional profiling of the gastrointestinal tract of ruminants from birth to adulthood reveals strong developmental stage specific gene expression

This study characterizes gene expression changes in the gastrointestinal tract of sheep from birth to adulthood, identifying developmental stage-specific differences, particularly in the rumen complex and immune-related genes.

Assembly and validation of conserved long non-coding RNAs in the ruminant transcriptome

The paper identifies a consensus set of ruminant lncRNAs by combining cross-species RNA-seq data and positional conservation, showing that stochastic sampling can be mitigated through this approach.

A High Resolution Atlas Of Gene Expression In The Domestic Sheep (Ovis aries)

This paper presents a high-resolution gene expression atlas for sheep, identifying transcriptional signatures and functional annotations across tissues and developmental stages.