A5086435813- Genetic and phenotypic traits in livestock
- Genetic Associations and Epidemiology
- Genomics and Phylogenetic Studies
- Genetic Mapping and Diversity in Plants and Animals
- Cancer-related molecular mechanisms research
- Genetic factors in colorectal cancer
- Genomics and Chromatin Dynamics
- Genomics and Rare Diseases
- Epigenetics and DNA Methylation
- Vector-Borne Animal Diseases
- RNA and protein synthesis mechanisms
- Vector-borne infectious diseases
- Genomic variations and chromosomal abnormalities
- Genetic diversity and population structure
- RNA modifications and cancer
- Cancer-related gene regulation
- Bioinformatics and Genomic Networks
- Animal Disease Management and Epidemiology
- Immune Cell Function and Interaction
- Immune Response and Inflammation
- Genetics and Neurodevelopmental Disorders
- Livestock Farming and Management
- Hedgehog Signaling Pathway Studies
- Congenital heart defects research
- T-cell and B-cell Immunology
University of Edinburgh
2015-2025
Roslin Institute
2015-2025
Cohort (United Kingdom)
2024
Wessex Regional Genetics Laboratory
2021-2022
Massachusetts General Hospital
2021
Broad Institute
2021
Genomics (United Kingdom)
2019
Munster Technological University
2001-2016
Institute of Genetics and Cancer
2005-2015
Western General Hospital
2007-2013
DNA methylation and the Polycomb repression system are epigenetic mechanisms that play important roles in maintaining transcriptional repression. Recent evidence suggests can attenuate binding of protein components to chromatin thus plays a role determining their genomic targeting. However, whether this is context regulation unclear. By genome-wide mapping Repressive Complex 2-signature histone mark, H3K27me3, severely hypomethylated mouse somatic cells, we show hypomethylation leads...
Abstract Despite only 8% of cattle being found in Europe, European breeds dominate current genetic resources. This adversely impacts research other important global breeds, especially those from Africa for which genomic resources are particularly limited, despite their disproportionate importance to the continent’s economies. To mitigate this issue, we have generated assemblies African been integrated with data 294 diverse into a graph genome that incorporates diversity. We illustrate how...
Genome-wide association studies (GWAS) have identified 14 tagging single nucleotide polymorphisms (tagSNPs) that are associated with the risk of colorectal cancer (CRC), and several these tagSNPs near bone morphogenetic protein (BMP) pathway loci. The penalty multiple testing implicit in GWAS increases attraction complementary approaches for disease gene discovery, including candidate gene- or pathway-based analyses. strongest loci additional predisposition SNPs arguably those already known...
BackgroundGermline variation in the 71 Crohn's disease (CD) loci implicated by genome-wide association studies (GWAS) only accounts for approximately 25% of estimated heritability. The contribution epigenetic alterations to pathogenesis is emerging as a research priority.
Graphia is an open-source platform created for the graph-based analysis of huge amounts quantitative and qualitative data currently being generated from study genomes, genes, proteins metabolites cells. Core to Graphia’s functionality support calculation correlation matrices any tabular matrix continuous or discrete values, whereupon software designed rapidly visualise often very large graphs that result in 2D 3D space. Following graph construction, extensive range measurement algorithms,...
Second generation sequencing has prompted a number of groups to re-interrogate the transcriptomes several bacterial and archaeal species. One central findings been identification complex networks small non-coding RNAs that play roles in transcriptional regulation all growth conditions for pathogen's interaction with survival within host cells. Legionella pneumophila is Gram-negative facultative intracellular human pathogen distinct biphasic lifestyle. its primary environmental hosts...
Understanding how the genome is shaped by selective processes forms an integral part of modern biology. However, as genomic datasets continue to grow larger it becoming increasingly difficult apply traditional statistics for detecting signatures selection these cohorts. There therefore a pressing need development next generation computational and analytical tools in large datasets. Here, we present hapbin, efficient multithreaded implementation extended haplotype homzygosity-based selection,...
Abstract More people globally depend on the water buffalo than any other domesticated species, and as most closely related species to cattle they can provide important insights into shared evolutionary basis of domestication. Here, we sequence genomes 79 across seven breeds compare patterns between breed selective sweeps with those seen for 294 representing 13 global breeds. The genomic regions under selection significantly overlap linked stature in human genetic studies, a disproportionate...
Evolutionary rates are not constant across the human genome but genes in close proximity have been shown to experience similar levels of divergence and selection. The higher-order organisation chromosomes has often invoked explain such phenomena previously there insufficient data on chromosome structure investigate this rigorously. Using results a recent genome-wide analysis open closed chromatin structures we investigated global association between divergence, selection for first time.In...
In this study we investigated the strengths and modes of selection associated with nucleosome positioning in human lineage through comparison interspecies intraspecies rates divergence. We identify significant evidence for both positive negative linked to first time, implicating a widespread important role DNA sequence location well-positioned nucleosomes. Selection appears be acting on particular base substitutions maintain optimum GC compositions core linker regions, with, e.g.,...
We have previously identified several colorectal cancer (CRC)-associated polymorphisms using genome-wide association (GWA) analysis. sought to fine-map the location of functional variants for three these regions at 8q23.3 (EIF3H), 16q22.1 (CDH1/CDH3) and 19q13.11 (RHPN2). genotyped two case–control sets high density in selected used existing data from four other sets, comprising a total 9328 CRC cases 10 480 controls. To improve marker density, we imputed genotypes 1000 Genomes Project...
Epithelial fusion underlies many vital organogenic processes during embryogenesis. Disruptions to these cause a significant number of human birth defects, including ocular coloboma. We provide robust spatial-temporal staging and unique anatomical detail optic fissure closure (OFC) in the embryonic chick, evidence for roles apoptosis epithelial remodelling. performed complementary transcriptomic profiling show that Netrin -1 ( NTN1 ) is precisely expressed chick margin but immediately...
Abstract Background Understanding the variation between well and poorly adapted cattle breeds to local environments pathogens is essential for breeding with improved climate disease-resistant phenotypes. Although considerable progress has been made towards identifying genetic differences breeds, at epigenetic chromatin levels remains characterized. Here, we generate, sequence analyse over 150 libraries base-pair resolution explore dynamics of DNA methylation accessibility bovine immune...
Gene expression is influenced by both genetic variants and the environment.As individuals age, changes in gene may be associated with decline physical cognitive abilities.We measured transcriptomewide levels lymphoblastoid cell lines derived from members of Lothian Birth Cohort 1936 at mean ages 70 76 years.Changes were identified for 1,741 transcripts 434 individuals.Gene Ontology enrichment analysis indicated an biological processes involved immune system.Transcriptome-wide association was...