J. Prendergast

发表

Widespread signatures of recent selection linked to nucleosome positioning in the human lineage.

C. Semple, J. Prendergast, 2011, Genome research.

Abundant pleiotropy in human complex diseases and traits.

F. Agakov, T. Manolio, P. McKeigue, 2011, American journal of human genetics.

nf-LO: A Scalable, Containerized Workflow for Genome-to-Genome Lift Over

J. Prendergast, A. Talenti, 2021, bioRxiv.

Meta-analysis of genome-wide association data identifies four new susceptibility loci for colorectal cancer

Steven Gallinger, Henry Völzke, Brent W Zanke, 2008, Nature Genetics.

Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication

D. Hume, A. Djikeng, W. Low, 2020, Nature Communications.

Sequencing and analysis of an Irish human genome

N. Friel, S. Cronin, O. Hardiman, 2010, Genome Biology.

Sequencing and analysis of an Irish human

N. Friel, S. Cronin, O. Hardiman, 2010 .

Side Effects: Substantial Non-Neutral Evolution Flanking Regulatory Sites

C. Semple, J. Prendergast, 2013, PLoS genetics.

Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes

Wendy A Bickmore, Judith Reichmann, Colm E. Nestor, 2013, Genome Biology.

Homozygous loss-of-function variants in European cosmopolitan and isolate populations

Martin S. Taylor, Ross M. Fraser, R. Durbin, 2015, Human molecular genetics.

A locus conferring tolerance to Theileria infection in African cattle

J. Prendergast, A. Talenti, Perle Latré de Laté, 2022, PLoS genetics.

Cancer, DNA repair and chromatin structure

J. Prendergast, 2008 .

Functional Predictors of Causative Cis-Regulatory Mutations in Mendelian Disease

D. Grozeva, P. Kind, H. R. Crollius, 2020, bioRxiv.

Examining the Impact of Imputation Errors on Fine-Mapping Using DNA Methylation QTL as a Model Trait

R. Marioni, P. Visscher, N. Wray, 2019, Genetics.

Increased ultra-rare variant load in an isolated Scottish population impacts exonic and regulatory regions

Martin S. Taylor, I. Deary, D. Hume, 2019, PLoS genetics.

A recurrent de novo mutation in ACTG1 causes isolated ocular coloboma

J. Prendergast, D. Soares, D. Fitzpatrick, 2017, Human mutation.

Germline susceptibility to colorectal cancer due to base-excision repair gene defects.

J. Prendergast, A. Tenesa, H. Campbell, 2005, American journal of human genetics.

Sexual differences in genetic architecture in UK Biobank

K. Rawlik, J. Prendergast, A. Tenesa, 2020, bioRxiv.

Age-related gene expression changes, and transcriptome wide association study of physical and cognitive aging traits, in the Lothian Birth Cohort 1936

Ian J. Deary, John M. Starr, Nicola Wrobel, 2017, Aging.

Optical mapping compendium of structural variants across global cattle breeds

J. Prendergast, A. Talenti, G. Mainda, 2022, bioRxiv.

Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle

A. Djikeng, J. Prendergast, A. Talenti, 2022, Genetics, selection, evolution : GSE.

Arginine to Glutamine Variant in Olfactomedin Like 3 (OLFML3) Is a Candidate for Severe Goniodysgenesis and Glaucoma in the Border Collie Dog Breed

J. Prendergast, A. Ewing, K. Summers, 2019, G3: Genes, Genomes, Genetics.

The conservation of human functional variants and their effects across livestock species

J. Prendergast, A. Tenesa, A. Talenti, 2022, Communications Biology.

Edinburgh Research Explorer Sequencing illustrates the transcriptional response of Legionella pneumophila during infection and identifies seventy novel small non-coding RNAs

J. Prendergast, B. Loftus, A. Lohan, 2017 .

Reply to Webb et al.

J. Prendergast, A. Tenesa, H. Campbell, 2006 .

Inverted CD4+/CD8+ T cell ratio in Boran (Bos indicus) cattle

J. Prendergast, Perle Latré de Laté, L. Morrison, 2020, Veterinary immunology and immunopathology.

Inherited Tolerance in Cattle to the Apicomplexan Protozoan Theileria parva is Associated with Decreased Proliferation of Parasite-Infected Lymphocytes

J. Prendergast, Perle Latré de Laté, E. Cook, 2021, Frontiers in Cellular and Infection Microbiology.

Genotype–phenotype characterisation of long survivors with motor neuron disease in Scotland

I. Deary, S. Chandran, J. Prendergast, 2022, Journal of Neurology.

A promoter-level mammalian expression atlas

Cesare Furlanello, Finn Drabløs, Carsten O. Daub, 2015 .

Shared regulatory sites are abundant in the human genome and shed light on genome evolution and disease pleiotropy

J. Prendergast, Pin Tong, J. Monahan, 2017, PLoS genetics.

Common variation near CDKN1A, POLD3 and SHROOM2 influences colorectal cancer risk

Steven Gallinger, Yusuke Nakamura, Graeme Grimes, 2012, Nature Genetics.

Linked Mutations at Adjacent Nucleotides Have Shaped Human Population Differentiation and Protein Evolution

I. Deary, D. Hume, S. Harris, 2018, bioRxiv.

A genome-wide screen in human embryonic stem cells reveals novel sites of allele-specific histone modification associated with known disease loci

C. Semple, J. Prendergast, D. Hay, 2012, Epigenetics & Chromatin.

Local Exome Sequences Facilitate Imputation of Less Common Variants and Increase Power of Genome Wide Association Studies

Ross M. Fraser, N. Hastie, I. Rudan, 2013, PloS one.

Identification and functional modelling of plausibly causative cis-regulatory variants in a highly-selected cohort with X-linked intellectual disability

D. Grozeva, P. Kind, J. Prendergast, 2021, PloS one.

Sequence-Level Mechanisms of Human Epigenome Evolution

Emily V. Chambers, C. Semple, J. Prendergast, 2014, Genome biology and evolution.

Sex differences in genetic architecture in the UK Biobank

K. Rawlik, J. Prendergast, A. Tenesa, 2021, Nature Genetics.

Genome-wide association scan identifies a colorectal cancer susceptibility locus on chromosome 8q24

Steven Gallinger, Vincent Ferretti, Brent W Zanke, 2007, Nature Genetics.

The host ubiquitin-dependent segregase VCP/p97 is required for the onset of human cytomegalovirus replication

J. Prendergast, Finn E. Grey, Yao-Tang Lin, 2017, PLoS pathogens.

Fine-mapping of colorectal cancer susceptibility loci at 8q23.3, 16q22.1 and 19q13.11: refinement of association signals and use of in silico analysis to suggest functional variation and unexpected candidate target genes.

D. Kerr, D. Duggan, J. Hopper, 2011, Human molecular genetics.

Meta-analysis of three genome-wide association studies identifies susceptibility loci for colorectal cancer at 1q41, 3q26.2, 12q13.13 and 20q13.33

Jean-Baptiste Cazier, Harry Campbell, Albert Tenesa, 2010, Nature Genetics.

Using regulatory variants to detect gene–gene interactions identifies networks of genes linked to cell immortalisation

I. Deary, D. Hume, I. Deary, 2020, Nature Communications.

A genome-wide association study identifies colorectal cancer susceptibility loci on chromosomes 10p14 and 8q23.3

Julian Peto, Henry Völzke, Sergi Castellví-Bel, 2008, Nature Genetics.

Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21

I. Deary, T. Hudson, C. Greenwood, 2008, Nature Genetics.

High performance imputation of structural and single nucleotide variants in Atlantic salmon using low-coverage whole genome sequencing

J. Prendergast, R. Houston, D. Robledo, 2023, bioRxiv.

Using machine learning to detect the differential usage of novel gene isoforms

Xiaopu Zhang, Musa A. Hassan, James G. D. Prendergast, 2022, BMC Bioinformatics.

Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures

S. Cockroft, B. Ylstra, J. Prendergast, 2013, Nature Structural &Molecular Biology.

Divergent selection experiments: a powerful tool for unravelling the genetic regulation of complex traits.

K. Rawlik, I. Jackson, J. Prendergast, 2018 .

hapbin: An Efficient Program for Performing Haplotype-Based Scans for Positive Selection in Large Genomic Datasets

Neil P. Chue Hong, Colin A. Maclean, James G.D. Prendergast, 2015, Molecular biology and evolution.

Arginine to Glutamine Variant in Olfactomedin Like 3 (OLFML3) Is a Candidate for Severe Goniodysgenesis and Glaucoma in the Border Collie Dog Breed

J. Prendergast, A. Ewing, K. Summers, 2019, G3: Genes, Genomes, Genetics.

Exome Sequencing to Detect Rare Variants Associated With General Cognitive Ability: A Pilot Study

Martin S. Taylor, R. Marioni, I. Deary, 2015, Twin Research and Human Genetics.

Chromatin structure and evolution in the human genome

C. Semple, W. Bickmore, J. Prendergast, 2007, BMC Evolutionary Biology.

Species-Specificity of Transcriptional Regulation and the Response to Lipopolysaccharide in Mammalian Macrophages

Mary E. B. McCulloch, D. Hume, J. Prendergast, 2020, Frontiers in Cell and Developmental Biology.

Genome‐wide methylation profiling in Crohn's disease identifies altered epigenetic regulation of key host defense mechanisms including the Th17 pathway

H. Drummond, E. Nimmo, J. Satsangi, 2012, Inflammatory bowel diseases.

Multiple Common Susceptibility Variants near BMP Pathway Loci GREM1, BMP4, and BMP2 Explain Part of the Missing Heritability of Colorectal Cancer

Steven Gallinger, Oliver Sieber, David J. Kerr, 2011, PLoS genetics.

A locus conferring tolerance to Theileria infection in African cattle

J. Prendergast, A. Talenti, Perle Latré de Laté, 2021, bioRxiv.

Increased ultra-rare variant load in an isolated Scottish population impacts exonic and regulatory regions

Martin S. Taylor, I. Deary, D. Hume, 2019, bioRxiv.

Whole-Genome Sequence Data Suggest Environmental Adaptation of Ethiopian Sheep Populations

D. Hume, A. Djikeng, J. Prendergast, 2021, Genome biology and evolution.

Rare Missense Functional Variants at COL4A1 and COL4A2 in Sporadic Intracerebral Hemorrhage

B. Kissela, C. Langefeld, S. Greenberg, 2021, Neurology.

Meta-analysis of three genome-wide association studies identifies susceptibility loci for colorectal cancer at 1q41, 3q26.2, 12q13.13 and 20q13.33

E. Dermitzakis, D. Kerr, L. Aaltonen, 2010, Nature Genetics.

Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21

Zanke, I. Deary, T. Hudson, 2008, Nature Genetics.

Loss‐of‐Function Mutations in the ALPL Gene Presenting with Adult Onset Osteoporosis and Low Serum Concentrations of Total Alkaline Phosphatase

I. Deary, S. Harris, P. Redmond, 2019, Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research.

Graphia: A platform for the graph-based visualisation and analysis of complex data

Tim Angus, David A. Hume, Tom C. Freeman, 2020, bioRxiv.

Sequencing Illustrates the Transcriptional Response of Legionella pneumophila during Infection and Identifies Seventy Novel Small Non-Coding RNAs

J. Prendergast, B. Loftus, A. Lohan, 2011, PloS one.

Detailed analysis of chick optic fissure closure reveals Netrin-1 as an essential mediator of epithelial fusion

J. Prendergast, L. Goodrich, B. Brooks, 2019, eLife.

Detailed analysis of chick optic fissure closure reveals Netrin-1 as an essential and conserved mediator of epithelial fusion during vertebrate embryogenesis

J. Prendergast, L. Goodrich, J. Sowden, 2018, bioRxiv.

Using machine learning to detect the differential usage of novel gene isoforms

Musa A. Hassan, J. Prendergast, Xiaopu Zhang, 2022, BMC Bioinform..

Rare genetic variants underlie outlying levels of DNA methylation and gene-expression

R. Marioni, P. Visscher, N. Wray, 2020, bioRxiv.

Sequencing and analysis of an Irish human genome

N. Friel, S. Cronin, O. Hardiman, 2010 .

Meta-analysis of three genome-wide association studies identifies susceptibility loci for at

E. Dermitzakis, D. Kerr, L. Aaltonen, 2016 .

Cumulative impact of 10 common genetic variants on colorectal cancer risk in 42,333 individuals from eight populations

T. Hudson, C. Greenwood, H. Brenner, 2013 .

Abundant pleiotropy in human complex diseases and traits.

F. Agakov, T. Manolio, P. McKeigue, 2011, American journal of human genetics.

The conservation of human functional variants and their effects across mammals

J. Prendergast, A. Tenesa, A. Talenti, 2022, bioRxiv.

Exome Sequencing to Detect Rare Variants Associated With General Cognitive Ability: A Pilot Study

Martin S. Taylor, R. Marioni, I. Deary, 2015, Twin Research and Human Genetics.

A promoter-level mammalian expression atlas

Martin S. Taylor, Jay W. Shin, Thomas J. Ha, 2014, Nature.

Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes

Colm E. Nestor, W. Bickmore, J. Prendergast, 2013, Genome Biology.