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Daniel J. Gaffney
Researcher at Wellcome Trust Sanger Institute
Publications - 84
Citations - 10172
Daniel J. Gaffney is an academic researcher from Wellcome Trust Sanger Institute. The author has contributed to research in topics: Gene & Induced pluripotent stem cell. The author has an hindex of 37, co-authored 80 publications receiving 7974 citations. Previous affiliations of Daniel J. Gaffney include Wellcome Trust & University of Chicago.
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Journal ArticleDOI
A survey of best practices for RNA-seq data analysis
Ana Conesa,Pedro Madrigal,Pedro Madrigal,Sonia Tarazona,David Gomez-Cabrero,Alejandra Cervera,Andrew McPherson,Michał Wojciech Szcześniak,Daniel J. Gaffney,Laura L. Elo,Xuegong Zhang,Ali Mortazavi +11 more
TL;DR: All of the major steps in RNA-seq data analysis are reviewed, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping.
Journal ArticleDOI
DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines.
Jordana T. Bell,Jordana T. Bell,Athma A. Pai,Joseph K. Pickrell,Daniel J. Gaffney,Daniel J. Gaffney,Roger Pique-Regi,Jacob F. Degner,Yoav Gilad,Jonathan K. Pritchard,Jonathan K. Pritchard +10 more
TL;DR: A strong genetic component to inter-individual variation in DNA methylation profiles is demonstrated, and there was an enrichment of SNPs that affect both methylation and gene expression, providing evidence for shared mechanisms in a fraction of genes.
Journal ArticleDOI
DNase I sensitivity QTLs are a major determinant of human expression variation
Jacob F. Degner,Athma A. Pai,Roger Pique-Regi,Jean Baptiste Veyrieras,Daniel J. Gaffney,Daniel J. Gaffney,Joseph K. Pickrell,Sherryl De Leon,Katelyn Michelini,Noah Lewellen,Gregory E. Crawford,Matthew Stephens,Yoav Gilad,Jonathan K. Pritchard,Jonathan K. Pritchard +14 more
TL;DR: It is shown that genetic variants that modify chromatin accessibility and transcription factor binding are a major mechanism through which genetic variation leads to gene expression differences among humans.
Journal ArticleDOI
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data.
Roger Pique-Regi,Jacob F. Degner,Athma A. Pai,Daniel J. Gaffney,Yoav Gilad,Jonathan K. Pritchard +5 more
TL;DR: A genome-wide map of 827,000 transcription factorbinding sites in human lymphoblastoid cell lines is reported, which is comprised of sites corresponding to 239 position weight matrices of known transcription factor binding motifs, and 49 novel sequence motifs.
Journal ArticleDOI
Common genetic variation drives molecular heterogeneity in human iPSCs
Helena Kilpinen,Angela Goncalves,Andreas Leha,Vackar Afzal,Kaur Alasoo,Sofie Ashford,Sendu Bala,Dalila Bensaddek,Francesco Paolo Casale,Oliver J. Culley,Petr Danacek,Adam Faulconbridge,Peter W. Harrison,Annie Kathuria,Davis J. McCarthy,Davis J. McCarthy,Shane A. McCarthy,Ruta Meleckyte,Yasin Memari,Nathalie Moens,Filipa A.C. Soares,Alice L. Mann,Ian Streeter,Chukwuma A. Agu,Alex Alderton,Rachel Nelson,Sarah Harper,Minal Patel,A. White,Sharad R. Patel,Laura Clarke,Reena Halai,Christopher M. Kirton,Anja Kolb-Kokocinski,Philip L. Beales,Ewan Birney,Davide Danovi,Angus I. Lamond,Willem H. Ouwehand,Willem H. Ouwehand,Willem H. Ouwehand,Ludovic Vallier,Ludovic Vallier,Fiona M. Watt,Richard Durbin,Oliver Stegle,Daniel J. Gaffney +46 more
TL;DR: This study outlines the major sources of genetic and phenotypic variation in iPS cells and establishes their suitability as models of complex human traits and cancer.