Daniel Gaffney
Daniel Gaffney
Directory, Therapeutics, Genomics plc
Verified email at genomicsplc.com
Title
Cited by
Cited by
Year
A survey of best practices for RNA-seq data analysis
A Conesa, P Madrigal, S Tarazona, D Gomez-Cabrero, A Cervera, ...
Genome biology 17 (1), 1-19, 2016
18482016
DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines
JT Bell, AA Pai, JK Pickrell, DJ Gaffney, R Pique-Regi, JF Degner, Y Gilad, ...
Genome biology 12 (1), 1-13, 2011
8662011
DNase I sensitivity QTLs are a major determinant of human expression variation
JF Degner, AA Pai, R Pique-Regi, JB Veyrieras, DJ Gaffney, JK Pickrell, ...
Nature 482 (7385), 390-394, 2012
6782012
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
R Pique-Regi, JF Degner, AA Pai, DJ Gaffney, Y Gilad, JK Pritchard
Genome research 21 (3), 447-455, 2011
5762011
DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina
JM Zullo, IA Demarco, R Piqué-Regi, DJ Gaffney, CB Epstein, CJ Spooner, ...
Cell 149 (7), 1474-1487, 2012
4002012
Common genetic variation drives molecular heterogeneity in human iPSCs
H Kilpinen, A Goncalves, A Leha, V Afzal, K Alasoo, S Ashford, S Bala, ...
Nature 546 (7658), 370-375, 2017
3542017
Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis
JZ Liu, MA Almarri, DJ Gaffney, GF Mells, L Jostins, HJ Cordell, SJ Ducker, ...
Nature genetics 44 (10), 1137-1141, 2012
2562012
Controls of nucleosome positioning in the human genome
DJ Gaffney, G McVicker, AA Pai, YN Fondufe-Mittendorf, N Lewellen, ...
PLoS genetics 8 (11), e1003036, 2012
2552012
Genetic background drives transcriptional variation in human induced pluripotent stem cells
F Rouhani, N Kumasaka, MC de Brito, A Bradley, L Vallier, D Gaffney
PLoS genetics 10 (6), e1004432, 2014
2502014
Dissecting the regulatory architecture of gene expression QTLs
DJ Gaffney, JB Veyrieras, JF Degner, R Pique-Regi, AA Pai, GE Crawford, ...
Genome biology 13 (1), 1-15, 2012
2182012
Epithelial IL-22RA1-mediated fucosylation promotes intestinal colonization resistance to an opportunistic pathogen
TAN Pham, S Clare, D Goulding, JM Arasteh, MD Stares, HP Browne, ...
Cell host & microbe 16 (4), 504-516, 2014
2152014
Quantifying the slightly deleterious mutation model of molecular evolution
A Eyre-Walker, PD Keightley, NGC Smith, D Gaffney
Molecular Biology and Evolution 19 (12), 2142-2149, 2002
2052002
Genome-wide association study of primary sclerosing cholangitis identifies new risk loci and quantifies the genetic relationship with inflammatory bowel disease
SG Ji, BD Juran, S Mucha, T Folseraas, L Jostins, E Melum, N Kumasaka, ...
Nature genetics 49 (2), 269-273, 2017
1742017
Fine-mapping cellular QTLs with RASQUAL and ATAC-seq
N Kumasaka, AJ Knights, DJ Gaffney
Nature genetics 48 (2), 206-213, 2016
1682016
Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response
K Alasoo, J Rodrigues, S Mukhopadhyay, AJ Knights, AL Mann, K Kundu, ...
Nature genetics 50 (3), 424-431, 2018
1512018
Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents
PD Keightley, DJ Gaffney
Proceedings of the National Academy of Sciences 100 (23), 13402-13406, 2003
1502003
Molecular and functional variation in iPSC-derived sensory neurons
J Schwartzentruber, S Foskolou, H Kilpinen, J Rodrigues, K Alasoo, ...
Nature genetics 50 (1), 54-61, 2018
1362018
The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels
AA Pai, CE Cain, O Mizrahi-Man, S De Leon, N Lewellen, JB Veyrieras, ...
Public Library of Science 8 (10), e1003000, 2012
1042012
Early maturation and distinct tau pathology in induced pluripotent stem cell-derived neurons from patients with MAPT mutations
M Iovino, S Agathou, A González-Rueda, M Del Castillo Velasco-Herrera, ...
Brain 138 (11), 3345-3359, 2015
1032015
The scale of mutational variation in the murid genome
DJ Gaffney, PD Keightley
Genome research 15 (8), 1086-1094, 2005
1032005
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Articles 1–20