Daniel Gaffney
TitleCited byYear
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), 13, 2016
10012016
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), R10, 2011
7192011
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, 2012
5232012
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
4722011
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
3282012
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, 2012
2042012
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
2032012
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
1862002
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
1762014
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), R7, 2012
1762012
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, 2017
1682017
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
1462014
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
1412003
The scale of mutational variation in the murid genome
DJ Gaffney, PD Keightley
Genome research 15 (8), 1086-1094, 2005
1002005
Fine-mapping cellular QTLs with RASQUAL and ATAC-seq
N Kumasaka, AJ Knights, DJ Gaffney
Nature genetics 48 (2), 206, 2016
932016
Gene expression and isoform variation analysis using Affymetrix Exon Arrays
A Bemmo, D Benovoy, T Kwan, DJ Gaffney, RV Jensen, J Majewski
BMC genomics 9 (1), 529, 2008
842008
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, 2017
812017
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, ...
PLoS genetics 8 (10), e1003000, 2012
782012
False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions
JK Pickrell, DJ Gaffney, Y Gilad, JK Pritchard
Bioinformatics 27 (15), 2144-2146, 2011
772011
Genomic selective constraints in murid noncoding DNA
DJ Gaffney, PD Keightley
PLoS genetics 2 (11), e204, 2006
732006
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Articles 1–20