Daniel Gaffney
Daniel Gaffney
Directory, Therapeutics, Genomics plc
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Cited by
Cited by
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
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, 1-13, 2011
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
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
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
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
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
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
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
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
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
Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer’s disease risk genes
J Schwartzentruber, S Cooper, JZ Liu, I Barrio-Hernandez, E Bello, ...
Nature genetics 53 (3), 392-402, 2021
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
Fine-mapping cellular QTLs with RASQUAL and ATAC-seq
N Kumasaka, AJ Knights, DJ Gaffney
Nature genetics 48 (2), 206-213, 2016
Dissecting the regulatory architecture of gene expression QTLs
DJ Gaffney, JB Veyrieras, JF Degner, R Pique-Regi, AA Pai, GE Crawford, ...
Genome biology 13, 1-15, 2012
Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes
H Heaton, AM Talman, A Knights, M Imaz, DJ Gaffney, R Durbin, ...
Nature methods 17 (6), 615-620, 2020
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
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
CRISPR/Cas9 editing in human pluripotent stem cell-cardiomyocytes highlights arrhythmias, hypocontractility, and energy depletion as potential therapeutic targets for …
D Mosqueira, I Mannhardt, JR Bhagwan, K Lis-Slimak, P Katili, E Scott, ...
European heart journal 39 (43), 3879-3892, 2018
N6-methyladenosine regulates the stability of RNA:DNA hybrids in human cells
A Abakir, TC Giles, A Cristini, JM Foster, N Dai, M Starczak, ...
Nature genetics 52 (1), 48-55, 2020
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