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Activities

Employment (4)

Wellcome Trust Sanger Institute: Cambridge, Cambridgeshire, GB

2015-10-02 to present | Group Leader (Cellular Genetics)
Employment
Source: Self-asserted source
Daniel Gaffney

Wellcome Trust Sanger Institute: Cambridge, Cambridgeshire, GB

2011-07-15 to 2015-10-01 | Career Development Fellow Group Leader (Computational Genomics)
Employment
Source: Self-asserted source
Daniel Gaffney

University of Chicago: Chicago, IL, US

2008-09-01 to 2011-07-12 | Postdoctoral Fellow (Human Genetics)
Employment
Source: Self-asserted source
Daniel Gaffney

McGill University and Genome Québec Innovation Centre: Montreal, QC, CA

2006-07-14 to 2008-09-01 | Postdoctoral Fellow
Employment
Source: Self-asserted source
Daniel Gaffney

Education and qualifications (3)

University of Edinburgh: Edinburgh, Edinburgh, GB

2002-09-01 to 2006-02-01 | PhD (Biological Sciences)
Education
Source: Self-asserted source
Daniel Gaffney

University of Edinburgh: Edinburgh, Edinburgh, GB

2000-09-01 to 2001-09-01 | M.Sc Quantitative Genetics and Genome Analysis (Biological Sciences)
Education
Source: Self-asserted source
Daniel Gaffney

National University of Ireland - Galway: Galway, Galway, IE

1995-09-01 to 1999-09-01 | B.Sc (Hons) Marine Science (Science)
Education
Source: Self-asserted source
Daniel Gaffney

Funding (1)

MICA: Development of Metrics and Quality Standards for Scale up of Human Pluripotent Stem Cells

Works (46)

Cell reprogramming shapes the mitochondrial DNA landscape

Nature Communications
2021-09-02 | Journal article
Contributors: Wei Wei; Daniel J. Gaffney; Patrick F. Chinnery
Source: check_circle
Crossref

Transposable element expression at unique loci in single cells with CELLO-seq

2020-10-02 | Preprint
Contributors: Rebecca V Berrens; Andrian Yang; Christopher E Laumer; Aaron TL Lun; Florian Bieberich; Cheuk-Ting Law; Guocheng Lan; Maria Imaz; Daniel Gaffney; John C Marioni
Source: check_circle
Crossref

Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes

Nature Methods
2020-06-04 | Journal article
Contributors: Haynes Heaton; Arthur M. Talman; Andrew Knights; Maria Imaz; Daniel J. Gaffney; Richard Durbin; Martin Hemberg; Mara K. N. Lawniczak
Source: check_circle
Crossref

Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes

Nature Methods
2020-04-16 | Journal article
Contributors: Davis J. McCarthy; Raghd Rostom; Yuanhua Huang; Daniel J. Kunz; Petr Danecek; Marc Jan Bonder; Tzachi Hagai; Ruqian Lyu; Wenyi Wang; Daniel J. Gaffney et al.
Source: check_circle
Crossref

Genome-wide meta-analysis, fine-mapping, and integrative prioritization identify new Alzheimer’s disease risk genes

2020-01-27 | Other
Contributors: Jeremy Schwartzentruber; Sarah Cooper; Jimmy Z Liu; Inigo Barrio-Hernandez; Erica Bello; Natsuhiko Kumasaka; Toby Johnson; Karol Estrada; Daniel J. Gaffney; Pedro Beltrao et al.
Source: check_circle
Crossref

Mapping and predicting gene–enhancer interactions

Nature Genetics
2019-12-29 | Journal article
Contributors: Daniel J. Gaffney
Source: check_circle
Crossref

souporcell: Robust clustering of single cell RNAseq by genotype and ambient RNA inference without reference genotypes

2019-07-14 | Other
Contributors: Haynes Heaton; Arthur M. Talman; Andrew Knights; Maria Imaz; Daniel Gaffney; Richard Durbin; Martin Hemberg; Mara Lawniczak
Source: check_circle
Crossref

High-resolution genetic mapping of putative causal interactions between regions of open chromatin

Nature Genetics
2019-01-26 | Journal article
Contributors: Natsuhiko Kumasaka; Andrew J. Knights; Daniel J. Gaffney
Source: check_circle
Crossref

Cardelino: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants

2018-09-10 | Other
Contributors: Davis J. McCarthy; Raghd Rostom; Yuanhua Huang; Daniel J. Kunz; Petr Danecek; Marc Jan Bonder; Tzachi Hagai; Wenyi Wang; Daniel J. Gaffney; Benjamin D. Simons et al.
Source: check_circle
Crossref

Genetic effects on promoter usage are highly context-specific and contribute to complex traits

2018-05-11 | Other
Contributors: Kaur Alasoo; Julia Rodrigues; John Danesh; Daniel F. Freitag; Dirk S. Paul; Daniel J. Gaffney
Source: check_circle
Crossref

Molecular and functional variation in iPSC-derived sensory neurons.

Nature genetics
2018-01 | Journal article
Contributors: Schwartzentruber J; Foskolou S; Kilpinen H; Rodrigues J; Alasoo K; Knights AJ; Patel M; Goncalves A; Ferreira R; Benn CL et al.
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response.

Nature genetics
2018-01 | Journal article
Contributors: Alasoo K; Rodrigues J; Mukhopadhyay S; Knights AJ; Mann AL; Kundu K; HIPSCI Consortium; Hale C; Dougan G; Gaffney DJ
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Common genetic variation drives molecular heterogeneity in human iPSCs.

Nature
2017-06 | Journal article
Contributors: Kilpinen H; Goncalves A; Leha A; Afzal V; Alasoo K; Ashford S; Bala S; Bensaddek D; Casale FP; Culley OJ et al.
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs.

Nature
2017-06 | Journal article
Contributors: Kilpinen H; Goncalves A; Leha A; Afzal V; Alasoo K; Ashford S; Bala S; Bensaddek D; Casale FP; Culley OJ et al.
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Shared genetic effects on chromatin and gene expression reveal widespread enhancer priming in immune response

2017-01-26 | Preprint
Contributors: Kaur Alasoo; Julia Rodrigues; Subhankar Mukhopadhyay; Andrew J. Knights; Alice L. Mann; Kousik Kundu; Christine Hale; Gordon Dougan; Daniel J. Gaffney
Source: check_circle
Crossref

Erratum to: A survey of best practices for RNA-seq data analysis.

2016 | Journal article
Contributors: Conesa A; Madrigal P; Tarazona S; Gomez-Cabrero D; Cervera A; McPherson A; Szcześniak MW; Gaffney DJ; Elo LL; Zhang X et al.
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Corrigendum: Fine-mapping cellular QTLs with RASQUAL and ATAC-seq.

2016-04 | Journal article
Contributors: Kumasaka N; Knights AJ; Gaffney DJ
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Fine-mapping cellular QTLs with RASQUAL and ATAC-seq.

2016-02 | Journal article
Contributors: Kumasaka N; Knights AJ; Gaffney DJ
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

A survey of best practices for RNA-seq data analysis.

2016-01 | Journal article
Contributors: Conesa A; Madrigal P; Tarazona S; Gomez-Cabrero D; Cervera A; McPherson A; Szcześniak MW; Gaffney DJ; Elo LL; Zhang X et al.
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Early maturation and distinct tau pathology in induced pluripotent stem cell-derived neurons from patients with MAPT mutations.

2015-11 | Journal article
Contributors: Iovino M; Agathou S; González-Rueda A; Del Castillo Velasco-Herrera M; Borroni B; Alberici A; Lynch T; O'Dowd S; Geti I; Gaffney D et al.
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Transcriptional profiling of macrophages derived from monocytes and iPS cells identifies a conserved response to LPS and novel alternative transcription.

2015-07 | Journal article
Contributors: Alasoo K; Martinez FO; Hale C; Gordon S; Powrie F; Dougan G; Mukhopadhyay S; Gaffney DJ
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Activin/nodal signaling and NANOG orchestrate human embryonic stem cell fate decisions by controlling the H3K4me3 chromatin mark.

2015-04 | Journal article
Contributors: Bertero A; Madrigal P; Galli A; Hubner NC; Moreno I; Burks D; Brown S; Pedersen RA; Gaffney D; Mendjan S et al.
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Epithelial IL-22RA1-mediated fucosylation promotes intestinal colonization resistance to an opportunistic pathogen.

2014-10 | Journal article
Contributors: Pham TA; Clare S; Goulding D; Arasteh JM; Stares MD; Browne HP; Keane JA; Page AJ; Kumasaka N; Kane L et al.
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Genetic background drives transcriptional variation in human induced pluripotent stem cells.

2014-06 | Journal article
Contributors: Rouhani F; Kumasaka N; de Brito MC; Bradley A; Vallier L; Gaffney D
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation.

2013-11 | Journal article
Contributors: Aldridge S; Watt S; Quail MA; Rayner T; Lukk M; Bimson MF; Gaffney D; Odom DT
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Global properties and functional complexity of human gene regulatory variation.

2013-05 | Journal article
Contributors: Gaffney DJ
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Controls of nucleosome positioning in the human genome.

2012 | Journal article
Contributors: Gaffney DJ; McVicker G; Pai AA; Fondufe-Mittendorf YN; Lewellen N; Michelini K; Widom J; Gilad Y; Pritchard JK
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data.

2012 | Journal article
Contributors: Veyrieras JB; Gaffney DJ; Pickrell JK; Gilad Y; Stephens M; Pritchard JK
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels.

2012 | Journal article
Contributors: Pai AA; Cain CE; Mizrahi-Man O; De Leon S; Lewellen N; Veyrieras JB; Degner JF; Gaffney DJ; Pickrell JK; Stephens M et al.
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis.

2012-10 | Journal article
Contributors: Liu JZ; Almarri MA; Gaffney DJ; Mells GF; Jostins L; Cordell HJ; Ducker SJ; Day DB; Heneghan MA; Neuberger JM et al.
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina.

2012-06 | Journal article
Contributors: Zullo JM; Demarco IA; Piqué-Regi R; Gaffney DJ; Epstein CB; Spooner CJ; Luperchio TR; Bernstein BE; Pritchard JK; Reddy KL et al.
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Dissecting the regulatory architecture of gene expression QTLs.

2012-01 | Journal article
Contributors: Gaffney DJ; Veyrieras JB; Degner JF; Pique-Regi R; Pai AA; Crawford GE; Stephens M; Gilad Y; Pritchard JK
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines.

2011 | Journal article
Contributors: Bell JT; Pai AA; Pickrell JK; Gaffney DJ; Pique-Regi R; Degner JF; Gilad Y; Pritchard JK
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions.

2011-08 | Journal article
Contributors: Pickrell JK; Gaffney DJ; Gilad Y; Pritchard JK
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data.

2011-03 | Journal article
Contributors: Pique-Regi R; Degner JF; Pai AA; Gaffney DJ; Gilad Y; Pritchard JK
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Gene expression and isoform variation analysis using Affymetrix exon arrays.

2009 | Journal article
Contributors: Bemmo A; Benovoy D; Kwan T; Gaffney DJ; Jensen RV; Majewski J
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Gene expression and isoform variation analysis using Affymetrix Exon Arrays.

2008 | Journal article
Contributors: Bemmo A; Benovoy D; Kwan T; Gaffney DJ; Jensen RV; Majewski J
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals.

2008-09 | Journal article
Contributors: Gaffney DJ; Keightley PD
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Genomic selective constraints in murid noncoding DNA.

2006-11 | Journal article
Contributors: Gaffney DJ; Keightley PD
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Evolutionary constraints in conserved nongenic sequences of mammals.

2005-10 | Journal article
Contributors: Keightley PD; Kryukov GV; Sunyaev S; Halligan DL; Gaffney DJ
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

The scale of mutational variation in the murid genome.

2005-08 | Journal article
Contributors: Gaffney DJ; Keightley PD
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

DNA sequence error rates in Genbank records estimated using the mouse genome as a reference.

2004 | Journal article
Contributors: Wesche PL; Gaffney DJ; Keightley PD
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Unexpected conserved non-coding DNA blocks in mammals.

2004-08 | Journal article
Contributors: Gaffney DJ; Keightley PD
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents.

2003-11 | Journal article
Contributors: Keightley PD; Gaffney DJ
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Quantifying the slightly deleterious mutation model of molecular evolution.

2002-12 | Journal article
Contributors: Eyre-Walker A; Keightley PD; Smith NG; Gaffney D
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central

Virulence in rodent malaria: host genotype by parasite genotype interactions.

2002-07 | Journal article
Contributors: Mackinnon MJ; Gaffney DJ; Read AF
Source: Self-asserted source
Daniel Gaffney via Europe PubMed Central