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Biology and Biochemistry

D-Index
50
Citations
16074
World Ranking
17426
National Ranking
1367

Overview

Daniel J. Gaffney is affiliated with the Wellcome Sanger Institute in the United Kingdom. Their research spans a range of topics within biochemistry, genetics, and molecular biology, with a focus on molecular biology, genetics, immunology, cancer research, and neurology.

Their scientific contributions focus on several main topics, including:

  • Single-cell and spatial transcriptomics
  • Genetic associations and epidemiology
  • CRISPR and genetic engineering
  • Neuroinflammation and neurodegeneration mechanisms
  • Pluripotent stem cells research
  • RNA modifications and cancer
  • Bioinformatics and genomic networks

Frequently publishing in high-impact journals, Daniel J. Gaffney has contributed notably to venues such as:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • Nature Genetics
  • Nature Communications
  • Nature Methods
  • Nature Neuroscience

Some recent significant papers include:

  • "Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer's disease risk genes" (2021), published in Nature Genetics
  • "Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes" (2020), published in Nature Methods
  • "Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain" (2022), published in Nature Neuroscience
  • "Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression" (2020), published in Nature Communications
  • "Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation" (2021), published in Nature Genetics

Throughout their career, Daniel J. Gaffney has collaborated extensively with several researchers, notably:

  • Andrew Knights
  • Natsuhiko Kumasaka
  • Maria Imaz
  • Adam M. H. Young
  • Robin J.M. Franklin

This body of work reflects a comprehensive engagement with cutting-edge methods in single-cell sequencing technologies, genetics, and neurobiology. Their research outputs contribute to understanding genetic influences on cellular function and disease mechanisms, particularly in neurological contexts.

Best Publications

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

    Ana Conesa;Pedro Madrigal;Pedro Madrigal;Sonia Tarazona;David Gomez-Cabrero

  • 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

  • DNase I sensitivity QTLs are a major determinant of human expression variation

    Jacob F. Degner;Athma A. Pai;Roger Pique-Regi;Jean Baptiste Veyrieras

  • 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

  • Common genetic variation drives molecular heterogeneity in human iPSCs

    Helena Kilpinen;Angela Goncalves;Andreas Leha;Vackar Afzal

  • DNA Sequence-Dependent Compartmentalization and Silencing of Chromatin at the Nuclear Lamina

    Joseph M. Zullo;Ignacio A. Demarco;Roger Piqué-Regi;Roger Piqué-Regi;Daniel J. Gaffney;Daniel J. Gaffney

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

    Jeremy Schwartzentruber;Jeremy Schwartzentruber;Sarah Cooper;Jimmy Z. Liu;Inigo Barrio-Hernandez

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

    Haynes Heaton;Arthur M Talman;Andrew Knights;Maria Imaz;Maria Imaz

  • Genome-wide association study of primary sclerosing cholangitis identifies new risk loci and quantifies the genetic relationship with inflammatory bowel disease

    Sun Gou Ji;Brian D. Juran;Sören Mucha;Trine Folseraas

  • Controls of Nucleosome Positioning in the Human Genome

    Daniel J. Gaffney;Graham McVicker;Graham McVicker;Athma A. Pai;Yvonne N. Fondufe-Mittendorf;Yvonne N. Fondufe-Mittendorf

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

    Foad Rouhani;Natsuhiko Kumasaka;Miguel Cardoso de Brito;Allan Bradley

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

    Kaur Alasoo;Julia Rodrigues;Subhankar Mukhopadhyay;Andrew J Knights

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

    Jimmy Z Liu;Mohamed A Almarri;Daniel J Gaffney;George F Mells

  • Epithelial IL-22RA1-Mediated Fucosylation Promotes Intestinal Colonization Resistance to an Opportunistic Pathogen

    Tu Anh N. Pham;Simon Clare;David Goulding;Julia M. Arasteh

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

    Natsuhiko Kumasaka;Andrew J Knights;Daniel J Gaffney

  • Dissecting the regulatory architecture of gene expression QTLs

    Daniel J Gaffney;Daniel J Gaffney;Daniel J Gaffney;Jean-Baptiste Veyrieras;Jacob F Degner;Roger Pique-Regi

  • CRISPR/Cas9 editing in human pluripotent stem cell-cardiomyocytes highlights arrhythmias, hypocontractility, and energy depletion as potential therapeutic targets for hypertrophic cardiomyopathy

    Diogo Mosqueira;Ingra Mannhardt;Jamie R Bhagwan;Katarzyna Lis-Slimak

  • Quantifying the Slightly Deleterious Mutation Model of Molecular Evolution

    Adam Eyre-Walker;Peter D. Keightley;Nick G. C. Smith;Daniel Gaffney

  • Molecular and functional variation in iPSC-derived sensory neurons.

    Jeremy Schwartzentruber;Jeremy Schwartzentruber;Stefanie Foskolou;Helena Kilpinen;Julia Rodrigues

  • Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation

    Julie Jerber;Daniel D Seaton;Anna S E Cuomo;Natsuhiko Kumasaka

Frequent Co-Authors

Jonathan K. Pritchard
Jonathan K. Pritchard Stanford University
John C. Marioni
John C. Marioni European Bioinformatics Institute
Ludovic Vallier
Ludovic Vallier University of Cambridge
Jeremy Schwartzentruber
Jeremy Schwartzentruber Wellcome Sanger Institute
Willem H. Ouwehand
Willem H. Ouwehand University of Cambridge
Oliver Stegle
Oliver Stegle German Cancer Research Center
Peter D. Keightley
Peter D. Keightley University of Edinburgh
Yoav Gilad
Yoav Gilad University of Chicago
Richard Durbin
Richard Durbin University of Cambridge
Gordon Dougan
Gordon Dougan University of Cambridge

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