Gaffney, Daniel J.

A survey of best practices for RNA-seq data analysis

Conesa, A., Madrigal, P., Tarazona, S., Gomez-Cabrero, D., Cervera, A., McPherson, A., Szcześniak, M. W., Gaffney, D. J., Elo, L. L., Zhang, X., et al. (2016) · Genome Biology

Genomics and Phylogenetic StudiesSingle-cell and spatial transcriptomics

Cited by 2,794

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

Bell, J. T., Pai, A. A., Pickrell, J. K., Gaffney, D. J., Pique-Regi, R., Degner, J. F., Gilad, Y., & Pritchard, J. K. (2011) · Genome Biology

Epigenetics and DNA MethylationGenetic Associations and Epidemiology

Cited by 838

Common genetic variation drives molecular heterogeneity in human iPSCs

Kilpinen, H., Goncalves, A., Leha, A., Afzal, V., Alasoo, K., Ashford, S., Bala, S., Bensaddek, D., Casale, F. P., Culley, O. J., et al. (2017) · Nature

Pluripotent Stem Cells ResearchGenetic Associations and Epidemiology

Cited by 586

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

Schwartzentruber, J., Cooper, S., Liu, J. Z., Barrio-Hernandez, I., Bello, E., Kumasaka, N., Young, A. M. H., Franklin, R. J. M., Johnson, T., Estrada, K., et al. (2021) · Nature Genetics

Alzheimer's disease research and treatmentsGenetic Associations and Epidemiology

Cited by 532

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

Pique-Regi, R., Degner, J. F., Pai, A. A., Gaffney, D. J., Gilad, Y., & Pritchard, J. K. (2011) · Genome Research

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 521

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

Heaton, H., Talman, A. M., Knights, A., Imaz, M., Gaffney, D. J., Durbin, R., Hemberg, M., & Lawniczak, M. K. N. (2020) · Nature Methods

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 506

Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain

Marsh, S. E., Walker, A. J., Kamath, T., Dissing-Olesen, L., Hammond, T. R., de Soysa, T. Y., Young, A. M. H., Murphy, S., Abdulraouf, A., Nadaf, N., et al. (2022) · Nature Neuroscience

Single-cell and spatial transcriptomicsNeuroinflammation and Neurodegeneration Mechanisms

Cited by 431

Single Cell Sequencing Reveals Glial Specific Responses to Tissue Processing & Enzymatic Dissociation in Mice and Humans

Marsh, S. E., Kamath, T., Walker, A. J., Dissing-Olesen, L., Hammond, T. R., Young, A. M. H., Abdulraouf, A., Nadaf, N., Dufort, C., Murphy, S., et al. (2020) · Nature Neuroscience

Single-cell and spatial transcriptomicsNeuroinflammation and Neurodegeneration Mechanisms

Cited by 430

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

The UK-PSC Consortium, Ji, S.-G., The International IBD Genetics Consortium, The International PSC Study Group, Juran, B. D., Mucha, S., Folseraas, T., Jostins, L., Melum, E., Kumasaka, N., et al. (2017) · Nature Genetics

Liver Diseases and ImmunityGenetic Associations and Epidemiology

Cited by 357

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

HIPSCI Consortium, Alasoo, K., Rodrigues, J., Mukhopadhyay, S., Knights, A. J., Mann, A. L., Kundu, K., Hale, C., Dougan, G., & Gaffney, D. J. (2018) · Nature Genetics

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 338

Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

Cuomo, A. S. E., Seaton, D. D., McCarthy, D. J., Martinez, I., Bonder, M. J., Garcia-Bernardo, J., Amatya, S., Madrigal, P., Isaacson, A., Buettner, F., et al. (2020) · Nature Communications

Pluripotent Stem Cells ResearchSingle-cell and spatial transcriptomics

Cited by 331

Genetic Background Drives Transcriptional Variation in Human Induced Pluripotent Stem Cells

Rouhani, F., Kumasaka, N., de Brito, M. C., Bradley, A., Vallier, L., & Gaffney, D. (2014) · PLoS Genetics

Pluripotent Stem Cells ResearchEpigenetics and DNA Methylation

Cited by 294

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

The UK Primary Biliary Cirrhosis (PBC) Consortium, Liu, J. Z., The Wellcome Trust Case Control Consortium 3, Almarri, M. A., Gaffney, D. J., Mells, G. F., Jostins, L., Cordell, H. J., Ducker, S. J., Day, D. B., et al. (2012) · Nature Genetics

Liver Diseases and ImmunityGenetic Associations and Epidemiology

Cited by 274

Molecular and functional variation in iPSC-derived sensory neurons

HIPSCI Consortium, Schwartzentruber, J., Foskolou, S., Kilpinen, H., Rodrigues, J., Alasoo, K., Knights, A. J., Patel, M., Goncalves, A., Ferreira, R., et al. (2018) · Nature Genetics

Genetic Associations and EpidemiologyPluripotent Stem Cells Research

Cited by 223

A Map of Transcriptional Heterogeneity and Regulatory Variation in Human Microglia

Young, A. M. H., Kumasaka, N., Calvert, F., Hammond, T. R., Knights, A., Panousis, N., Park, J. S., Schwartzentruber, J., Liu, J., Kundu, K., et al. (2021) · Nature Genetics

Neuroinflammation and Neurodegeneration MechanismsSingle-cell and spatial transcriptomics

Cited by 213

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

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. (2015) · Brain

Alzheimer's disease research and treatmentsAmyotrophic Lateral Sclerosis Research

Cited by 155

Niacin-mediated rejuvenation of macrophage/microglia enhances remyelination of the aging central nervous system

Rawji, K. S., Young, A. M. H., Ghosh, T., Michaels, N. J., Mirzaei, R., Kappen, J., Kolehmainen, K. L., Alaeiilkhchi, N., Lozinski, B., Mishra, M. K., et al. (2020) · Acta Neuropathologica

Multiple Sclerosis Research StudiesNeuroinflammation and Neurodegeneration Mechanisms

Cited by 153

Single-cell atlas of human liver development reveals pathways directing hepatic cell fates

Wesley, B. T., Ross, A. D. B., Muraro, D., Miao, Z., Saxton, S., Tomaz, R. A., Morell, C. M., Ridley, K., Zacharis, E. D., Petrus-Reurer, S., et al. (2022) · Nature Cell Biology

Single-cell and spatial transcriptomicsLiver physiology and pathology

Cited by 146

Substantial somatic genomic variation and selection for BCOR mutations in human induced pluripotent stem cells

Rouhani, F. J., Zou, X., Danecek, P., Badja, C., Amarante, T. D., Koh, G., Wu, Q., Memari, Y., Durbin, R., Martincorena, I., et al. (2022) · Nature Genetics

Pluripotent Stem Cells ResearchCRISPR and Genetic Engineering

Cited by 105

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

Alasoo, K., Martinez, F. O., Hale, C., Gordon, S., Powrie, F., Dougan, G., Mukhopadhyay, S., & Gaffney, D. J. (2015) · Scientific Reports

Pluripotent Stem Cells ResearchImmune cells in cancer

Cited by 102