Daniel J Gaffney

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc Global properties and functional complexity of human gene regulatory variation
    Daniel J Gaffney
    Wellcome Trust Sanger Institute, Cambridge, United Kingdom
    PLoS Genet 9:e1003501. 2013
  2. pmc Controls of nucleosome positioning in the human genome
    Daniel J Gaffney
    Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
    PLoS Genet 8:e1003036. 2012
  3. pmc Dissecting the regulatory architecture of gene expression QTLs
    Daniel J Gaffney
    Department of Human Genetics, University of Chicago, 920 E58th Street, Chicago, IL 60637, USA
    Genome Biol 13:R7. 2012
  4. pmc DNase‚ÄČI sensitivity QTLs are a major determinant of human expression variation
    Jacob F Degner
    Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
    Nature 482:390-4. 2012
  5. pmc The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels
    Athma A Pai
    Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
    PLoS Genet 8:e1003000. 2012
  6. pmc DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines
    Jordana T Bell
    Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
    Genome Biol 12:R10. 2011
  7. pmc Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data
    Jean Baptiste Veyrieras
    Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
    PLoS ONE 7:e30629. 2012
  8. pmc Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
    Roger Pique-Regi
    Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
    Genome Res 21:447-55. 2011
  9. doi request reprint DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina
    Joseph M Zullo
    Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
    Cell 149:1474-87. 2012
  10. pmc False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions
    Joseph K Pickrell
    Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
    Bioinformatics 27:2144-6. 2011

Collaborators

Detail Information

Publications11

  1. pmc Global properties and functional complexity of human gene regulatory variation
    Daniel J Gaffney
    Wellcome Trust Sanger Institute, Cambridge, United Kingdom
    PLoS Genet 9:e1003501. 2013
    ..Finally, I highlight outstanding problems and future directions for development...
  2. pmc Controls of nucleosome positioning in the human genome
    Daniel J Gaffney
    Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
    PLoS Genet 8:e1003036. 2012
    ....
  3. pmc Dissecting the regulatory architecture of gene expression QTLs
    Daniel J Gaffney
    Department of Human Genetics, University of Chicago, 920 E58th Street, Chicago, IL 60637, USA
    Genome Biol 13:R7. 2012
    ..Using the HapMap lymphoblastoid cell lines, we combine 1000 Genomes genotypes and an extensive catalogue of human functional elements to investigate the biological mechanisms that eQTLs perturb...
  4. pmc DNase‚ÄČI sensitivity QTLs are a major determinant of human expression variation
    Jacob F Degner
    Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
    Nature 482:390-4. 2012
    ..Our observations indicate that dsQTLs are highly abundant in the human genome and are likely to be important contributors to phenotypic variation...
  5. pmc The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels
    Athma A Pai
    Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
    PLoS Genet 8:e1003000. 2012
    ..By analyzing our data within the context of known steady-state eQTLs, we estimate that a substantial fraction of eQTLs are associated with inter-individual variation in mRNA decay rates...
  6. pmc DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines
    Jordana T Bell
    Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
    Genome Biol 12:R10. 2011
    ..Here we measured methylation levels at 22,290 CpG dinucleotides in lymphoblastoid cell lines from 77 HapMap Yoruba individuals, for which genome-wide gene expression and genotype data were also available...
  7. pmc Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data
    Jean Baptiste Veyrieras
    Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
    PLoS ONE 7:e30629. 2012
    ..Nonetheless, we do observe an overall enrichment of eQTLs in exons versus introns in all three data sets, consistent with an important role for exonic sequences in gene regulation...
  8. pmc Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
    Roger Pique-Regi
    Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
    Genome Res 21:447-55. 2011
    ..We anticipate that this approach will be a valuable tool for genome-wide studies of gene regulation in a wide variety of cell types or tissues under diverse conditions...
  9. doi request reprint DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina
    Joseph M Zullo
    Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
    Cell 149:1474-87. 2012
    ..Knockdown of cKrox or HDAC3 results in dissociation of LASs/LADs from the nuclear lamina. These results reveal a mechanism that couples nuclear compartmentalization of chromatin domains with the control of gene activity...
  10. pmc False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions
    Joseph K Pickrell
    Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
    Bioinformatics 27:2144-6. 2011
    ..Here, we consider whether false positive peak calls can be caused by particular type of error in the reference genome: multicopy sequences which have been incorrectly assembled and collapsed into a single copy...
  11. pmc Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis
    Jimmy Z Liu
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Genet 44:1137-41. 2012
    ..8) with the most associated variant. This study shows how data from dense fine-mapping arrays coupled with functional genomic data can be used to identify candidate causal variants for functional follow-up...