Global Properties and Functional Complexity of Human Gene Regulatory Variation

by Gaffney, Daniel J.
Published 2013

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

by Keightley, Peter D., Gaffney, Daniel J.
Published 2003

The scale of mutational variation in the murid genome

by Gaffney, Daniel J., Keightley, Peter D.
Published 2005

Genomic Selective Constraints in Murid Noncoding DNA

by Gaffney, Daniel J, Keightley, Peter D
Published 2006

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

by Gaffney, Daniel J, Keightley, Peter D
Published 2008

Selective Constraints in Experimentally Defined Primate Regulatory Regions

by Gaffney, Daniel J., Blekhman, Ran, Majewski, Jacek
Published 2008

Fine-mapping cellular QTLs with RASQUAL and ATAC-seq

by Kumasaka, Natsuhiko, Knights, Andrew J, Gaffney, Daniel J
Published in Nat Genet (2015)

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

by Pickrell, Joseph K., Gaffney, Daniel J., Gilad, Yoav, Pritchard, Jonathan K.
Published 2011

Evolutionary constraints in conserved nongenic sequences of mammals

by Keightley, Peter D., Kryukov, Gregory V., Sunyaev, Shamil, Halligan, Daniel L., Gaffney, Daniel J.
Published 2005

Gene Expression and Isoform Variation Analysis using Affymetrix Exon Arrays

by Bemmo, Amandine, Benovoy, David, Kwan, Tony, Gaffney, Daniel J, Jensen, Roderick V, Majewski, Jacek
Published 2008

Gene expression and isoform variation analysis using Affymetrix exon arrays

by Bemmo, Amandine, Benovoy, David, Kwan, Tony, Gaffney, Daniel J, Jensen, Roderick V, Majewski, Jacek
Published 2009

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

by Alasoo, Kaur, Rodrigues, Julia, Danesh, John, Freitag, Daniel F, Paul, Dirk S, Gaffney, Daniel J
Published in eLife (2019)

Exon-Specific QTLs Skew the Inferred Distribution of Expression QTLs Detected Using Gene Expression Array Data

by Veyrieras, Jean-Baptiste, Gaffney, Daniel J., Pickrell, Joseph K., Gilad, Yoav, Stephens, Matthew, Pritchard, Jonathan K.
Published 2012

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

by Pique-Regi, Roger, Degner, Jacob F., Pai, Athma A., Gaffney, Daniel J., Gilad, Yoav, Pritchard, Jonathan K.
Published 2011

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

by Alasoo, Kaur, Martinez, Fernando O., Hale, Christine, Gordon, Siamon, Powrie, Fiona, Dougan, Gordon, Mukhopadhyay, Subhankar, Gaffney, Daniel J.
Published in Sci Rep (2015)

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

by Alasoo, Kaur, Rodrigues, Julia, Mukhopadhyay, Subhankar, Knights, Andrew J., Mann, Alice L., Kundu, Kousik, Hale, Christine, Dougan, Gordon, Gaffney, Daniel J.
Published in Nat Genet (2018)

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

by Bell, Jordana T, Pai, Athma A, Pickrell, Joseph K, Gaffney, Daniel J, Pique-Regi, Roger, Degner, Jacob F, Gilad, Yoav, Pritchard, Jonathan K
Published 2011

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

by Bell, Jordana T, Pai, Athma A, Pickrell, Joseph K, Gaffney, Daniel J, Pique-Regi, Roger, Degner, Jacob F, Gilad, Yoav, Pritchard, Jonathan K
Published 2011

Controls of Nucleosome Positioning in the Human Genome

by Gaffney, Daniel J., McVicker, Graham, Pai, Athma A., Fondufe-Mittendorf, Yvonne N., Lewellen, Noah, Michelini, Katelyn, Widom, Jonathan, Gilad, Yoav, Pritchard, Jonathan K.
Published 2012

Dissecting the regulatory architecture of gene expression QTLs

by Gaffney, Daniel J, Veyrieras, Jean-Baptiste, Degner, Jacob F, Pique-Regi, Roger, Pai, Athma A, Crawford, Gregory E, Stephens, Matthew, Gilad, Yoav, Pritchard, Jonathan K
Published 2012