Global Properties and Functional Complexity of Human Gene Regulatory Variation

por Gaffney, Daniel J.
Publicado 2013

Genomic Selective Constraints in Murid Noncoding DNA

por Gaffney, Daniel J, Keightley, Peter D
Publicado 2006

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

por Gaffney, Daniel J, Keightley, Peter D
Publicado 2008

Selective Constraints in Experimentally Defined Primate Regulatory Regions

por Gaffney, Daniel J., Blekhman, Ran, Majewski, Jacek
Publicado 2008

Fine-mapping cellular QTLs with RASQUAL and ATAC-seq

por Kumasaka, Natsuhiko, Knights, Andrew J, Gaffney, Daniel J
Publicado 2015

Cell reprogramming shapes the mitochondrial DNA landscape

por Wei, Wei, Gaffney, Daniel J., Chinnery, Patrick F.
Publicado 2021

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

por Pickrell, Joseph K., Gaffney, Daniel J., Gilad, Yoav, Pritchard, Jonathan K.
Publicado 2011

Gene Expression and Isoform Variation Analysis using Affymetrix Exon Arrays

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

Gene expression and isoform variation analysis using Affymetrix exon arrays

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

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

por Alasoo, Kaur, Rodrigues, Julia, Danesh, John, Freitag, Daniel F, Paul, Dirk S, Gaffney, Daniel J
Publicado 2019

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

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

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

por Alasoo, Kaur, Martinez, Fernando O., Hale, Christine, Gordon, Siamon, Powrie, Fiona, Dougan, Gordon, Mukhopadhyay, Subhankar, Gaffney, Daniel J.
Publicado 2015

Signatures of TSPAN8 variants associated with human metabolic regulation and diseases

por De, Tisham, Goncalves, Angela, Speed, Doug, Froguel, Philippe, Gaffney, Daniel J., Johnson, Michael R., Jarvelin, Marjo-Riitta, Coin, Lachlan JM.
Publicado 2021

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

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

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

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

Controls of Nucleosome Positioning in the Human Genome

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

Dissecting the regulatory architecture of gene expression QTLs

por 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
Publicado 2012

A survey of best practices for RNA-seq data analysis

por Conesa, Ana, Madrigal, Pedro, Tarazona, Sonia, Gomez-Cabrero, David, Cervera, Alejandra, McPherson, Andrew, Szcześniak, Michał Wojciech, Gaffney, Daniel J., Elo, Laura L., Zhang, Xuegong, Mortazavi, Ali
Publicado 2016

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

por Conesa, Ana, Madrigal, Pedro, Tarazona, Sonia, Gomez-Cabrero, David, Cervera, Alejandra, McPherson, Andrew, Szcześniak, Michal Wojciech, Gaffney, Daniel J., Elo, Laura L., Zhang, Xuegong, Mortazavi, Ali
Publicado 2016

The Contribution of RNA Decay Quantitative Trait Loci to Inter-Individual Variation in Steady-State Gene Expression Levels

por Pai, Athma A., Cain, Carolyn E., Mizrahi-Man, Orna, De Leon, Sherryl, Lewellen, Noah, Veyrieras, Jean-Baptiste, Degner, Jacob F., Gaffney, Daniel J., Pickrell, Joseph K., Stephens, Matthew, Pritchard, Jonathan K., Gilad, Yoav
Publicado 2012