Daniel J Gaffney

Daniel J Gaffney

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Daniel J Gaffney

Daniel J Gaffney

Publications by authors named "Daniel J Gaffney"

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Mapping and predicting gene-enhancer interactions.

Authors:
Daniel J Gaffney

Nat Genet 2019 Dec;51(12):1662-1663

Wellcome Sanger Institute, Hinxton, UK.

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http://dx.doi.org/10.1038/s41588-019-0540-6DOI Listing
December 2019

High-resolution genetic mapping of putative causal interactions between regions of open chromatin.

Nat Genet 2019 01 26;51(1):128-137. Epub 2018 Nov 26.

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.

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http://www.nature.com/articles/s41588-018-0278-6
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http://dx.doi.org/10.1038/s41588-018-0278-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6330062PMC
January 2019

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

Nat Genet 2017 Feb 19;49(2):269-273. Epub 2016 Dec 19.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.

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http://dx.doi.org/10.1038/ng.3745DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5540332PMC
February 2017

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

Genome Biol 2016 Aug 26;17(1):181. Epub 2016 Aug 26.

Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697-2300, USA.

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http://dx.doi.org/10.1186/s13059-016-1047-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5000515PMC
August 2016

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

Nat Genet 2016 Feb 14;48(2):206-13. Epub 2015 Dec 14.

Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK.

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http://biorxiv.org/content/biorxiv/early/2015/04/30/018788.f
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http://www.nature.com/doifinder/10.1038/ng.3467
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http://dx.doi.org/10.1038/ng.3467DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5098600PMC
February 2016

Controls of nucleosome positioning in the human genome.

PLoS Genet 2012 15;8(11):e1003036. Epub 2012 Nov 15.

Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.

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https://dx.plos.org/10.1371/journal.pgen.1003036
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http://dx.doi.org/10.1371/journal.pgen.1003036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3499251PMC
May 2013

Global properties and functional complexity of human gene regulatory variation.

Authors:
Daniel J Gaffney

PLoS Genet 2013 May 30;9(5):e1003501. Epub 2013 May 30.

Wellcome Trust Sanger Institute, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1003501DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3667745PMC
May 2013

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

Bioinformatics 2011 Aug 19;27(15):2144-6. Epub 2011 Jun 19.

Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr354DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137225PMC
August 2011

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

Genome Res 2011 Mar 24;21(3):447-55. Epub 2010 Nov 24.

Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1101/gr.112623.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3044858PMC
March 2011

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

BMC Evol Biol 2008 Sep 30;8:265. Epub 2008 Sep 30.

McGill University and Genome Québec Innovation Centre, 740 ave Dr Penfield Rm 7208, Montréal, Québec, H3A 1A4, Canada.

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http://dx.doi.org/10.1186/1471-2148-8-265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2576242PMC
September 2008

Selective constraints in experimentally defined primate regulatory regions.

PLoS Genet 2008 Aug 15;4(8):e1000157. Epub 2008 Aug 15.

McGill University, Montréal, Québec, Canada.

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http://dx.doi.org/10.1371/journal.pgen.1000157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2490716PMC
August 2008

Genomic selective constraints in murid noncoding DNA.

PLoS Genet 2006 Nov 18;2(11):e204. Epub 2006 Oct 18.

Institute of Evolutionary Biology, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.0020204DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1657059PMC
November 2006

Evolutionary constraints in conserved nongenic sequences of mammals.

Genome Res 2005 Oct;15(10):1373-8

Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom.

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http://www.genome.org/cgi/doi/10.1101/gr.3942005
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http://dx.doi.org/10.1101/gr.3942005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240079PMC
October 2005

The scale of mutational variation in the murid genome.

Genome Res 2005 Aug 15;15(8):1086-94. Epub 2005 Jul 15.

Institute of Evolutionary Biology, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom.

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http://dx.doi.org/10.1101/gr.3895005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182221PMC
August 2005

DNA sequence error rates in Genbank records estimated using the mouse genome as a reference.

DNA Seq 2004 Oct-Dec;15(5-6):362-4

University of Edinburgh, School of Biological Sciences, Ashworth Laboratories, UK.

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http://dx.doi.org/10.1080/10425170400008972DOI Listing
June 2005

Unexpected conserved non-coding DNA blocks in mammals.

Trends Genet 2004 Aug;20(8):332-7

Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, Scotland, United Kingdom.

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http://dx.doi.org/10.1016/j.tig.2004.06.011DOI Listing
August 2004

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

Proc Natl Acad Sci U S A 2003 Nov 3;100(23):13402-6. Epub 2003 Nov 3.

Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, United Kingdom.

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http://dx.doi.org/10.1073/pnas.2233252100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC263826PMC
November 2003