Daniel Gaffney - Publications

Affiliations: 
University of Edinburgh, Edinburgh, Scotland, United Kingdom 

24 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A. A survey of best practices for RNA-seq data analysis. Genome Biology. 17: 13. PMID 26813401 DOI: 10.1186/s13059-016-0881-8  0.36
2015 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, Vallier L, Paulsen O, Káradóttir RT, Spillantini MG. Early maturation and distinct tau pathology in induced pluripotent stem cell-derived neurons from patients with MAPT mutations. Brain : a Journal of Neurology. PMID 26220942 DOI: 10.1093/Brain/Awv222  0.36
2015 Bertero A, Madrigal P, Galli A, Hubner NC, Moreno I, Burks D, Brown S, Pedersen RA, Gaffney D, Mendjan S, Pauklin S, Vallier L. Activin/nodal signaling and NANOG orchestrate human embryonic stem cell fate decisions by controlling the H3K4me3 chromatin mark. Genes & Development. 29: 702-17. PMID 25805847 DOI: 10.1101/Gad.255984.114  0.36
2014 Rouhani F, Kumasaka N, de Brito MC, Bradley A, Vallier L, Gaffney D. Genetic background drives transcriptional variation in human induced pluripotent stem cells. Plos Genetics. 10: e1004432. PMID 24901476 DOI: 10.1371/journal.pgen.1004432  0.36
2013 Aldridge S, Watt S, Quail MA, Rayner T, Lukk M, Bimson MF, Gaffney D, Odom DT. AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation. Genome Biology. 14: R124. PMID 24200198 DOI: 10.1186/gb-2013-14-11-r124  0.36
2012 Gaffney DJ, McVicker G, Pai AA, Fondufe-Mittendorf YN, Lewellen N, Michelini K, Widom J, Gilad Y, Pritchard JK. Controls of nucleosome positioning in the human genome. Plos Genetics. 8: e1003036. PMID 23166509 DOI: 10.1371/Journal.Pgen.1003036  0.36
2012 Pai AA, Cain CE, Mizrahi-Man O, De Leon S, Lewellen N, Veyrieras JB, Degner JF, Gaffney DJ, Pickrell JK, Stephens M, Pritchard JK, Gilad Y. The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels. Plos Genetics. 8: e1003000. PMID 23071454 DOI: 10.1371/Journal.Pgen.1003000  0.36
2012 Liu JZ, Almarri MA, Gaffney DJ, Mells GF, Jostins L, Cordell HJ, Ducker SJ, Day DB, Heneghan MA, Neuberger JM, Donaldson PT, Bathgate AJ, Burroughs A, Davies MH, Jones DE, et al. Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis. Nature Genetics. 44: 1137-41. PMID 22961000 DOI: 10.1038/ng.2395  0.36
2012 Zullo JM, Demarco IA, Piqué-Regi R, Gaffney DJ, Epstein CB, Spooner CJ, Luperchio TR, Bernstein BE, Pritchard JK, Reddy KL, Singh H. DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina. Cell. 149: 1474-87. PMID 22726435 DOI: 10.1016/J.Cell.2012.04.035  0.36
2012 Veyrieras JB, Gaffney DJ, Pickrell JK, Gilad Y, Stephens M, Pritchard JK. Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data. Plos One. 7: e30629. PMID 22359548 DOI: 10.1371/Journal.Pone.0030629  0.36
2012 Degner JF, Pai AA, Pique-Regi R, Veyrieras JB, Gaffney DJ, Pickrell JK, De Leon S, Michelini K, Lewellen N, Crawford GE, Stephens M, Gilad Y, Pritchard JK. DNase I sensitivity QTLs are a major determinant of human expression variation. Nature. 482: 390-4. PMID 22307276 DOI: 10.1038/Nature10808  0.36
2012 Gaffney DJ, Veyrieras JB, Degner JF, Pique-Regi R, Pai AA, Crawford GE, Stephens M, Gilad Y, Pritchard JK. Dissecting the regulatory architecture of gene expression QTLs. Genome Biology. 13: R7. PMID 22293038 DOI: 10.1186/Gb-2012-13-1-R7  0.36
2011 Pickrell JK, Gaffney DJ, Gilad Y, Pritchard JK. False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions. Bioinformatics (Oxford, England). 27: 2144-6. PMID 21690102 DOI: 10.1093/bioinformatics/btr354  0.36
2011 Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF, Gilad Y, Pritchard JK. DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biology. 12: R10. PMID 21251332 DOI: 10.1186/Gb-2011-12-1-R10  0.36
2011 Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Research. 21: 447-55. PMID 21106904 DOI: 10.1101/Gr.112623.110  0.36
2008 Gaffney DJ, Keightley PD. Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals. Bmc Evolutionary Biology. 8: 265. PMID 18826599 DOI: 10.1186/1471-2148-8-265  1
2008 Gaffney DJ, Blekhman R, Majewski J. Selective constraints in experimentally defined primate regulatory regions. Plos Genetics. 4: e1000157. PMID 18704158 DOI: 10.1371/Journal.Pgen.1000157  0.36
2006 Gaffney DJ, Keightley PD. Genomic selective constraints in murid noncoding DNA. Plos Genetics. 2: e204. PMID 17166057 DOI: 10.1371/journal.pgen.0020204  1
2005 Keightley PD, Kryukov GV, Sunyaev S, Halligan DL, Gaffney DJ. Evolutionary constraints in conserved nongenic sequences of mammals. Genome Research. 15: 1373-8. PMID 16204190 DOI: 10.1101/Gr.3942005  0.36
2005 Gaffney DJ, Keightley PD. The scale of mutational variation in the murid genome. Genome Research. 15: 1086-94. PMID 16024822 DOI: 10.1101/gr.3895005  1
2004 Wesche PL, Gaffney DJ, Keightley PD. DNA sequence error rates in Genbank records estimated using the mouse genome as a reference. Dna Sequence : the Journal of Dna Sequencing and Mapping. 15: 362-4. PMID 15621661 DOI: 10.1080/10425170400008972  1
2004 Gaffney DJ, Keightley PD. Unexpected conserved non-coding DNA blocks in mammals. Trends in Genetics : Tig. 20: 332-7. PMID 15262402 DOI: 10.1016/j.tig.2004.06.011  1
2003 Keightley PD, Gaffney DJ. Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents. Proceedings of the National Academy of Sciences of the United States of America. 100: 13402-6. PMID 14597721 DOI: 10.1073/pnas.2233252100  1
2002 Eyre-Walker A, Keightley PD, Smith NG, Gaffney D. Quantifying the slightly deleterious mutation model of molecular evolution. Molecular Biology and Evolution. 19: 2142-9. PMID 12446806  1
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