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Items: 37

1.

Mapping and predicting gene-enhancer interactions.

Gaffney DJ.

Nat Genet. 2019 Dec;51(12):1662-1663. doi: 10.1038/s41588-019-0540-6. No abstract available.

PMID:
31784730
2.

Publisher Correction: Molecular and functional variation in iPSC-derived sensory neurons.

Schwartzentruber J, Foskolou S, Kilpinen H, Rodrigues J, Alasoo K, Knights AJ, Patel M, Goncalves A, Ferreira R, Benn CL, Wilbrey A, Bictash M, Impey E, Cao L, Lainez S, Loucif AJ, Whiting PJ; HIPSCI Consortium, Gutteridge A, Gaffney DJ.

Nat Genet. 2019 Jul;51(7):1190. doi: 10.1038/s41588-019-0445-4.

PMID:
31160811
3.

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

Alasoo K, Rodrigues J, Danesh J, Freitag DF, Paul DS, Gaffney DJ.

Elife. 2019 Jan 8;8. pii: e41673. doi: 10.7554/eLife.41673.

4.

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

Kumasaka N, Knights AJ, Gaffney DJ.

Nat Genet. 2019 Jan;51(1):128-137. doi: 10.1038/s41588-018-0278-6. Epub 2018 Nov 26.

5.

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

Alasoo K, Rodrigues J, Mukhopadhyay S, Knights AJ, Mann AL, Kundu K; HIPSCI Consortium, Hale C, Dougan G, Gaffney DJ.

Nat Genet. 2018 Mar;50(3):424-431. doi: 10.1038/s41588-018-0046-7. Epub 2018 Jan 29.

6.

Molecular and functional variation in iPSC-derived sensory neurons.

Schwartzentruber J, Foskolou S, Kilpinen H, Rodrigues J, Alasoo K, Knights AJ, Patel M, Goncalves A, Ferreira R, Benn CL, Wilbrey A, Bictash M, Impey E, Cao L, Lainez S, Loucif AJ, Whiting PJ; HIPSCI Consortium, Gutteridge A, Gaffney DJ.

Nat Genet. 2018 Jan;50(1):54-61. doi: 10.1038/s41588-017-0005-8. Epub 2017 Dec 11. Erratum in: Nat Genet. 2019 Jul;51(7):1190.

7.

Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs.

Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, Danecek P, Faulconbridge A, Harrison PW, Kathuria A, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Mann A, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, White A, Patel SR, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ.

Nature. 2017 Jun 29;546(7660):686. doi: 10.1038/nature23012. Epub 2017 Jun 14.

PMID:
28614302
8.

Common genetic variation drives molecular heterogeneity in human iPSCs.

Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, Danecek P, Faulconbridge A, Harrison PW, Kathuria A, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Mann A, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, White A, Patel SR, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ.

Nature. 2017 Jun 15;546(7658):370-375. doi: 10.1038/nature22403. Epub 2017 May 10. Erratum in: Nature. 2017 Jun 29;546(7660):686.

9.

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

Ji SG, Juran BD, Mucha S, Folseraas T, Jostins L, Melum E, Kumasaka N, Atkinson EJ, Schlicht EM, Liu JZ, Shah T, Gutierrez-Achury J, Boberg KM, Bergquist A, Vermeire S, Eksteen B, Durie PR, Farkkila M, Müller T, Schramm C, Sterneck M, Weismüller TJ, Gotthardt DN, Ellinghaus D, Braun F, Teufel A, Laudes M, Lieb W, Jacobs G, Beuers U, Weersma RK, Wijmenga C, Marschall HU, Milkiewicz P, Pares A, Kontula K, Chazouillères O, Invernizzi P, Goode E, Spiess K, Moore C, Sambrook J, Ouwehand WH, Roberts DJ, Danesh J, Floreani A, Gulamhusein AF, Eaton JE, Schreiber S, Coltescu C, Bowlus CL, Luketic VA, Odin JA, Chopra KB, Kowdley KV, Chalasani N, Manns MP, Srivastava B, Mells G, Sandford RN, Alexander G, Gaffney DJ, Chapman RW, Hirschfield GM, de Andrade M; UK-PSC Consortium; International IBD Genetics Consortium; International PSC Study Group, Rushbrook SM, Franke A, Karlsen TH, Lazaridis KN, Anderson CA.

Nat Genet. 2017 Feb;49(2):269-273. doi: 10.1038/ng.3745. Epub 2016 Dec 19.

10.

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

Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A.

Genome Biol. 2016 Aug 26;17(1):181. No abstract available.

11.

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

Kumasaka N, Knights AJ, Gaffney DJ.

Nat Genet. 2016 Apr;48(4):473. doi: 10.1038/ng0329-473e. No abstract available.

PMID:
27023776
12.

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

Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A.

Genome Biol. 2016 Jan 26;17:13. doi: 10.1186/s13059-016-0881-8. Review. Erratum in: Genome Biol. 2016;17(1):181.

13.

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

Kumasaka N, Knights AJ, Gaffney DJ.

Nat Genet. 2016 Feb;48(2):206-13. doi: 10.1038/ng.3467. Epub 2015 Dec 14. Erratum in: Nat Genet. 2016 Apr;48(4):473.

14.

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

Alasoo K, Martinez FO, Hale C, Gordon S, Powrie F, Dougan G, Mukhopadhyay S, Gaffney DJ.

Sci Rep. 2015 Jul 30;5:12524. doi: 10.1038/srep12524.

15.

Epithelial IL-22RA1-mediated fucosylation promotes intestinal colonization resistance to an opportunistic pathogen.

Pham TA, Clare S, Goulding D, Arasteh JM, Stares MD, Browne HP, Keane JA, Page AJ, Kumasaka N, Kane L, Mottram L, Harcourt K, Hale C, Arends MJ, Gaffney DJ; Sanger Mouse Genetics Project, Dougan G, Lawley TD.

Cell Host Microbe. 2014 Oct 8;16(4):504-16. doi: 10.1016/j.chom.2014.08.017. Epub 2014 Sep 25.

16.

Global properties and functional complexity of human gene regulatory variation.

Gaffney DJ.

PLoS Genet. 2013 May;9(5):e1003501. doi: 10.1371/journal.pgen.1003501. Epub 2013 May 30. Review.

17.

Controls of nucleosome positioning in the human genome.

Gaffney DJ, McVicker G, Pai AA, Fondufe-Mittendorf YN, Lewellen N, Michelini K, Widom J, Gilad Y, Pritchard JK.

PLoS Genet. 2012;8(11):e1003036. doi: 10.1371/journal.pgen.1003036. Epub 2012 Nov 15.

18.

The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels.

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.

PLoS Genet. 2012;8(10):e1003000. doi: 10.1371/journal.pgen.1003000. Epub 2012 Oct 11.

19.

Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis.

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, Alexander GJ, Barrett JC, Sandford RN, Anderson CA; UK Primary Biliary Cirrhosis (PBC) Consortium; Wellcome Trust Case Control Consortium 3.

Nat Genet. 2012 Oct;44(10):1137-41. doi: 10.1038/ng.2395. Epub 2012 Sep 9.

20.

DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina.

Zullo JM, Demarco IA, Piqué-Regi R, Gaffney DJ, Epstein CB, Spooner CJ, Luperchio TR, Bernstein BE, Pritchard JK, Reddy KL, Singh H.

Cell. 2012 Jun 22;149(7):1474-87. doi: 10.1016/j.cell.2012.04.035.

21.

Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data.

Veyrieras JB, Gaffney DJ, Pickrell JK, Gilad Y, Stephens M, Pritchard JK.

PLoS One. 2012;7(2):e30629. doi: 10.1371/journal.pone.0030629. Epub 2012 Feb 16.

22.

DNase I sensitivity QTLs are a major determinant of human expression variation.

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.

Nature. 2012 Feb 5;482(7385):390-4. doi: 10.1038/nature10808.

23.

Dissecting the regulatory architecture of gene expression QTLs.

Gaffney DJ, Veyrieras JB, Degner JF, Pique-Regi R, Pai AA, Crawford GE, Stephens M, Gilad Y, Pritchard JK.

Genome Biol. 2012 Jan 31;13(1):R7. doi: 10.1186/gb-2012-13-1-r7.

24.

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

Pickrell JK, Gaffney DJ, Gilad Y, Pritchard JK.

Bioinformatics. 2011 Aug 1;27(15):2144-6. doi: 10.1093/bioinformatics/btr354. Epub 2011 Jun 19.

25.

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

Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF, Gilad Y, Pritchard JK.

Genome Biol. 2011;12(1):R10. doi: 10.1186/gb-2011-12-1-r10. Epub 2011 Jan 20. Erratum in: Genome Biol. 2011;12(6):405.

26.

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

Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK.

Genome Res. 2011 Mar;21(3):447-55. doi: 10.1101/gr.112623.110. Epub 2010 Nov 24.

27.

Decisions made on a rollercoaster.

Gaffney DJ.

Radiol Manage. 2009 Mar-Apr;31(2):56. No abstract available.

PMID:
19634800
28.

Gene expression and isoform variation analysis using Affymetrix Exon Arrays.

Bemmo A, Benovoy D, Kwan T, Gaffney DJ, Jensen RV, Majewski J.

BMC Genomics. 2008 Nov 7;9:529. doi: 10.1186/1471-2164-9-529. Erratum in: BMC Genomics. 2009 Mar 23;10. doi: 10.1186/1471-2164-10-121.

29.

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

Gaffney DJ, Keightley PD.

BMC Evol Biol. 2008 Sep 30;8:265. doi: 10.1186/1471-2148-8-265.

30.

Selective constraints in experimentally defined primate regulatory regions.

Gaffney DJ, Blekhman R, Majewski J.

PLoS Genet. 2008 Aug 15;4(8):e1000157. doi: 10.1371/journal.pgen.1000157.

31.

Genomic selective constraints in murid noncoding DNA.

Gaffney DJ, Keightley PD.

PLoS Genet. 2006 Nov 24;2(11):e204. Epub 2006 Oct 18.

32.

Evolutionary constraints in conserved nongenic sequences of mammals.

Keightley PD, Kryukov GV, Sunyaev S, Halligan DL, Gaffney DJ.

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

33.

The scale of mutational variation in the murid genome.

Gaffney DJ, Keightley PD.

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

34.

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

Wesche PL, Gaffney DJ, Keightley PD.

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

PMID:
15621661
35.

Unexpected conserved non-coding DNA blocks in mammals.

Gaffney DJ, Keightley PD.

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

PMID:
15262402
36.

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

Keightley PD, Gaffney DJ.

Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13402-6. Epub 2003 Nov 3.

37.

Virulence in rodent malaria: host genotype by parasite genotype interactions.

Mackinnon MJ, Gaffney DJ, Read AF.

Infect Genet Evol. 2002 Jul;1(4):287-96.

PMID:
12798007

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