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Items: 35

1.

Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data.

Cairns J, Orchard WR, Malysheva V, Spivakov M.

Bioinformatics. 2019 Jun 14. pii: btz450. doi: 10.1093/bioinformatics/btz450. [Epub ahead of print]

PMID:
31197313
2.

Publisher Correction: Disease-relevant transcriptional signatures identified in individual smooth muscle cells from healthy mouse vessels.

Dobnikar L, Taylor AL, Chappell J, Oldach P, Harman JL, Oerton E, Dzierzak E, Bennett MR, Spivakov M, Jørgensen HF.

Nat Commun. 2018 Dec 17;9(1):5401. doi: 10.1038/s41467-018-07887-3.

3.

Author Correction: Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks.

Choy MK, Javierre BM, Williams SG, Baross SL, Liu Y, Wingett SW, Akbarov A, Wallace C, Freire-Pritchett P, Rugg-Gunn PJ, Spivakov M, Fraser P, Keavney BD.

Nat Commun. 2018 Nov 12;9(1):4792. doi: 10.1038/s41467-018-07399-0.

4.

Disease-relevant transcriptional signatures identified in individual smooth muscle cells from healthy mouse vessels.

Dobnikar L, Taylor AL, Chappell J, Oldach P, Harman JL, Oerton E, Dzierzak E, Bennett MR, Spivakov M, Jørgensen HF.

Nat Commun. 2018 Nov 1;9(1):4567. doi: 10.1038/s41467-018-06891-x. Erratum in: Nat Commun. 2018 Dec 17;9(1):5401.

5.

Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells.

Koohy H, Bolland DJ, Matheson LS, Schoenfelder S, Stellato C, Dimond A, Várnai C, Chovanec P, Chessa T, Denizot J, Manzano Garcia R, Wingett SW, Freire-Pritchett P, Nagano T, Hawkins P, Stephens L, Elderkin S, Spivakov M, Fraser P, Corcoran AE, Varga-Weisz PD.

Genome Biol. 2018 Sep 5;19(1):126. doi: 10.1186/s13059-018-1489-y.

6.

Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks.

Choy MK, Javierre BM, Williams SG, Baross SL, Liu Y, Wingett SW, Akbarov A, Wallace C, Freire-Pritchett P, Rugg-Gunn PJ, Spivakov M, Fraser P, Keavney BD.

Nat Commun. 2018 Jun 28;9(1):2526. doi: 10.1038/s41467-018-04931-0. Erratum in: Nat Commun. 2018 Nov 12;9(1):4792.

7.

Chromosome contacts in activated T cells identify autoimmune disease candidate genes.

Burren OS, Rubio García A, Javierre BM, Rainbow DB, Cairns J, Cooper NJ, Lambourne JJ, Schofield E, Castro Dopico X, Ferreira RC, Coulson R, Burden F, Rowlston SP, Downes K, Wingett SW, Frontini M, Ouwehand WH, Fraser P, Spivakov M, Todd JA, Wicker LS, Cutler AJ, Wallace C.

Genome Biol. 2017 Sep 4;18(1):165. doi: 10.1186/s13059-017-1285-0.

8.

Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation.

Rubin AJ, Barajas BC, Furlan-Magaril M, Lopez-Pajares V, Mumbach MR, Howard I, Kim DS, Boxer LD, Cairns J, Spivakov M, Wingett SW, Shi M, Zhao Z, Greenleaf WJ, Kundaje A, Snyder M, Chang HY, Fraser P, Khavari PA.

Nat Genet. 2017 Oct;49(10):1522-1528. doi: 10.1038/ng.3935. Epub 2017 Aug 14.

9.

Platelet function is modified by common sequence variation in megakaryocyte super enhancers.

Petersen R, Lambourne JJ, Javierre BM, Grassi L, Kreuzhuber R, Ruklisa D, Rosa IM, Tomé AR, Elding H, van Geffen JP, Jiang T, Farrow S, Cairns J, Al-Subaie AM, Ashford S, Attwood A, Batista J, Bouman H, Burden F, Choudry FA, Clarke L, Flicek P, Garner SF, Haimel M, Kempster C, Ladopoulos V, Lenaerts AS, Materek PM, McKinney H, Meacham S, Mead D, Nagy M, Penkett CJ, Rendon A, Seyres D, Sun B, Tuna S, van der Weide ME, Wingett SW, Martens JH, Stegle O, Richardson S, Vallier L, Roberts DJ, Freson K, Wernisch L, Stunnenberg HG, Danesh J, Fraser P, Soranzo N, Butterworth AS, Heemskerk JW, Turro E, Spivakov M, Ouwehand WH, Astle WJ, Downes K, Kostadima M, Frontini M.

Nat Commun. 2017 Jul 13;8:16058. doi: 10.1038/ncomms16058.

10.

Dynamic Rewiring of Promoter-Anchored Chromatin Loops during Adipocyte Differentiation.

Siersbæk R, Madsen JGS, Javierre BM, Nielsen R, Bagge EK, Cairns J, Wingett SW, Traynor S, Spivakov M, Fraser P, Mandrup S.

Mol Cell. 2017 May 4;66(3):420-435.e5. doi: 10.1016/j.molcel.2017.04.010.

11.

Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells.

Freire-Pritchett P, Schoenfelder S, Várnai C, Wingett SW, Cairns J, Collier AJ, García-Vílchez R, Furlan-Magaril M, Osborne CS, Fraser P, Rugg-Gunn PJ, Spivakov M.

Elife. 2017 Mar 23;6. pii: e21926. doi: 10.7554/eLife.21926.

12.

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters.

Javierre BM, Burren OS, Wilder SP, Kreuzhuber R, Hill SM, Sewitz S, Cairns J, Wingett SW, Várnai C, Thiecke MJ, Burden F, Farrow S, Cutler AJ, Rehnström K, Downes K, Grassi L, Kostadima M, Freire-Pritchett P, Wang F; BLUEPRINT Consortium, Stunnenberg HG, Todd JA, Zerbino DR, Stegle O, Ouwehand WH, Frontini M, Wallace C, Spivakov M, Fraser P.

Cell. 2016 Nov 17;167(5):1369-1384.e19. doi: 10.1016/j.cell.2016.09.037.

13.

Defining cell type with chromatin profiling.

Spivakov M, Fraser P.

Nat Biotechnol. 2016 Nov 8;34(11):1126-1128. doi: 10.1038/nbt.3724. No abstract available.

PMID:
27824844
14.

Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity.

Pancaldi V, Carrillo-de-Santa-Pau E, Javierre BM, Juan D, Fraser P, Spivakov M, Valencia A, Rico D.

Genome Biol. 2016 Jul 8;17(1):152. doi: 10.1186/s13059-016-1003-3.

15.

CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data.

Cairns J, Freire-Pritchett P, Wingett SW, Várnai C, Dimond A, Plagnol V, Zerbino D, Schoenfelder S, Javierre BM, Osborne C, Fraser P, Spivakov M.

Genome Biol. 2016 Jun 15;17(1):127. doi: 10.1186/s13059-016-0992-2.

16.

Two Mutually Exclusive Local Chromatin States Drive Efficient V(D)J Recombination.

Bolland DJ, Koohy H, Wood AL, Matheson LS, Krueger F, Stubbington MJ, Baizan-Edge A, Chovanec P, Stubbs BA, Tabbada K, Andrews SR, Spivakov M, Corcoran AE.

Cell Rep. 2016 Jun 14;15(11):2475-87. doi: 10.1016/j.celrep.2016.05.020. Epub 2016 Jun 2.

17.

CHiCP: a web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets.

Schofield EC, Carver T, Achuthan P, Freire-Pritchett P, Spivakov M, Todd JA, Burren OS.

Bioinformatics. 2016 Aug 15;32(16):2511-3. doi: 10.1093/bioinformatics/btw173. Epub 2016 Apr 8.

18.

Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model.

Wilson NK, Schoenfelder S, Hannah R, Sánchez Castillo M, Schütte J, Ladopoulos V, Mitchelmore J, Goode DK, Calero-Nieto FJ, Moignard V, Wilkinson AC, Jimenez-Madrid I, Kinston S, Spivakov M, Fraser P, Göttgens B.

Blood. 2016 Mar 31;127(13):e12-23. doi: 10.1182/blood-2015-10-677393. Epub 2016 Jan 25.

19.

Dynamic Reorganization of Extremely Long-Range Promoter-Promoter Interactions between Two States of Pluripotency.

Joshi O, Wang SY, Kuznetsova T, Atlasi Y, Peng T, Fabre PJ, Habibi E, Shaik J, Saeed S, Handoko L, Richmond T, Spivakov M, Burgess D, Stunnenberg HG.

Cell Stem Cell. 2015 Dec 3;17(6):748-757. doi: 10.1016/j.stem.2015.11.010.

20.

A new phosphate-starvation response in fission yeast requires the endocytic function of myosin I.

Petrini E, Baillet V, Cridge J, Hogan CJ, Guillaume C, Ke H, Brandetti E, Walker S, Koohy H, Spivakov M, Varga-Weisz P.

J Cell Sci. 2015 Oct 15;128(20):3707-13. doi: 10.1242/jcs.171314. Epub 2015 Sep 7.

21.

Spurious transcription factor binding: non-functional or genetically redundant?

Spivakov M.

Bioessays. 2014 Aug;36(8):798-806. doi: 10.1002/bies.201400036. Epub 2014 May 30.

22.

A comparison of peak callers used for DNase-Seq data.

Koohy H, Down TA, Spivakov M, Hubbard T.

PLoS One. 2014 May 8;9(5):e96303. doi: 10.1371/journal.pone.0096303. eCollection 2014. Erratum in: PLoS One. 2014;9(8):e105136.

23.

Spatial separation of Xist RNA and polycomb proteins revealed by superresolution microscopy.

Cerase A, Smeets D, Tang YA, Gdula M, Kraus F, Spivakov M, Moindrot B, Leleu M, Tattermusch A, Demmerle J, Nesterova TB, Green C, Otte AP, Schermelleh L, Brockdorff N.

Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):2235-40. doi: 10.1073/pnas.1312951111. Epub 2014 Jan 27.

24.

Genomic and phenotypic characterization of a wild medaka population: towards the establishment of an isogenic population genetic resource in fish.

Spivakov M, Auer TO, Peravali R, Dunham I, Dolle D, Fujiyama A, Toyoda A, Aizu T, Minakuchi Y, Loosli F, Naruse K, Birney E, Wittbrodt J.

G3 (Bethesda). 2014 Mar 20;4(3):433-45. doi: 10.1534/g3.113.008722.

25.

Genome-wide identification of Ikaros targets elucidates its contribution to mouse B-cell lineage specification and pre-B-cell differentiation.

Ferreirós-Vidal I, Carroll T, Taylor B, Terry A, Liang Z, Bruno L, Dharmalingam G, Khadayate S, Cobb BS, Smale ST, Spivakov M, Srivastava P, Petretto E, Fisher AG, Merkenschlager M.

Blood. 2013 Mar 7;121(10):1769-82. doi: 10.1182/blood-2012-08-450114. Epub 2013 Jan 9.

26.

Analysis of variation at transcription factor binding sites in Drosophila and humans.

Spivakov M, Akhtar J, Kheradpour P, Beal K, Girardot C, Koscielny G, Herrero J, Kellis M, Furlong EE, Birney E.

Genome Biol. 2012 Sep 28;13(9):R49. doi: 10.1186/gb-2012-13-9-r49.

27.

A transcription factor collective defines cardiac cell fate and reflects lineage history.

Junion G, Spivakov M, Girardot C, Braun M, Gustafson EH, Birney E, Furlong EE.

Cell. 2012 Feb 3;148(3):473-86. doi: 10.1016/j.cell.2012.01.030.

28.

Jarid2 is a PRC2 component in embryonic stem cells required for multi-lineage differentiation and recruitment of PRC1 and RNA Polymerase II to developmental regulators.

Landeira D, Sauer S, Poot R, Dvorkina M, Mazzarella L, Jørgensen HF, Pereira CF, Leleu M, Piccolo FM, Spivakov M, Brookes E, Pombo A, Fisher C, Skarnes WC, Snoek T, Bezstarosti K, Demmers J, Klose RJ, Casanova M, Tavares L, Brockdorff N, Merkenschlager M, Fisher AG.

Nat Cell Biol. 2010 Jun;12(6):618-24. doi: 10.1038/ncb2065. Epub 2010 May 16.

29.

T cell receptor signaling controls Foxp3 expression via PI3K, Akt, and mTOR.

Sauer S, Bruno L, Hertweck A, Finlay D, Leleu M, Spivakov M, Knight ZA, Cobb BS, Cantrell D, O'Connor E, Shokat KM, Fisher AG, Merkenschlager M.

Proc Natl Acad Sci U S A. 2008 Jun 3;105(22):7797-802. doi: 10.1073/pnas.0800928105. Epub 2008 May 28.

30.

Cohesins functionally associate with CTCF on mammalian chromosome arms.

Parelho V, Hadjur S, Spivakov M, Leleu M, Sauer S, Gregson HC, Jarmuz A, Canzonetta C, Webster Z, Nesterova T, Cobb BS, Yokomori K, Dillon N, Aragon L, Fisher AG, Merkenschlager M.

Cell. 2008 Feb 8;132(3):422-33. doi: 10.1016/j.cell.2008.01.011. Epub 2008 Jan 31.

31.

The impact of chromatin modifiers on the timing of locus replication in mouse embryonic stem cells.

Jørgensen HF, Azuara V, Amoils S, Spivakov M, Terry A, Nesterova T, Cobb BS, Ramsahoye B, Merkenschlager M, Fisher AG.

Genome Biol. 2007;8(8):R169.

32.

Epigenetic signatures of stem-cell identity.

Spivakov M, Fisher AG.

Nat Rev Genet. 2007 Apr;8(4):263-71. Review.

PMID:
17363975
33.

Distinct promoters mediate the regulation of Ebf1 gene expression by interleukin-7 and Pax5.

Roessler S, Györy I, Imhof S, Spivakov M, Williams RR, Busslinger M, Fisher AG, Grosschedl R.

Mol Cell Biol. 2007 Jan;27(2):579-94. Epub 2006 Nov 13.

34.

Chromatin signatures of pluripotent cell lines.

Azuara V, Perry P, Sauer S, Spivakov M, Jørgensen HF, John RM, Gouti M, Casanova M, Warnes G, Merkenschlager M, Fisher AG.

Nat Cell Biol. 2006 May;8(5):532-8. Epub 2006 Mar 29.

PMID:
16570078
35.

A dynamic switch in the replication timing of key regulator genes in embryonic stem cells upon neural induction.

Perry P, Sauer S, Billon N, Richardson WD, Spivakov M, Warnes G, Livesey FJ, Merkenschlager M, Fisher AG, Azuara V.

Cell Cycle. 2004 Dec;3(12):1645-50. Epub 2004 Dec 4.

PMID:
15611653

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