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Items: 26

1.

Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes.

Miguel-Escalada I, Bonàs-Guarch S, Cebola I, Ponsa-Cobas J, Mendieta-Esteban J, Atla G, Javierre BM, Rolando DMY, Farabella I, Morgan CC, García-Hurtado J, Beucher A, Morán I, Pasquali L, Ramos-Rodríguez M, Appel EVR, Linneberg A, Gjesing AP, Witte DR, Pedersen O, Grarup N, Ravassard P, Torrents D, Mercader JM, Piemonti L, Berney T, de Koning EJP, Kerr-Conte J, Pattou F, Fedko IO, Groop L, Prokopenko I, Hansen T, Marti-Renom MA, Fraser P, Ferrer J.

Nat Genet. 2019 Jul;51(7):1137-1148. doi: 10.1038/s41588-019-0457-0. Epub 2019 Jun 28.

2.

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.

3.

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions.

Schoenfelder S, Javierre BM, Furlan-Magaril M, Wingett SW, Fraser P.

J Vis Exp. 2018 Jun 28;(136). doi: 10.3791/57320.

4.

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.

5.

The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia.

Beekman R, Chapaprieta V, Russiñol N, Vilarrasa-Blasi R, Verdaguer-Dot N, Martens JHA, Duran-Ferrer M, Kulis M, Serra F, Javierre BM, Wingett SW, Clot G, Queirós AC, Castellano G, Blanc J, Gut M, Merkel A, Heath S, Vlasova A, Ullrich S, Palumbo E, Enjuanes A, Martín-García D, Beà S, Pinyol M, Aymerich M, Royo R, Puiggros M, Torrents D, Datta A, Lowy E, Kostadima M, Roller M, Clarke L, Flicek P, Agirre X, Prosper F, Baumann T, Delgado J, López-Guillermo A, Fraser P, Yaspo ML, Guigó R, Siebert R, Martí-Renom MA, Puente XS, López-Otín C, Gut I, Stunnenberg HG, Campo E, Martin-Subero JI.

Nat Med. 2018 Jun;24(6):868-880. doi: 10.1038/s41591-018-0028-4. Epub 2018 May 21.

6.

Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition.

Novo CL, Javierre BM, Cairns J, Segonds-Pichon A, Wingett SW, Freire-Pritchett P, Furlan-Magaril M, Schoenfelder S, Fraser P, Rugg-Gunn PJ.

Cell Rep. 2018 Mar 6;22(10):2615-2627. doi: 10.1016/j.celrep.2018.02.040.

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.

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.

9.

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.

10.

Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes.

Aymard F, Aguirrebengoa M, Guillou E, Javierre BM, Bugler B, Arnould C, Rocher V, Iacovoni JS, Biernacka A, Skrzypczak M, Ginalski K, Rowicka M, Fraser P, Legube G.

Nat Struct Mol Biol. 2017 Apr;24(4):353-361. doi: 10.1038/nsmb.3387. Epub 2017 Mar 6.

11.

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.

12.

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.

13.

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.

14.

IL-4 orchestrates STAT6-mediated DNA demethylation leading to dendritic cell differentiation.

Vento-Tormo R, Company C, Rodríguez-Ubreva J, de la Rica L, Urquiza JM, Javierre BM, Sabarinathan R, Luque A, Esteller M, Aran JM, Álvarez-Errico D, Ballestar E.

Genome Biol. 2016 Jan 13;17:4. doi: 10.1186/s13059-015-0863-2.

15.

Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome.

Schoenfelder S, Sugar R, Dimond A, Javierre BM, Armstrong H, Mifsud B, Dimitrova E, Matheson L, Tavares-Cadete F, Furlan-Magaril M, Segonds-Pichon A, Jurkowski W, Wingett SW, Tabbada K, Andrews S, Herman B, LeProust E, Osborne CS, Koseki H, Fraser P, Luscombe NM, Elderkin S.

Nat Genet. 2015 Oct;47(10):1179-1186. doi: 10.1038/ng.3393. Epub 2015 Aug 31.

16.

Comparison of Hi-C results using in-solution versus in-nucleus ligation.

Nagano T, Várnai C, Schoenfelder S, Javierre BM, Wingett SW, Fraser P.

Genome Biol. 2015 Aug 26;16:175. doi: 10.1186/s13059-015-0753-7.

17.

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements.

Schoenfelder S, Furlan-Magaril M, Mifsud B, Tavares-Cadete F, Sugar R, Javierre BM, Nagano T, Katsman Y, Sakthidevi M, Wingett SW, Dimitrova E, Dimond A, Edelman LB, Elderkin S, Tabbada K, Darbo E, Andrews S, Herman B, Higgs A, LeProust E, Osborne CS, Mitchell JA, Luscombe NM, Fraser P.

Genome Res. 2015 Apr;25(4):582-97. doi: 10.1101/gr.185272.114. Epub 2015 Mar 9.

18.

The B cell transcription program mediates hypomethylation and overexpression of key genes in Epstein-Barr virus-associated proliferative conversion.

Hernando H, Shannon-Lowe C, Islam AB, Al-Shahrour F, Rodríguez-Ubreva J, Rodríguez-Cortez VC, Javierre BM, Mangas C, Fernández AF, Parra M, Delecluse HJ, Esteller M, López-Granados E, Fraga MF, López-Bigas N, Ballestar E.

Genome Biol. 2013 Jan 15;14(1):R3. doi: 10.1186/gb-2013-14-1-r3.

19.

Environmental triggers and epigenetic deregulation in autoimmune disease.

Javierre BM, Hernando H, Ballestar E.

Discov Med. 2011 Dec;12(67):535-45. Review.

20.

Long-range epigenetic silencing associates with deregulation of Ikaros targets in colorectal cancer cells.

Javierre BM, Rodriguez-Ubreva J, Al-Shahrour F, Corominas M, Graña O, Ciudad L, Agirre X, Pisano DG, Valencia A, Roman-Gomez J, Calasanz MJ, Prosper F, Esteller M, Gonzalez-Sarmiento R, Ballestar E.

Mol Cancer Res. 2011 Aug;9(8):1139-51. doi: 10.1158/1541-7786.MCR-10-0515. Epub 2011 Jul 7. Erratum in: Mol Cancer Res. 2011 Oct;9(10):1429-32.

21.

A new epigenetic challenge: systemic lupus erythematosus.

Javierre BM, Richardson B.

Adv Exp Med Biol. 2011;711:117-36. Review.

PMID:
21627046
22.

Leptin and TNF-alpha promoter methylation levels measured by MSP could predict the response to a low-calorie diet.

Cordero P, Campion J, Milagro FI, Goyenechea E, Steemburgo T, Javierre BM, Martinez JA.

J Physiol Biochem. 2011 Sep;67(3):463-70. doi: 10.1007/s13105-011-0084-4. Epub 2011 Apr 5.

23.

Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus.

Javierre BM, Fernandez AF, Richter J, Al-Shahrour F, Martin-Subero JI, Rodriguez-Ubreva J, Berdasco M, Fraga MF, O'Hanlon TP, Rider LG, Jacinto FV, Lopez-Longo FJ, Dopazo J, Forn M, Peinado MA, Carreño L, Sawalha AH, Harley JB, Siebert R, Esteller M, Miller FW, Ballestar E.

Genome Res. 2010 Feb;20(2):170-9. doi: 10.1101/gr.100289.109. Epub 2009 Dec 22.

24.

The dynamic DNA methylomes of double-stranded DNA viruses associated with human cancer.

Fernandez AF, Rosales C, Lopez-Nieva P, Graña O, Ballestar E, Ropero S, Espada J, Melo SA, Lujambio A, Fraga MF, Pino I, Javierre B, Carmona FJ, Acquadro F, Steenbergen RD, Snijders PJ, Meijer CJ, Pineau P, Dejean A, Lloveras B, Capella G, Quer J, Buti M, Esteban JI, Allende H, Rodriguez-Frias F, Castellsague X, Minarovits J, Ponce J, Capello D, Gaidano G, Cigudosa JC, Gomez-Lopez G, Pisano DG, Valencia A, Piris MA, Bosch FX, Cahir-McFarland E, Kieff E, Esteller M.

Genome Res. 2009 Mar;19(3):438-51. doi: 10.1101/gr.083550.108. Epub 2009 Feb 10.

25.

Epigenetic connections between autoimmune disorders and haematological malignancies.

Javierre BM, Esteller M, Ballestar E.

Trends Immunol. 2008 Dec;29(12):616-23. doi: 10.1016/j.it.2008.08.008. Epub 2008 Oct 24. Review.

PMID:
18951845
26.

Increased expression of VEGF121/VEGF165-189 ratio results in a significant enhancement of human prostate tumor angiogenesis.

Catena R, Muniz-Medina V, Moralejo B, Javierre B, Best CJ, Emmert-Buck MR, Green JE, Baker CC, Calvo A.

Int J Cancer. 2007 May 15;120(10):2096-109.

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