CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data
Cairns, Jonathan, Freire-Pritchett, Paula, Wingett, Steven W, Várnai, Csilla, Dimond, Andrew, Plagnol, Vincent, Zerbino, Daniel, Schoenfelder, Stefan, Javierre, Biola-Maria, Osborne, Cameron, Fraser, Peter, Spivakov, Mikhail
Published in Genome Biology (15.06.2016)
Published in Genome Biology (15.06.2016)
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Comparison of Hi-C results using in-solution versus in-nucleus ligation
Nagano, Takashi, Várnai, Csilla, Schoenfelder, Stefan, Javierre, Biola-Maria, Wingett, Steven W, Fraser, Peter
Published in Genome Biology (26.08.2015)
Published in Genome Biology (26.08.2015)
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Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation
Rubin, Adam J, Barajas, Brook C, Furlan-Magaril, Mayra, Lopez-Pajares, Vanessa, Mumbach, Maxwell R, Howard, Imani, Kim, Daniel S, Boxer, Lisa D, Cairns, Jonathan, Spivakov, Mikhail, Wingett, Steven W, Shi, Minyi, Zhao, Zhixin, Greenleaf, William J, Kundaje, Anshul, Snyder, Michael, Chang, Howard Y, Fraser, Peter, Khavari, Paul A
Published in Nature genetics (01.10.2017)
Published in Nature genetics (01.10.2017)
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Active and repressed biosynthetic gene clusters have spatially distinct chromosome states
Nützmann, Hans-Wilhelm, Doerr, Daniel, Ramírez-Colmenero, América, Sotelo-Fonseca, Jesús Emiliano, Wegel, Eva, Di Stefano, Marco, Wingett, Steven W., Fraser, Peter, Hurst, Laurence, Fernandez-Valverde, Selene L., Osbourn, Anne
Published in Proceedings of the National Academy of Sciences - PNAS (16.06.2020)
Published in Proceedings of the National Academy of Sciences - PNAS (16.06.2020)
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HiCUP: pipeline for mapping and processing Hi-C data [version 1; peer review: 2 approved, 1 approved with reservations]
Wingett, Steven W, Ewels, Philip, Furlan-Magaril, Mayra, Nagano, Takashi, Schoenfelder, Stefan, Fraser, Peter, Andrews, Simon
Published in F1000 research (2015)
Published in F1000 research (2015)
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Capture Hi-C identifies putative target genes at 33 breast cancer risk loci
Baxter, Joseph S, Leavy, Olivia C, Dryden, Nicola H, Maguire, Sarah, Johnson, Nichola, Fedele, Vita, Simigdala, Nikiana, Martin, Lesley-Ann, Andrews, Simon, Wingett, Steven W, Assiotis, Ioannis, Fenwick, Kerry, Chauhan, Ritika, Rust, Alistair G, Orr, Nick, Dudbridge, Frank, Haider, Syed, Fletcher, Olivia
Published in Nature communications (12.03.2018)
Published in Nature communications (12.03.2018)
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Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition
Novo, Clara Lopes, Javierre, Biola-Maria, Cairns, Jonathan, Segonds-Pichon, Anne, Wingett, Steven W., Freire-Pritchett, Paula, Furlan-Magaril, Mayra, Schoenfelder, Stefan, Fraser, Peter, Rugg-Gunn, Peter J.
Published in Cell reports (Cambridge) (06.03.2018)
Published in Cell reports (Cambridge) (06.03.2018)
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Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans
Chauve, Laetitia, Hodge, Francesca, Murdoch, Sharlene, Masoudzadeh, Fatemeh, Mann, Harry-Jack, Lopez-Clavijo, Andrea F, Okkenhaug, Hanneke, West, Greg, Sousa, Bebiana C, Segonds-Pichon, Anne, Li, Cheryl, Wingett, Steven W, Kienberger, Hermine, Kleigrewe, Karin, de Bono, Mario, Wakelam, Michael J O, Casanueva, Olivia
Published in PLoS biology (01.11.2021)
Published in PLoS biology (01.11.2021)
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Global reorganisation of cis -regulatory units upon lineage commitment of human embryonic stem cells
Freire-Pritchett, Paula, Schoenfelder, Stefan, Várnai, Csilla, Wingett, Steven W, Cairns, Jonathan, Collier, Amanda J, García-Vílchez, Raquel, Furlan-Magaril, Mayra, Osborne, Cameron S, Fraser, Peter, Rugg-Gunn, Peter J, Spivakov, Mikhail
Published in eLife (23.03.2017)
Published in eLife (23.03.2017)
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The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle
Furlan-Magaril, Mayra, Ando-Kuri, Masami, Arzate-Mejía, Rodrigo G, Morf, Jörg, Cairns, Jonathan, Román-Figueroa, Abraham, Tenorio-Hernández, Luis, Poot-Hernández, A César, Andrews, Simon, Várnai, Csilla, Virk, Boo, Wingett, Steven W, Fraser, Peter
Published in Genome Biology (08.06.2021)
Published in Genome Biology (08.06.2021)
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Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks
Choy, Mun-Kit, Javierre, Biola M, Williams, Simon G, Baross, Stephanie L, Liu, Yingjuan, Wingett, Steven W, Akbarov, Artur, Wallace, Chris, Freire-Pritchett, Paula, Rugg-Gunn, Peter J, Spivakov, Mikhail, Fraser, Peter, Keavney, Bernard D
Published in Nature communications (28.06.2018)
Published in Nature communications (28.06.2018)
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Chromosome contacts in activated T cells identify autoimmune disease candidate genes
Burren, Oliver S, Rubio García, Arcadio, Javierre, Biola-Maria, Rainbow, Daniel B, Cairns, Jonathan, Cooper, Nicholas J, Lambourne, John J, Schofield, Ellen, Castro Dopico, Xaquin, Ferreira, Ricardo C, Coulson, Richard, Burden, Frances, Rowlston, Sophia P, Downes, Kate, Wingett, Steven W, Frontini, Mattia, Ouwehand, Willem H, Fraser, Peter, Spivakov, Mikhail, Todd, John A, Wicker, Linda S, Cutler, Antony J, Wallace, Chris
Published in Genome Biology (04.09.2017)
Published in Genome Biology (04.09.2017)
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Intra- and interchromosomal contact mapping reveals the Igh locus has extensive conformational heterogeneity and interacts with B-lineage genes
Mielczarek, Olga, Rogers, Carolyn H., Zhan, Yinxiu, Matheson, Louise S., Stubbington, Michael J.T., Schoenfelder, Stefan, Bolland, Daniel J., Javierre, Biola M., Wingett, Steven W., Várnai, Csilla, Segonds-Pichon, Anne, Conn, Simon J., Krueger, Felix, Andrews, Simon, Fraser, Peter, Giorgetti, Luca, Corcoran, Anne E.
Published in Cell reports (Cambridge) (26.09.2023)
Published in Cell reports (Cambridge) (26.09.2023)
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Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells
Koohy, Hashem, Bolland, Daniel J, Matheson, Louise S, Schoenfelder, Stefan, Stellato, Claudia, Dimond, Andrew, Várnai, Csilla, Chovanec, Peter, Chessa, Tamara, Denizot, Jeremy, Manzano Garcia, Raquel, Wingett, Steven W, Freire-Pritchett, Paula, Nagano, Takashi, Hawkins, Phillip, Stephens, Len, Elderkin, Sarah, Spivakov, Mikhail, Fraser, Peter, Corcoran, Anne E, Varga-Weisz, Patrick D
Published in Genome Biology (05.09.2018)
Published in Genome Biology (05.09.2018)
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Author Correction: Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks
Choy, Mun-Kit, Javierre, Biola M, Williams, Simon G, Baross, Stephanie L, Liu, Yingjuan, Wingett, Steven W, Akbarov, Artur, Wallace, Chris, Freire-Pritchett, Paula, Rugg-Gunn, Peter J, Spivakov, Mikhail, Fraser, Peter, Keavney, Bernard D
Published in Nature communications (12.11.2018)
Published in Nature communications (12.11.2018)
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Journal Article
Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C
Mifsud, Borbala, Tavares-Cadete, Filipe, Young, Alice N, Sugar, Robert, Schoenfelder, Stefan, Ferreira, Lauren, Wingett, Steven W, Andrews, Simon, Grey, William, Ewels, Philip A, Herman, Bram, Happe, Scott, Higgs, Andy, LeProust, Emily, Follows, George A, Fraser, Peter, Luscombe, Nicholas M, Osborne, Cameron S
Published in Nature genetics (01.06.2015)
Published in Nature genetics (01.06.2015)
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