Works matching AU Schoenfelder, Stefan

Results: 27

DNA G-quadruplex structures act as functional elements in α- and β-globin enhancers.

Published in:

Genome Biology, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s13059-025-03627-1

By:

Doyle, Colm;
Herka, Krzysztof;
Flynn, Sean M.;
Melidis, Larry;
Dhir, Somdutta;
Schoenfelder, Stefan;
Tannahill, David;
Balasubramanian, Shankar

Publication type:

Article

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

Published in:

Nature Genetics, 2015, v. 47, n. 10, p. 1179, doi. 10.1038/ng.3393

By:

Mifsud, Borbala;
Dimitrova, Emilia;
Wingett, Steven W;
Luscombe, Nicholas M;
Schoenfelder, Stefan;
Dimond, Andrew;
Javierre, Biola-Maria;
Armstrong, Harry;
Matheson, Louise;
Furlan-Magaril, Mayra;
Jurkowski, Wiktor;
Tabbada, Kristina;
Osborne, Cameron S;
Fraser, Peter;
Elderkin, Sarah;
Sugar, Robert;
Tavares-Cadete, Filipe;
Segonds-Pichon, Anne;
Andrews, Simon;
Herman, Bram

Publication type:

Article

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C.

Published in:

Nature Genetics, 2015, v. 47, n. 6, p. 598, doi. 10.1038/ng.3286

By:

Mifsud, Borbala;
Tavares-Cadete, Filipe;
Sugar, Robert;
Young, Alice N;
Schoenfelder, Stefan;
Ferreira, Lauren;
Ewels, Philip A;
Fraser, Peter;
Wingett, Steven W;
Andrews, Simon;
Grey, William;
Herman, Bram;
Happe, Scott;
Higgs, Andy;
LeProust, Emily;
Follows, George A;
Luscombe, Nicholas M;
Osborne, Cameron S

Publication type:

Article

Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells.

Published in:

Nature Genetics, 2010, v. 42, n. 1, p. 53, doi. 10.1038/ng.496

By:

Schoenfelder, Stefan;
Sexton, Tom;
Chakalova, Lyubomira;
Cope, Nathan F.;
Horton, Alice;
Andrews, Simon;
Kurukuti, Sreenivasulu;
Mitchell, Jennifer A.;
Umlauf, David;
Dimitrova, Daniela S.;
Eskiw, Christopher H.;
Yanquan Luo;
Chia-Lin Wei;
Yijun Ruan;
Bieker, James J.;
Fraser, Peter

Publication type:

Article

Widespread allele-specific topological domains in the human genome are not confined to imprinted gene clusters.

Published in:

Genome Biology, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s13059-023-02876-2

By:

Richer, Stephen;
Tian, Yuan;
Schoenfelder, Stefan;
Hurst, Laurence;
Murrell, Adele;
Pisignano, Giuseppina

Publication type:

Article

Nuclear RNA Sequencing of the Mouse Erythroid Cell Transcriptome.

Published in:

PLoS ONE, 2012, v. 7, n. 11, p. 1, doi. 10.1371/journal.pone.0049274

By:

Mitchell, Jennifer A.;
Clay, Ieuan;
Umlauf, David;
Chen, Chih-yu;
Moir, Catherine A.;
Eskiw, Christopher H.;
Schoenfelder, Stefan;
Chakalova, Lyubomira;
Nagano, Takashi;
Fraser, Peter

Publication type:

Article

Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins.

Published in:

EMBO Journal, 2017, v. 36, n. 24, p. 3573, doi. 10.15252/embj.201798004

By:

Wutz, Gordana;
Várnai, Csilla;
Nagasaka, Kota;
Cisneros, David A;
Stocsits, Roman R;
Tang, Wen;
Schoenfelder, Stefan;
Jessberger, Gregor;
Muhar, Matthias;
Hossain, M Julius;
Walther, Nike;
Koch, Birgit;
Kueblbeck, Moritz;
Ellenberg, Jan;
Zuber, Johannes;
Fraser, Peter;
Peters, Jan‐Michael

Publication type:

Article

Short- and long-range cis interactions between integrated HPV genomes and cellular chromatin dysregulate host gene expression in early cervical carcinogenesis.

Published in:

PLoS Pathogens, 2021, v. 17, n. 8, p. 1, doi. 10.1371/journal.ppat.1009875

By:

Groves, Ian J.;
Drane, Emma L. A.;
Michalski, Marco;
Monahan, Jack M.;
Scarpini, Cinzia G.;
Smith, Stephen P.;
Bussotti, Giovanni;
Várnai, Csilla;
Schoenfelder, Stefan;
Fraser, Peter;
Enright, Anton J.;
Coleman, Nicholas

Publication type:

Article

Divergent wiring of repressive and active chromatin interactions between mouse embryonic and trophoblast lineages.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-06666-4

By:

Schoenfelder, Stefan;
Mifsud, Borbala;
Senner, Claire E.;
Todd, Christopher D.;
Chrysanthou, Stephanie;
Darbo, Elodie;
Hemberger, Myriam;
Branco, Miguel R.

Publication type:

Article

GOTHiC, a probabilistic model to resolve complex biases and to identify real interactions in Hi-C data.

Published in:

PLoS ONE, 2017, v. 12, n. 4, p. 1, doi. 10.1371/journal.pone.0174744

By:

Martincorena, Inigo;
Darbo, Elodie;
Sugar, Robert;
Mifsud, Borbala;
Luscombe, Nicholas M.;
Schoenfelder, Stefan;
Fraser, Peter

Publication type:

Article

Identifying Causal Genes at the Multiple Sclerosis Associated Region 6q23 Using Capture Hi-C.

Published in:

PLoS ONE, 2016, v. 11, n. 11, p. 1, doi. 10.1371/journal.pone.0166923

By:

Martin, Paul;
McGovern, Amanda;
Massey, Jonathan;
Schoenfelder, Stefan;
Duffus, Kate;
Yarwood, Annie;
Barton, Anne;
Worthington, Jane;
Fraser, Peter;
Eyre, Stephen;
Orozco, Gisela

Publication type:

Article

Non-coding transcripts in the H19 imprinting control region mediate gene silencing in transgenic Drosophila.

Published in:

EMBO Reports, 2007, v. 8, n. 11, p. 1068, doi. 10.1038/sj.embor.7401094

By:

Schoenfelder, Stefan;
Smits, Guillaume;
Fraser, Peter;
Reik, Wolf;
Paro, Renato

Publication type:

Article

Widespread reorganisation of pluripotent factor binding and gene regulatory interactions between human pluripotent states.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-22201-4

By:

Chovanec, Peter;
Collier, Amanda J.;
Krueger, Christel;
Várnai, Csilla;
Semprich, Claudia I.;
Schoenfelder, Stefan;
Corcoran, Anne E.;
Rugg-Gunn, Peter J.

Publication type:

Article

Transcription-dependent cohesin repositioning rewires chromatin loops in cellular senescence.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. N.PAG, doi. 10.1038/s41467-020-19878-4

By:

Olan, Ioana;
Parry, Aled J.;
Schoenfelder, Stefan;
Narita, Masako;
Ito, Yoko;
Chan, Adelyne S. L.;
Slater, Guy St.C.;
Bihary, Dóra;
Bando, Masashige;
Shirahige, Katsuhiko;
Kimura, Hiroshi;
Samarajiwa, Shamith A.;
Fraser, Peter;
Narita, Masashi

Publication type:

Article

Cis-Regulatory Control of Mammalian Sex Determination.

Published in:

Sexual Development, 2021, v. 15, n. 5/6, p. 317, doi. 10.1159/000519244

By:

Ridnik, Meshi;
Schoenfelder, Stefan;
Gonen, Nitzan

Publication type:

Article

HMGA1 orchestrates chromatin compartmentalization and sequesters genes into 3D networks coordinating senescence heterogeneity.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-51153-8

By:

Olan, Ioana;
Ando-Kuri, Masami;
Parry, Aled J.;
Handa, Tetsuya;
Schoenfelder, Stefan;
Fraser, Peter;
Ohkawa, Yasuyuki;
Kimura, Hiroshi;
Narita, Masako;
Narita, Masashi

Publication type:

Article

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

Published in:

Genome Biology, 2018, v. 19, n. 1, p. N.PAG, doi. 10.1186/s13059-018-1489-y

By:

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.

Publication type:

Article

Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci.

Published in:

Nature Communications, 2015, v. 6, n. 11, p. 10069, doi. 10.1038/ncomms10069

By:

Martin, Paul;
McGovern, Amanda;
Orozco, Gisela;
Duffus, Kate;
Yarwood, Annie;
Schoenfelder, Stefan;
Cooper, Nicholas J.;
Barton, Anne;
Wallace, Chris;
Fraser, Peter;
Worthington, Jane;
Eyre, Steve

Publication type:

Article

Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci.

Published in:

Nature Communications, 2015, v. 6, n. 2, p. 6178, doi. 10.1038/ncomms7178

By:

Jäger, Roland;
Migliorini, Gabriele;
Henrion, Marc;
Kandaswamy, Radhika;
Speedy, Helen E.;
Heindl, Andreas;
Whiffin, Nicola;
Carnicer, Maria J.;
Broome, Laura;
Dryden, Nicola;
Nagano, Takashi;
Schoenfelder, Stefan;
Enge, Martin;
Yuan, Yinyin;
Taipale, Jussi;
Fraser, Peter;
Fletcher, Olivia;
Houlston, Richard S.

Publication type:

Article

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

Published in:

Genome Biology, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s13059-015-0753-7

By:

Takashi Nagano;
Várnai, Csilla;
Schoenfelder, Stefan;
Javierre, Biola-Maria;
Wingett, Steven W.;
Fraser, Peter

Publication type:

Article

Improved simultaneous mapping of epigenetic features and 3D chromatin structure via ViCAR.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03377-6

By:

Flynn, Sean M.;
Dhir, Somdutta;
Herka, Krzysztof;
Doyle, Colm;
Melidis, Larry;
Simeone, Angela;
Hui, Winnie W. I.;
Araujo Tavares, Rafael de Cesaris;
Schoenfelder, Stefan;
Tannahill, David;
Balasubramanian, Shankar

Publication type:

Article

Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours.

Published in:

Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1253-8

By:

Harewood, Louise;
Kishore, Kamal;
Eldridge, Matthew D.;
Wingett, Steven;
Pearson, Danita;
Schoenfelder, Stefan;
Collins, V. Peter;
Fraser, Peter

Publication type:

Article

Capture Hi-C identifies a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23.

Published in:

Genome Biology, 2016, v. 17, p. 1, doi. 10.1186/s13059-016-1078-x

By:

McGovern, Amanda;
Schoenfelder, Stefan;
Martin, Paul;
Massey, Jonathan;
Duffus, Kate;
Plant, Darren;
Yarwood, Annie;
Pratt, Arthur G.;
Anderson, Amy E.;
Isaacs, John D.;
Diboll, Julie;
Thalayasingam, Nishanthi;
Ospelt, Caroline;
Barton, Anne;
Worthington, Jane;
Fraser, Peter;
Eyre, Stephen;
Orozco, Gisela

Publication type:

Article

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

Published in:

Genome Biology, 2016, v. 17, p. 1, doi. 10.1186/s13059-016-0992-2

By:

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

Publication type:

Article

High‐resolution three‐dimensional chromatin profiling of the Chinese hamster ovary cell genome.

Published in:

Biotechnology & Bioengineering, 2021, v. 118, n. 2, p. 784, doi. 10.1002/bit.27607

By:

Bevan, Stephen;
Schoenfelder, Stefan;
Young, Robert J.;
Zhang, Lin;
Andrews, Simon;
Fraser, Peter;
O'Callaghan, Peter M.

Publication type:

Article

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure.

Published in:

Nature, 2013, v. 502, n. 7469, p. 59, doi. 10.1038/nature12593

By:

Nagano, Takashi;
Lubling, Yaniv;
Stevens, Tim J.;
Schoenfelder, Stefan;
Yaffe, Eitan;
Dean, Wendy;
Laue, Ernest D.;
Tanay, Amos;
Fraser, Peter

Publication type:

Article

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

Published in:

eLife, 2017, p. 1, doi. 10.7554/eLife.21926

By:

Freire-Pritchett, Paula;
Schoenfelder, Stefan;
Vá Rnai, 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

Publication type:

Article