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

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

Source: Genome Biology, Vol 25, Iss 1, Pp 1-10 (2024)

Subject Terms: 3D genome structure, Hi-C, Histone marks, G-quadruplex DNA, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/64f8f18f52c349d5bcf820beb8d79a27

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

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

Source: Nature Communications, Vol 15, Iss 1, Pp 1-18 (2024)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/7476e4a7107d49bfbd49a2a4b2b12352

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

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

Source: Genome Biology, Vol 24, Iss 1, Pp 1-35 (2023)

Subject Terms: Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/82621c9e5c664c34abfd6e15dd050f64

Intra- and interchromosomal contact mapping reveals the Igh locus has extensive conformational heterogeneity and interacts with B-lineage genes

Authors: Olga Mielczarek, Carolyn H. Rogers, Yinxiu Zhan, Louise S. Matheson, Michael J.T. Stubbington, Stefan Schoenfelder, Daniel J. Bolland, Biola M. Javierre, Steven W. Wingett, Csilla Várnai, Anne Segonds-Pichon, Simon J. Conn, Felix Krueger, Simon Andrews, Peter Fraser, Luca Giorgetti, Anne E. Corcoran

Source: Cell Reports, Vol 42, Iss 9, Pp 113074- (2023)

Subject Terms: CP: Immunology, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124723010859; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/125cbc8ecfba40ce99ab9245a423021d

3D genome organization links non-coding disease-associated variants to genes

Authors: Gisela Orozco, Stefan Schoenfelder, Nicolas Walker, Stephan Eyre, Peter Fraser

Source: Frontiers in Cell and Developmental Biology, Vol 10 (2022)

Subject Terms: 3D genomics, GWAS, gene expression, SNP, causality, promoter-capture Hi-C, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fcell.2022.995388/full; https://doaj.org/toc/2296-634X

Access URL: https://doaj.org/article/a1a0157e13b7444a9022c9b749de2d9a

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

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

Source: Nature Communications, Vol 12, Iss 1, Pp 1-18 (2021)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/7b14988f9bbd452bb5b113c07a446d36

Transcription-dependent cohesin repositioning rewires chromatin loops in cellular senescence

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

Source: Nature Communications, Vol 11, Iss 1, Pp 1-14 (2020)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/cfcc6e6ce1f94a00978bd38e7e46977b

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

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

Source: PLoS Pathogens, Vol 17, Iss 8, p e1009875 (2021)

Subject Terms: Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1553-7366; https://doaj.org/toc/1553-7374

Access URL: https://doaj.org/article/c2ebaa15d87542a8b9191e3a5a74e587

The impact of courier-, express- and parcel (CEP) service providers on urban road traffic: The case of Vienna

Authors: Sebastian Kummer, Marko Hribernik, David M. Herold, Jasmin Mikl, Mario Dobrovnik, Stefan Schoenfelder

Source: Transportation Research Interdisciplinary Perspectives, Vol 9, Iss , Pp 100278- (2021)

Subject Terms: Urban road traffic, Last-mile, CEP, City logistics, Survey, Transportation and communications, HE1-9990

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2590198220301895; https://doaj.org/toc/2590-1982

Access URL: https://doaj.org/article/f4f974f776b34106a0e7f354c15bf572

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

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

Source: Nature Communications, Vol 9, Iss 1, Pp 1-10 (2018)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/b406d78bb61b40df9e736ae3f1f1e49a

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

Authors: Hashem Koohy, Daniel J. Bolland, Louise S. Matheson, Stefan Schoenfelder, Claudia Stellato, Andrew Dimond, Csilla Várnai, Peter Chovanec, Tamara Chessa, Jeremy Denizot, Raquel Manzano Garcia, Steven W. Wingett, Paula Freire-Pritchett, Takashi Nagano, Phillip Hawkins, Len Stephens, Sarah Elderkin, Mikhail Spivakov, Peter Fraser, Anne E. Corcoran, Patrick D. Varga-Weisz

Source: Genome Biology, Vol 19, Iss 1, Pp 1-24 (2018)

Subject Terms: Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s13059-018-1489-y; https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/6176506a0b014dd1a2e2a5beb2a2e029

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

Authors: Clara Lopes Novo, Biola-Maria Javierre, Jonathan Cairns, Anne Segonds-Pichon, Steven W. Wingett, Paula Freire-Pritchett, Mayra Furlan-Magaril, Stefan Schoenfelder, Peter Fraser, Peter J. Rugg-Gunn

Source: Cell Reports, Vol 22, Iss 10, Pp 2615-2627 (2018)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124718302213; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/a9fe24befd3e4a119da1557f07e1eacc

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

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

Source: Genome Biology, Vol 18, Iss 1, Pp 1-11 (2017)

Subject Terms: Hi-C, Chromosome conformation capture, Cancer, Tumour, Glioblastoma, Anaplastic astrocytoma, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s13059-017-1253-8; https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/6927c847dd604636bfaaaa54b97b4973

ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL

Authors: Gordana Wutz, Rene Ladurner, Brian Glenn St Hilaire, Roman R Stocsits, Kota Nagasaka, Benoit Pignard, Adrian Sanborn, Wen Tang, Csilla Várnai, Miroslav P Ivanov, Stefan Schoenfelder, Petra van der Lelij, Xingfan Huang, Gerhard Dürnberger, Elisabeth Roitinger, Karl Mechtler, Iain Finley Davidson, Peter Fraser, Erez Lieberman-Aiden, Jan-Michael Peters

Source: eLife, Vol 9 (2020)

Subject Terms: chromatin structure, genome organization, cohesin, CTCF, TADs, loops, Medicine, Science, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://elifesciences.org/articles/52091; https://doaj.org/toc/2050-084X

Access URL: https://doaj.org/article/50f9b518193c4de2ba8e04afd984547d

Global Reorganization of the Nuclear Landscape in Senescent Cells

Authors: Tamir Chandra, Philip Andrew Ewels, Stefan Schoenfelder, Mayra Furlan-Magaril, Steven William Wingett, Kristina Kirschner, Jean-Yves Thuret, Simon Andrews, Peter Fraser, Wolf Reik

Source: Cell Reports, Vol 10, Iss 4, Pp 471-483 (2015)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S221112471401122X; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/3c24731ad6c0489a928431702a77252b

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

Authors: Paula Freire-Pritchett, Stefan Schoenfelder, Csilla Várnai, Steven W Wingett, Jonathan Cairns, Amanda J Collier, Raquel García-Vílchez, Mayra Furlan-Magaril, Cameron S Osborne, Peter Fraser, Peter J Rugg-Gunn, Mikhail Spivakov

Source: eLife, Vol 6 (2017)

Subject Terms: gene regulation, cis-regulatory units, human embryonic stem cells, lineage committment, nuclear architecture, promoter capture Hi-C, Medicine, Science, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://elifesciences.org/articles/21926; https://doaj.org/toc/2050-084X

Access URL: https://doaj.org/article/6b57a130ecbc478aaa570feb12bd03e6

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

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

Source: PLoS ONE, Vol 12, Iss 4, p e0174744 (2017)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC5381888?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/34572f7f552f4608b385e9edc53e4c30

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

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

Source: PLoS ONE, Vol 11, Iss 11, p e0166923 (2016)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/8522a4146c414caba49e01a735871ae1

HiCUP: pipeline for mapping and processing Hi-C data [version 1; referees: 2 approved, 1 approved with reservations]

Authors: Steven Wingett, Philip Ewels, Mayra Furlan-Magaril, Takashi Nagano, Stefan Schoenfelder, Peter Fraser, Simon Andrews

Source: F1000Research, Vol 4 (2015)

Subject Terms: Bioinformatics, Genomics, Medicine, Science

File Description: electronic resource

Relation: http://f1000research.com/articles/4-1310/v1; https://doaj.org/toc/2046-1402

Access URL: https://doaj.org/article/3062fe9e657b4a0ab4c1ad31fc61ef9f

Nuclear RNA sequencing of the mouse erythroid cell transcriptome.

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

Source: PLoS ONE, Vol 7, Iss 11, p e49274 (2012)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC3510205?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/0244b07b53fe4a4486c1b6e6aab8d9a8