{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,14]],"date-time":"2026-02-14T10:35:23Z","timestamp":1771065323761,"version":"3.50.1"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2020,8,31]],"date-time":"2020-08-31T00:00:00Z","timestamp":1598832000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MC_UU_12025"],"award-info":[{"award-number":["MC_UU_12025"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["106130\/Z\/14\/B"],"award-info":[{"award-number":["106130\/Z\/14\/B"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The 3D structure of chromatin in the nucleus is important for gene expression and regulation. Chromosome conformation capture techniques, such as Hi-C, generate large amounts of data showing interaction points on the genome but these are hard to interpret using standard tools.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have developed CSynth, an interactive 3D genome browser and real-time chromatin restraint-based modeller to visualize models of any chromosome conformation capture (3C) data. Unlike other modelling systems, CSynth allows dynamic interaction with the modelling parameters to allow experimentation and effects on the model. It also allows comparison of models generated from data in different tissues\/cell states and the results of third-party 3D modelling outputs. In addition, we include an option to view and manipulate these complicated structures using Virtual Reality (VR) so scientists can immerse themselves in the models for further understanding. This VR component has also proven to be a valuable teaching and a public engagement tool.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availabilityand implementation<\/jats:title>\n                  <jats:p>CSynth is web based and available to use at csynth.org.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa757","type":"journal-article","created":{"date-parts":[[2020,8,24]],"date-time":"2020-08-24T19:28:08Z","timestamp":1598297288000},"page":"951-955","source":"Crossref","is-referenced-by-count":20,"title":["CSynth: an interactive modelling and visualization tool for 3D chromatin structure"],"prefix":"10.1093","volume":"37","author":[{"given":"Stephen","family":"Todd","sequence":"first","affiliation":[{"name":"Department of Computing, Goldsmiths, University of London , London, UK"},{"name":"London Geometry, Ltd. , London, UK"}]},{"given":"Peter","family":"Todd","sequence":"additional","affiliation":[{"name":"London Geometry, Ltd. , London, UK"}]},{"given":"Simon J","family":"McGowan","sequence":"additional","affiliation":[{"name":"Analysis, Visualization and Informatics, MRC Weatherall Institute of Molecular Medicine , Oxford, UK"}]},{"given":"James R","family":"Hughes","sequence":"additional","affiliation":[{"name":"Genome Biology Group, MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine , Oxford, UK"}]},{"given":"Yasutaka","family":"Kakui","sequence":"additional","affiliation":[{"name":"The Francis Crick Institute, Chromosome Segregation Laboratory , London, UK"}]},{"given":"Frederic Fol","family":"Leymarie","sequence":"additional","affiliation":[{"name":"Department of Computing, Goldsmiths, University of London , London, UK"},{"name":"London Geometry, Ltd. , London, UK"}]},{"given":"William","family":"Latham","sequence":"additional","affiliation":[{"name":"Department of Computing, Goldsmiths, University of London , London, UK"},{"name":"London Geometry, Ltd. , London, UK"}]},{"given":"Stephen","family":"Taylor","sequence":"additional","affiliation":[{"name":"Analysis, Visualization and Informatics, MRC Weatherall Institute of Molecular Medicine , Oxford, UK"}]}],"member":"286","published-online":{"date-parts":[[2020,8,31]]},"reference":[{"key":"2023051612173217300_btaa757-B1","doi-asserted-by":"crossref","first-page":"886","DOI":"10.1186\/s12864-016-3210-4","article-title":"Chromosome3D: reconstructing three-dimensional chromosomal structures from Hi-C interaction frequency data using distance geometry simulated annealing","volume":"17","author":"Adhikari","year":"2016","journal-title":"BMC Genomics"},{"key":"2023051612173217300_btaa757-B2","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1186\/1471-2105-11-444","article-title":"Genome3D: a viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome","volume":"11","author":"Asbury","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023051612173217300_btaa757-B0680254","doi-asserted-by":"publisher","first-page":"2125","DOI":"10.1016\/j.celrep.2020.01.044","article-title":"A Dynamic Folded Hairpin Conformation Is Associated with \u03b1-Globin Activation in Erythroid Cells","volume":"30","author":"Chiariello","year":"2020","journal-title":"Cell Reports"},{"key":"2023051612173217300_btaa757-B4","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1038\/nmeth.4146","article-title":"How best to identify chromosomal interactions: a comparison of approaches","volume":"14","author":"Davies","year":"2017","journal-title":"Nat. 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