Modeling chromosomes: Beyond pretty pictures
Recently, Chromosome Conformation Capture (3C) based experiments have highlighted the importance of computational models for the study of chromosome organization. In this review, we propose that current computational models can be grouped into roughly four classes, with two classes of data-driven mo...
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| Other Authors: | |
| Format: | Article |
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Elsevier
2017
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| Online Access: | http://hdl.handle.net/1721.1/112798 https://orcid.org/0000-0002-5320-2728 https://orcid.org/0000-0001-5905-6517 https://orcid.org/0000-0002-0785-5410 |
| _version_ | 1826199182051901440 |
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| author | Imakaev, Maksim Viktorovich Fudenberg, Geoffrey Mirny, Leonid A |
| author2 | Institute for Medical Engineering and Science |
| author_facet | Institute for Medical Engineering and Science Imakaev, Maksim Viktorovich Fudenberg, Geoffrey Mirny, Leonid A |
| author_sort | Imakaev, Maksim Viktorovich |
| collection | MIT |
| description | Recently, Chromosome Conformation Capture (3C) based experiments have highlighted the importance of computational models for the study of chromosome organization. In this review, we propose that current computational models can be grouped into roughly four classes, with two classes of data-driven models: consensus structures and data-driven ensembles, and two classes of de novo models: structural ensembles and mechanistic ensembles. Finally, we highlight specific questions mechanistic ensembles can address. |
| first_indexed | 2024-09-23T11:16:01Z |
| format | Article |
| id | mit-1721.1/112798 |
| institution | Massachusetts Institute of Technology |
| last_indexed | 2024-09-23T11:16:01Z |
| publishDate | 2017 |
| publisher | Elsevier |
| record_format | dspace |
| spelling | mit-1721.1/1127982022-10-01T02:27:24Z Modeling chromosomes: Beyond pretty pictures Imakaev, Maksim Viktorovich Fudenberg, Geoffrey Mirny, Leonid A Institute for Medical Engineering and Science Massachusetts Institute of Technology. Department of Physics Imakaev, Maksim Viktorovich Fudenberg, Geoffrey Mirny, Leonid A Recently, Chromosome Conformation Capture (3C) based experiments have highlighted the importance of computational models for the study of chromosome organization. In this review, we propose that current computational models can be grouped into roughly four classes, with two classes of data-driven models: consensus structures and data-driven ensembles, and two classes of de novo models: structural ensembles and mechanistic ensembles. Finally, we highlight specific questions mechanistic ensembles can address. National Institutes of Health (U.S.) (Grant R01HG003143) National Institutes of Health (U.S.) (Grant R01 GM114190) 2017-12-19T14:38:30Z 2017-12-19T14:38:30Z 2015-09 2015-09 2017-12-18T20:46:11Z Article http://purl.org/eprint/type/JournalArticle 0014-5793 1873-3468 http://hdl.handle.net/1721.1/112798 Imakaev, Maxim V. et al. “Modeling Chromosomes: Beyond Pretty Pictures.” FEBS Letters 589, 20 (September 2015): 3031–3036 © 2015 Federation of European Biochemical Societies https://orcid.org/0000-0002-5320-2728 https://orcid.org/0000-0001-5905-6517 https://orcid.org/0000-0002-0785-5410 http://dx.doi.org/10.1016/J.FEBSLET.2015.09.004 FEBS Letters Creative Commons Attribution-Noncommercial-Share Alike http://creativecommons.org/licenses/by-nc-sa/4.0/ application/pdf Elsevier PMC |
| spellingShingle | Imakaev, Maksim Viktorovich Fudenberg, Geoffrey Mirny, Leonid A Modeling chromosomes: Beyond pretty pictures |
| title | Modeling chromosomes: Beyond pretty pictures |
| title_full | Modeling chromosomes: Beyond pretty pictures |
| title_fullStr | Modeling chromosomes: Beyond pretty pictures |
| title_full_unstemmed | Modeling chromosomes: Beyond pretty pictures |
| title_short | Modeling chromosomes: Beyond pretty pictures |
| title_sort | modeling chromosomes beyond pretty pictures |
| url | http://hdl.handle.net/1721.1/112798 https://orcid.org/0000-0002-5320-2728 https://orcid.org/0000-0001-5905-6517 https://orcid.org/0000-0002-0785-5410 |
| work_keys_str_mv | AT imakaevmaksimviktorovich modelingchromosomesbeyondprettypictures AT fudenberggeoffrey modelingchromosomesbeyondprettypictures AT mirnyleonida modelingchromosomesbeyondprettypictures |