A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains
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DOI: 10.1038/s41467-024-48593-7
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- Jesse R. Dixon & Siddarth Selvaraj & Feng Yue & Audrey Kim & Yan Li & Yin Shen & Ming Hu & Jun S. Liu & Bing Ren, 2012. "Topological domains in mammalian genomes identified by analysis of chromatin interactions," Nature, Nature, vol. 485(7398), pages 376-380, May.
- Wenbao Yu & Bing He & Kai Tan, 2017. "Identifying topologically associating domains and subdomains by Gaussian Mixture model And Proportion test," Nature Communications, Nature, vol. 8(1), pages 1-9, December.
- Michael A. Willcockson & Sean E. Healton & Cary N. Weiss & Boris A. Bartholdy & Yair Botbol & Laxmi N. Mishra & Dhruv S. Sidhwani & Tommy J. Wilson & Hugo B. Pinto & Maxim I. Maron & Karin A. Skalina , 2021. "H1 histones control the epigenetic landscape by local chromatin compaction," Nature, Nature, vol. 589(7841), pages 293-298, January.
- Michael Mitter & Catherina Gasser & Zsuzsanna Takacs & Christoph C. H. Langer & Wen Tang & Gregor Jessberger & Charlie T. Beales & Eva Neuner & Stefan L. Ameres & Jan-Michael Peters & Anton Goloborodk, 2020. "Conformation of sister chromatids in the replicated human genome," Nature, Nature, vol. 586(7827), pages 139-144, October.
- Gil Ron & Yuval Globerson & Dror Moran & Tommy Kaplan, 2017. "Promoter-enhancer interactions identified from Hi-C data using probabilistic models and hierarchical topological domains," Nature Communications, Nature, vol. 8(1), pages 1-12, December.
- Jesse R. Dixon & Inkyung Jung & Siddarth Selvaraj & Yin Shen & Jessica E. Antosiewicz-Bourget & Ah Young Lee & Zhen Ye & Audrey Kim & Nisha Rajagopal & Wei Xie & Yarui Diao & Jing Liang & Huimin Zhao , 2015. "Chromatin architecture reorganization during stem cell differentiation," Nature, Nature, vol. 518(7539), pages 331-336, February.
- Takashi Nagano & Yaniv Lubling & Csilla Várnai & Carmel Dudley & Wing Leung & Yael Baran & Netta Mendelson Cohen & Steven Wingett & Peter Fraser & Amos Tanay, 2017. "Cell-cycle dynamics of chromosomal organization at single-cell resolution," Nature, Nature, vol. 547(7661), pages 61-67, July.
- Elphège P. Nora & Laura Caccianini & Geoffrey Fudenberg & Kevin So & Vasumathi Kameswaran & Abigail Nagle & Alec Uebersohn & Bassam Hajj & Agnès Le Saux & Antoine Coulon & Leonid A. Mirny & Katherine , 2020. "Molecular basis of CTCF binding polarity in genome folding," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
- Elphège P. Nora & Bryan R. Lajoie & Edda G. Schulz & Luca Giorgetti & Ikuhiro Okamoto & Nicolas Servant & Tristan Piolot & Nynke L. van Berkum & Johannes Meisig & John Sedat & Joost Gribnau & Emmanuel, 2012. "Spatial partitioning of the regulatory landscape of the X-inactivation centre," Nature, Nature, vol. 485(7398), pages 381-385, May.
- Samuel Collombet & Noémie Ranisavljevic & Takashi Nagano & Csilla Varnai & Tarak Shisode & Wing Leung & Tristan Piolot & Rafael Galupa & Maud Borensztein & Nicolas Servant & Peter Fraser & Katia Ancel, 2020. "Parental-to-embryo switch of chromosome organization in early embryogenesis," Nature, Nature, vol. 580(7801), pages 142-146, April.
- Yan Zhang & Lin An & Jie Xu & Bo Zhang & W. Jim Zheng & Ming Hu & Jijun Tang & Feng Yue, 2018. "Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus," Nature Communications, Nature, vol. 9(1), pages 1-9, December.
- Alessandro Magli & June Baik & Pruthvi Pota & Carolina Ortiz Cordero & Il-Youp Kwak & Daniel J. Garry & Paul E. Love & Brian D. Dynlacht & Rita C. R. Perlingeiro, 2019. "Pax3 cooperates with Ldb1 to direct local chromosome architecture during myogenic lineage specification," Nature Communications, Nature, vol. 10(1), pages 1-17, December.
- Andrew J. King & Duantida Songdej & Damien J. Downes & Robert A. Beagrie & Siyu Liu & Megan Buckley & Peng Hua & Maria C. Suciu & A. Marieke Oudelaar & Lars L. P. Hanssen & Danuta Jeziorska & Nigel Ro, 2021. "Reactivation of a developmentally silenced embryonic globin gene," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
- Job Dekker & Andrew S. Belmont & Mitchell Guttman & Victor O. Leshyk & John T. Lis & Stavros Lomvardas & Leonid A. Mirny & Clodagh C. O’Shea & Peter J. Park & Bing Ren & Joan C. Ritland Politz & Jay S, 2017. "Correction: Corrigendum: The 4D nucleome project," Nature, Nature, vol. 552(7684), pages 278-278, December.
- Job Dekker & Andrew S. Belmont & Mitchell Guttman & Victor O. Leshyk & John T. Lis & Stavros Lomvardas & Leonid A. Mirny & Clodagh C. O’Shea & Peter J. Park & Bing Ren & Joan C. Ritland Politz & Jay S, 2017. "The 4D nucleome project," Nature, Nature, vol. 549(7671), pages 219-226, September.
- Haoyue Zhang & Daniel J. Emerson & Thomas G. Gilgenast & Katelyn R. Titus & Yemin Lan & Peng Huang & Di Zhang & Hongxin Wang & Cheryl A. Keller & Belinda Giardine & Ross C. Hardison & Jennifer E. Phil, 2019. "Chromatin structure dynamics during the mitosis-to-G1 phase transition," Nature, Nature, vol. 576(7785), pages 158-162, December.
- Angsheng Li & Xianchen Yin & Bingxiang Xu & Danyang Wang & Jimin Han & Yi Wei & Yun Deng & Ying Xiong & Zhihua Zhang, 2018. "Decoding topologically associating domains with ultra-low resolution Hi-C data by graph structural entropy," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
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