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@article{Schmitt:2016aa,
	Abstract = {The three-dimensional configuration of DNA is integral to all nuclear processes in eukaryotes, yet our knowledge of the chromosome architecture is still limited. Genome-wide chromosome conformation capture studies have uncovered features of chromatin organization in cultured cells, but genome architecture in human tissues has yet to be explored. Here, we report the most comprehensive survey to date of chromatin organization in human tissues. Through integrative analysis of chromatin contact maps in 21 primary human tissues and cell types, we find topologically associating domains highly conserved in different tissues. We also discover genomic regions that exhibit unusually high levels of local chromatin interactions. These frequently interacting regions (FIREs) are enriched for super-enhancers and are near tissue-specifically expressed genes. They display strong tissue-specificity in local chromatin interactions. Additionally, FIRE formation is partially dependent on CTCF and the Cohesin complex. We further show that FIREs can help annotate the function of non-coding sequence variants.},
	Author = {Schmitt, Anthony D and Hu, Ming and Jung, Inkyung and Xu, Zheng and Qiu, Yunjiang and Tan, Catherine L and Li, Yun and Lin, Shin and Lin, Yiing and Barr, Cathy L and Ren, Bing},
	Date-Added = {2019-11-27 08:16:49 -0500},
	Date-Modified = {2019-11-27 08:16:49 -0500},
	Doi = {10.1016/j.celrep.2016.10.061},
	Journal = {Cell Rep},
	Journal-Full = {Cell reports},
	Month = {Nov},
	Number = {8},
	Pages = {2042-2059},
	Pmid = {27851967},
	Pst = {ppublish},
	Title = {A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome},
	Volume = {17},
	Year = {2016},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.celrep.2016.10.061}}

@article{Cresswell:2019aa,
	Author = {Cresswell, Kellen G and Stansfield, John C and Dozmorov, Mikhail G},
	Date = {2019/01/01},
	Date-Added = {2019-11-27 08:13:23 -0500},
	Date-Modified = {2019-11-27 08:13:23 -0500},
	Doi = {10.1101/549170},
	Journal = {bioRxiv},
	Month = {01},
	N2 = {The three-dimensional (3D) structure of the genome plays a crucial role in regulating gene expression. Chromatin conformation capture technologies (Hi-C) have revealed that the genome is organized in a hierarchy of topologically associated domains (TADs), the fundamental building blocks of the genome. Identifying such hierarchical structures is a critical step in understanding regulatory interactions within the genome. Existing tools for TAD calling frequently require tunable parameters, are sensitive to biases such as sequencing depth, resolution, and sparsity of Hi-C data, and are computationally inefficient. Furthermore, the choice of TAD callers within the R/Bioconductor ecosystem is limited. To address these challenges, we frame the problem of TAD detection in a spectral clustering framework. Our SpectralTAD R package has automatic parameter selection, robust to sequencing depth, resolution and sparsity of Hi-C data, and detects hierarchical, biologically relevant TAD structure. Using simulated and real-life Hi-C data, we show that SpectralTAD outperforms rGMAP and TopDom, two state-of-the-art R-based TAD callers. TAD boundaries that are shared among multiple levels of the hierarchy were more enriched in relevant genomic annotations, e.g., CTCF binding sites, suggesting their higher biological importance. In contrast, boundaries of primary TADs, defined as TADs which cannot be split into sub-TADs, were found to be less enriched in genomic annotations, suggesting their more dynamic role in genome regulation. In summary, we present a simple, fast, and user-friendly R package for robust detection of TAD hierarchies supported by biological evidence. SpectralTAD is available on https://github.com/dozmorovlab/SpectralTAD and Bioconductor (submitted).},
	Pages = {549170},
	Title = {SpectralTAD: an R package for defining a hierarchy of Topologically Associated Domains using spectral clustering},
	Ty = {JOUR},
	Url = {http://biorxiv.org/content/early/2019/02/13/549170.abstract},
	Year = {2019},
	Bdsk-Url-1 = {http://biorxiv.org/content/early/2019/02/13/549170.abstract},
	Bdsk-Url-2 = {https://doi.org/10.1101/549170}}

@article{Rao:2014aa,
	Author = {Suhas~S.P. Rao and Miriam~H. Huntley and Neva~C. Durand and Elena~K. Stamenova and Ivan~D. Bochkov and James~T. Robinson and Adrian~L. Sanborn and Ido Machol and Arina~D. Omer and Eric~S. Lander and Erez~Lieberman Aiden},
	Doi = {10.1016/j.cell.2014.11.021},
	Journal = {Cell},
	Month = {dec},
	Number = {7},
	Pages = {1665--1680},
	Publisher = {Elsevier {BV}},
	Title = {A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping},
	Volume = {159},
	Year = {2014},
	Bdsk-Url-1 = {https://doi.org/10.1016/j.cell.2014.11.021}}

@article{Rao:2017aa,
	Author = {Suhas S.P. Rao and Su-Chen Huang and Brian Glenn St Hilaire and Jesse M. Engreitz and Elizabeth M. Perez and Kyong-Rim Kieffer-Kwon and Adrian L. Sanborn and Sarah E. Johnstone and Gavin D. Bascom and Ivan D. Bochkov and Xingfan Huang and Muhammad S. Shamim and Jaeweon Shin and Douglass Turner and Ziyi Ye and Arina D. Omer and James T. Robinson and Tamar Schlick and Bradley E. Bernstein and Rafael Casellas and Eric S. Lander and Erez Lieberman Aiden},
	Doi = {10.1016/j.cell.2017.09.026},
	Journal = {Cell},
	Month = {oct},
	Number = {2},
	Pages = {305--320.e24},
	Publisher = {Elsevier {BV}},
	Title = {Cohesin Loss Eliminates All Loop Domains},
	Volume = {171},
	Year = {2017},
	Bdsk-Url-1 = {https://doi.org/10.1016/j.cell.2017.09.026}}

@article{Durand:2016aa,
	Author = {Neva C. Durand and Muhammad S. Shamim and Ido Machol and Suhas S.P. Rao and Miriam H. Huntley and Eric S. Lander and Erez Lieberman Aiden},
	Doi = {10.1016/j.cels.2016.07.002},
	Journal = {Cell Systems},
	Month = {jul},
	Number = {1},
	Pages = {95--98},
	Publisher = {Elsevier {BV}},
	Title = {Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments},
	Volume = {3},
	Year = {2016},
	Bdsk-Url-1 = {https://doi.org/10.1016/j.cels.2016.07.002}}
