Mapping the spectrum of 3D communities in human chromosome conformation capture data
暂无分享,去创建一个
Sang Hoon Lee | Xavier Durang | Yeonghoon Kim | Sungmin Lee | Per Stenberg | Jae-Hyung Jeon | Ludvig Lizana | Sungmin Lee | Jae-Hyung Jeon | L. Lizana | P. Stenberg | Xavier Durang | Sang Hoon Lee | Yeonghoon Kim
[1] M. Nicodemi,et al. Structure of the human chromosome interaction network , 2017, PloS one.
[2] L. Mirny. The fractal globule as a model of chromatin architecture in the cell , 2011, Chromosome Research.
[3] Shlomo Havlin,et al. Crumpled globule model of the three-dimensional structure of DNA , 1993 .
[4] S. Q. Xie,et al. Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation , 2015, Molecular systems biology.
[5] Data production leads,et al. An integrated encyclopedia of DNA elements in the human genome , 2012 .
[6] Mason A. Porter,et al. Communities in Networks , 2009, ArXiv.
[7] M E J Newman,et al. Finding and evaluating community structure in networks. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.
[8] Caroline Uhler,et al. Network analysis identifies chromosome intermingling regions as regulatory hotspots for transcription , 2017, Proceedings of the National Academy of Sciences.
[9] Simona Bianco,et al. Predicting chromatin architecture from models of polymer physics , 2017, Chromosome Research.
[10] Manolis Kellis,et al. Discovery and characterization of chromatin states for systematic annotation of the human genome , 2010, Nature Biotechnology.
[11] A. Grosberg. Extruding Loops to Make Loopy Globules? , 2016, Biophysical journal.
[12] Santo Fortunato,et al. Community detection in graphs , 2009, ArXiv.
[13] M V Tamm,et al. Anomalous diffusion in fractal globules. , 2014, Physical review letters.
[14] Neva C. Durand,et al. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes , 2015, Proceedings of the National Academy of Sciences.
[15] Neva C. Durand,et al. A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.
[16] Timothy J. Durham,et al. "Systematic" , 1966, Comput. J..
[17] Purnamrita Sarkar,et al. NETWORK MODELLING OF TOPOLOGICAL DOMAINS USING HI-C DATA. , 2017, The annals of applied statistics.
[18] E. M. Muro,et al. Co-regulation of paralog genes in the three-dimensional chromatin architecture , 2016, Nucleic acids research.
[19] ENCODEConsortium,et al. An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.
[20] Danielle S Bassett,et al. Detecting hierarchical genome folding with network modularity , 2018, Nature Methods.
[21] Daniel Ruiz,et al. A Fast Algorithm for Matrix Balancing , 2013, Web Information Retrieval and Linear Algebra Algorithms.
[22] M. Newman. Community detection in networks: Modularity optimization and maximum likelihood are equivalent , 2016, Physical review. E.
[23] Maitreya J. Dunham,et al. Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps , 2014, G3: Genes, Genomes, Genetics.
[24] L. Mirny,et al. Chromosome Compaction by Active Loop Extrusion , 2016, Biophysical journal.
[25] I. Amit,et al. Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .
[26] Anton Goloborodko,et al. Compaction and segregation of sister chromatids via active loop extrusion , 2016, bioRxiv.
[27] Rasha E. Boulos,et al. Revealing long-range interconnected hubs in human chromatin interaction data using graph theory. , 2013, Physical review letters.
[28] Pasquale De Meo,et al. Generalized Louvain method for community detection in large networks , 2011, 2011 11th International Conference on Intelligent Systems Design and Applications.
[29] Mark E. J. Newman,et al. An efficient and principled method for detecting communities in networks , 2011, Physical review. E, Statistical, nonlinear, and soft matter physics.
[30] Aristotelis Tsirigos,et al. Detecting community structures in Hi-C genomic data , 2015, 2016 Annual Conference on Information Science and Systems (CISS).
[31] Bing He,et al. Identifying topologically associating domains and subdomains by Gaussian Mixture model And Proportion test , 2017, Nature Communications.
[32] Mark Gerstein,et al. MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions , 2016, bioRxiv.
[33] J. Sedat,et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre , 2012, Nature.
[34] Jean-Loup Guillaume,et al. Fast unfolding of communities in large networks , 2008, 0803.0476.
[35] Jesse R. Dixon,et al. Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.
[36] David M Blei,et al. Efficient discovery of overlapping communities in massive networks , 2013, Proceedings of the National Academy of Sciences.
[37] Michael S. Becker,et al. Spatial Organization of the Mouse Genome and Its Role in Recurrent Chromosomal Translocations , 2012, Cell.
[38] Daniel Jost,et al. IC-Finder: inferring robustly the hierarchical organization of chromatin folding , 2017, Nucleic acids research.
[39] Jing Liang,et al. Chromatin architecture reorganization during stem cell differentiation , 2015, Nature.
[40] Benjamin J. Raphael,et al. Identification of hierarchical chromatin domains , 2016, Bioinform..