{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,10]],"date-time":"2024-09-10T18:28:00Z","timestamp":1725992880569},"reference-count":61,"publisher":"Elsevier","isbn-type":[{"type":"print","value":"9780128114322"}],"license":[{"start":{"date-parts":[[2019,1,1]],"date-time":"2019-01-01T00:00:00Z","timestamp":1546300800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019]]},"DOI":"10.1016\/b978-0-12-809633-8.20243-4","type":"book-chapter","created":{"date-parts":[[2018,4,23]],"date-time":"2018-04-23T04:21:44Z","timestamp":1524457304000},"page":"318-323","source":"Crossref","is-referenced-by-count":0,"title":["Learning Chromatin Interaction Using Hi-C Datasets"],"prefix":"10.1016","author":[{"given":"Wing-Kin","family":"Sung","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib1","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1186\/s13059-015-0767-1","article-title":"Hicplotter integrates genomic data with interaction matrices","volume":"16","author":"Akdemir","year":"2015","journal-title":"Genome Biology"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib60","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1007\/s004390050630","article-title":"The human histone gene cluster at the D6S105 locus","volume":"101","author":"Albig","year":"1997","journal-title":"Hum. Genet."},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib2","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1101\/gr.160374.113","article-title":"Statistical confidence estimation for hi-c data reveals regulatory chromatin contacts","volume":"24","author":"Ay","year":"2014","journal-title":"Genome Research"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib3","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1016\/j.ymeth.2012.04.004","article-title":"Genome structure determination via 3c-based data integration by the integrative modeling platform","volume":"58","author":"Bau","year":"2012","journal-title":"Methods (San Diego, CA)"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib4","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1038\/nature14450","article-title":"Condensin-driven remodelling of X chromosome topology during dosage compensation","volume":"523","author":"Crane","year":"2015","journal-title":"Nature"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib5","doi-asserted-by":"crossref","first-page":"2994","DOI":"10.1093\/nar\/gkx145","article-title":"A critical assessment of topologically associating domain prediction tools","volume":"45","author":"Dali","year":"2017","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib6","doi-asserted-by":"crossref","first-page":"1306","DOI":"10.1126\/science.1067799","article-title":"Capturing chromosome conformation","volume":"295","author":"Dekker","year":"2002","journal-title":"Science (New York, N.Y.)"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib7","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nature11082","article-title":"Topological domains in mammalian genomes identified by analysis of chromatin interactions","volume":"485","author":"Dixon","year":"2012","journal-title":"Nature"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib8","doi-asserted-by":"crossref","first-page":"1299","DOI":"10.1101\/gr.5571506","article-title":"Chromosome conformation capture carbon copy (5c): A massively parallel solution for mapping interactions between genomic elements","volume":"16","author":"Dostie","year":"2006","journal-title":"Genome Research"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib9","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/nature08973","article-title":"A three-dimensional model of the yeast genome","volume":"465","author":"Duan","year":"2010","journal-title":"Nature"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib10","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/1748-7188-9-14","article-title":"Identification of alternative topological domains in chromatin","volume":"9","author":"Filippova","year":"2014","journal-title":"Algorithms for Molecular Biology"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib11","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1038\/nmeth.4325","article-title":"Carmen Maria Livi, Francesco Ferrari, and Silvio Bicciato. Comparison of computational methods for hi-c data analysis","volume":"14","author":"Forcato","year":"2017","journal-title":"Nature Methods"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib12","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1038\/nature08497","article-title":"An oestrogen-receptor-alpha-bound human chromatin interactome","volume":"462","author":"Fullwood","year":"2009","journal-title":"Nature"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib13","first-page":"e81","article-title":"Ic-finder: Inferring robustly the hierarchical organization of chromatin folding","volume":"45","author":"Haddad","year":"2017","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib14","doi-asserted-by":"crossref","first-page":"1068.e1","DOI":"10.1016\/j.cell.2012.02.019","article-title":"Snapshot: Chromosome confirmation capture","volume":"148","author":"Hakim","year":"2012","journal-title":"Cell"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib15","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","article-title":"Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and b cell identities","volume":"38","author":"Heinz","year":"2010","journal-title":"Molecular Cell"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib16","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1186\/s13059-015-0740-z","article-title":"Predicting chromatin organization using histone marks","volume":"16","author":"Huang","year":"2015","journal-title":"Genome Biology"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib17","doi-asserted-by":"crossref","first-page":"e1002893","DOI":"10.1371\/journal.pcbi.1002893","article-title":"Bayesian inference of spatial organizations of chromosomes","volume":"9","author":"Hu","year":"2013","journal-title":"PLOS Computational Biology"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib18","doi-asserted-by":"crossref","first-page":"3131","DOI":"10.1093\/bioinformatics\/bts570","article-title":"Hicnorm: Removing biases in hi-c data via poisson regression","volume":"28","author":"Hu","year":"2012","journal-title":"Bioinformatics (Oxford)"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib19","doi-asserted-by":"crossref","first-page":"1290","DOI":"10.1093\/bioinformatics\/btu801","article-title":"Hippie: A high-throughput identification pipeline for promoter interacting enhancer elements","volume":"31","author":"Hwang","year":"2015","journal-title":"Bioinformatics (Oxford)"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib20","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1038\/nmeth.2148","article-title":"Iterative correction of hi-c data reveals hallmarks of chromosome organization","volume":"9","author":"Imakaev","year":"2012","journal-title":"Nature Methods"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib21","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/nature12644","article-title":"A high-resolution map of the three-dimensional chromatin interactome in human cells","volume":"503","author":"Jin","year":"2013","journal-title":"Nature"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib22","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1038\/nbt.2057","article-title":"Genome architectures revealed by tethered chromosome conformation capture and population-based modeling","volume":"30","author":"Kalhor","year":"2011","journal-title":"Nature Biotechnology"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib23","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1038\/nrm.2016.138","article-title":"Regulation of disease-associated gene expression in the 3d genome","volume":"17","author":"Krijger","year":"2016","journal-title":"Nature Reviews. Molecular Cell Biology"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib24","doi-asserted-by":"crossref","first-page":"875","DOI":"10.1101\/gr.737703","article-title":"Genomic gene clustering analysis of pathways in eukaryotes","volume":"13","author":"Lee","year":"2003","journal-title":"Genome Research"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib25","doi-asserted-by":"crossref","first-page":"1141","DOI":"10.1038\/nmeth.3104","article-title":"3d genome reconstruction from chromosomal contacts","volume":"11","author":"Lesne","year":"2014","journal-title":"Nature Methods"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib26","doi-asserted-by":"crossref","first-page":"i386","DOI":"10.1093\/bioinformatics\/btu443","article-title":"Two-dimensional segmentation for analyzing hi-c data","volume":"30","author":"Levy-Leduc","year":"2014","journal-title":"Bioinformatics (Oxford)"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib27","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1126\/science.1181369","article-title":"Comprehensive mapping of long-range interactions reveals folding principles of the human genome","volume":"326","author":"Lieberman-Aiden","year":"2009","journal-title":"Science (New York, N.Y.)"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib28","doi-asserted-by":"crossref","first-page":"e0174744","DOI":"10.1371\/journal.pone.0174744","article-title":"Gothic, a probabilistic model to resolve complex biases and to identify real interactions in hi-c data","volume":"12","author":"Mifsud","year":"2017","journal-title":"PLOS ONE"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib29","doi-asserted-by":"crossref","first-page":"R44","DOI":"10.1186\/gb-2004-5-7-r44","article-title":"Tissue-specific spatial organization of genomes","volume":"5","author":"Parada","year":"2004","journal-title":"Genome Biology"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib30","doi-asserted-by":"crossref","first-page":"e183","DOI":"10.1093\/nar\/gkt745","article-title":"The sequencing bias relaxed characteristics of hi-c derived data and implications for chromatin 3d modeling","volume":"41","author":"Peng","year":"2013","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib61","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1056\/NEJM199307083290205","article-title":"Charcot-Marie-Tooth Disease Type 1A -- Association with a Spontaneous Point Mutation in the PMP22 Gene","volume":"329","author":"Rao","year":"1993","journal-title":"N Engl J Med."},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib31","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1016\/j.cell.2014.11.021","article-title":"A 3d map of the human genome at kilobase resolution reveals principles of chromatin looping","volume":"159","author":"Rao","year":"2014","journal-title":"Cell"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib32","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1186\/1471-2105-12-414","article-title":"Three-dimensional modeling of chromatin structure from interaction frequency data using markov chain monte carlo sampling","volume":"12","author":"Rousseau","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib33","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1186\/s13059-015-0806-y","article-title":"Hifive: A tool suite for easy and efficient hic and 5c data analysis","volume":"16","author":"Sauria","year":"2015","journal-title":"Genome Biology"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib34","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1186\/s12859-015-0678-x","article-title":"Hicdat: A fast and easy-to-use hi-c data analysis tool","volume":"16","author":"Schmid","year":"2015","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib35","doi-asserted-by":"crossref","first-page":"e1005665","DOI":"10.1371\/journal.pcbi.1005665","article-title":"Automatic analysis and 3d-modelling of hi-c data using tadbit reveals structural features of the fly chromatin colors","volume":"13","author":"Serra","year":"2017","journal-title":"PLOS Computational Biology"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib36","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1186\/s13059-015-0831-x","article-title":"Hic-pro: An optimized and flexible pipeline for hi-c data processing","volume":"16","author":"Servant","year":"2015","journal-title":"Genome Biology"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib37","doi-asserted-by":"crossref","first-page":"1206","DOI":"10.1093\/bioinformatics\/btt120","article-title":"Cytohic: A cytoscape plugin for visual comparison of hi-c networks","volume":"29","author":"Shavit","year":"2013","journal-title":"Bioinformatics (Oxford)"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib38","doi-asserted-by":"crossref","first-page":"1121","DOI":"10.1093\/bioinformatics\/btv736","article-title":"Hierarchical block matrices as efficient representations of chromosome topologies and their application for 3c data integration","volume":"32","author":"Shavit","year":"2016","journal-title":"Bioinformatics (Oxford)"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib39","doi-asserted-by":"crossref","first-page":"e70","DOI":"10.1093\/nar\/gkv1505","article-title":"Topdom: An efficient and deterministic method for identifying topological domains in genomes","volume":"44","author":"Shin","year":"2016","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib40","doi-asserted-by":"crossref","first-page":"1348","DOI":"10.1038\/ng1896","article-title":"Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4c)","volume":"38","author":"Simonis","year":"2006","journal-title":"Nature Genetics"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib41","doi-asserted-by":"crossref","first-page":"W288","DOI":"10.1093\/nar\/gkw437","article-title":"3d-gnome: An integrated web service for structural modeling of the 3d genome","volume":"44","author":"Szalaj","year":"2016","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib42","doi-asserted-by":"crossref","first-page":"8164","DOI":"10.1093\/nar\/gkq955","article-title":"Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation","volume":"38","author":"Tanizawa","year":"2010","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib43","doi-asserted-by":"crossref","first-page":"e1004809","DOI":"10.1371\/journal.pcbi.1004809","article-title":"Quin: A web server for querying and visualizing chromatin interaction networks","volume":"12","author":"Thibodeau","year":"2016","journal-title":"PLOS Computational Biology"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib44","doi-asserted-by":"crossref","first-page":"e52","DOI":"10.1093\/nar\/gkt1411","article-title":"Large-scale reconstruction of 3d structures of human chromosomes from chromosomal contact data","volume":"42","author":"Trieu","year":"2014","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib45","doi-asserted-by":"crossref","first-page":"1286","DOI":"10.1093\/bioinformatics\/btv754","article-title":"Mogen: A tool for reconstructing 3d models of genomes from chromosomal conformation capturing data","volume":"32","author":"Trieu","year":"2016","journal-title":"Bioinformatics (Oxford)"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib46","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1093\/nar\/gkw1155","article-title":"3d genome structure modeling by lorentzian objective function","volume":"45","author":"Trieu","year":"2017","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib47","doi-asserted-by":"crossref","first-page":"i26","DOI":"10.1093\/bioinformatics\/btu268","article-title":"A statistical approach for inferring the 3d structure of the genome","volume":"30","author":"Varoquaux","year":"2014","journal-title":"Bioinformatics (Oxford)"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib48","doi-asserted-by":"crossref","first-page":"e163","DOI":"10.1093\/nar\/gkx735","article-title":"Hitad: Detecting the structural and functional hierarchies of topologically associating domains from chromatin interactions","volume":"45","author":"Wang","year":"2017","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib49","doi-asserted-by":"crossref","first-page":"e54","DOI":"10.1093\/nar\/gkv100","article-title":"Inferential modeling of 3d chromatin structure","volume":"43","author":"Wang","year":"2015","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib50","article-title":"The 3d genome browser: A web-based browser for visualizing 3d genome organization and long-range chromatin interactions","author":"Wang","year":"2017","journal-title":"bioRxiv"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib51","doi-asserted-by":"crossref","first-page":"1601","DOI":"10.1093\/bioinformatics\/btv485","article-title":"Identification of hierarchical chromatin domains","volume":"32","author":"Weinreb","year":"2016","journal-title":"Bioinformatics (Oxford)"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib52","doi-asserted-by":"crossref","first-page":"1310","DOI":"10.12688\/f1000research.7334.1","article-title":"Hicup: Pipeline for mapping and processing hi-c data","volume":"4","author":"Wingett","year":"2015","journal-title":"F1000Research"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib53","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1093\/bioinformatics\/btv650","article-title":"A hidden markov random field-based bayesian method for the detection of long-range chromosomal interactions in hi-c data","volume":"32","author":"Xu","year":"2016","journal-title":"Bioinformatics (Oxford)"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib54","doi-asserted-by":"crossref","first-page":"2692","DOI":"10.1093\/bioinformatics\/btw240","article-title":"Fasthic: A fast and accurate algorithm to detect long-range chromosomal interactions from hi-c data","volume":"32","author":"Xu","year":"2016","journal-title":"Bioinformatics (Oxford)"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib55","doi-asserted-by":"crossref","first-page":"1059","DOI":"10.1038\/ng.947","article-title":"Probabilistic modeling of hi-c contact maps eliminates systematic biases to characterize global chromosomal architecture","volume":"43","author":"Yaffe","year":"2011","journal-title":"Nature Genetics"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib56","doi-asserted-by":"crossref","unstructured":"Zhang, Z.Z., Li, G., Toh, K.-C., Sung, W.-K., 2013. Inference of spatial organizations of chromosomes using semi-definite embedding approach and hi-c data. In: RECOMB, pp. 317\u2013332.","DOI":"10.1007\/978-3-642-37195-0_31"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib57","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1101\/gr.212803.116","article-title":"Reciprocal insulation analysis of hi-c data shows that tads represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes","volume":"27","author":"Zhan","year":"2017","journal-title":"Genome Research"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib58","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1038\/nmeth.2440","article-title":"Exploring long-range genome interactions using the washu epigenome browser","volume":"10","author":"Zhou","year":"2013","journal-title":"Nature Methods"},{"key":"10.1016\/B978-0-12-809633-8.20243-4_bib59","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/s13059-016-0896-1","article-title":"Hsa: Integrating multi-track hi-c data for genome-scale reconstruction of 3d chromatin structure","volume":"17","author":"Zou","year":"2016","journal-title":"Genome Biology"}],"container-title":["Encyclopedia of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:B9780128096338202434?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:B9780128096338202434?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T00:22:10Z","timestamp":1548116530000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/B9780128096338202434"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019]]},"ISBN":["9780128114322"],"references-count":61,"URL":"https:\/\/doi.org\/10.1016\/b978-0-12-809633-8.20243-4","relation":{},"subject":[],"published":{"date-parts":[[2019]]}}}