{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,18]],"date-time":"2026-07-18T18:24:07Z","timestamp":1784399047603,"version":"3.55.0"},"reference-count":46,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2013,1,31]],"date-time":"2013-01-31T00:00:00Z","timestamp":1359590400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1002893","type":"journal-article","created":{"date-parts":[[2013,1,31]],"date-time":"2013-01-31T21:27:31Z","timestamp":1359667651000},"page":"e1002893","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":199,"title":["Bayesian Inference of Spatial Organizations of Chromosomes"],"prefix":"10.1371","volume":"9","author":[{"given":"Ming","family":"Hu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ke","family":"Deng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhaohui","family":"Qin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jesse","family":"Dixon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siddarth","family":"Selvaraj","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer","family":"Fang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bing","family":"Ren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun S.","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2013,1,31]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"1793","DOI":"10.1126\/science.1152850","article-title":"Gene regulation in the third dimension","volume":"319","author":"J Dekker","year":"2008","journal-title":"Science"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1038\/nature05916","article-title":"Nuclear organization of the genome and the potential for gene regulation","volume":"447","author":"P Fraser","year":"2007","journal-title":"Nature"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"1046","DOI":"10.1039\/b803580f","article-title":"Long-range chromosomal interactions and gene regulation","volume":"4","author":"A Miele","year":"2008","journal-title":"Mol Biosyst"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1016\/j.cell.2007.01.028","article-title":"Beyond the sequence: cellular organization of genome function","volume":"128","author":"T Misteli","year":"2007","journal-title":"Cell"},{"key":"ref5","first-page":"153","article-title":"Spatial positioning; a new dimension in genome function","volume":"119","author":"T Misteli","year":"2004","journal-title":"Cell"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1412","DOI":"10.1126\/science.1067703","article-title":"Visualizing chromatin dynamics in interphase nuclei","volume":"296","author":"SM Gasser","year":"2002","journal-title":"Science"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1038\/nrg2041","article-title":"Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions","volume":"8","author":"C Lanctot","year":"2007","journal-title":"Nat Rev Genet"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1016\/S0092-8674(03)00189-2","article-title":"Global chromosome positions are transmitted through mitosis in mammalian cells","volume":"112","author":"D Gerlich","year":"2003","journal-title":"Cell"},{"key":"ref9","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":"E Lieberman-Aiden","year":"2009","journal-title":"Science"},{"key":"ref10","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":"R Kalhor","year":"2011","journal-title":"Nat Biotechnol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1038\/nsmb.1936","article-title":"The three-dimensional folding of the alpha-globin gene domain reveals formation of chromatin globules","volume":"18","author":"D Bau","year":"2011","journal-title":"Nat Struct Mol Biol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1038\/nature06404","article-title":"Determining the architectures of macromolecular assemblies","volume":"450","author":"F Alber","year":"2007","journal-title":"Nature"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/nature08973","article-title":"A three-dimensional model of the yeast genome","volume":"465","author":"Z Duan","year":"2010","journal-title":"Nature"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1007\/s10107-004-0559-y","article-title":"On the Implementation of an Interior-Point Filter Line-Search Algorithm for Large-Scale Nonlinear Programming","volume":"106","author":"A Wachter","year":"2006","journal-title":"Mathematical Programming"},{"key":"ref15","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":"H Tanizawa","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"ref16","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":"M Rousseau","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"ref17","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":"E Yaffe","year":"2011","journal-title":"Nat Genet"},{"key":"ref18","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":"J Dixon","year":"2012","journal-title":"Nature"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1126\/science.1110428","article-title":"Inferential structure determination","volume":"309","author":"W Rieping","year":"2005","journal-title":"Science"},{"key":"ref20","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":"M Hu","year":"2012","journal-title":"Bioinformatics"},{"key":"ref21","unstructured":"Liu J (2001) Monte Carlo Strategies in scientific computing. New York: Springer-Verlag."},{"key":"ref22","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1109\/TAC.1974.1100705","article-title":"A new look at the statistical model identification","volume":"19","author":"H Akaike","year":"1974","journal-title":"IEEE Transactions on Automatic Control"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/S0969-2126(01)00572-X","article-title":"Computational modeling predicts the structure and dynamics of chromatin fiber","volume":"9","author":"DA Beard","year":"2001","journal-title":"Structure"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1016\/j.molcel.2010.02.032","article-title":"Ring1B compacts chromatin structure and represses gene expression independent of histone ubiquitination","volume":"38","author":"R Eskeland","year":"2010","journal-title":"Mol Cell"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1038\/nature11243","article-title":"A map of the cis-regulatory sequences in the mouse genome","volume":"488","author":"Y Shen","year":"2012","journal-title":"Nature"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1016\/j.cell.2008.07.020","article-title":"Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells","volume":"134","author":"A Marson","year":"2008","journal-title":"Cell"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1038\/nature06008","article-title":"Genome-wide maps of chromatin state in pluripotent and lineage-committed cells","volume":"448","author":"TS Mikkelsen","year":"2007","journal-title":"Nature"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"2484","DOI":"10.1101\/gad.1837309","article-title":"SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state","volume":"23","author":"S Bilodeau","year":"2009","journal-title":"Genes Dev"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"e1001023","DOI":"10.1371\/journal.pgen.1001023","article-title":"CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression","volume":"6","author":"MP Schnetz","year":"2010","journal-title":"PLoS Genet"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1016\/j.molcel.2010.03.016","article-title":"Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation","volume":"38","author":"D Peric-Hupkes","year":"2010","journal-title":"Mol Cell"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1101\/gr.099796.109","article-title":"Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis","volume":"20","author":"I Hiratani","year":"2009","journal-title":"Genome Res"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"4475","DOI":"10.1128\/MCB.00208-07","article-title":"The three-dimensional structure of human interphase chromosomes is related to the transcriptome map","volume":"27","author":"S Goetze","year":"2007","journal-title":"Mol Cell Biol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"908","DOI":"10.1016\/j.cell.2012.02.002","article-title":"Spatial Organization of the Mouse Genome and Its Role in Recurrent Chromosomal Translocations","volume":"148","author":"Y Zhang","year":"2012","journal-title":"Cell"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/nature11049","article-title":"Spatial partitioning of the regulatory landscape of the X-inactivation centre","volume":"485","author":"EP Nora","year":"2012","journal-title":"Nature"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"2710","DOI":"10.1073\/pnas.92.7.2710","article-title":"A random-walk\/giant-loop model for interphase chromosomes","volume":"92","author":"RK Sachs","year":"1995","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"1239","DOI":"10.1083\/jcb.130.6.1239","article-title":"Evidence for the organization of chromatin in megabase pair-sized loops arranged along a random walk path in the human G0\/G1 interphase nucleus","volume":"130","author":"H Yokota","year":"1995","journal-title":"J Cell Biol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1038\/nrm2894","article-title":"The nuclear envelope in genome organization, expression and stability","volume":"11","author":"K Mekhail","year":"2010","journal-title":"Nat Rev Mol Cell Biol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1038\/nbt.1680","article-title":"Genomics tools for unraveling chromosome architecture","volume":"28","author":"B van Steensel","year":"2010","journal-title":"Nat Biotechnol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"16495","DOI":"10.1073\/pnas.0402766101","article-title":"Long-range compaction and flexibility of interphase chromatin in budding yeast analyzed by high-resolution imaging techniques","volume":"101","author":"K Bystricky","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"e125","DOI":"10.1093\/nar\/gkl675","article-title":"3D reconstruction and comparison of shapes of DNA minicircles observed by cryo-electron microscopy","volume":"34","author":"A Amzallag","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref41","doi-asserted-by":"crossref","unstructured":"McCullagh P, Nelder JA (1989) Generalized linear models. Chapman &amp; Hall\/CRC.","DOI":"10.1007\/978-1-4899-3242-6"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"1032","DOI":"10.1080\/01621459.1998.10473765","article-title":"Sequential Monte-Carlo Methods For Dynamic-Systems","volume":"93","author":"JS Liu","year":"1998","journal-title":"Journal of the American Statistical Association"},{"key":"ref43","doi-asserted-by":"crossref","unstructured":"Gelman A, Carlin JB, Stern HS, Rubin DB (1995) Bayesian data analysis. London: Chapman &amp; Hall. xix, 526 p.","DOI":"10.1201\/9780429258411"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1016\/0370-2693(87)91197-X","article-title":"Hybrid Monte-Carlo","volume":"195","author":"S Duane","year":"1987","journal-title":"Physics Letters B"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"337","DOI":"10.2307\/2347565","article-title":"Adaptive rejection sampling for Gibbs sampling","volume":"41","author":"W Gilks","year":"1992","journal-title":"Applied Statistics"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"698","DOI":"10.1109\/TPAMI.1987.4767965","article-title":"Least-squares fitting of two 3-d point sets","volume":"9","author":"KS Arun","year":"1987","journal-title":"IEEE Trans Pattern Anal Mach Intell"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002893","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,7,9]],"date-time":"2019-07-09T03:14:28Z","timestamp":1562642068000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002893"}},"subtitle":[],"editor":[{"given":"Amos","family":"Tanay","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2013,1,31]]},"references-count":46,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2013,1,31]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1002893","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,1,31]]}}}