{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T08:23:08Z","timestamp":1778055788733,"version":"3.51.4"},"reference-count":44,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2015,5,12]],"date-time":"2015-05-12T00:00:00Z","timestamp":1431388800000},"content-version":"vor","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.1004221","type":"journal-article","created":{"date-parts":[[2015,5,12]],"date-time":"2015-05-12T18:02:37Z","timestamp":1431453757000},"page":"e1004221","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":44,"title":["Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex"],"prefix":"10.1371","volume":"11","author":[{"given":"Sepideh","family":"Babaei","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ahmed","family":"Mahfouz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marc","family":"Hulsman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Boudewijn P. F.","family":"Lelieveldt","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeroen","family":"de Ridder","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marcel","family":"Reinders","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2015,5,12]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1038\/nature11245","article-title":"Architecture of the human regulatory network derived from ENCODE data","volume":"489","author":"MB Gerstein","year":"2012","journal-title":"Nature"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1186\/1471-2164-11-704","article-title":"Human transcriptional interactome of chromatin contribute to gene co-expression","volume":"11","author":"X Dong","year":"2010","journal-title":"BMC Genomics"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"e54699","DOI":"10.1371\/journal.pone.0054699","article-title":"The 3D organization of the yeast genome correlates with co-expression and reflects functional relations between genes","volume":"8","author":"D Homouz","year":"2013","journal-title":"PloS One"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"7690","DOI":"10.1093\/nar\/gks501","article-title":"Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages","volume":"40","author":"X Lan","year":"2012","journal-title":"Nucleic Acids Research"},{"key":"ref5","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":"F Jin","year":"2013","journal-title":"Nature"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1038\/msb.2010.79","article-title":"Intra- and inter-chromosomal interactions correlate with CTCF binding genome wide","volume":"6","author":"M Botta","year":"2010","journal-title":"Molecular Systems Biology"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"221","DOI":"10.3389\/fgene.2012.00221","article-title":"Transcription factories","volume":"3","author":"D Rieder","year":"2012","journal-title":"Frontiers in Genetics"},{"key":"ref8","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":"ref9","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1038\/ng.496","article-title":"Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells","volume":"42","author":"S Schoenfelder","year":"2010","journal-title":"Nature Genetics"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"8683","DOI":"10.1021\/cr300513p","article-title":"Transcription factories: genome organization and gene regulation","volume":"113","author":"A Papantonis","year":"2013","journal-title":"Chemical Reviews"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1038\/nrg3454","article-title":"Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data","volume":"14","author":"J Dekker","year":"2013","journal-title":"Nature Reviews Genetics"},{"key":"ref12","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":"ref13","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":"2012","journal-title":"Nature Biotechnology"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"3028","DOI":"10.1093\/nar\/gkt1294","article-title":"Dissecting the chromatin interactome of microRNA genes","volume":"42","author":"D Chen","year":"2014","journal-title":"Nucleic Acids Research"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"1207","DOI":"10.1016\/j.celrep.2012.09.022","article-title":"Large-scale functional organization of long-range chromatin interaction networks","volume":"2","author":"KS Sandhu","year":"2012","journal-title":"Cell Reports"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"118102","DOI":"10.1103\/PhysRevLett.111.118102","article-title":"Revealing long-range interconnected hubs in human chromatin interaction data using graph theory","volume":"111","author":"R Boulos","year":"2013","journal-title":"Physical Review Letters"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1186\/1752-0509-7-90","article-title":"Topology of molecular interaction networks","volume":"7","author":"W Winterbach","year":"2013","journal-title":"BMC Systems Biology"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"556","DOI":"10.1016\/j.jtbi.2010.01.014","article-title":"Generalized walks-based centrality measures for complex biological networks","volume":"263","author":"E Estrada","year":"2010","journal-title":"Journal of Theoretical Biology"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"1169","DOI":"10.1038\/nmeth.2728","article-title":"Using networks to measure similarity between genes: association index selection","volume":"10","author":"JI Fuxman Bass","year":"2013","journal-title":"Nature Methods"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1093\/bioinformatics\/bth167","article-title":"Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph","volume":"20","author":"HW Ma","year":"2004","journal-title":"Bioinformatics"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"i237","DOI":"10.1093\/bioinformatics\/btu283","article-title":"Scale-space measures for graph topology link protein network architecture to function","volume":"30","author":"M Hulsman","year":"2014","journal-title":"Bioinformatics"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1186\/1752-0509-1-19","article-title":"Study of gene function based on spatial co-expression in a high-resolution mouse brain atlas","volume":"1","author":"Z Liu","year":"2007","journal-title":"BMC Systems Biology"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"e1003128","DOI":"10.1371\/journal.pcbi.1003128","article-title":"Co-expression profiling of autism genes in the mouse brain","volume":"9","author":"I Menashe","year":"2013","journal-title":"PLoS Computational Biology"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1038\/nature05453","article-title":"Genome-wide atlas of gene expression in the adult mouse brain","volume":"445","author":"ES Lein","year":"2007","journal-title":"Nature"},{"key":"ref25","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":"Nature Genetics"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1101\/gad.179804.111","article-title":"A decade of 3C technologies: insights into nuclear organization","volume":"26","author":"E de Wit","year":"2012","journal-title":"Genes & Development"},{"key":"ref27","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":"JR Dixon","year":"2012","journal-title":"Nature"},{"key":"ref28","article-title":"Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements","volume":"gkt227","author":"J Paulsen","year":"2013","journal-title":"Nucleic Acids Research"},{"key":"ref29","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":"ref30","unstructured":"Kondor R, Lafferty J (2002) Diffusion kernels on graphs and other discrete input spaces. Machin Learning-Int. Workshop and Conf.: 315\u2013322."},{"key":"ref31","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1186\/1471-2105-14-29","article-title":"Detecting recurrent gene mutation in interaction network context using multi-scale graph diffusion","volume":"14","author":"S Babaei","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"ref32","article-title":"3D hotspots of recurrent retroviral insertions reveal long-range interactions with cancer genes","volume":"6","author":"S Babaei","year":"2014","journal-title":"Nature Communications"},{"key":"ref33","first-page":"2579","article-title":"Visualizing data using t-SNE","volume":"9","author":"LVD Maaten","year":"2008","journal-title":"Journal of Machine Learning Research"},{"key":"ref34","unstructured":"van der Maaten L (2013) Barnes-Hut-SNE. arXiv preprint arXiv:13013342: 1\u201311."},{"key":"ref35","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1016\/j.gde.2009.09.006","article-title":"Finding distal regulatory elements in the human genome","volume":"19","author":"ND Heintzman","year":"2009","journal-title":"Current Opinion in Genetics & Development"},{"key":"ref36","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":"M Imakaev","year":"2012","journal-title":"Nature Methods"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"11794","DOI":"10.1073\/pnas.0812608106","article-title":"Genomic-anatomic evidence for distinct functional domains in hippocampal field ca1","volume":"106","author":"HW Dong","year":"2009","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"5397","DOI":"10.1073\/pnas.1312098111","article-title":"Cell-type-based model explaining coexpression patterns of genes in the brain","volume":"111","author":"P Grange","year":"2014","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"e1001049","DOI":"10.1371\/journal.pcbi.1001049","article-title":"Relationships between gene expression and brain wiring in the adult rodent brain","volume":"7","author":"L French","year":"2011","journal-title":"PLoS Computational Biology"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"e1002040","DOI":"10.1371\/journal.pcbi.1002040","article-title":"Gene expression in the rodent brain is associated with its regional connectivity","volume":"7","author":"L Wolf","year":"2011","journal-title":"PLoS Computational Biology"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/j.neuroimage.2013.08.049","article-title":"NeuroImage Integrative analysis of the connectivity and gene expression atlases in the mouse brain","volume":"84","author":"S Ji","year":"2014","journal-title":"NeuroImage"},{"key":"ref42","first-page":"71","article-title":"High-resolution prediction of mouse brain connectivity using gene expression patterns","volume":"73C","author":"A Fakhry","year":"2014","journal-title":"Methods"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1038\/nrg3413","article-title":"From neural development to cognition: unexpected roles for chromatin","volume":"14","author":"JL Ronan","year":"2013","journal-title":"Nature Reviews Genetics"},{"key":"ref44","unstructured":"Duin R (2004). Pr-tools. URL <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.prtools.org\" xlink:type=\"simple\">http:\/\/www.prtools.org<\/ext-link>."}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004221","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,25]],"date-time":"2019-08-25T00:39:43Z","timestamp":1566693583000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004221"}},"subtitle":[],"editor":[{"given":"Guillaume Joseph","family":"Filion","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2015,5,12]]},"references-count":44,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2015,5,12]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1004221","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,5,12]]}}}