{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T18:36:00Z","timestamp":1761676560061,"version":"3.37.3"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2017,7,28]],"date-time":"2017-07-28T00:00:00Z","timestamp":1501200000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The availability of powerful analysis tools will further understanding of genome organization and its relationship to phenotype in dynamical settings.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>The 4D Nucleome Analysis Toolbox (NAT) is a user-friendly and powerful MATLAB toolbox for time series analysis of genome-wide chromosome conformation capture (Hi-C) data and gene expression (RNA-seq). NAT can load and normalize data, define topologically associating domains, analyse translocations, produce visualization, and study time course data. We provide examples that include time series data sets and karyotypically abnormal cell lines demonstrating the flexibility of NAT.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/laseaman\/4D_Nucleome_Analysis_Toolbox<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx484","type":"journal-article","created":{"date-parts":[[2017,7,27]],"date-time":"2017-07-27T19:13:20Z","timestamp":1501182800000},"page":"104-106","source":"Crossref","is-referenced-by-count":8,"title":["4D nucleome Analysis Toolbox: analysis of Hi-C data with abnormal karyotype and time series capabilities"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9111-9776","authenticated-orcid":false,"given":"Laura","family":"Seaman","sequence":"first","affiliation":[{"name":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA"}]},{"given":"Indika","family":"Rajapakse","sequence":"additional","affiliation":[{"name":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,7,28]]},"reference":[{"key":"2023020208303421100_btx484-B1","doi-asserted-by":"crossref","first-page":"8002","DOI":"10.1073\/pnas.1505822112","article-title":"Functional organization of the human 4D nucleome","volume":"112","author":"Chen","year":"2015","journal-title":"Proc. Natl. Acad. Sci"},{"key":"2023020208303421100_btx484-B2","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":"2023020208303421100_btx484-B3","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.cels.2015.07.012","article-title":"Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom","volume":"3","author":"Durand","year":"2016","journal-title":"Cell Syst"},{"key":"2023020208303421100_btx484-B4","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.cels.2016.07.002","article-title":"Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments","volume":"3","author":"Durand","year":"2016","journal-title":"Cell Syst"},{"year":"2013","author":"Filippova","key":"2023020208303421100_btx484-B5"},{"key":"2023020208303421100_btx484-B6","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":"Nat. Methods"},{"key":"2023020208303421100_btx484-B7","doi-asserted-by":"crossref","first-page":"22.","DOI":"10.1186\/s12864-016-3387-6","article-title":"HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking","volume":"18","author":"Lazaris","year":"2017","journal-title":"BMC Genomics"},{"key":"2023020208303421100_btx484-B8","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"},{"key":"2023020208303421100_btx484-B9","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"},{"year":"2017","author":"Seaman","key":"2023020208303421100_btx484-B10"},{"key":"2023020208303421100_btx484-B11","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 Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/1\/104\/49043508\/bioinformatics_34_1_104.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/1\/104\/49043508\/bioinformatics_34_1_104.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T08:41:34Z","timestamp":1675327294000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/1\/104\/4054460"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,7,28]]},"references-count":11,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2018,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx484","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2018,1,1]]},"published":{"date-parts":[[2017,7,28]]}}}