{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:50Z","timestamp":1772138090810,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2018,8,23]],"date-time":"2018-08-23T00:00:00Z","timestamp":1534982400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"PCC\/Movember Foundation","award":["RS2014-04"],"award-info":[{"award-number":["RS2014-04"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The 3D genome architecture influences the regulation of genes by facilitating chromatin interactions between distal cis-regulatory elements and gene promoters. We implement Cross Cell-type Correlation based on DNA accessibility (C3D), a customizable computational tool that predicts chromatin interactions using an unsupervised algorithm that utilizes correlations in chromatin measurements, such as DNaseI hypersensitivity signals.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>C3D accurately predicts 32.7%, 18.3% and 24.1% of interactions, validated by ChIA-PET assays, between promoters and distal regions that overlie DNaseI hypersensitive sites in K562, MCF-7 and GM12878 cells, respectively.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Source code is open-source and freely available on GitHub (https:\/\/github.com\/LupienLabOrganization\/C3D) under the GNU GPLv3 license. C3D is implemented in Bash and R; it runs on any platform with Bash (\u22654.0), R (\u22653.1.1) and BEDTools (\u22652.19.0). It requires the following R packages: GenomicRanges, Sushi, data.table, preprocessCore and dynamicTreeCut.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty717","type":"journal-article","created":{"date-parts":[[2018,8,22]],"date-time":"2018-08-22T15:19:20Z","timestamp":1534951160000},"page":"877-879","source":"Crossref","is-referenced-by-count":13,"title":["C3D: a tool to predict 3D genomic interactions between cis-regulatory elements"],"prefix":"10.1093","volume":"35","author":[{"given":"Tahmid","family":"Mehdi","sequence":"first","affiliation":[{"name":"Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada"},{"name":"Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, ON, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Swneke D","family":"Bailey","sequence":"additional","affiliation":[{"name":"Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul","family":"Guilhamon","sequence":"additional","affiliation":[{"name":"Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0929-9478","authenticated-orcid":false,"given":"Mathieu","family":"Lupien","sequence":"additional","affiliation":[{"name":"Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada"},{"name":"Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada"},{"name":"Ontario Institute for Cancer Research, Toronto, ON, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,8,23]]},"reference":[{"key":"2023013107254838100_bty717-B1","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1093\/bioinformatics\/19.2.185","article-title":"A comparison of normalization methods for high density oligonucleotide array data based on variance and bias","volume":"19","author":"Bolstad","year":"2003","journal-title":"Bioinformatics"},{"key":"2023013107254838100_bty717-B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1101\/gr.164079.113","article-title":"Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits","volume":"24","author":"Corradin","year":"2014","journal-title":"Genome Res"},{"key":"2023013107254838100_bty717-B3","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":"Dekker","year":"2013","journal-title":"Nat. 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