{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T22:22:33Z","timestamp":1792794153748,"version":"4.5.0"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2018,3,15]],"date-time":"2018-03-15T00:00:00Z","timestamp":1521072000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"Howard Hughes Medical Institute International Student Research","id":[{"id":"https:\/\/ror.org\/006w34k90","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Gabilan Stanford Graduate Fellowship"},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["1DP2GM12348501"],"award-info":[{"award-number":["1DP2GM12348501"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["3U41HG007000-04S1"],"award-info":[{"award-number":["3U41HG007000-04S1"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["3R01ES02500902S1"],"award-info":[{"award-number":["3R01ES02500902S1"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["1U01HG009431-01"],"award-info":[{"award-number":["1U01HG009431-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The three-dimensional organization of chromatin plays a critical role in gene regulation and disease. High-throughput chromosome conformation capture experiments such as Hi-C are used to obtain genome-wide maps of three-dimensional chromatin contacts. However, robust estimation of data quality and systematic comparison of these contact maps is challenging due to the multi-scale, hierarchical structure of chromatin contacts and the resulting properties of experimental noise in the data. Measuring concordance of contact maps is important for assessing reproducibility of replicate experiments and for modeling variation between different cellular contexts.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We introduce a concordance measure called DIfferences between Smoothed COntact maps (GenomeDISCO) for assessing the similarity of a pair of contact maps obtained from chromosome conformation capture experiments. The key idea is to smooth contact maps using random walks on the contact map graph, before estimating concordance. We use simulated datasets to benchmark GenomeDISCO's sensitivity to different types of noise that affect chromatin contact maps. When applied to a large collection of Hi-C datasets, GenomeDISCO accurately distinguishes biological replicates from samples obtained from different cell types. GenomeDISCO also generalizes to other chromosome conformation capture assays, such as HiChIP.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Software implementing GenomeDISCO is available at https:\/\/github.com\/kundajelab\/genomedisco.<\/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\/bty164","type":"journal-article","created":{"date-parts":[[2018,3,15]],"date-time":"2018-03-15T09:24:19Z","timestamp":1521105859000},"page":"2701-2707","source":"Crossref","is-referenced-by-count":132,"title":["GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs"],"prefix":"10.1093","volume":"34","author":[{"given":"Oana","family":"Ursu","sequence":"first","affiliation":[{"name":"Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathan","family":"Boley","sequence":"additional","affiliation":[{"name":"Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maryna","family":"Taranova","sequence":"additional","affiliation":[{"name":"Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Y X Rachel","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Statistics, Stanford University, Stanford, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Galip Gurkan","family":"Yardimci","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington, WA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William","family":"Stafford Noble","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington, WA, USA"},{"name":"Department of Computer Science and Engineering, University of Washington, WA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3084-2287","authenticated-orcid":false,"given":"Anshul","family":"Kundaje","sequence":"additional","affiliation":[{"name":"Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA"},{"name":"Department of Computer Science, Stanford University, Stanford, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,3,15]]},"reference":[{"key":"2023012712481574900_bty164-B1","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 Res"},{"key":"2023012712481574900_bty164-B2","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1016\/j.stem.2016.04.004","article-title":"Local genome topology can exhibit an incompletely rewired 3D-folding state during somatic cell reprogramming","volume":"18","author":"Beagan","year":"2016","journal-title":"Cell Stem Cell"},{"key":"2023012712481574900_bty164-B3","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1186\/s13059-016-0992-2","article-title":"CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data","volume":"17","author":"Cairns","year":"2016","journal-title":"Genome Biol"},{"key":"2023012712481574900_bty164-B4","doi-asserted-by":"crossref","first-page":"15454","DOI":"10.1038\/ncomms15454","article-title":"An integrated model for detecting significant chromatin interactions from high-resolution Hi-C data","volume":"8","author":"Carty","year":"2017","journal-title":"Nat. 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