{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,27]],"date-time":"2025-03-27T18:18:16Z","timestamp":1743099496240,"version":"3.40.3"},"publisher-location":"Cham","reference-count":13,"publisher":"Springer Nature Switzerland","isbn-type":[{"type":"print","value":"9783031451690"},{"type":"electronic","value":"9783031451706"}],"license":[{"start":{"date-parts":[[2023,1,1]],"date-time":"2023-01-01T00:00:00Z","timestamp":1672531200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2023,1,1]],"date-time":"2023-01-01T00:00:00Z","timestamp":1672531200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023]]},"DOI":"10.1007\/978-3-031-45170-6_91","type":"book-chapter","created":{"date-parts":[[2023,11,14]],"date-time":"2023-11-14T13:03:02Z","timestamp":1699966982000},"page":"871-878","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["ccLoopER: Deep Prediction of\u00a0CTCF and\u00a0cohesin Mediated Chromatin looping Using DNA Transformer Model"],"prefix":"10.1007","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4825-1901","authenticated-orcid":false,"given":"Anup Kumar","family":"Halder","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4981-8746","authenticated-orcid":false,"given":"Abhishek","family":"Agarwal","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7357-3315","authenticated-orcid":false,"given":"Sevastianos","family":"Korsak","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6103-5915","authenticated-orcid":false,"given":"Karolina","family":"Jodkowska","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3840-7610","authenticated-orcid":false,"given":"Dariusz","family":"Plewczynski","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,12,4]]},"reference":[{"issue":"2","key":"91_CR1","doi-asserted-by":"crossref","first-page":"155","DOI":"10.15302\/J-QB-022-0315","volume":"11","author":"M Chili\u0144ski","year":"2023","unstructured":"Chili\u0144ski, M., Halder, A.K., Plewczynski, D.: Prediction of chromatin looping using deep hybrid learning (DHL). Quant. Biol. 11(2), 155\u2013162 (2023)","journal-title":"Quant. Biol."},{"issue":"6","key":"91_CR2","doi-asserted-by":"publisher","first-page":"1110","DOI":"10.1016\/j.cell.2016.02.007","volume":"164","author":"J Dekker","year":"2016","unstructured":"Dekker, J., Mirny, L.: The 3D genome as moderator of chromosomal communication. Cell 164(6), 1110\u20131121 (2016)","journal-title":"Cell"},{"issue":"7398","key":"91_CR3","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1038\/nature11082","volume":"485","author":"JR Dixon","year":"2012","unstructured":"Dixon, J.R., et al.: Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485(7398), 376\u2013380 (2012)","journal-title":"Nature"},{"issue":"1","key":"91_CR4","doi-asserted-by":"publisher","first-page":"1337","DOI":"10.1038\/s41467-021-21583-9","volume":"12","author":"R Fang","year":"2021","unstructured":"Fang, R., et al.: Comprehensive analysis of single cell ATAC-seq data with SnapATAC. Nat. Commun. 12(1), 1337 (2021)","journal-title":"Nat. Commun."},{"issue":"12","key":"91_CR5","doi-asserted-by":"publisher","first-page":"1345","DOI":"10.1038\/cr.2016.137","volume":"26","author":"R Fang","year":"2016","unstructured":"Fang, R., et al.: Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. Cell Res. 26(12), 1345\u20131348 (2016)","journal-title":"Cell Res."},{"issue":"6384","key":"91_CR6","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1126\/science.aar7831","volume":"360","author":"M Ganji","year":"2018","unstructured":"Ganji, M., et al.: Real-time imaging of DNA loop extrusion by condensin. Science 360(6384), 102\u2013105 (2018)","journal-title":"Science"},{"issue":"15","key":"91_CR7","doi-asserted-by":"publisher","first-page":"2112","DOI":"10.1093\/bioinformatics\/btab083","volume":"37","author":"Y Ji","year":"2021","unstructured":"Ji, Y., Zhou, Z., Liu, H., Davuluri, R.V.: DNABERT: pre-trained bidirectional encoder representations from transformers model for DNA-language in genome. Bioinformatics 37(15), 2112\u20132120 (2021)","journal-title":"Bioinformatics"},{"key":"91_CR8","unstructured":"Kenton, J.D.M.W.C., Toutanova, L.K.: BERT: pre-training of deep bidirectional transformers for language understanding. In: Proceedings of naacL-HLT, vol. 1, p. 2 (2019)"},{"issue":"1\u20132","key":"91_CR9","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1016\/j.cell.2011.12.014","volume":"148","author":"G Li","year":"2012","unstructured":"Li, G., et al.: Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148(1\u20132), 84\u201398 (2012)","journal-title":"Cell"},{"key":"91_CR10","doi-asserted-by":"crossref","unstructured":"Lieberman-Aiden, E., et al.: Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326(5950), 289\u2013293 (2009)","DOI":"10.1126\/science.1181369"},{"issue":"11","key":"91_CR11","doi-asserted-by":"publisher","first-page":"919","DOI":"10.1038\/nmeth.3999","volume":"13","author":"MR Mumbach","year":"2016","unstructured":"Mumbach, M.R., et al.: Hichip: efficient and sensitive analysis of protein-directed genome architecture. Nat. Methods 13(11), 919\u2013922 (2016)","journal-title":"Nat. Methods"},{"issue":"7","key":"91_CR12","doi-asserted-by":"publisher","first-page":"1665","DOI":"10.1016\/j.cell.2014.11.021","volume":"159","author":"SS Rao","year":"2014","unstructured":"Rao, S.S., et al.: A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159(7), 1665\u20131680 (2014)","journal-title":"Cell"},{"issue":"7","key":"91_CR13","doi-asserted-by":"publisher","first-page":"1611","DOI":"10.1016\/j.cell.2015.11.024","volume":"163","author":"Z Tang","year":"2015","unstructured":"Tang, Z., et al.: CTCF-mediated human 3D genome architecture reveals chromatin topology for transcription. Cell 163(7), 1611\u20131627 (2015)","journal-title":"Cell"}],"container-title":["Lecture Notes in Computer Science","Pattern Recognition and Machine Intelligence"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-031-45170-6_91","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,25]],"date-time":"2023-12-25T20:11:48Z","timestamp":1703535108000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-031-45170-6_91"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023]]},"ISBN":["9783031451690","9783031451706"],"references-count":13,"URL":"https:\/\/doi.org\/10.1007\/978-3-031-45170-6_91","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2023]]},"assertion":[{"value":"4 December 2023","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"PReMI","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Conference on Pattern Recognition and Machine Intelligence","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Kolkata","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"India","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2023","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"12 December 2023","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"15 December 2023","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"10","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"premi2023","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"https:\/\/www.isical.ac.in\/~premi23\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Double-blind","order":1,"name":"type","label":"Type","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"EquinOCS","order":2,"name":"conference_management_system","label":"Conference Management System","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"311","order":3,"name":"number_of_submissions_sent_for_review","label":"Number of Submissions Sent for Review","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"91","order":4,"name":"number_of_full_papers_accepted","label":"Number of Full Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"0","order":5,"name":"number_of_short_papers_accepted","label":"Number of Short Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"29% - The value is computed by the equation \"Number of Full Papers Accepted \/ Number of Submissions Sent for Review * 100\" and then rounded to a whole number.","order":6,"name":"acceptance_rate_of_full_papers","label":"Acceptance Rate of Full Papers","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"3","order":7,"name":"average_number_of_reviews_per_paper","label":"Average Number of Reviews per Paper","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"3","order":8,"name":"average_number_of_papers_per_reviewer","label":"Average Number of Papers per Reviewer","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"Yes","order":9,"name":"external_reviewers_involved","label":"External Reviewers Involved","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}}]}}