{"id":"https://openalex.org/W7118577116","doi":"https://doi.org/10.1093/bib/bbaf704","title":"iceDP: identifying inter-chromatin engagement via density peaks clustering algorithm","display_name":"iceDP: identifying inter-chromatin engagement via density peaks clustering algorithm","publication_year":2025,"publication_date":"2025-12-18","ids":{"openalex":"https://openalex.org/W7118577116","doi":"https://doi.org/10.1093/bib/bbaf704","pmid":"https://pubmed.ncbi.nlm.nih.gov/41499218"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf704","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf704","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bib/bbaf704","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5122169316","display_name":"Ruhai Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I159948400","display_name":"Jinan University","ror":"https://ror.org/02xe5ns62","country_code":"CN","type":"education","lineage":["https://openalex.org/I159948400"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Ruhai Chen","raw_affiliation_strings":["Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hong Kong-Macau Institute of CNS Regeneration, Department of Chemistry, Jinan University , No. 601, Huangpu Avenue West, Guangzhou, Guangdong 510632 ,"],"raw_orcid":"https://orcid.org/0000-0001-5907-9954","affiliations":[{"raw_affiliation_string":"Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hong Kong-Macau Institute of CNS Regeneration, Department of Chemistry, Jinan University , No. 601, Huangpu Avenue West, Guangzhou, Guangdong 510632 ,","institution_ids":["https://openalex.org/I159948400"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100297377","display_name":"JieKai CHEN","orcid":null},"institutions":[{"id":"https://openalex.org/I2802148028","display_name":"Guangzhou Institutes of Biomedicine and Health","ror":"https://ror.org/02c31t502","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2802148028"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiekai Chen","raw_affiliation_strings":["Center for Biomedical Digital Science, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190 Kaiyuan Avenue, Guangzhou, Guangdong 510530 ,"],"raw_orcid":"https://orcid.org/0000-0001-5168-7074","affiliations":[{"raw_affiliation_string":"Center for Biomedical Digital Science, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , No. 190 Kaiyuan Avenue, Guangzhou, Guangdong 510530 ,","institution_ids":["https://openalex.org/I2802148028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104277001","display_name":"Lingling Shi","orcid":null},"institutions":[{"id":"https://openalex.org/I159948400","display_name":"Jinan University","ror":"https://ror.org/02xe5ns62","country_code":"CN","type":"education","lineage":["https://openalex.org/I159948400"]},{"id":"https://openalex.org/I199305430","display_name":"Nantong University","ror":"https://ror.org/02afcvw97","country_code":"CN","type":"education","lineage":["https://openalex.org/I199305430"]},{"id":"https://openalex.org/I4210162753","display_name":"First Affiliated Hospital of Jinan University","ror":"https://ror.org/05d5vvz89","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210162753"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lingling Shi","raw_affiliation_strings":["Co-innovation Center of Neuro-regeneration, Nantong University , No. 9, Seyuan Road, Nantong, Jiangsu 226019 ,","Department of Psychiatry, the First Affiliated Hospital of Jinan University , No. 613, Huangpu Avenue West, Guangzhou, Guangdong 510632 ,","Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hong Kong-Macau Institute of CNS Regeneration, Department of Chemistry, Jinan University , No. 601, Huangpu Avenue West, Guangzhou, Guangdong 510632 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Co-innovation Center of Neuro-regeneration, Nantong University , No. 9, Seyuan Road, Nantong, Jiangsu 226019 ,","institution_ids":["https://openalex.org/I199305430"]},{"raw_affiliation_string":"Department of Psychiatry, the First Affiliated Hospital of Jinan University , No. 613, Huangpu Avenue West, Guangzhou, Guangdong 510632 ,","institution_ids":["https://openalex.org/I4210162753"]},{"raw_affiliation_string":"Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hong Kong-Macau Institute of CNS Regeneration, Department of Chemistry, Jinan University , No. 601, Huangpu Avenue West, Guangzhou, Guangdong 510632 ,","institution_ids":["https://openalex.org/I159948400"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003413234","display_name":"Jun He","orcid":"https://orcid.org/0000-0002-1479-285X"},"institutions":[{"id":"https://openalex.org/I4210090512","display_name":"Guangzhou Experimental Station","ror":"https://ror.org/00f2c2516","country_code":"CN","type":"facility","lineage":["https://openalex.org/I107851509","https://openalex.org/I4210090512","https://openalex.org/I4210127390","https://openalex.org/I4210151987"]},{"id":"https://openalex.org/I4210145292","display_name":"Shenzhen University Health Science Center","ror":"https://ror.org/04yjbr930","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210145292"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiangping He","raw_affiliation_strings":["Faculty of Life and Health Sciences , Shenzhen University of Advanced Technology, No. 1 Gongchang Road, Shenzhen 518107,","Guangzhou National Laboratory , No. 9 Xinghuan Road, 510320\uff0cGuangzhou,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Life and Health Sciences , Shenzhen University of Advanced Technology, No. 1 Gongchang Road, Shenzhen 518107,","institution_ids":["https://openalex.org/I4210145292"]},{"raw_affiliation_string":"Guangzhou National Laboratory , No. 9 Xinghuan Road, 510320\uff0cGuangzhou,","institution_ids":["https://openalex.org/I4210090512"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5122169316"],"corresponding_institution_ids":["https://openalex.org/I159948400"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.62846051,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9067000150680542,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9067000150680542,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.02889999933540821,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10184","display_name":"Plant Molecular Biology Research","score":0.006500000134110451,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.8428999781608582},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6586999893188477},{"id":"https://openalex.org/keywords/chromosome-conformation-capture","display_name":"Chromosome conformation capture","score":0.578499972820282},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4499000012874603},{"id":"https://openalex.org/keywords/chromosome","display_name":"Chromosome","score":0.41200000047683716},{"id":"https://openalex.org/keywords/range","display_name":"Range (aeronautics)","score":0.3407000005245209},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3100999891757965}],"concepts":[{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.8428999781608582},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6586999893188477},{"id":"https://openalex.org/C93946551","wikidata":"https://www.wikidata.org/wiki/Q5113914","display_name":"Chromosome conformation capture","level":5,"score":0.578499972820282},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5662000179290771},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5412999987602234},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4499000012874603},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4138000011444092},{"id":"https://openalex.org/C30481170","wikidata":"https://www.wikidata.org/wiki/Q37748","display_name":"Chromosome","level":3,"score":0.41200000047683716},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.3407000005245209},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33880001306533813},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3100999891757965},{"id":"https://openalex.org/C145103041","wikidata":"https://www.wikidata.org/wiki/Q1151519","display_name":"Embryonic stem cell","level":3,"score":0.3091000020503998},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.3068999946117401},{"id":"https://openalex.org/C67258246","wikidata":"https://www.wikidata.org/wiki/Q5065897","display_name":"ChIA-PET","level":5,"score":0.30320000648498535},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.30300000309944153},{"id":"https://openalex.org/C134320426","wikidata":"https://www.wikidata.org/wiki/Q901026","display_name":"Chromatin immunoprecipitation","level":5,"score":0.259799987077713},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.2540999948978424},{"id":"https://openalex.org/C3018263672","wikidata":"https://www.wikidata.org/wiki/Q1296251","display_name":"Efficient algorithm","level":2,"score":0.2531000077724457},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.25130000710487366}],"mesh":[{"descriptor_ui":"D000066450","descriptor_name":"Mouse Embryonic Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000066450","descriptor_name":"Mouse Embryonic Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000066450","descriptor_name":"Mouse Embryonic Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000066450","descriptor_name":"Mouse Embryonic Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000098430","descriptor_name":"Clustering Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098430","descriptor_name":"Clustering Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098430","descriptor_name":"Clustering Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098430","descriptor_name":"Clustering Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf704","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf704","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41499218","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41499218","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12777978","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12777978/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf704","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf704","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1992682476","display_name":null,"funder_award_id":"2024YFA1802300","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G2120846650","display_name":null,"funder_award_id":"32570664","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2338753390","display_name":null,"funder_award_id":"82471562","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3479153688","display_name":null,"funder_award_id":"2023B1515020111","funder_id":"https://openalex.org/F4320337111","funder_display_name":"Basic and Applied Basic Research Foundation of Guangdong Province"},{"id":"https://openalex.org/G5966987922","display_name":null,"funder_award_id":"2025A1515012444","funder_id":"https://openalex.org/F4320321921","funder_display_name":"Natural Science Foundation of Guangdong Province"},{"id":"https://openalex.org/G6190039103","display_name":null,"funder_award_id":"32370856","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6347846689","display_name":null,"funder_award_id":"2023YFF1204701","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G6891310715","display_name":null,"funder_award_id":"2024A1515010690","funder_id":"https://openalex.org/F4320321921","funder_display_name":"Natural Science Foundation of Guangdong Province"},{"id":"https://openalex.org/G690265133","display_name":null,"funder_award_id":"81771222","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7190675542","display_name":null,"funder_award_id":"32225012","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8867091002","display_name":null,"funder_award_id":"2019A1515011316","funder_id":"https://openalex.org/F4320321921","funder_display_name":"Natural Science Foundation of Guangdong Province"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321921","display_name":"Natural Science Foundation of Guangdong Province","ror":null},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320337111","display_name":"Basic and Applied Basic Research Foundation of Guangdong Province","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":62,"referenced_works":["https://openalex.org/W1569301647","https://openalex.org/W1862913282","https://openalex.org/W1973860395","https://openalex.org/W1991269963","https://openalex.org/W2009576540","https://openalex.org/W2028163659","https://openalex.org/W2043024569","https://openalex.org/W2049070625","https://openalex.org/W2063124224","https://openalex.org/W2073026107","https://openalex.org/W2090037139","https://openalex.org/W2091287100","https://openalex.org/W2106880776","https://openalex.org/W2134221701","https://openalex.org/W2135204824","https://openalex.org/W2137065828","https://openalex.org/W2142270559","https://openalex.org/W2163679188","https://openalex.org/W2165835468","https://openalex.org/W2168887077","https://openalex.org/W2243544746","https://openalex.org/W2481029670","https://openalex.org/W2573731673","https://openalex.org/W2590568317","https://openalex.org/W2594764564","https://openalex.org/W2616052794","https://openalex.org/W2755246242","https://openalex.org/W2765567136","https://openalex.org/W2768603011","https://openalex.org/W2785060777","https://openalex.org/W2790140187","https://openalex.org/W2804270751","https://openalex.org/W2806123558","https://openalex.org/W2891879783","https://openalex.org/W2900583157","https://openalex.org/W2908798728","https://openalex.org/W2909545741","https://openalex.org/W2942431730","https://openalex.org/W2950195808","https://openalex.org/W2951458958","https://openalex.org/W2969310280","https://openalex.org/W2969687360","https://openalex.org/W2988126442","https://openalex.org/W2991518271","https://openalex.org/W2997518667","https://openalex.org/W3002964216","https://openalex.org/W3013167866","https://openalex.org/W3013371767","https://openalex.org/W3015099573","https://openalex.org/W3041895828","https://openalex.org/W3092475374","https://openalex.org/W3117820463","https://openalex.org/W3127763277","https://openalex.org/W3136813783","https://openalex.org/W3164028935","https://openalex.org/W4206655024","https://openalex.org/W4235139267","https://openalex.org/W4285006497","https://openalex.org/W4311100591","https://openalex.org/W4379977950","https://openalex.org/W4384928858","https://openalex.org/W4389991923"],"related_works":[],"abstract_inverted_index":{"Chromatin":[0],"topological":[1],"structure":[2],"is":[3,148],"critical":[4],"for":[5,44],"gene":[6],"regulation.":[7],"Hi-C":[8,95],"based":[9],"experiments":[10],"have":[11,21],"significantly":[12],"advanced":[13],"our":[14],"understanding":[15],"chromatin":[16,155],"organization.":[17],"Numerous":[18],"computational":[19],"tools":[20,43],"been":[22],"developed":[23],"to":[24,34,72,86,93,133],"identify":[25,73],"various":[26],"structural":[27],"levels":[28],"of":[29,41,154],"chromatin,":[30],"ranging":[31],"from":[32],"compartments":[33],"loops.":[35],"However,":[36],"there":[37],"remains":[38],"a":[39,63,151],"lack":[40],"specialized":[42],"identifying":[45],"non-homologous":[46],"inter-chromatin":[47],"contacts":[48],"(NHCCs),":[49],"which":[50],"play":[51],"important":[52],"roles":[53],"in":[54,106,117],"chromosome":[55],"territories.":[56],"In":[57],"this":[58],"study,":[59],"we":[60],"present":[61],"iceDP,":[62],"tool":[64],"that":[65],"leverages":[66],"the":[67,142],"Density":[68],"Peaks":[69],"clustering":[70],"algorithm":[71],"local":[74],"high-density":[75],"regions":[76,80],"within":[77],"inter-chromatin.":[78],"These":[79],"undergo":[81],"two":[82],"subsequent":[83],"filtering":[84],"steps":[85],"eliminate":[87],"obvious":[88],"false":[89],"positives.":[90],"When":[91],"applied":[92],"three":[94],"datasets,":[96],"iceDP":[97,124,137,147],"accurately":[98],"identified":[99],"known":[100],"NHCCs,":[101],"including":[102,159],"olfactory":[103,108],"receptor":[104],"genes":[105,116],"mature":[107],"sensory":[109],"neurons":[110],"and":[111,135,164,169],"Polycomb":[112],"repressive":[113],"complex-regulated":[114],"developmental":[115],"mouse":[118],"embryonic":[119],"stem":[120],"cells":[121],"(mESCs).":[122],"Notably,":[123],"also":[125],"uncovered":[126],"previously":[127],"unreported":[128],"transcriptionally":[129],"active":[130],"NHCCs.":[131],"Compared":[132],"diffHiC":[134],"FitHiC,":[136],"exhibited":[138],"superior":[139],"performance":[140],"with":[141,150],"highest":[143],"positive":[144],"rate.":[145],"Moreover,":[146],"compatible":[149],"wide":[152],"range":[153],"conformation":[156],"capture":[157],"techniques,":[158],"in-situ":[160],"Hi-C,":[161],"Micro-C,":[162],"HiChIP,":[163],"BL-HiC,":[165],"demonstrating":[166],"its":[167],"versatility":[168],"utility.":[170]},"counts_by_year":[],"updated_date":"2026-01-08T20:10:11.968330","created_date":"2026-01-08T00:00:00"}