{"id":"https://openalex.org/W4323353603","doi":"https://doi.org/10.1093/bib/bbad072","title":"A comprehensive review of bioinformatics tools for chromatin loop calling","display_name":"A comprehensive review of bioinformatics tools for chromatin loop calling","publication_year":2023,"publication_date":"2023-03-01","ids":{"openalex":"https://openalex.org/W4323353603","doi":"https://doi.org/10.1093/bib/bbad072","pmid":"https://pubmed.ncbi.nlm.nih.gov/36882016"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad072","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad072","pdf_url":"https://academic.oup.com/bib/article-pdf/24/2/bbad072/49560694/bbad072.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/24/2/bbad072/49560694/bbad072.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010244714","display_name":"Li Liu","orcid":"https://orcid.org/0000-0003-0535-4361"},"institutions":[{"id":"https://openalex.org/I150229711","display_name":"University of Electronic Science and Technology of China","ror":"https://ror.org/04qr3zq92","country_code":"CN","type":"education","lineage":["https://openalex.org/I150229711"]},{"id":"https://openalex.org/I4210123686","display_name":"Quzhou University","ror":"https://ror.org/024nfx323","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210123686"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Li Liu","raw_affiliation_strings":["University of Electronic Science and Technology of China Yangtze Delta Region Institute (Quzhou), , Quzhou 324003 , China"],"raw_orcid":"https://orcid.org/0000-0003-0535-4361","affiliations":[{"raw_affiliation_string":"University of Electronic Science and Technology of China Yangtze Delta Region Institute (Quzhou), , Quzhou 324003 , China","institution_ids":["https://openalex.org/I4210123686","https://openalex.org/I150229711"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091011429","display_name":"Kaiyuan Han","orcid":"https://orcid.org/0000-0003-0801-3271"},"institutions":[{"id":"https://openalex.org/I150229711","display_name":"University of Electronic Science and Technology of China","ror":"https://ror.org/04qr3zq92","country_code":"CN","type":"education","lineage":["https://openalex.org/I150229711"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kaiyuan Han","raw_affiliation_strings":["University of Electronic Science and Technology of China Center for Informational Biology, School of Life Science and Technology, , Chengdu 610054 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Electronic Science and Technology of China Center for Informational Biology, School of Life Science and Technology, , Chengdu 610054 , China","institution_ids":["https://openalex.org/I150229711"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101297351","display_name":"Huimin Sun","orcid":"https://orcid.org/0000-0002-5532-0883"},"institutions":[{"id":"https://openalex.org/I2722730","display_name":"Inner Mongolia University","ror":"https://ror.org/0106qb496","country_code":"CN","type":"education","lineage":["https://openalex.org/I2722730"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huimin Sun","raw_affiliation_strings":["Inner Mongolia University School of Physical Science and Technology, , Hohhot 010021 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inner Mongolia University School of Physical Science and Technology, , Hohhot 010021 , China","institution_ids":["https://openalex.org/I2722730"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101891640","display_name":"Lu Han","orcid":"https://orcid.org/0000-0003-4228-768X"},"institutions":[{"id":"https://openalex.org/I2722730","display_name":"Inner Mongolia University","ror":"https://ror.org/0106qb496","country_code":"CN","type":"education","lineage":["https://openalex.org/I2722730"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lu Han","raw_affiliation_strings":["Inner Mongolia University School of Physical Science and Technology, , Hohhot 010021 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inner Mongolia University School of Physical Science and Technology, , Hohhot 010021 , China","institution_ids":["https://openalex.org/I2722730"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030507718","display_name":"Dong Gao","orcid":"https://orcid.org/0000-0003-0425-5134"},"institutions":[{"id":"https://openalex.org/I150229711","display_name":"University of Electronic Science and Technology of China","ror":"https://ror.org/04qr3zq92","country_code":"CN","type":"education","lineage":["https://openalex.org/I150229711"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dong Gao","raw_affiliation_strings":["University of Electronic Science and Technology of China Center for Informational Biology, School of Life Science and Technology, , Chengdu 610054 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Electronic Science and Technology of China Center for Informational Biology, School of Life Science and Technology, , Chengdu 610054 , China","institution_ids":["https://openalex.org/I150229711"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071202132","display_name":"Qilemuge Xi","orcid":null},"institutions":[{"id":"https://openalex.org/I2722730","display_name":"Inner Mongolia University","ror":"https://ror.org/0106qb496","country_code":"CN","type":"education","lineage":["https://openalex.org/I2722730"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qilemuge Xi","raw_affiliation_strings":["Inner Mongolia University State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, , Hohhot 010070 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inner Mongolia University State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, , Hohhot 010070 , China","institution_ids":["https://openalex.org/I2722730"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062026165","display_name":"Lirong Zhang","orcid":"https://orcid.org/0000-0001-7466-1029"},"institutions":[{"id":"https://openalex.org/I2722730","display_name":"Inner Mongolia University","ror":"https://ror.org/0106qb496","country_code":"CN","type":"education","lineage":["https://openalex.org/I2722730"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Lirong Zhang","raw_affiliation_strings":["Inner Mongolia University School of Physical Science and Technology, , Hohhot 010021 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inner Mongolia University School of Physical Science and Technology, , Hohhot 010021 , China","institution_ids":["https://openalex.org/I2722730"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041539298","display_name":"Hao Lin","orcid":"https://orcid.org/0000-0001-6265-2862"},"institutions":[{"id":"https://openalex.org/I150229711","display_name":"University of Electronic Science and Technology of China","ror":"https://ror.org/04qr3zq92","country_code":"CN","type":"education","lineage":["https://openalex.org/I150229711"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Hao Lin","raw_affiliation_strings":["University of Electronic Science and Technology of China Center for Informational Biology, School of Life Science and Technology, , Chengdu 610054 , China"],"raw_orcid":"https://orcid.org/0000-0001-6265-2862","affiliations":[{"raw_affiliation_string":"University of Electronic Science and Technology of China Center for Informational Biology, School of Life Science and Technology, , Chengdu 610054 , China","institution_ids":["https://openalex.org/I150229711"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5041539298","https://openalex.org/A5062026165"],"corresponding_institution_ids":["https://openalex.org/I150229711","https://openalex.org/I2722730"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.5991,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.82854531,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"24","issue":"2","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":0.9998999834060669,"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":0.9998999834060669,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9944000244140625,"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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9932000041007996,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7491213083267212},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.6246723532676697},{"id":"https://openalex.org/keywords/loop","display_name":"Loop (graph theory)","score":0.5320319533348083},{"id":"https://openalex.org/keywords/completeness","display_name":"Completeness (order theory)","score":0.5169579386711121},{"id":"https://openalex.org/keywords/variety","display_name":"Variety (cybernetics)","score":0.4248015582561493},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.42159461975097656},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.380041241645813},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3210378885269165},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.29212018847465515},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1523972749710083},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10325956344604492},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.089599609375}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7491213083267212},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.6246723532676697},{"id":"https://openalex.org/C184670325","wikidata":"https://www.wikidata.org/wiki/Q512604","display_name":"Loop (graph theory)","level":2,"score":0.5320319533348083},{"id":"https://openalex.org/C17231256","wikidata":"https://www.wikidata.org/wiki/Q5156540","display_name":"Completeness (order theory)","level":2,"score":0.5169579386711121},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.4248015582561493},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.42159461975097656},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.380041241645813},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3210378885269165},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29212018847465515},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1523972749710083},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10325956344604492},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.089599609375},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"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":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D002875","descriptor_name":"Chromosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbad072","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad072","pdf_url":"https://academic.oup.com/bib/article-pdf/24/2/bbad072/49560694/bbad072.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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:36882016","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36882016","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}],"best_oa_location":{"id":"doi:10.1093/bib/bbad072","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad072","pdf_url":"https://academic.oup.com/bib/article-pdf/24/2/bbad072/49560694/bbad072.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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/G1303004423","display_name":null,"funder_award_id":"62172078","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1437965613","display_name":null,"funder_award_id":"62272085","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7595737103","display_name":null,"funder_award_id":"61962041","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8896417337","display_name":null,"funder_award_id":"61961031","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4323353603.pdf","grobid_xml":"https://content.openalex.org/works/W4323353603.grobid-xml"},"referenced_works_count":150,"referenced_works":["https://openalex.org/W1565385417","https://openalex.org/W1605145036","https://openalex.org/W1660678623","https://openalex.org/W1790765732","https://openalex.org/W1831401007","https://openalex.org/W1859117663","https://openalex.org/W1862913282","https://openalex.org/W1915573037","https://openalex.org/W1965863160","https://openalex.org/W1970831058","https://openalex.org/W1973062929","https://openalex.org/W1985621639","https://openalex.org/W2001576815","https://openalex.org/W2011463791","https://openalex.org/W2014677321","https://openalex.org/W2018436502","https://openalex.org/W2031057223","https://openalex.org/W2049633694","https://openalex.org/W2053323016","https://openalex.org/W2058560100","https://openalex.org/W2064727535","https://openalex.org/W2065006553","https://openalex.org/W2070021921","https://openalex.org/W2078059415","https://openalex.org/W2082912595","https://openalex.org/W2090037139","https://openalex.org/W2097798909","https://openalex.org/W2102368172","https://openalex.org/W2105778988","https://openalex.org/W2111880238","https://openalex.org/W2114104545","https://openalex.org/W2123227077","https://openalex.org/W2125263315","https://openalex.org/W2125636389","https://openalex.org/W2128106349","https://openalex.org/W2130116522","https://openalex.org/W2133083672","https://openalex.org/W2134907628","https://openalex.org/W2141407136","https://openalex.org/W2142270559","https://openalex.org/W2145174846","https://openalex.org/W2152531901","https://openalex.org/W2163412235","https://openalex.org/W2166760304","https://openalex.org/W2171808845","https://openalex.org/W2182733429","https://openalex.org/W2185693210","https://openalex.org/W2258346454","https://openalex.org/W2303393194","https://openalex.org/W2345951097","https://openalex.org/W2429188508","https://openalex.org/W2481029670","https://openalex.org/W2491201136","https://openalex.org/W2519241029","https://openalex.org/W2523285811","https://openalex.org/W2530292798","https://openalex.org/W2551092411","https://openalex.org/W2553838260","https://openalex.org/W2597274540","https://openalex.org/W2600121124","https://openalex.org/W2616052794","https://openalex.org/W2625231465","https://openalex.org/W2755353730","https://openalex.org/W2761883725","https://openalex.org/W2789833802","https://openalex.org/W2800968671","https://openalex.org/W2804657285","https://openalex.org/W2805705799","https://openalex.org/W2806123558","https://openalex.org/W2883453789","https://openalex.org/W2887206273","https://openalex.org/W2888206159","https://openalex.org/W2898577086","https://openalex.org/W2914156189","https://openalex.org/W2914971047","https://openalex.org/W2945038365","https://openalex.org/W2949773289","https://openalex.org/W2950020758","https://openalex.org/W2950960548","https://openalex.org/W2951184828","https://openalex.org/W2951196462","https://openalex.org/W2951448241","https://openalex.org/W2951458958","https://openalex.org/W2951858712","https://openalex.org/W2952664869","https://openalex.org/W2952947531","https://openalex.org/W2953369069","https://openalex.org/W2969310280","https://openalex.org/W2973702082","https://openalex.org/W2984969073","https://openalex.org/W2989713781","https://openalex.org/W2991042659","https://openalex.org/W2991248607","https://openalex.org/W2991283206","https://openalex.org/W3002964216","https://openalex.org/W3003909932","https://openalex.org/W3009259903","https://openalex.org/W3010189944","https://openalex.org/W3010968994","https://openalex.org/W3013977756","https://openalex.org/W3016357852","https://openalex.org/W3016522754","https://openalex.org/W3017323102","https://openalex.org/W3017665189","https://openalex.org/W3037015477","https://openalex.org/W3041895828","https://openalex.org/W3042010229","https://openalex.org/W3044680723","https://openalex.org/W3082989829","https://openalex.org/W3086683161","https://openalex.org/W3087813728","https://openalex.org/W3091034669","https://openalex.org/W3106437999","https://openalex.org/W3112525717","https://openalex.org/W3112889838","https://openalex.org/W3120569827","https://openalex.org/W3125832420","https://openalex.org/W3126733217","https://openalex.org/W3127438792","https://openalex.org/W3127763277","https://openalex.org/W3134809854","https://openalex.org/W3136813783","https://openalex.org/W3188463051","https://openalex.org/W3194691506","https://openalex.org/W3198409039","https://openalex.org/W3198741502","https://openalex.org/W3200314447","https://openalex.org/W3206351987","https://openalex.org/W3207880742","https://openalex.org/W3212499419","https://openalex.org/W4200214589","https://openalex.org/W4206413332","https://openalex.org/W4220688679","https://openalex.org/W4225259708","https://openalex.org/W4225836315","https://openalex.org/W4226185665","https://openalex.org/W4229940030","https://openalex.org/W4281869774","https://openalex.org/W4285006497","https://openalex.org/W4286203308","https://openalex.org/W4362523504","https://openalex.org/W6680991062","https://openalex.org/W6731376107","https://openalex.org/W6774179507","https://openalex.org/W6781007629","https://openalex.org/W6800385033","https://openalex.org/W6800946031","https://openalex.org/W6803112162","https://openalex.org/W6805666649","https://openalex.org/W6839025469"],"related_works":["https://openalex.org/W4237277701","https://openalex.org/W4286930115","https://openalex.org/W2032233321","https://openalex.org/W3121970507","https://openalex.org/W24774503","https://openalex.org/W3004891660","https://openalex.org/W2110028391","https://openalex.org/W2969540308","https://openalex.org/W54497855","https://openalex.org/W217960748"],"abstract_inverted_index":{"Precisely":[0],"calling":[1],"chromatin":[2,19,29],"loops":[3,30,54,142],"has":[4],"profound":[5],"implications":[6],"for":[7,89,155],"further":[8,144],"analysis":[9],"of":[10,37,45,74,85,113,125,129],"gene":[11],"regulation":[12],"and":[13,104,111,118,143],"disease":[14],"mechanisms.":[15],"Technological":[16],"advances":[17],"in":[18,31,42],"conformation":[20],"capture":[21],"(3C)":[22],"assays":[23],"make":[24],"it":[25],"possible":[26],"to":[27,51,65,77,121,140,159],"identify":[28],"the":[32,56,86,96,105,109,122,136],"genome.":[33],"However,":[34],"a":[35,72],"variety":[36],"experimental":[38,102],"protocols":[39],"have":[40,62],"resulted":[41],"different":[43,101],"levels":[44],"biases,":[46],"which":[47],"require":[48],"distinct":[49],"methods":[50],"call":[52,141],"true":[53],"from":[55],"background.":[57],"Although":[58],"many":[59],"bioinformatics":[60,156],"tools":[61,88],"been":[63],"developed":[64],"address":[66],"this":[67,150],"problem,":[68],"there":[69],"is":[70,152],"still":[71],"lack":[73],"special":[75],"introduction":[76],"loop-calling":[78,87,162],"algorithms.":[79,107,163],"This":[80],"review":[81],"provides":[82],"an":[83],"overview":[84],"various":[90],"3C-based":[91],"techniques.":[92],"We":[93],"first":[94],"discuss":[95],"background":[97],"biases":[98],"produced":[99],"by":[100],"techniques":[103],"denoising":[106],"Then,":[108],"completeness":[110],"priority":[112],"each":[114],"tool":[115],"are":[116],"categorized":[117],"summarized":[119],"according":[120],"data":[123],"source":[124],"application.":[126],"The":[127],"summary":[128],"these":[130],"works":[131],"can":[132],"help":[133],"researchers":[134],"select":[135],"most":[137],"appropriate":[138],"method":[139],"perform":[145],"downstream":[146],"analysis.":[147],"In":[148],"addition,":[149],"survey":[151],"also":[153],"useful":[154],"scientists":[157],"aiming":[158],"develop":[160],"new":[161]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
