{"id":"https://openalex.org/W4392112960","doi":"https://doi.org/10.1093/bib/bbae044","title":"Chromosome structure modeling tools and their evaluation in bacteria","display_name":"Chromosome structure modeling tools and their evaluation in bacteria","publication_year":2024,"publication_date":"2024-01-22","ids":{"openalex":"https://openalex.org/W4392112960","doi":"https://doi.org/10.1093/bib/bbae044","pmid":"https://pubmed.ncbi.nlm.nih.gov/38385874"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae044","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae044","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae044/56728474/bbae044.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae044/56728474/bbae044.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5112131321","display_name":"Tong Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]},{"id":"https://openalex.org/I4210157677","display_name":"Hubei Academy of Agricultural Sciences","ror":"https://ror.org/04qg81z57","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210157677"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tong Liu","raw_affiliation_strings":["College of Informatics, Huazhong Agricultural University , , Wuhan 430070 , China","Hubei Key Laboratory of Agricultural Bioinformatics , , Wuhan 430070 , China","Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Informatics, Huazhong Agricultural University , , Wuhan 430070 , China","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"Hubei Key Laboratory of Agricultural Bioinformatics , , Wuhan 430070 , China","institution_ids":["https://openalex.org/I4210157677"]},{"raw_affiliation_string":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108847909","display_name":"Qin-Tian Qiu","orcid":null},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]},{"id":"https://openalex.org/I4210157677","display_name":"Hubei Academy of Agricultural Sciences","ror":"https://ror.org/04qg81z57","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210157677"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qin-Tian Qiu","raw_affiliation_strings":["College of Informatics, Huazhong Agricultural University , , Wuhan 430070 , China","Hubei Key Laboratory of Agricultural Bioinformatics , , Wuhan 430070 , China","Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Informatics, Huazhong Agricultural University , , Wuhan 430070 , China","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"Hubei Key Laboratory of Agricultural Bioinformatics , , Wuhan 430070 , China","institution_ids":["https://openalex.org/I4210157677"]},{"raw_affiliation_string":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086191036","display_name":"Kang-Jian Hua","orcid":null},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]},{"id":"https://openalex.org/I4210157677","display_name":"Hubei Academy of Agricultural Sciences","ror":"https://ror.org/04qg81z57","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210157677"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kang-Jian Hua","raw_affiliation_strings":["College of Informatics, Huazhong Agricultural University , , Wuhan 430070 , China","Hubei Key Laboratory of Agricultural Bioinformatics , , Wuhan 430070 , China","Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Informatics, Huazhong Agricultural University , , Wuhan 430070 , China","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"Hubei Key Laboratory of Agricultural Bioinformatics , , Wuhan 430070 , China","institution_ids":["https://openalex.org/I4210157677"]},{"raw_affiliation_string":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013464460","display_name":"Bin\u2010Guang Ma","orcid":"https://orcid.org/0000-0002-9531-6643"},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]},{"id":"https://openalex.org/I4210157677","display_name":"Hubei Academy of Agricultural Sciences","ror":"https://ror.org/04qg81z57","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210157677"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Bin-Guang Ma","raw_affiliation_strings":["College of Informatics, Huazhong Agricultural University , , Wuhan 430070 , China","Hubei Key Laboratory of Agricultural Bioinformatics , , Wuhan 430070 , China","Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China"],"raw_orcid":"https://orcid.org/0000-0002-9531-6643","affiliations":[{"raw_affiliation_string":"College of Informatics, Huazhong Agricultural University , , Wuhan 430070 , China","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"Hubei Key Laboratory of Agricultural Bioinformatics , , Wuhan 430070 , China","institution_ids":["https://openalex.org/I4210157677"]},{"raw_affiliation_string":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China","institution_ids":["https://openalex.org/I204823248"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5013464460"],"corresponding_institution_ids":["https://openalex.org/I204823248","https://openalex.org/I4210157677"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.211,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.52341068,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"25","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9973999857902527,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9944000244140625,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/caulobacter-crescentus","display_name":"Caulobacter crescentus","score":0.8365623950958252},{"id":"https://openalex.org/keywords/chromosome","display_name":"Chromosome","score":0.6870967149734497},{"id":"https://openalex.org/keywords/circular-bacterial-chromosome","display_name":"Circular bacterial chromosome","score":0.5406003594398499},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5322707891464233},{"id":"https://openalex.org/keywords/bacterial-artificial-chromosome","display_name":"Bacterial artificial chromosome","score":0.5258553624153137},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5227211117744446},{"id":"https://openalex.org/keywords/constraint","display_name":"Constraint (computer-aided design)","score":0.4560222327709198},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4454715847969055},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.31479310989379883},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.24560397863388062},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22980231046676636},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.10996592044830322},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.0901576578617096},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08794260025024414}],"concepts":[{"id":"https://openalex.org/C2778767192","wikidata":"https://www.wikidata.org/wiki/Q2943106","display_name":"Caulobacter crescentus","level":4,"score":0.8365623950958252},{"id":"https://openalex.org/C30481170","wikidata":"https://www.wikidata.org/wiki/Q37748","display_name":"Chromosome","level":3,"score":0.6870967149734497},{"id":"https://openalex.org/C58167604","wikidata":"https://www.wikidata.org/wiki/Q5121654","display_name":"Circular bacterial chromosome","level":4,"score":0.5406003594398499},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5322707891464233},{"id":"https://openalex.org/C182901222","wikidata":"https://www.wikidata.org/wiki/Q419061","display_name":"Bacterial artificial chromosome","level":4,"score":0.5258553624153137},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5227211117744446},{"id":"https://openalex.org/C2776036281","wikidata":"https://www.wikidata.org/wiki/Q48769818","display_name":"Constraint (computer-aided design)","level":2,"score":0.4560222327709198},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4454715847969055},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31479310989379883},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.24560397863388062},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22980231046676636},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.10996592044830322},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0901576578617096},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08794260025024414},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C2993175405","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Bacterial protein","level":3,"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":"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":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002876","descriptor_name":"Chromosomes, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002876","descriptor_name":"Chromosomes, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002876","descriptor_name":"Chromosomes, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002876","descriptor_name":"Chromosomes, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002876","descriptor_name":"Chromosomes, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011387","descriptor_name":"Prokaryotic Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011387","descriptor_name":"Prokaryotic Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011387","descriptor_name":"Prokaryotic Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011387","descriptor_name":"Prokaryotic Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011387","descriptor_name":"Prokaryotic Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022004","descriptor_name":"Chromosome Structures","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D022004","descriptor_name":"Chromosome Structures","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D022004","descriptor_name":"Chromosome Structures","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D022004","descriptor_name":"Chromosome Structures","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D022004","descriptor_name":"Chromosome Structures","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae044","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae044","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae044/56728474/bbae044.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38385874","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38385874","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:10883143","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10883143","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10883143/pdf/bbae044.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae044","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae044","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae044/56728474/bbae044.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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/G8053634594","display_name":null,"funder_award_id":"31971184","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":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4392112960.pdf"},"referenced_works_count":95,"referenced_works":["https://openalex.org/W144339231","https://openalex.org/W1531468991","https://openalex.org/W1605334561","https://openalex.org/W1654084651","https://openalex.org/W1910205447","https://openalex.org/W1963866954","https://openalex.org/W1973654613","https://openalex.org/W1974463674","https://openalex.org/W1978496023","https://openalex.org/W1981861937","https://openalex.org/W1991232135","https://openalex.org/W1994536648","https://openalex.org/W2000448104","https://openalex.org/W2001576815","https://openalex.org/W2009653511","https://openalex.org/W2012842652","https://openalex.org/W2013898056","https://openalex.org/W2014031166","https://openalex.org/W2015128055","https://openalex.org/W2033766178","https://openalex.org/W2045864964","https://openalex.org/W2051798038","https://openalex.org/W2053871313","https://openalex.org/W2053929098","https://openalex.org/W2056568469","https://openalex.org/W2056900498","https://openalex.org/W2070021921","https://openalex.org/W2073026107","https://openalex.org/W2082852695","https://openalex.org/W2090037139","https://openalex.org/W2097557319","https://openalex.org/W2101249563","https://openalex.org/W2102526163","https://openalex.org/W2102707800","https://openalex.org/W2107935250","https://openalex.org/W2110174983","https://openalex.org/W2123596692","https://openalex.org/W2137940450","https://openalex.org/W2141913814","https://openalex.org/W2141952839","https://openalex.org/W2148450265","https://openalex.org/W2152825437","https://openalex.org/W2163965181","https://openalex.org/W2165780114","https://openalex.org/W2167319364","https://openalex.org/W2168999925","https://openalex.org/W2169371330","https://openalex.org/W2192926654","https://openalex.org/W2296334390","https://openalex.org/W2321233811","https://openalex.org/W2338496560","https://openalex.org/W2416744721","https://openalex.org/W2418338772","https://openalex.org/W2430846749","https://openalex.org/W2521980880","https://openalex.org/W2552583736","https://openalex.org/W2559000278","https://openalex.org/W2569095710","https://openalex.org/W2570093425","https://openalex.org/W2580178967","https://openalex.org/W2584813526","https://openalex.org/W2593043670","https://openalex.org/W2698669422","https://openalex.org/W2731989040","https://openalex.org/W2738924259","https://openalex.org/W2765567136","https://openalex.org/W2775377317","https://openalex.org/W2783742719","https://openalex.org/W2790578518","https://openalex.org/W2790671385","https://openalex.org/W2801885583","https://openalex.org/W2806062033","https://openalex.org/W2912635573","https://openalex.org/W2915396787","https://openalex.org/W2945135442","https://openalex.org/W2949391446","https://openalex.org/W2951074257","https://openalex.org/W2952117848","https://openalex.org/W2977744221","https://openalex.org/W2980442871","https://openalex.org/W3039284858","https://openalex.org/W3042402374","https://openalex.org/W3087813728","https://openalex.org/W3088572354","https://openalex.org/W3095576387","https://openalex.org/W3118481910","https://openalex.org/W3134081044","https://openalex.org/W3184944554","https://openalex.org/W4206996735","https://openalex.org/W4210727401","https://openalex.org/W4213457705","https://openalex.org/W4231020221","https://openalex.org/W4280582334","https://openalex.org/W4310376024","https://openalex.org/W6653777321"],"related_works":["https://openalex.org/W4318482186","https://openalex.org/W3127279613","https://openalex.org/W2128999749","https://openalex.org/W2104967054","https://openalex.org/W2134826931","https://openalex.org/W2113979580","https://openalex.org/W2974256862","https://openalex.org/W2073025457","https://openalex.org/W2004599440","https://openalex.org/W1584505729"],"abstract_inverted_index":{"The":[0],"three-dimensional":[1],"(3D)":[2],"structure":[3,26,37,51,68,139],"of":[4,17],"bacterial":[5,35,122,137],"chromosomes":[6],"is":[7,41],"crucial":[8],"for":[9,121,136],"understanding":[10],"chromosome":[11,19,36,50,66,138],"function.":[12,39],"With":[13],"the":[14,24,49,56,117],"growing":[15],"availability":[16],"high-throughput":[18],"conformation":[20],"capture":[21],"(3C/Hi-C)":[22],"data,":[23],"3D":[25,58,67,118],"reconstruction":[27,52,69,119,140],"algorithms":[28,70,92,120],"have":[29,45],"become":[30],"powerful":[31],"tools":[32,53],"to":[33,44,54],"study":[34],"and":[38,71,85,96,104],"It":[40],"highly":[42],"desired":[43],"a":[46],"recommendation":[47],"on":[48,75,126],"facilitate":[55],"prokaryotic":[57],"genomics.":[59],"In":[60],"this":[61],"work,":[62],"we":[63,130],"review":[64],"existing":[65],"classify":[72],"them":[73],"based":[74],"their":[76],"underlying":[77],"computational":[78],"models":[79],"into":[80],"two":[81],"categories:":[82],"constraint-based":[83],"modeling":[84],"thermodynamics-based":[86],"modeling.":[87],"We":[88,112],"briefly":[89,131],"compare":[90],"these":[91],"utilizing":[93],"3C/Hi-C":[94],"datasets":[95],"fluorescence":[97],"microscopy":[98],"data":[99],"obtained":[100],"from":[101],"Escherichia":[102],"coli":[103],"Caulobacter":[105],"crescentus,":[106],"as":[107,109],"well":[108],"simulated":[110],"datasets.":[111],"discuss":[113],"current":[114],"challenges":[115],"in":[116],"chromosomes,":[123],"primarily":[124],"focusing":[125],"software":[127],"usability.":[128],"Finally,":[129],"prospect":[132],"future":[133],"research":[134],"directions":[135],"algorithms.":[141]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
