{"id":"https://openalex.org/W4400420270","doi":"https://doi.org/10.1093/bib/bbae320","title":"Spatial proximity and gene function: a new dimension in prokaryotic gene association network analysis with 3D-GeneNet","display_name":"Spatial proximity and gene function: a new dimension in prokaryotic gene association network analysis with 3D-GeneNet","publication_year":2024,"publication_date":"2024-05-23","ids":{"openalex":"https://openalex.org/W4400420270","doi":"https://doi.org/10.1093/bib/bbae320","pmid":"https://pubmed.ncbi.nlm.nih.gov/38975892"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae320","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae320","pdf_url":"https://academic.oup.com/bib/article-pdf/25/4/bbae320/58468926/bbae320.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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://academic.oup.com/bib/article-pdf/25/4/bbae320/58468926/bbae320.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100722722","display_name":"Yuan Gao","orcid":"https://orcid.org/0000-0002-5083-8624"},"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"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuan Gao","raw_affiliation_strings":["College of Veterinary Medicine, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China","Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District , Wuhan 430070, Hubei , China","State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Veterinary Medicine, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District , Wuhan 430070, Hubei , China","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076509097","display_name":"Bin Ma","orcid":"https://orcid.org/0000-0001-5744-9667"},"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"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bin Ma","raw_affiliation_strings":["College of Veterinary Medicine, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China","Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District , Wuhan 430070, Hubei , China","State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Veterinary Medicine, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District , Wuhan 430070, Hubei , China","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101336752","display_name":"Qianshuai Xu","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"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qianshuai Xu","raw_affiliation_strings":["College of Veterinary Medicine, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China","Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District , Wuhan 430070, Hubei , China","State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Veterinary Medicine, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District , Wuhan 430070, Hubei , China","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107699404","display_name":"Yuna Peng","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"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuna Peng","raw_affiliation_strings":["College of Veterinary Medicine, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China","Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District , Wuhan 430070, Hubei , China","State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Veterinary Medicine, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District , Wuhan 430070, Hubei , China","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000182682","display_name":"Huimin Gong","orcid":"https://orcid.org/0000-0001-9572-2353"},"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"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huimin Gong","raw_affiliation_strings":["College of Veterinary Medicine, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China","Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District , Wuhan 430070, Hubei , China","State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Veterinary Medicine, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District , Wuhan 430070, Hubei , China","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025070286","display_name":"Aohan Guan","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"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Aohan Guan","raw_affiliation_strings":["College of Veterinary Medicine, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China","Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District , Wuhan 430070, Hubei , China","State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Veterinary Medicine, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District , Wuhan 430070, Hubei , China","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025048843","display_name":"Kexin Hua","orcid":"https://orcid.org/0000-0003-4078-8018"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kexin Hua","raw_affiliation_strings":["Swine Genome and Breeding Team, Yazhouwan National Laboratory , No. 8 Huanjin Road, Yazhou District, Sanya City, Hainan Province 572024 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Swine Genome and Breeding Team, Yazhouwan National Laboratory , No. 8 Huanjin Road, Yazhou District, Sanya City, Hainan Province 572024 , China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023693692","display_name":"Paul R. Langford","orcid":"https://orcid.org/0000-0002-6368-4724"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Paul R Langford","raw_affiliation_strings":["Section of Paediatric Infectious Disease, Imperial College London, St Mary\u2019s Campus, Norfolk Place , London W2 1PG , United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Section of Paediatric Infectious Disease, Imperial College London, St Mary\u2019s Campus, Norfolk Place , London W2 1PG , United Kingdom","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045973583","display_name":"Hui Jin","orcid":"https://orcid.org/0000-0001-8004-2662"},"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"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Hui Jin","raw_affiliation_strings":["College of Veterinary Medicine, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China","Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District , Wuhan 430070, Hubei , China","State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China"],"raw_orcid":"https://orcid.org/0000-0001-8004-2662","affiliations":[{"raw_affiliation_string":"College of Veterinary Medicine, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District , Wuhan 430070, Hubei , China","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100710204","display_name":"Rui Luo","orcid":"https://orcid.org/0000-0002-1966-251X"},"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"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Rui Luo","raw_affiliation_strings":["College of Veterinary Medicine, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China","Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District , Wuhan 430070, Hubei , China","State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Veterinary Medicine, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District , Wuhan 430070, Hubei , China","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei , China","institution_ids":["https://openalex.org/I204823248"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5045973583","https://openalex.org/A5100710204"],"corresponding_institution_ids":["https://openalex.org/I204823248"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.1866,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.52646343,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"25","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9983000159263611,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9983000159263611,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9980999827384949,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9965999722480774,"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/computational-biology","display_name":"Computational biology","score":0.6668396592140198},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6235734224319458},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.46041232347488403},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.43650782108306885}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6668396592140198},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6235734224319458},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.46041232347488403},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.43650782108306885}],"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":"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":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae320","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae320","pdf_url":"https://academic.oup.com/bib/article-pdf/25/4/bbae320/58468926/bbae320.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38975892","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38975892","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:11229033","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11229033","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11229033/pdf/bbae320.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae320","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae320","pdf_url":"https://academic.oup.com/bib/article-pdf/25/4/bbae320/58468926/bbae320.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.4099999964237213}],"awards":[{"id":"https://openalex.org/G1179218761","display_name":null,"funder_award_id":"2662023PY005","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G3242354017","display_name":null,"funder_award_id":"CARS-41","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G4028963664","display_name":null,"funder_award_id":"BB/S019901/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G5196018293","display_name":null,"funder_award_id":"2021CFA016","funder_id":"https://openalex.org/F4320322186","funder_display_name":"Natural Science Foundation of Hubei Province"},{"id":"https://openalex.org/G6230799193","display_name":null,"funder_award_id":"2021YFD1800405","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G7807978518","display_name":null,"funder_award_id":"CARS-41","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G8070222486","display_name":"China Partnering Award: Imperial College London - China collaboration on Actinobacillus pleuropneumoniae vaccines, diagnostics, and pathogenesis","funder_award_id":"BB/S019901/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320322186","display_name":"Natural Science Foundation of Hubei Province","ror":null},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4400420270.pdf"},"referenced_works_count":64,"referenced_works":["https://openalex.org/W121381176","https://openalex.org/W1527927437","https://openalex.org/W1582212884","https://openalex.org/W1636448922","https://openalex.org/W1654084651","https://openalex.org/W1776547251","https://openalex.org/W1969353942","https://openalex.org/W1990315216","https://openalex.org/W1995117714","https://openalex.org/W2009576540","https://openalex.org/W2009653511","https://openalex.org/W2009966494","https://openalex.org/W2025853251","https://openalex.org/W2030889455","https://openalex.org/W2044426892","https://openalex.org/W2044606399","https://openalex.org/W2056482755","https://openalex.org/W2063450668","https://openalex.org/W2063571454","https://openalex.org/W2073026107","https://openalex.org/W2090037139","https://openalex.org/W2090632681","https://openalex.org/W2092533385","https://openalex.org/W2096173332","https://openalex.org/W2097798909","https://openalex.org/W2098497185","https://openalex.org/W2101125257","https://openalex.org/W2106391842","https://openalex.org/W2107109782","https://openalex.org/W2107424557","https://openalex.org/W2107717979","https://openalex.org/W2110095004","https://openalex.org/W2117994680","https://openalex.org/W2123500593","https://openalex.org/W2138865250","https://openalex.org/W2145506897","https://openalex.org/W2154529762","https://openalex.org/W2159482845","https://openalex.org/W2159675211","https://openalex.org/W2162142896","https://openalex.org/W2166755915","https://openalex.org/W2169507523","https://openalex.org/W2185236314","https://openalex.org/W2185693210","https://openalex.org/W2270112065","https://openalex.org/W2338496560","https://openalex.org/W2395289335","https://openalex.org/W2569570762","https://openalex.org/W2583187415","https://openalex.org/W2783742719","https://openalex.org/W2990771302","https://openalex.org/W3107527779","https://openalex.org/W3111355925","https://openalex.org/W3175752499","https://openalex.org/W3184675023","https://openalex.org/W4224298492","https://openalex.org/W4239919700","https://openalex.org/W4280626237","https://openalex.org/W4281832579","https://openalex.org/W4294216483","https://openalex.org/W4298400103","https://openalex.org/W4387707437","https://openalex.org/W6634734262","https://openalex.org/W6797786779"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W1971568933"],"abstract_inverted_index":{"Understanding":[0],"the":[1,30,102,105,147,172,193,218,228],"biological":[2],"functions":[3],"and":[4,19,40,61,101,132,142,207,213,221],"processes":[5],"of":[6,33,73,95,149,152,174,195,224,230],"genes,":[7],"particularly":[8],"those":[9],"not":[10,169],"yet":[11],"characterized,":[12],"is":[13,28,235],"crucial":[14],"for":[15],"advancing":[16],"molecular":[17],"biology":[18],"identifying":[20],"therapeutic":[21],"targets.":[22],"The":[23],"hypothesis":[24],"guiding":[25],"this":[26,225],"study":[27],"that":[29,51,192],"3D":[31],"proximity":[32],"genes":[34],"correlates":[35],"with":[36],"their":[37],"functional":[38,90],"interactions":[39,155],"relevance":[41],"in":[42,227],"prokaryotes.":[43],"We":[44],"introduced":[45],"3D-GeneNet,":[46],"an":[47],"innovative":[48],"software":[49],"tool":[50],"utilizes":[52],"high-throughput":[53],"sequencing":[54,212],"data":[55],"from":[56],"chromosome":[57],"conformation":[58],"capture":[59],"techniques":[60],"integrates":[62],"topological":[63,88],"metrics":[64],"to":[65,121,126,199],"construct":[66],"gene":[67,99,154,231],"association":[68,232],"networks.":[69],"Through":[70],"a":[71],"series":[72],"comparative":[74],"analyses":[75],"focused":[76],"on":[77,162],"spatial":[78],"versus":[79],"linear":[80,96,175],"distances,":[81],"we":[82],"explored":[83],"various":[84,200],"dimensions":[85],"such":[86],"as":[87],"structure,":[89],"enrichment":[91],"levels,":[92],"distribution":[93],"patterns":[94],"distances":[97],"among":[98],"pairs,":[100],"area":[103],"under":[104],"receiver":[106],"operating":[107],"characteristic":[108],"curve":[109],"by":[110,158,184],"utilizing":[111],"model":[112],"organism":[113],"Escherichia":[114],"coli":[115,164],"K-12.":[116],"Furthermore,":[117],"3D-GeneNet":[118,168,196,234],"was":[119,156],"shown":[120],"maintain":[122],"good":[123],"accuracy":[124,148,173,183],"compared":[125],"multiple":[127,135],"algorithms":[128],"(neighbourhood,":[129],"co-occurrence,":[130],"coexpression,":[131],"fusion)":[133],"across":[134],"bacteria,":[136],"including":[137,203],"E.":[138,163],"coli,":[139],"Brucella":[140],"abortus,":[141],"Vibrio":[143],"cholerae.":[144],"In":[145],"addition,":[146],"3D-GeneNet's":[150],"prediction":[151],"long-distance":[153],"identified":[157],"bacterial":[159,201],"two-hybrid":[160],"assays":[161],"K-12":[165],"MG1655,":[166],"where":[167],"only":[170],"increased":[171],"genomic":[176],"distance":[177],"tripled":[178],"but":[179],"also":[180],"achieved":[181],"60%":[182],"running":[185],"alone.":[186],"Finally,":[187],"it":[188],"can":[189],"be":[190],"concluded":[191],"applicability":[194,220],"will":[197],"extend":[198],"forms,":[202],"Gram-negative,":[204],"Gram-positive,":[205],"single-,":[206],"multi-chromosomal":[208],"bacteria":[209],"through":[210],"Hi-C":[211],"analysis.":[214],"Such":[215],"findings":[216],"highlight":[217],"broad":[219],"significant":[222],"promise":[223],"method":[226],"realm":[229],"network.":[233],"freely":[236],"accessible":[237],"at":[238],"https://github.com/gaoyuanccc/3D-GeneNet.":[239]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
