{"id":"https://openalex.org/W2587287902","doi":"https://doi.org/10.1093/bioinformatics/btx062","title":"cooccurNet: an R package for co-occurrence network construction and analysis","display_name":"cooccurNet: an R package for co-occurrence network construction and analysis","publication_year":2017,"publication_date":"2017-02-08","ids":{"openalex":"https://openalex.org/W2587287902","doi":"https://doi.org/10.1093/bioinformatics/btx062","mag":"2587287902","pmid":"https://pubmed.ncbi.nlm.nih.gov/28174895"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx062","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx062","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102910308","display_name":"Yuanqiang Zou","orcid":"https://orcid.org/0000-0003-3293-5858"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuanqiang Zou","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University, Changsha, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University, Changsha, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101439426","display_name":"Zhiqiang Wu","orcid":"https://orcid.org/0000-0001-9227-3062"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhiqiang Wu","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University, Changsha, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University, Changsha, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080371739","display_name":"Lizong Deng","orcid":"https://orcid.org/0000-0001-9314-262X"},"institutions":[{"id":"https://openalex.org/I200296433","display_name":"Chinese Academy of Medical Sciences & Peking Union Medical College","ror":"https://ror.org/02drdmm93","country_code":"CN","type":"education","lineage":["https://openalex.org/I200296433"]},{"id":"https://openalex.org/I4210122727","display_name":"Suzhou Institute of Systems Medicine","ror":"https://ror.org/02szepc22","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210122727","https://openalex.org/I4210141683"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lizong Deng","raw_affiliation_strings":["Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China","Suzhou Institute of Systems Medicine, Suzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China","institution_ids":["https://openalex.org/I200296433"]},{"raw_affiliation_string":"Suzhou Institute of Systems Medicine, Suzhou, China","institution_ids":["https://openalex.org/I4210122727"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047692460","display_name":"Aiping Wu","orcid":"https://orcid.org/0000-0002-5869-651X"},"institutions":[{"id":"https://openalex.org/I200296433","display_name":"Chinese Academy of Medical Sciences & Peking Union Medical College","ror":"https://ror.org/02drdmm93","country_code":"CN","type":"education","lineage":["https://openalex.org/I200296433"]},{"id":"https://openalex.org/I4210122727","display_name":"Suzhou Institute of Systems Medicine","ror":"https://ror.org/02szepc22","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210122727","https://openalex.org/I4210141683"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Aiping Wu","raw_affiliation_strings":["Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China","Suzhou Institute of Systems Medicine, Suzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China","institution_ids":["https://openalex.org/I200296433"]},{"raw_affiliation_string":"Suzhou Institute of Systems Medicine, Suzhou, China","institution_ids":["https://openalex.org/I4210122727"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081439040","display_name":"Fan Wu","orcid":"https://orcid.org/0000-0001-9392-2597"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fan Wu","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University, Changsha, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University, Changsha, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078793726","display_name":"Kenli Li","orcid":"https://orcid.org/0000-0002-2635-7716"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kenli Li","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University, Changsha, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University, Changsha, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101823373","display_name":"Taijiao Jiang","orcid":"https://orcid.org/0000-0002-6071-0122"},"institutions":[{"id":"https://openalex.org/I200296433","display_name":"Chinese Academy of Medical Sciences & Peking Union Medical College","ror":"https://ror.org/02drdmm93","country_code":"CN","type":"education","lineage":["https://openalex.org/I200296433"]},{"id":"https://openalex.org/I4210122727","display_name":"Suzhou Institute of Systems Medicine","ror":"https://ror.org/02szepc22","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210122727","https://openalex.org/I4210141683"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Taijiao Jiang","raw_affiliation_strings":["Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China","Suzhou Institute of Systems Medicine, Suzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China","institution_ids":["https://openalex.org/I200296433"]},{"raw_affiliation_string":"Suzhou Institute of Systems Medicine, Suzhou, China","institution_ids":["https://openalex.org/I4210122727"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037335167","display_name":"Yousong Peng","orcid":"https://orcid.org/0000-0002-5482-9506"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yousong Peng","raw_affiliation_strings":["College of Biology, Hunan University, Changsha, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Biology, Hunan University, Changsha, China","institution_ids":["https://openalex.org/I16609230"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5037335167","https://openalex.org/A5101823373"],"corresponding_institution_ids":["https://openalex.org/I16609230","https://openalex.org/I200296433","https://openalex.org/I4210122727"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.3279,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.57855202,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"33","issue":"12","first_page":"1881","last_page":"1882"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.19840000569820404,"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":0.19840000569820404,"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/T10167","display_name":"Influenza Virus Research Studies","score":0.12150000035762787,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10064","display_name":"Complex Network Analysis Techniques","score":0.11299999803304672,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6230283975601196},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.5314592123031616},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.4947316348552704},{"id":"https://openalex.org/keywords/network-analysis","display_name":"Network analysis","score":0.48398566246032715},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.32467374205589294},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.22378283739089966},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.11394745111465454}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6230283975601196},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.5314592123031616},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.4947316348552704},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.48398566246032715},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.32467374205589294},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.22378283739089966},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.11394745111465454},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009975","descriptor_name":"Orthomyxoviridae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009975","descriptor_name":"Orthomyxoviridae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009975","descriptor_name":"Orthomyxoviridae","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btx062","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx062","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28174895","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28174895","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.47999998927116394,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320323137","display_name":"Chinese Academy of Medical Sciences","ror":"https://ror.org/03cve4549"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":9,"referenced_works":["https://openalex.org/W1509095134","https://openalex.org/W1860923284","https://openalex.org/W1973805239","https://openalex.org/W2040661539","https://openalex.org/W2095805667","https://openalex.org/W2099487753","https://openalex.org/W2139447922","https://openalex.org/W2166701319","https://openalex.org/W2345242111"],"related_works":["https://openalex.org/W4389426664","https://openalex.org/W2566205467","https://openalex.org/W3012616639","https://openalex.org/W3126000805","https://openalex.org/W3198565742","https://openalex.org/W2010064959","https://openalex.org/W2157390150","https://openalex.org/W2119742499","https://openalex.org/W1985266044","https://openalex.org/W4387011503"],"abstract_inverted_index":{"MOTIVATION:":[0],"Previously,":[1],"we":[2],"developed":[3],"a":[4,60],"computational":[5],"model":[6],"to":[7,15],"identify":[8],"genomic":[9],"co-occurrence":[10,56,70,82],"networks":[11],"that":[12],"was":[13],"applied":[14],"capture":[16],"the":[17,81,95],"coevolution":[18],"patterns":[19],"within":[20],"genomes":[21],"of":[22,30,44,48],"influenza":[23],"viruses.":[24],"To":[25],"facilitate":[26],"easy":[27],"public":[28],"use":[29],"this":[31],"model,":[32],"an":[33],"R":[34],"package":[35],"'cooccurNet'":[36,41,78,87],"is":[37,73,88],"presented":[38],"here.":[39],"RESULTS:":[40],"includes":[42],"functionalities":[43],"construction":[45],"and":[46,54,75],"analysis":[47],"residues":[49,65],"(e.g.":[50],"nucleotides,":[51],"amino":[52],"acids":[53],"SNPs)":[55],"network.":[57,83],"In":[58],"addition,":[59],"new":[61],"method":[62],"for":[63],"measuring":[64],"coevolution,":[66],"defined":[67],"as":[68],"residue":[69],"score":[71],"(RCOS),":[72],"proposed":[74],"implemented":[76],"in":[77],"based":[79],"on":[80,91],"AVAILABILITY":[84],"AND":[85],"IMPLEMENTATION:":[86],"publicly":[89],"available":[90,112],"CRAN":[92],"repositories":[93],"under":[94],"GPL-3":[96],"Open":[97],"Source":[98],"License":[99],"(":[100],"http://cran.r-project.org/package=cooccurNet":[101],").":[102],"CONTACT:":[103],"taijiao@ibms.pumc.edu.cn":[104],"or":[105],"pys2013@hnu.edu.cn.":[106],"SUPPLEMENTARY":[107],"INFORMATION:":[108],"Supplementary":[109],"data":[110],"are":[111],"at":[113],"Bioinformatics":[114],"online.":[115]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
