{"id":"https://openalex.org/W2949773212","doi":"https://doi.org/10.1186/s12859-019-2915-1","title":"Difficulty in inferring microbial community structure based on co-occurrence network approaches","display_name":"Difficulty in inferring microbial community structure based on co-occurrence network approaches","publication_year":2019,"publication_date":"2019-06-13","ids":{"openalex":"https://openalex.org/W2949773212","doi":"https://doi.org/10.1186/s12859-019-2915-1","mag":"2949773212","pmid":"https://pubmed.ncbi.nlm.nih.gov/31195956"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-2915-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2915-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-019-2915-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-019-2915-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078094527","display_name":"Hokuto Hirano","orcid":null},"institutions":[{"id":"https://openalex.org/I207014233","display_name":"Kyushu Institute of Technology","ror":"https://ror.org/02278tr80","country_code":"JP","type":"education","lineage":["https://openalex.org/I207014233"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hokuto Hirano","raw_affiliation_strings":["Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, 820-8502, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, 820-8502, Japan","institution_ids":["https://openalex.org/I207014233"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013426338","display_name":"Kazuhiro Takemoto","orcid":"https://orcid.org/0000-0002-6355-1366"},"institutions":[{"id":"https://openalex.org/I207014233","display_name":"Kyushu Institute of Technology","ror":"https://ror.org/02278tr80","country_code":"JP","type":"education","lineage":["https://openalex.org/I207014233"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kazuhiro Takemoto","raw_affiliation_strings":["Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, 820-8502, Japan. takemoto@bio.kyutech.ac.jp","Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, 820-8502, Japan"],"raw_orcid":"https://orcid.org/0000-0002-6355-1366","affiliations":[{"raw_affiliation_string":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, 820-8502, Japan. takemoto@bio.kyutech.ac.jp","institution_ids":["https://openalex.org/I207014233"]},{"raw_affiliation_string":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, 820-8502, Japan","institution_ids":["https://openalex.org/I207014233"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":9.5737,"has_fulltext":true,"cited_by_count":172,"citation_normalized_percentile":{"value":0.98758022,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"20","issue":"1","first_page":"329","last_page":"329"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.6660000085830688,"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/T10066","display_name":"Gut microbiota and health","score":0.6660000085830688,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.21119999885559082,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12134","display_name":"Insect symbiosis and bacterial influences","score":0.029999999329447746,"subfield":{"id":"https://openalex.org/subfields/1109","display_name":"Insect Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5819723606109619},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5374467968940735},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.523106575012207},{"id":"https://openalex.org/keywords/co-occurrence","display_name":"Co-occurrence","score":0.5230715870857239},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.38124433159828186},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37020206451416016},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3304627537727356},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3208909034729004},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19696027040481567},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1269221305847168},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.08465132117271423}],"concepts":[{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5819723606109619},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5374467968940735},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.523106575012207},{"id":"https://openalex.org/C154290570","wikidata":"https://www.wikidata.org/wiki/Q1756768","display_name":"Co-occurrence","level":2,"score":0.5230715870857239},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.38124433159828186},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37020206451416016},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3304627537727356},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3208909034729004},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19696027040481567},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1269221305847168},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08465132117271423}],"mesh":[{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-019-2915-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2915-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-019-2915-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31195956","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31195956","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:76a1217589944912b49ff9ab3c82d32e","is_oa":false,"landing_page_url":"https://doaj.org/article/76a1217589944912b49ff9ab3c82d32e","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 20, Iss 1, Pp 1-14 (2019)","raw_type":"article"},{"id":"pmh:oai:irdb.nii.ac.jp:01216:0004073013","is_oa":true,"landing_page_url":"https://kyutech.repo.nii.ac.jp/records/6058","pdf_url":null,"source":{"id":"https://openalex.org/S7407056385","display_name":"Institutional Repositories DataBase (IRDB)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184597095","host_organization_name":"National Institute of Informatics","host_organization_lineage":["https://openalex.org/I184597095"],"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":"BMC Bioinformatics","raw_type":"journal article"},{"id":"pmh:oai:kyutech.repo.nii.ac.jp:00006058","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"VoR"},{"id":"pmh:oai:pubmedcentral.nih.gov:6567618","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6567618","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-2915-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2915-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-019-2915-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","score":0.6899999976158142,"display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G160385374","display_name":null,"funder_award_id":"JP17H04703","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2949773212.pdf","grobid_xml":"https://content.openalex.org/works/W2949773212.grobid-xml"},"referenced_works_count":52,"referenced_works":["https://openalex.org/W1556776055","https://openalex.org/W1581963595","https://openalex.org/W1864161604","https://openalex.org/W1891411045","https://openalex.org/W1966327575","https://openalex.org/W1971061059","https://openalex.org/W2011312755","https://openalex.org/W2015077700","https://openalex.org/W2044712133","https://openalex.org/W2055754079","https://openalex.org/W2058927331","https://openalex.org/W2066918346","https://openalex.org/W2069994241","https://openalex.org/W2083278075","https://openalex.org/W2106399600","https://openalex.org/W2112090702","https://openalex.org/W2112976607","https://openalex.org/W2113977541","https://openalex.org/W2124637492","https://openalex.org/W2126452774","https://openalex.org/W2136737152","https://openalex.org/W2147637673","https://openalex.org/W2163056825","https://openalex.org/W2165700458","https://openalex.org/W2261537921","https://openalex.org/W2280650020","https://openalex.org/W2301173600","https://openalex.org/W2340637042","https://openalex.org/W2423440312","https://openalex.org/W2529100136","https://openalex.org/W2558664061","https://openalex.org/W2614665773","https://openalex.org/W2745757065","https://openalex.org/W2753353801","https://openalex.org/W2754579667","https://openalex.org/W2762906919","https://openalex.org/W2767110145","https://openalex.org/W2771045365","https://openalex.org/W2773368689","https://openalex.org/W2775040279","https://openalex.org/W2775315818","https://openalex.org/W2783192416","https://openalex.org/W2800234325","https://openalex.org/W2809621815","https://openalex.org/W2810660502","https://openalex.org/W2895043543","https://openalex.org/W2897946500","https://openalex.org/W2900697674","https://openalex.org/W2910384792","https://openalex.org/W2950714739","https://openalex.org/W3037000643","https://openalex.org/W4239135575"],"related_works":["https://openalex.org/W2415545834","https://openalex.org/W2069695727","https://openalex.org/W2150084125","https://openalex.org/W2118505788","https://openalex.org/W1802639773","https://openalex.org/W1972196578","https://openalex.org/W1490878237","https://openalex.org/W1542823905","https://openalex.org/W2990314835","https://openalex.org/W4254166511"],"abstract_inverted_index":{"BACKGROUND:":[0],"Co-occurrence":[1,32,149],"networks-ecological":[2],"associations":[3,38],"between":[4],"sampled":[5],"populations":[6],"of":[7,49,52,83,114,130,204,216,219,226],"microbial":[8,23,70,88,232],"communities":[9,163,173],"inferred":[10],"from":[11,16],"taxonomic":[12],"composition":[13],"data":[14,121],"obtained":[15],"high-throughput":[17],"sequencing":[18],"techniques-are":[19],"widely":[20,99],"used":[21,42,100],"in":[22,105,142,161,170,189,193],"ecology.":[24],"Several":[25],"co-occurrence":[26,53,116,183],"network":[27,33,54,117,150,184],"methods":[28,34,55,85,101,118,132,137,222,229],"have":[29],"been":[30],"proposed.":[31],"only":[35],"infer":[36],"ecological":[37,89,106,233],"and":[39,223],"are":[40,72],"often":[41],"to":[43,109,125],"discuss":[44],"species":[45,191],"interactions.":[46],"However,":[47,196],"validity":[48,82,218],"this":[50],"application":[51],"is":[56],"currently":[57],"debated.":[58],"In":[59],"particular,":[60],"they":[61,208],"simply":[62],"evaluate":[63],"using":[64],"parametric":[65],"statistical":[66],"models,":[67],"even":[68],"though":[69],"compositions":[71],"determined":[73],"through":[74,91],"population":[75],"dynamics.":[76],"RESULTS:":[77],"We":[78,94],"comprehensively":[79],"evaluated":[80,95],"the":[81,112,115,139,158,197,202,210,217,224],"common":[84],"for":[86,212,230],"inferring":[87,231],"networks":[90,146],"realistic":[92],"simulations.":[93],"how":[96],"correctly":[97],"nine":[98],"describe":[102],"interaction":[103,140,155,159],"patterns":[104,141,160],"communities.":[107],"Contrary":[108],"previous":[110],"studies,":[111],"performance":[113,151],"on":[119],"compositional":[120],"was":[122],"almost":[123],"equal":[124],"or":[126],"less":[127],"than":[128],"that":[129,182],"classical":[131],"(e.g.,":[133],"Pearson's":[134],"correlation).":[135],"The":[136],"described":[138],"dense":[143],"and/or":[144],"heterogeneous":[145],"rather":[147],"inadequately.":[148],"also":[152],"depended":[153],"upon":[154],"types;":[156],"specifically,":[157],"competitive":[162],"were":[164,174],"relatively":[165,175],"accurately":[166],"predicted":[167],"while":[168],"those":[169],"predator-prey":[171],"(parasitic)":[172],"inadequately":[176],"predicted.":[177],"CONCLUSIONS:":[178],"Our":[179],"findings":[180],"indicated":[181],"approaches":[185],"may":[186],"be":[187],"insufficient":[188],"interpreting":[190],"interactions":[192],"microbiome":[194],"studies.":[195],"results":[198],"do":[199],"not":[200],"diminish":[201],"importance":[203],"these":[205,220],"approaches.":[206],"Rather,":[207],"highlight":[209],"need":[211],"further":[213],"careful":[214],"evaluation":[215],"much-used":[221],"development":[225],"more":[227],"suitable":[228],"networks.":[234]},"counts_by_year":[{"year":2026,"cited_by_count":9},{"year":2025,"cited_by_count":18},{"year":2024,"cited_by_count":23},{"year":2023,"cited_by_count":24},{"year":2022,"cited_by_count":37},{"year":2021,"cited_by_count":33},{"year":2020,"cited_by_count":26},{"year":2019,"cited_by_count":2}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}