{"id":"https://openalex.org/W4382630876","doi":"https://doi.org/10.1093/bioinformatics/btad236","title":"Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities","display_name":"Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities","publication_year":2023,"publication_date":"2023-06-01","ids":{"openalex":"https://openalex.org/W4382630876","doi":"https://doi.org/10.1093/bioinformatics/btad236","pmid":"https://pubmed.ncbi.nlm.nih.gov/37387148"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad236","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad236","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/Supplement_1/i47/50741508/btad236.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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/bioinformatics/article-pdf/39/Supplement_1/i47/50741508/btad236.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100341248","display_name":"Qi Wang","orcid":"https://orcid.org/0000-0002-0134-1726"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qi Wang","raw_affiliation_strings":["Systems, Synthetic, and Physical Biology (SSPB) Graduate Program, Rice University , Houston, TX 77005, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Systems, Synthetic, and Physical Biology (SSPB) Graduate Program, Rice University , Houston, TX 77005, United States","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025825738","display_name":"Michael Nute","orcid":"https://orcid.org/0000-0003-4129-6525"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Nute","raw_affiliation_strings":["Department of Computer Science, Rice University , Houston, TX 77005, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Rice University , Houston, TX 77005, United States","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054369332","display_name":"Todd J. Treangen","orcid":"https://orcid.org/0000-0002-3760-564X"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Todd J Treangen","raw_affiliation_strings":["Department of Computer Science, Rice University , Houston, TX 77005, United States"],"raw_orcid":"https://orcid.org/0000-0002-3760-564X","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Rice University , Houston, TX 77005, United States","institution_ids":["https://openalex.org/I74775410"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5054369332"],"corresponding_institution_ids":["https://openalex.org/I74775410"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":0.5528,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.61358243,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"39","issue":"Supplement_1","first_page":"i47","last_page":"i56"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.44359999895095825,"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":0.44359999895095825,"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/T11288","display_name":"Clostridium difficile and Clostridium perfringens research","score":0.3788999915122986,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"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/T10897","display_name":"Antibiotic Use and Resistance","score":0.03020000085234642,"subfield":{"id":"https://openalex.org/subfields/2402","display_name":"Applied Microbiology and Biotechnology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.6090871095657349},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.39440277218818665},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3161669969558716}],"concepts":[{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6090871095657349},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.39440277218818665},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3161669969558716},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003424","descriptor_name":"Crohn Disease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003424","descriptor_name":"Crohn Disease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003424","descriptor_name":"Crohn Disease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad236","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad236","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/Supplement_1/i47/50741508/btad236.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37387148","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37387148","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":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10311314","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10311314","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10311314/pdf/btad236.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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad236","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad236","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/Supplement_1/i47/50741508/btad236.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","score":0.7400000095367432,"display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G143167659","display_name":null,"funder_award_id":"P01\u2010AI152999","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G1734186762","display_name":null,"funder_award_id":"R21NS106640","funder_id":"https://openalex.org/F4320337359","funder_display_name":"National Institute of Neurological Disorders and Stroke"},{"id":"https://openalex.org/G2239731442","display_name":"MIM: Elucidating the Rules of Cooperation and Resiliency in Microbial Communities through Stochastic Graph Grammars","funder_award_id":"2126387","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2640905883","display_name":null,"funder_award_id":"T15LM007093","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G2996460108","display_name":"Project 3: Functional Microbiome and Host Signatures in Transition from Commensal to pathogen","funder_award_id":"5p01ai152999-04","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3511783147","display_name":"NLM Research Training Program in Biomedical Informatics and Data Science for Predoctoral and Postdoctoral Fellows","funder_award_id":"5t15lm007093-32","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8942470891","display_name":"The role of the gut microbiome in the neuropathology of traumatic brain injury","funder_award_id":"5r21ns106640-03","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310133","display_name":"Rice University","ror":"https://ror.org/008zs3103"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"},{"id":"https://openalex.org/F4320337359","display_name":"National Institute of Neurological Disorders and Stroke","ror":"https://ror.org/01s5ya894"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4382630876.pdf","grobid_xml":"https://content.openalex.org/works/W4382630876.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1831504143","https://openalex.org/W2040720350","https://openalex.org/W2058508948","https://openalex.org/W2118816584","https://openalex.org/W2126452774","https://openalex.org/W2133290123","https://openalex.org/W2159954944","https://openalex.org/W2225916722","https://openalex.org/W2331416186","https://openalex.org/W2409622550","https://openalex.org/W2559597060","https://openalex.org/W2745757065","https://openalex.org/W2750588931","https://openalex.org/W2771485505","https://openalex.org/W2773368689","https://openalex.org/W2778827740","https://openalex.org/W2792021903","https://openalex.org/W2804854320","https://openalex.org/W2889311756","https://openalex.org/W2895474878","https://openalex.org/W2897558112","https://openalex.org/W2900189879","https://openalex.org/W2904450188","https://openalex.org/W2914355353","https://openalex.org/W2920387023","https://openalex.org/W2920934181","https://openalex.org/W2922150224","https://openalex.org/W2945412501","https://openalex.org/W2947189704","https://openalex.org/W2948246500","https://openalex.org/W2949773212","https://openalex.org/W2952564192","https://openalex.org/W3002175424","https://openalex.org/W3003257820","https://openalex.org/W3012081453","https://openalex.org/W3034922513","https://openalex.org/W3037682416","https://openalex.org/W3039446139","https://openalex.org/W3080728491","https://openalex.org/W3083321322","https://openalex.org/W3103145119","https://openalex.org/W4200055542","https://openalex.org/W4200489997","https://openalex.org/W4280615884","https://openalex.org/W6747216723"],"related_works":["https://openalex.org/W2748952813","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/W2117258802"],"abstract_inverted_index":{"MOTIVATION:":[0],"Interactions":[1],"among":[2],"microbes":[3],"within":[4,29,54],"microbial":[5,27,41,180],"communities":[6],"have":[7],"been":[8],"shown":[9],"to":[10,36,93,132,149,157],"play":[11],"crucial":[12],"roles":[13],"in":[14,81,142],"human":[15],"health.":[16],"In":[17,115],"spite":[18],"of":[19,24,60,69],"recent":[20],"progress,":[21],"low-level":[22],"knowledge":[23],"bacteria":[25],"driving":[26,52],"interactions":[28,53],"microbiomes":[30],"remains":[31],"unknown,":[32],"limiting":[33],"our":[34],"ability":[35],"fully":[37],"decipher":[38],"and":[39,65,105,129,162,188],"control":[40,74],"communities.":[42],"RESULTS:":[43],"We":[44,153],"present":[45],"a":[46,111,150,175],"novel":[47,176],"approach":[48,177],"for":[49,178],"identifying":[50,121],"species":[51,71,123,168],"microbiomes.":[55],"Bakdrive":[56,76,156,173,185],"infers":[57],"ecological":[58,113],"networks":[59],"given":[61],"metagenomic":[62,90],"sequencing":[63,91],"samples":[64,92,128],"identifies":[66],"minimum":[67],"sets":[68],"driver":[70,95,122,167],"(MDS)":[72],"using":[73],"theory.":[75],"has":[77],"three":[78],"key":[79],"innovations":[80],"this":[82],"space:":[83],"(i)":[84],"it":[85,98,107],"leverages":[86],"inherent":[87],"information":[88],"from":[89,125],"identify":[94],"species,":[96],"(ii)":[97],"explicitly":[99],"takes":[100],"host-specific":[101],"variation":[102],"into":[103],"consideration,":[104],"(iii)":[106],"does":[108],"not":[109],"require":[110],"known":[112],"network.":[114],"extensive":[116],"simulated":[117],"data,":[118],"we":[119,136],"demonstrate":[120],"identified":[124],"healthy":[126,151],"donor":[127],"introducing":[130],"them":[131],"the":[133,139],"disease":[134,164],"samples,":[135],"can":[137],"restore":[138],"gut":[140],"microbiome":[141],"recurrent":[143],"Clostridioides":[144],"difficile":[145],"(rCDI)":[146],"infection":[147],"patients":[148],"state.":[152],"also":[154],"applied":[155],"two":[158],"real":[159],"datasets,":[160],"rCDI":[161],"Crohn's":[163],"patients,":[165],"uncovering":[166],"consistent":[169],"with":[170],"previous":[171],"work.":[172],"represents":[174],"capturing":[179],"interactions.":[181],"AVAILABILITY":[182],"AND":[183],"IMPLEMENTATION:":[184],"is":[186],"open-source":[187],"available":[189],"at:":[190],"https://gitlab.com/treangenlab/bakdrive.":[191]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}