{"id":"https://openalex.org/W4404242848","doi":"https://doi.org/10.1093/bib/bbae580","title":"mbDriver: identifying driver microbes in microbial communities based on time-series microbiome data","display_name":"mbDriver: identifying driver microbes in microbial communities based on time-series microbiome data","publication_year":2024,"publication_date":"2024-09-23","ids":{"openalex":"https://openalex.org/W4404242848","doi":"https://doi.org/10.1093/bib/bbae580","pmid":"https://pubmed.ncbi.nlm.nih.gov/39526854"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae580","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae580","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bib/bbae580","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5113987311","display_name":"Xiaoxiu Tan","orcid":null},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiaoxiu Tan","raw_affiliation_strings":["Department of Bioinformatics and Biostatistics , School of Life Sciences and Biotechnology, , 800 Dongchuan Road, Minhang District, Shanghai 200240 ,","Shanghai Jiao Tong University , School of Life Sciences and Biotechnology, , 800 Dongchuan Road, Minhang District, Shanghai 200240 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Biostatistics , School of Life Sciences and Biotechnology, , 800 Dongchuan Road, Minhang District, Shanghai 200240 ,","institution_ids":[]},{"raw_affiliation_string":"Shanghai Jiao Tong University , School of Life Sciences and Biotechnology, , 800 Dongchuan Road, Minhang District, Shanghai 200240 ,","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100656874","display_name":"Feng Xue","orcid":"https://orcid.org/0000-0003-2630-8460"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Feng Xue","raw_affiliation_strings":["Department of Bioinformatics and Biostatistics , School of Life Sciences and Biotechnology, , 800 Dongchuan Road, Minhang District, Shanghai 200240 ,","Shanghai Jiao Tong University , School of Life Sciences and Biotechnology, , 800 Dongchuan Road, Minhang District, Shanghai 200240 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Biostatistics , School of Life Sciences and Biotechnology, , 800 Dongchuan Road, Minhang District, Shanghai 200240 ,","institution_ids":[]},{"raw_affiliation_string":"Shanghai Jiao Tong University , School of Life Sciences and Biotechnology, , 800 Dongchuan Road, Minhang District, Shanghai 200240 ,","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005334123","display_name":"Chenhong Zhang","orcid":"https://orcid.org/0000-0002-4462-892X"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I4391767884","display_name":"State Key Laboratory of Microbial Metabolism","ror":"https://ror.org/04t3q5q03","country_code":null,"type":"facility","lineage":["https://openalex.org/I183067930","https://openalex.org/I4391767884"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chenhong Zhang","raw_affiliation_strings":["Shanghai Jiao Tong University , School of Life Sciences and Biotechnology, , 800 Dongchuan Road, Minhang District, Shanghai 200240 ,","State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine , School of Life Sciences and Biotechnology, , 800 Dongchuan Road, Minhang District, Shanghai 200240 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University , School of Life Sciences and Biotechnology, , 800 Dongchuan Road, Minhang District, Shanghai 200240 ,","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine , School of Life Sciences and Biotechnology, , 800 Dongchuan Road, Minhang District, Shanghai 200240 ,","institution_ids":["https://openalex.org/I4391767884"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023727941","display_name":"Tao Wang","orcid":"https://orcid.org/0000-0002-1218-4017"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tao Wang","raw_affiliation_strings":["Department of Bioinformatics and Biostatistics , School of Life Sciences and Biotechnology, , 800 Dongchuan Road, Minhang District, Shanghai 200240 ,","MoE Key Lab of Artificial Intelligence , AI Institute, , 800 Dongchuan Road, Minhang District, Shanghai 200240 ,","SJTU-Yale Joint Center of Biostatistics and Data Science, Shanghai Jiao Tong University , 800 Dongchuan Road, Minhang District, Shanghai 200240 ,","Shanghai Jiao Tong University , AI Institute, , 800 Dongchuan Road, Minhang District, Shanghai 200240 ,","Shanghai Jiao Tong University , School of Life Sciences and Biotechnology, , 800 Dongchuan Road, Minhang District, Shanghai 200240 ,"],"raw_orcid":"https://orcid.org/0000-0002-1218-4017","affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Biostatistics , School of Life Sciences and Biotechnology, , 800 Dongchuan Road, Minhang District, Shanghai 200240 ,","institution_ids":[]},{"raw_affiliation_string":"MoE Key Lab of Artificial Intelligence , AI Institute, , 800 Dongchuan Road, Minhang District, Shanghai 200240 ,","institution_ids":[]},{"raw_affiliation_string":"SJTU-Yale Joint Center of Biostatistics and Data Science, Shanghai Jiao Tong University , 800 Dongchuan Road, Minhang District, Shanghai 200240 ,","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Shanghai Jiao Tong University , AI Institute, , 800 Dongchuan Road, Minhang District, Shanghai 200240 ,","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Shanghai Jiao Tong University , School of Life Sciences and Biotechnology, , 800 Dongchuan Road, Minhang District, Shanghai 200240 ,","institution_ids":["https://openalex.org/I183067930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5113987311"],"corresponding_institution_ids":["https://openalex.org/I183067930"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.4453,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.65162234,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"25","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9922999739646912,"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":0.988099992275238,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.8502583503723145},{"id":"https://openalex.org/keywords/series","display_name":"Series (stratigraphy)","score":0.6195216178894043},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5057525634765625},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4059872627258301},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.373007595539093},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28998732566833496},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.22238364815711975},{"id":"https://openalex.org/keywords/paleontology","display_name":"Paleontology","score":0.05637630820274353}],"concepts":[{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.8502583503723145},{"id":"https://openalex.org/C143724316","wikidata":"https://www.wikidata.org/wiki/Q312468","display_name":"Series (stratigraphy)","level":2,"score":0.6195216178894043},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5057525634765625},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4059872627258301},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.373007595539093},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28998732566833496},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.22238364815711975},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.05637630820274353}],"mesh":[{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae580","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae580","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39526854","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39526854","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:11551971","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11551971","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11551971/pdf/bbae580.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae580","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae580","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.7300000190734863,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G197011403","display_name":null,"funder_award_id":"12222111","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4766654764","display_name":null,"funder_award_id":"12331009","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322999","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":81,"referenced_works":["https://openalex.org/W1513618424","https://openalex.org/W1966623514","https://openalex.org/W1968512837","https://openalex.org/W1972883069","https://openalex.org/W1983314776","https://openalex.org/W2000844307","https://openalex.org/W2012994611","https://openalex.org/W2027763661","https://openalex.org/W2032356948","https://openalex.org/W2039813252","https://openalex.org/W2044712133","https://openalex.org/W2055631148","https://openalex.org/W2056036338","https://openalex.org/W2067810199","https://openalex.org/W2073924079","https://openalex.org/W2083503429","https://openalex.org/W2084624623","https://openalex.org/W2097360283","https://openalex.org/W2101420429","https://openalex.org/W2105018820","https://openalex.org/W2107279356","https://openalex.org/W2110936821","https://openalex.org/W2122825543","https://openalex.org/W2135046866","https://openalex.org/W2147637673","https://openalex.org/W2148171446","https://openalex.org/W2159482845","https://openalex.org/W2161590746","https://openalex.org/W2165108567","https://openalex.org/W2328506293","https://openalex.org/W2413154614","https://openalex.org/W2481949923","https://openalex.org/W2487770199","https://openalex.org/W2531800017","https://openalex.org/W2568184332","https://openalex.org/W2578482213","https://openalex.org/W2584072963","https://openalex.org/W2597588799","https://openalex.org/W2743502656","https://openalex.org/W2773368689","https://openalex.org/W2774486220","https://openalex.org/W2804854320","https://openalex.org/W2895474878","https://openalex.org/W2896618349","https://openalex.org/W2903406988","https://openalex.org/W2904450188","https://openalex.org/W2920387023","https://openalex.org/W2953093188","https://openalex.org/W2955323986","https://openalex.org/W2980709830","https://openalex.org/W3006380141","https://openalex.org/W3006796998","https://openalex.org/W3009727385","https://openalex.org/W3020261810","https://openalex.org/W3026078206","https://openalex.org/W3030441098","https://openalex.org/W3039446139","https://openalex.org/W3112717819","https://openalex.org/W3127101777","https://openalex.org/W3127794728","https://openalex.org/W3132416946","https://openalex.org/W3167638709","https://openalex.org/W3201482214","https://openalex.org/W3210537005","https://openalex.org/W4200075747","https://openalex.org/W4211050664","https://openalex.org/W4223988084","https://openalex.org/W4234698323","https://openalex.org/W4281252130","https://openalex.org/W4281394935","https://openalex.org/W4294216483","https://openalex.org/W4294541781","https://openalex.org/W4295929883","https://openalex.org/W4320914026","https://openalex.org/W4321243485","https://openalex.org/W4324032719","https://openalex.org/W4383723770","https://openalex.org/W4388823618","https://openalex.org/W4391689636","https://openalex.org/W4400014436","https://openalex.org/W6728541980"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2604155846","https://openalex.org/W4390658901","https://openalex.org/W3121185202","https://openalex.org/W4393043634","https://openalex.org/W4206185765","https://openalex.org/W2900546243","https://openalex.org/W3020516445"],"abstract_inverted_index":{"Alterations":[0],"in":[1,200,219],"human":[2],"microbial":[3],"communities":[4],"are":[5,183],"intricately":[6],"linked":[7],"to":[8,46,139],"the":[9,16,60,115,123,140,146,176,201,210,220],"onset":[10],"and":[11,36,132,159,179,191],"progression":[12],"of":[13,67,106,135,155,181,212],"diseases.":[14],"Identifying":[15],"key":[17],"microbes":[18,87,198],"driving":[19],"these":[20],"community":[21],"changes":[22],"is":[23,56,164],"crucial,":[24],"as":[25,29],"they":[26],"may":[27],"serve":[28],"valuable":[30],"biomarkers":[31],"for":[32,43,50,84,122],"disease":[33],"prevention,":[34],"diagnosis,":[35],"treatment.":[37],"However,":[38],"there":[39],"remains":[40],"a":[41,79,186,225],"need":[42],"further":[44],"research":[45],"develop":[47],"effective":[48],"methods":[49],"addressing":[51],"this":[52],"critical":[53],"task.":[54],"This":[55,76],"primarily":[57],"because":[58],"defining":[59],"driver":[61,86,197],"microbe":[62],"requires":[63],"consideration":[64],"not":[65],"only":[66],"each":[68,136],"microbe's":[69,137],"individual":[70],"contributions":[71],"but":[72],"also":[73],"their":[74],"interactions.":[75],"paper":[77],"introduces":[78],"novel":[80],"framework,":[81],"called":[82],"mbDriver,":[83],"identifying":[85],"based":[88,113],"on":[89,114,167,209],"microbiome":[90],"abundance":[91,108],"data":[92,104,109],"collected":[93],"at":[94],"discrete":[95],"time":[96],"points.":[97],"mbDriver":[98,182],"comprises":[99],"three":[100],"main":[101],"components:":[102],"(i)":[103],"preprocessing":[105],"time-series":[107],"using":[110,128,185],"smoothing":[111],"splines":[112],"negative":[116],"binomial":[117],"distribution,":[118],"(ii)":[119],"parameter":[120],"estimation":[121,163],"generalized":[124],"Lotka-Volterra":[125],"(gLV)":[126],"model":[127],"regularized":[129,160],"least":[130,161],"squares,":[131],"(iii)":[133],"quantification":[134],"contribution":[138],"community's":[141],"steady":[142],"state":[143],"by":[144,150],"manipulating":[145],"causal":[147],"graph":[148],"implied":[149],"gLV":[151],"equations.":[152],"The":[153],"performance":[154],"nonparametric":[156],"spline-based":[157],"denoising":[158],"squares":[162],"comprehensively":[165],"evaluated":[166],"simulated":[168],"datasets,":[169],"demonstrating":[170],"superiority":[171],"over":[172],"existing":[173],"methods.":[174],"Furthermore,":[175],"practical":[177],"applicability":[178],"effectiveness":[180],"showcased":[184],"dietary":[187,202],"fiber":[188,203],"intervention":[189,204],"dataset":[190,205,223],"an":[192],"ulcerative":[193,221],"colitis":[194,222],"dataset.":[195],"Notably,":[196],"identified":[199,218],"exhibit":[206],"significant":[207,226],"effects":[208],"abundances":[211],"short-chain":[213],"fatty":[214],"acids,":[215],"while":[216],"those":[217],"show":[224],"correlation":[227],"with":[228],"metabolism-related":[229],"pathways.":[230]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2025-12-27T23:08:20.325037","created_date":"2025-10-10T00:00:00"}
