{"id":"https://openalex.org/W3178958851","doi":"https://doi.org/10.1093/bioinformatics/btab287","title":"Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model","display_name":"Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model","publication_year":2021,"publication_date":"2021-04-26","ids":{"openalex":"https://openalex.org/W3178958851","doi":"https://doi.org/10.1093/bioinformatics/btab287","mag":"3178958851","pmid":"https://pubmed.ncbi.nlm.nih.gov/34252954"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab287","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab287","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/Supplement_1/i16/39620131/btab287.pdf","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":"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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/Supplement_1/i16/39620131/btab287.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085261724","display_name":"Shion Hosoda","orcid":"https://orcid.org/0000-0001-5093-6833"},"institutions":[{"id":"https://openalex.org/I150744194","display_name":"Waseda University","ror":"https://ror.org/00ntfnx83","country_code":"JP","type":"education","lineage":["https://openalex.org/I150744194"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Shion Hosoda","raw_affiliation_strings":["Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University , Tokyo 169-8555, Japan","Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University , Tokyo 169-8555, Japan"],"affiliations":[{"raw_affiliation_string":"Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University , Tokyo 169-8555, Japan","institution_ids":["https://openalex.org/I150744194"]},{"raw_affiliation_string":"Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University , Tokyo 169-8555, Japan","institution_ids":["https://openalex.org/I150744194"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085566781","display_name":"Tsukasa Fukunaga","orcid":"https://orcid.org/0000-0003-4442-6049"},"institutions":[{"id":"https://openalex.org/I150744194","display_name":"Waseda University","ror":"https://ror.org/00ntfnx83","country_code":"JP","type":"education","lineage":["https://openalex.org/I150744194"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Tsukasa Fukunaga","raw_affiliation_strings":["Department of Computer Science, Graduate School of Information Science and Technology, The University of Tokyo , Tokyo 113-8656, Japan","Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University , Tokyo 169-8555, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Graduate School of Information Science and Technology, The University of Tokyo , Tokyo 113-8656, Japan","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University , Tokyo 169-8555, Japan","institution_ids":["https://openalex.org/I150744194"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025857432","display_name":"Michiaki Hamada","orcid":"https://orcid.org/0000-0001-9466-1034"},"institutions":[{"id":"https://openalex.org/I80188885","display_name":"Nippon Medical School","ror":"https://ror.org/00krab219","country_code":"JP","type":"education","lineage":["https://openalex.org/I80188885"]},{"id":"https://openalex.org/I150744194","display_name":"Waseda University","ror":"https://ror.org/00ntfnx83","country_code":"JP","type":"education","lineage":["https://openalex.org/I150744194"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Michiaki Hamada","raw_affiliation_strings":["Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University , Tokyo 169-8555, Japan","Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University , Tokyo 169-8555, Japan","Graduate School of Medicine, Nippon Medical School , Tokyo 113-8602, Japan"],"affiliations":[{"raw_affiliation_string":"Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University , Tokyo 169-8555, Japan","institution_ids":["https://openalex.org/I150744194"]},{"raw_affiliation_string":"Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University , Tokyo 169-8555, Japan","institution_ids":["https://openalex.org/I150744194"]},{"raw_affiliation_string":"Graduate School of Medicine, Nippon Medical School , Tokyo 113-8602, Japan","institution_ids":["https://openalex.org/I80188885"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5085261724"],"corresponding_institution_ids":["https://openalex.org/I150744194"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.3254,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.56158959,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"37","issue":"Supplement_1","first_page":"i16","last_page":"i24"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9998999834060669,"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":0.9998999834060669,"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/T10141","display_name":"Probiotics and Fermented Foods","score":0.9632999897003174,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food 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"}},{"id":"https://openalex.org/T11667","display_name":"Advanced Chemical Sensor Technologies","score":0.9574000239372253,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6606433391571045},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6151921153068542},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5613190531730652},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.5061232447624207},{"id":"https://openalex.org/keywords/bayesian-network","display_name":"Bayesian network","score":0.5034253001213074},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.49964332580566406},{"id":"https://openalex.org/keywords/regression","display_name":"Regression","score":0.4908793568611145},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.47929543256759644},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4760275185108185},{"id":"https://openalex.org/keywords/regression-analysis","display_name":"Regression analysis","score":0.45705199241638184},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.44800928235054016},{"id":"https://openalex.org/keywords/conditional-dependence","display_name":"Conditional dependence","score":0.4283387064933777},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.2841688394546509},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.19592785835266113}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6606433391571045},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6151921153068542},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5613190531730652},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.5061232447624207},{"id":"https://openalex.org/C33724603","wikidata":"https://www.wikidata.org/wiki/Q812540","display_name":"Bayesian network","level":2,"score":0.5034253001213074},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.49964332580566406},{"id":"https://openalex.org/C83546350","wikidata":"https://www.wikidata.org/wiki/Q1139051","display_name":"Regression","level":2,"score":0.4908793568611145},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.47929543256759644},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4760275185108185},{"id":"https://openalex.org/C152877465","wikidata":"https://www.wikidata.org/wiki/Q208042","display_name":"Regression analysis","level":2,"score":0.45705199241638184},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.44800928235054016},{"id":"https://openalex.org/C174920663","wikidata":"https://www.wikidata.org/wiki/Q5159256","display_name":"Conditional dependence","level":2,"score":0.4283387064933777},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.2841688394546509},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.19592785835266113},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"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":"D016011","descriptor_name":"Normal Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016011","descriptor_name":"Normal Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016011","descriptor_name":"Normal Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056265","descriptor_name":"Microbial Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056265","descriptor_name":"Microbial Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056265","descriptor_name":"Microbial Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab287","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab287","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/Supplement_1/i16/39620131/btab287.pdf","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":"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:34252954","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34252954","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},{"id":"pmh:oai:pubmedcentral.nih.gov:8275348","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8275348","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab287","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab287","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/Supplement_1/i16/39620131/btab287.pdf","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":"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":[],"awards":[{"id":"https://openalex.org/G4986525417","display_name":null,"funder_award_id":"JP20H05582","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G553283399","display_name":null,"funder_award_id":"JP18KT0016","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G5693266671","display_name":null,"funder_award_id":"JP19H01152","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G6746580654","display_name":null,"funder_award_id":"JP20H00624","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G7840787119","display_name":null,"funder_award_id":"JP19J20117","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"},{"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/W3178958851.pdf","grobid_xml":"https://content.openalex.org/works/W3178958851.grobid-xml"},"referenced_works_count":51,"referenced_works":["https://openalex.org/W1575431606","https://openalex.org/W1605035807","https://openalex.org/W1864161604","https://openalex.org/W1891411045","https://openalex.org/W1971061059","https://openalex.org/W1988691705","https://openalex.org/W1993830991","https://openalex.org/W2012994611","https://openalex.org/W2027763661","https://openalex.org/W2040539560","https://openalex.org/W2053080660","https://openalex.org/W2058402249","https://openalex.org/W2069305293","https://openalex.org/W2101515427","https://openalex.org/W2113977541","https://openalex.org/W2117076645","https://openalex.org/W2120563211","https://openalex.org/W2126452774","https://openalex.org/W2127175247","https://openalex.org/W2131186249","https://openalex.org/W2136737152","https://openalex.org/W2141137078","https://openalex.org/W2161523118","https://openalex.org/W2164386968","https://openalex.org/W2172085063","https://openalex.org/W2186184898","https://openalex.org/W2208966601","https://openalex.org/W2334002433","https://openalex.org/W2413154614","https://openalex.org/W2463312000","https://openalex.org/W2500593481","https://openalex.org/W2550570544","https://openalex.org/W2561761056","https://openalex.org/W2593928562","https://openalex.org/W2748607273","https://openalex.org/W2793465863","https://openalex.org/W2802240472","https://openalex.org/W2895859043","https://openalex.org/W2900937147","https://openalex.org/W2962960682","https://openalex.org/W2969872083","https://openalex.org/W2974721962","https://openalex.org/W2982906277","https://openalex.org/W3013117258","https://openalex.org/W3025757981","https://openalex.org/W3087499068","https://openalex.org/W6677459581","https://openalex.org/W6684042573","https://openalex.org/W6686512395","https://openalex.org/W6724198773","https://openalex.org/W6751152636"],"related_works":["https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W1699080303","https://openalex.org/W4297799326","https://openalex.org/W2374924985","https://openalex.org/W2102053756","https://openalex.org/W2170757954","https://openalex.org/W2620337387","https://openalex.org/W2203247113"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":2}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
