{"id":"https://openalex.org/W4409121215","doi":"https://doi.org/10.1093/bioinformatics/btaf139","title":"Demixer: a probabilistic generative model to delineate different strains of a microbial species in a mixed infection sample","display_name":"Demixer: a probabilistic generative model to delineate different strains of a microbial species in a mixed infection sample","publication_year":2025,"publication_date":"2025-03-29","ids":{"openalex":"https://openalex.org/W4409121215","doi":"https://doi.org/10.1093/bioinformatics/btaf139","pmid":"https://pubmed.ncbi.nlm.nih.gov/40178927"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf139","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf139","pdf_url":null,"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://doi.org/10.1093/bioinformatics/btaf139","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091917294","display_name":"V P Brintha","orcid":null},"institutions":[{"id":"https://openalex.org/I24676775","display_name":"Indian Institute of Technology Madras","ror":"https://ror.org/03v0r5n49","country_code":"IN","type":"facility","lineage":["https://openalex.org/I24676775"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Brintha VP","raw_affiliation_strings":["Center for Integrative Biology and Systems Medicine (IBSE), IIT Madras , Chennai, 600036,","Department of Computer Science and Engineering, Indian Institute of Technology (IIT) Madras , Chennai, 600036,","Wadhwani School of Data Science and AI, IIT Madras , Chennai, 600036,","Indian Institute of Technology (IIT) Madras Department of Computer Science and Engineering, , Chennai,","IIT Madras Wadhwani School of Data Science and AI, , Chennai,","IIT Madras Center for Integrative Biology and Systems Medicine (IBSE), , Chennai,"],"affiliations":[{"raw_affiliation_string":"Center for Integrative Biology and Systems Medicine (IBSE), IIT Madras , Chennai, 600036,","institution_ids":["https://openalex.org/I24676775"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Indian Institute of Technology (IIT) Madras , Chennai, 600036,","institution_ids":["https://openalex.org/I24676775"]},{"raw_affiliation_string":"Wadhwani School of Data Science and AI, IIT Madras , Chennai, 600036,","institution_ids":["https://openalex.org/I24676775"]},{"raw_affiliation_string":"Indian Institute of Technology (IIT) Madras Department of Computer Science and Engineering, , Chennai,","institution_ids":["https://openalex.org/I24676775"]},{"raw_affiliation_string":"IIT Madras Wadhwani School of Data Science and AI, , Chennai,","institution_ids":["https://openalex.org/I24676775"]},{"raw_affiliation_string":"IIT Madras Center for Integrative Biology and Systems Medicine (IBSE), , Chennai,","institution_ids":["https://openalex.org/I24676775"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077782872","display_name":"Manikandan Narayanan","orcid":"https://orcid.org/0000-0002-8490-4087"},"institutions":[{"id":"https://openalex.org/I24676775","display_name":"Indian Institute of Technology Madras","ror":"https://ror.org/03v0r5n49","country_code":"IN","type":"facility","lineage":["https://openalex.org/I24676775"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Manikandan Narayanan","raw_affiliation_strings":["Center for Integrative Biology and Systems Medicine (IBSE), IIT Madras , Chennai, 600036,","Department of Computer Science and Engineering, Indian Institute of Technology (IIT) Madras , Chennai, 600036,","Wadhwani School of Data Science and AI, IIT Madras , Chennai, 600036,","Indian Institute of Technology (IIT) Madras Department of Computer Science and Engineering, , Chennai,","IIT Madras Center for Integrative Biology and Systems Medicine (IBSE), , Chennai,","IIT Madras Wadhwani School of Data Science and AI, , Chennai,"],"affiliations":[{"raw_affiliation_string":"Center for Integrative Biology and Systems Medicine (IBSE), IIT Madras , Chennai, 600036,","institution_ids":["https://openalex.org/I24676775"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Indian Institute of Technology (IIT) Madras , Chennai, 600036,","institution_ids":["https://openalex.org/I24676775"]},{"raw_affiliation_string":"Wadhwani School of Data Science and AI, IIT Madras , Chennai, 600036,","institution_ids":["https://openalex.org/I24676775"]},{"raw_affiliation_string":"Indian Institute of Technology (IIT) Madras Department of Computer Science and Engineering, , Chennai,","institution_ids":["https://openalex.org/I24676775"]},{"raw_affiliation_string":"IIT Madras Center for Integrative Biology and Systems Medicine (IBSE), , Chennai,","institution_ids":["https://openalex.org/I24676775"]},{"raw_affiliation_string":"IIT Madras Wadhwani School of Data Science and AI, , Chennai,","institution_ids":["https://openalex.org/I24676775"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5091917294"],"corresponding_institution_ids":["https://openalex.org/I24676775"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.8149,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.70704536,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"41","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9889000058174133,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9889000058174133,"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/T10038","display_name":"Tuberculosis Research and Epidemiology","score":0.9886999726295471,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9851999878883362,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.6203992962837219},{"id":"https://openalex.org/keywords/generative-model","display_name":"Generative model","score":0.6014842987060547},{"id":"https://openalex.org/keywords/heuristics","display_name":"Heuristics","score":0.5776379704475403},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.560638427734375},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.515133261680603},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4623526334762573},{"id":"https://openalex.org/keywords/tuberculosis","display_name":"Tuberculosis","score":0.4325940012931824},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.41301652789115906},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.392686128616333},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.35558587312698364},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.34692150354385376},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.32288241386413574},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.30151426792144775},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.14105376601219177},{"id":"https://openalex.org/keywords/cartography","display_name":"Cartography","score":0.07648307085037231}],"concepts":[{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.6203992962837219},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.6014842987060547},{"id":"https://openalex.org/C127705205","wikidata":"https://www.wikidata.org/wiki/Q5748245","display_name":"Heuristics","level":2,"score":0.5776379704475403},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.560638427734375},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.515133261680603},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4623526334762573},{"id":"https://openalex.org/C2781069245","wikidata":"https://www.wikidata.org/wiki/Q12204","display_name":"Tuberculosis","level":2,"score":0.4325940012931824},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.41301652789115906},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.392686128616333},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.35558587312698364},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.34692150354385376},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.32288241386413574},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.30151426792144775},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.14105376601219177},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.07648307085037231},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","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":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018088","descriptor_name":"Tuberculosis, Multidrug-Resistant","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":true},{"descriptor_ui":"D018088","descriptor_name":"Tuberculosis, Multidrug-Resistant","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":true},{"descriptor_ui":"D018088","descriptor_name":"Tuberculosis, Multidrug-Resistant","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":true},{"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":"D060085","descriptor_name":"Coinfection","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":true},{"descriptor_ui":"D060085","descriptor_name":"Coinfection","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":true},{"descriptor_ui":"D060085","descriptor_name":"Coinfection","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf139","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf139","pdf_url":null,"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:40178927","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40178927","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:12011361","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12011361","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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/btaf139","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf139","pdf_url":null,"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":[{"score":0.46000000834465027,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"},{"score":0.4000000059604645,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1952362346","https://openalex.org/W2009018119","https://openalex.org/W2107340859","https://openalex.org/W2155465294","https://openalex.org/W2157539385","https://openalex.org/W2205393402","https://openalex.org/W2522581443","https://openalex.org/W2589642545","https://openalex.org/W2887960483","https://openalex.org/W2952463453","https://openalex.org/W2963699930","https://openalex.org/W2987479663","https://openalex.org/W3005424591","https://openalex.org/W3008594856","https://openalex.org/W3079060667","https://openalex.org/W3111672821","https://openalex.org/W3175871955","https://openalex.org/W4205435626","https://openalex.org/W4224216683","https://openalex.org/W4252845385","https://openalex.org/W4291019294","https://openalex.org/W4291020280","https://openalex.org/W4321497407","https://openalex.org/W4387872798","https://openalex.org/W6639619044","https://openalex.org/W6675301171","https://openalex.org/W6920401330"],"related_works":["https://openalex.org/W4365211920","https://openalex.org/W3014948380","https://openalex.org/W4391584540","https://openalex.org/W4380551139","https://openalex.org/W4317695495","https://openalex.org/W4395044357","https://openalex.org/W4287117424","https://openalex.org/W4387506531","https://openalex.org/W2087346071","https://openalex.org/W2967848559"],"abstract_inverted_index":{"All":[0],"code":[1],"relevant":[2],"to":[3],"Demixer":[4],"is":[5],"available":[6],"at":[7],"https://github.com/BIRDSgroup/Demixer.":[8]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-03-27T14:29:43.386196","created_date":"2025-04-03T00:00:00"}