{"id":"https://openalex.org/W4389076127","doi":"https://doi.org/10.1093/bioinformatics/btad706","title":"mb-PHENIX: diffusion and supervised uniform manifold approximation for denoizing microbiota data","display_name":"mb-PHENIX: diffusion and supervised uniform manifold approximation for denoizing microbiota data","publication_year":2023,"publication_date":"2023-11-28","ids":{"openalex":"https://openalex.org/W4389076127","doi":"https://doi.org/10.1093/bioinformatics/btad706","pmid":"https://pubmed.ncbi.nlm.nih.gov/38015858"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad706","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad706","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad706/53895999/btad706.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/advance-article-pdf/doi/10.1093/bioinformatics/btad706/53895999/btad706.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017243953","display_name":"Cristian Padr\u00f3n-Manrique","orcid":"https://orcid.org/0000-0001-9956-3484"},"institutions":[{"id":"https://openalex.org/I4210110970","display_name":"National Institute of Genomic Medicine","ror":"https://ror.org/01qjckx08","country_code":"MX","type":"government","lineage":["https://openalex.org/I4210095685","https://openalex.org/I4210110970"]},{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Cristian Padron-Manrique","raw_affiliation_strings":["Human Systems Biology Laboratory, Instituto Nacional de Medicina Gen\u00f3mica (INMEGEN) , Mexico City, 14610, Mexico","Programa de Doctorado en Ciencias Biom\u00e9dicas, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM) , Mexico City, 04510, Mexico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Human Systems Biology Laboratory, Instituto Nacional de Medicina Gen\u00f3mica (INMEGEN) , Mexico City, 14610, Mexico","institution_ids":["https://openalex.org/I4210110970"]},{"raw_affiliation_string":"Programa de Doctorado en Ciencias Biom\u00e9dicas, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM) , Mexico City, 04510, Mexico","institution_ids":["https://openalex.org/I8961855"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025799655","display_name":"Aar\u00f3n V\u00e1zquez-Jim\u00e9nez","orcid":"https://orcid.org/0000-0003-2688-6463"},"institutions":[{"id":"https://openalex.org/I4210110970","display_name":"National Institute of Genomic Medicine","ror":"https://ror.org/01qjckx08","country_code":"MX","type":"government","lineage":["https://openalex.org/I4210095685","https://openalex.org/I4210110970"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Aar\u00f3n V\u00e1zquez-Jim\u00e9nez","raw_affiliation_strings":["Human Systems Biology Laboratory, Instituto Nacional de Medicina Gen\u00f3mica (INMEGEN) , Mexico City, 14610, Mexico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Human Systems Biology Laboratory, Instituto Nacional de Medicina Gen\u00f3mica (INMEGEN) , Mexico City, 14610, Mexico","institution_ids":["https://openalex.org/I4210110970"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014927161","display_name":"Diego Esquivel-Hern\u00e1ndez","orcid":"https://orcid.org/0000-0002-3636-4514"},"institutions":[{"id":"https://openalex.org/I4210110970","display_name":"National Institute of Genomic Medicine","ror":"https://ror.org/01qjckx08","country_code":"MX","type":"government","lineage":["https://openalex.org/I4210095685","https://openalex.org/I4210110970"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Diego Armando Esquivel-Hernandez","raw_affiliation_strings":["Human Systems Biology Laboratory, Instituto Nacional de Medicina Gen\u00f3mica (INMEGEN) , Mexico City, 14610, Mexico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Human Systems Biology Laboratory, Instituto Nacional de Medicina Gen\u00f3mica (INMEGEN) , Mexico City, 14610, Mexico","institution_ids":["https://openalex.org/I4210110970"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108881039","display_name":"Yoscelina Estrella Martinez Lopez","orcid":null},"institutions":[{"id":"https://openalex.org/I4210110970","display_name":"National Institute of Genomic Medicine","ror":"https://ror.org/01qjckx08","country_code":"MX","type":"government","lineage":["https://openalex.org/I4210095685","https://openalex.org/I4210110970"]},{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Yoscelina Estrella Martinez Lopez","raw_affiliation_strings":["Human Systems Biology Laboratory, Instituto Nacional de Medicina Gen\u00f3mica (INMEGEN) , Mexico City, 14610, Mexico","Programa de Doctorado en Ciencias M\u00e9dicas, Odontol\u00f3gicas y de la Salud, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM) , Mexico City, 04510, Mexico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Human Systems Biology Laboratory, Instituto Nacional de Medicina Gen\u00f3mica (INMEGEN) , Mexico City, 14610, Mexico","institution_ids":["https://openalex.org/I4210110970"]},{"raw_affiliation_string":"Programa de Doctorado en Ciencias M\u00e9dicas, Odontol\u00f3gicas y de la Salud, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM) , Mexico City, 04510, Mexico","institution_ids":["https://openalex.org/I8961855"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081351949","display_name":"Daniel Neri-Rosario","orcid":"https://orcid.org/0000-0002-3899-5133"},"institutions":[{"id":"https://openalex.org/I4210110970","display_name":"National Institute of Genomic Medicine","ror":"https://ror.org/01qjckx08","country_code":"MX","type":"government","lineage":["https://openalex.org/I4210095685","https://openalex.org/I4210110970"]},{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Daniel Neri-Rosario","raw_affiliation_strings":["Human Systems Biology Laboratory, Instituto Nacional de Medicina Gen\u00f3mica (INMEGEN) , Mexico City, 14610, Mexico","Programa de Maestr\u00eda en Ciencias Bioqu\u00edmicas, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM) , Mexico City, 04510, Mexico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Human Systems Biology Laboratory, Instituto Nacional de Medicina Gen\u00f3mica (INMEGEN) , Mexico City, 14610, Mexico","institution_ids":["https://openalex.org/I4210110970"]},{"raw_affiliation_string":"Programa de Maestr\u00eda en Ciencias Bioqu\u00edmicas, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM) , Mexico City, 04510, Mexico","institution_ids":["https://openalex.org/I8961855"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076055634","display_name":"Jean Paul S\u00e1nchez-Casta\u00f1eda","orcid":null},"institutions":[{"id":"https://openalex.org/I4210110970","display_name":"National Institute of Genomic Medicine","ror":"https://ror.org/01qjckx08","country_code":"MX","type":"government","lineage":["https://openalex.org/I4210095685","https://openalex.org/I4210110970"]},{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Jean Paul S\u00e1nchez-Casta\u00f1eda","raw_affiliation_strings":["Human Systems Biology Laboratory, Instituto Nacional de Medicina Gen\u00f3mica (INMEGEN) , Mexico City, 14610, Mexico","Programa de Maestr\u00eda en Ciencias Bioqu\u00edmicas, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM) , Mexico City, 04510, Mexico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Human Systems Biology Laboratory, Instituto Nacional de Medicina Gen\u00f3mica (INMEGEN) , Mexico City, 14610, Mexico","institution_ids":["https://openalex.org/I4210110970"]},{"raw_affiliation_string":"Programa de Maestr\u00eda en Ciencias Bioqu\u00edmicas, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM) , Mexico City, 04510, Mexico","institution_ids":["https://openalex.org/I8961855"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053310134","display_name":"David Giron-Villalobos","orcid":"https://orcid.org/0000-0002-4848-3713"},"institutions":[{"id":"https://openalex.org/I4210110970","display_name":"National Institute of Genomic Medicine","ror":"https://ror.org/01qjckx08","country_code":"MX","type":"government","lineage":["https://openalex.org/I4210095685","https://openalex.org/I4210110970"]},{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"David Giron-Villalobos","raw_affiliation_strings":["Human Systems Biology Laboratory, Instituto Nacional de Medicina Gen\u00f3mica (INMEGEN) , Mexico City, 14610, Mexico","Programa de Maestr\u00eda en Ciencias Bioqu\u00edmicas, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM) , Mexico City, 04510, Mexico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Human Systems Biology Laboratory, Instituto Nacional de Medicina Gen\u00f3mica (INMEGEN) , Mexico City, 14610, Mexico","institution_ids":["https://openalex.org/I4210110970"]},{"raw_affiliation_string":"Programa de Maestr\u00eda en Ciencias Bioqu\u00edmicas, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM) , Mexico City, 04510, Mexico","institution_ids":["https://openalex.org/I8961855"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017937746","display_name":"Osbaldo Res\u00e9ndis-Antonio","orcid":"https://orcid.org/0000-0001-5220-541X"},"institutions":[{"id":"https://openalex.org/I4210110970","display_name":"National Institute of Genomic Medicine","ror":"https://ror.org/01qjckx08","country_code":"MX","type":"government","lineage":["https://openalex.org/I4210095685","https://openalex.org/I4210110970"]},{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["MX"],"is_corresponding":true,"raw_author_name":"Osbaldo Resendis-Antonio","raw_affiliation_strings":["Coordinaci\u00f3n de la Investigaci\u00f3n Cient\u00edfica\u2014Red de Apoyo a la Investigaci\u00f3n\u2014Centro de Ciencias de la Complejidad, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM) , Mexico City, 04510, Mexico","Human Systems Biology Laboratory, Instituto Nacional de Medicina Gen\u00f3mica (INMEGEN) , Mexico City, 14610, Mexico"],"raw_orcid":"https://orcid.org/0000-0001-5220-541X","affiliations":[{"raw_affiliation_string":"Coordinaci\u00f3n de la Investigaci\u00f3n Cient\u00edfica\u2014Red de Apoyo a la Investigaci\u00f3n\u2014Centro de Ciencias de la Complejidad, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM) , Mexico City, 04510, Mexico","institution_ids":["https://openalex.org/I8961855"]},{"raw_affiliation_string":"Human Systems Biology Laboratory, Instituto Nacional de Medicina Gen\u00f3mica (INMEGEN) , Mexico City, 14610, Mexico","institution_ids":["https://openalex.org/I4210110970"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5017937746"],"corresponding_institution_ids":["https://openalex.org/I4210110970","https://openalex.org/I8961855"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.8073,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.74002456,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":97},"biblio":{"volume":"39","issue":"12","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":0.9843000173568726,"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":0.9843000173568726,"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":0.0015999999595806003,"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/T11331","display_name":"Fecal contamination and water quality","score":0.00139999995008111,"subfield":{"id":"https://openalex.org/subfields/2312","display_name":"Water Science and Technology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6364642977714539},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.5976393222808838},{"id":"https://openalex.org/keywords/imputation","display_name":"Imputation (statistics)","score":0.5538031458854675},{"id":"https://openalex.org/keywords/curse-of-dimensionality","display_name":"Curse of dimensionality","score":0.5380915999412537},{"id":"https://openalex.org/keywords/initialization","display_name":"Initialization","score":0.5043066740036011},{"id":"https://openalex.org/keywords/dimensionality-reduction","display_name":"Dimensionality reduction","score":0.4529891312122345},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.41683629155158997},{"id":"https://openalex.org/keywords/nonlinear-dimensionality-reduction","display_name":"Nonlinear dimensionality reduction","score":0.41008061170578003},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.39288491010665894},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.35737085342407227},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3434954881668091},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.32406869530677795},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.31116434931755066}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6364642977714539},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5976393222808838},{"id":"https://openalex.org/C58041806","wikidata":"https://www.wikidata.org/wiki/Q1660484","display_name":"Imputation (statistics)","level":3,"score":0.5538031458854675},{"id":"https://openalex.org/C111030470","wikidata":"https://www.wikidata.org/wiki/Q1430460","display_name":"Curse of dimensionality","level":2,"score":0.5380915999412537},{"id":"https://openalex.org/C114466953","wikidata":"https://www.wikidata.org/wiki/Q6034165","display_name":"Initialization","level":2,"score":0.5043066740036011},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.4529891312122345},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.41683629155158997},{"id":"https://openalex.org/C151876577","wikidata":"https://www.wikidata.org/wiki/Q7049464","display_name":"Nonlinear dimensionality reduction","level":3,"score":0.41008061170578003},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.39288491010665894},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.35737085342407227},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3434954881668091},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.32406869530677795},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.31116434931755066},{"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/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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},{"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/btad706","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad706","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad706/53895999/btad706.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:38015858","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38015858","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:10699834","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10699834","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10699834/pdf/btad706.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad706","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad706","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad706/53895999/btad706.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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320323401","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25"},{"id":"https://openalex.org/F4320327956","display_name":"Instituto Nacional de Medicina Gen\u00f3mica","ror":"https://ror.org/01qjckx08"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4389076127.pdf"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W2805619986","https://openalex.org/W2889326414","https://openalex.org/W3118966073","https://openalex.org/W3174029804","https://openalex.org/W3204834823","https://openalex.org/W4282559099","https://openalex.org/W4365148555","https://openalex.org/W4382242087","https://openalex.org/W6766725701","https://openalex.org/W6839125717"],"related_works":["https://openalex.org/W2181530120","https://openalex.org/W4211215373","https://openalex.org/W2024529227","https://openalex.org/W1574575415","https://openalex.org/W3144172081","https://openalex.org/W3179858851","https://openalex.org/W3028371478","https://openalex.org/W2081476516","https://openalex.org/W2581984549","https://openalex.org/W3123177881"],"abstract_inverted_index":{"MOTIVATION:":[0],"Microbiota":[1],"data":[2,55],"encounters":[3],"challenges":[4],"arising":[5],"from":[6,71],"technical":[7,32],"noise":[8],"and":[9,31,74,90],"the":[10,16,52,72,81],"curse":[11],"of":[12,18,54,84],"dimensionality,":[13],"which":[14],"affect":[15],"reliability":[17],"scientific":[19],"findings.":[20],"Furthermore,":[21],"abundance":[22,120,127],"matrices":[23],"exhibit":[24],"a":[25,37],"zero-inflated":[26],"distribution":[27],"due":[28],"to":[29,114],"biological":[30],"influences.":[33],"Consequently,":[34],"there":[35],"is":[36,136,143],"growing":[38],"demand":[39],"for":[40],"advanced":[41],"algorithms":[42],"that":[43,67],"can":[44],"effectively":[45],"recover":[46],"missing":[47,82],"taxa":[48,69],"while":[49],"also":[50],"considering":[51],"preservation":[53],"structure.":[56],"RESULTS:":[57],"We":[58],"present":[59],"mb-PHENIX,":[60],"an":[61],"open-source":[62],"algorithm":[63,135],"developed":[64],"in":[65],"Python":[66],"recovers":[68],"abundances":[70],"noisy":[73],"sparse":[75],"microbiota":[76,89,116],"data.":[77],"Our":[78,108],"method":[79],"infers":[80],"information":[83],"count":[85],"matrix":[86],"(in":[87],"16S":[88],"shotgun":[91],"studies)":[92],"by":[93],"applying":[94],"imputation":[95],"via":[96],"diffusion":[97],"with":[98],"supervised":[99],"Uniform":[100],"Manifold":[101],"Approximation":[102],"Projection":[103],"(sUMAP)":[104],"space":[105],"as":[106],"initialization.":[107],"hybrid":[109],"machine":[110],"learning":[111],"approach":[112],"allows":[113],"denoise":[115],"data,":[117],"revealing":[118],"differential":[119],"microbes":[121],"among":[122],"study":[123],"groups":[124],"where":[125],"traditional":[126],"analysis":[128],"fails.":[129],"AVAILABILITY":[130],"AND":[131],"IMPLEMENTATION:":[132],"The":[133],"mb-PHENIX":[134],"available":[137,144],"at":[138],"https://github.com/resendislab/mb-PHENIX.":[139],"An":[140],"easy-to-use":[141],"implementation":[142],"on":[145],"Google":[146],"Colab":[147],"(see":[148],"GitHub).":[149]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
