{"id":"https://openalex.org/W4406292104","doi":"https://doi.org/10.1093/bioinformatics/btaf014","title":"PhyloMix: enhancing microbiome-trait association prediction through phylogeny-mixing augmentation","display_name":"PhyloMix: enhancing microbiome-trait association prediction through phylogeny-mixing augmentation","publication_year":2025,"publication_date":"2025-01-08","ids":{"openalex":"https://openalex.org/W4406292104","doi":"https://doi.org/10.1093/bioinformatics/btaf014","pmid":"https://pubmed.ncbi.nlm.nih.gov/39799515"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf014","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf014","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf014/61416299/btaf014.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/btaf014/61416299/btaf014.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101505105","display_name":"Yifan Jiang","orcid":"https://orcid.org/0009-0007-5334-9627"},"institutions":[{"id":"https://openalex.org/I151746483","display_name":"University of Waterloo","ror":"https://ror.org/01aff2v68","country_code":"CA","type":"education","lineage":["https://openalex.org/I151746483"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Yifan Jiang","raw_affiliation_strings":["Cheriton School of Computer Science, University of Waterloo , Waterloo, ON, N2L 3G1,","Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada"],"affiliations":[{"raw_affiliation_string":"Cheriton School of Computer Science, University of Waterloo , Waterloo, ON, N2L 3G1,","institution_ids":["https://openalex.org/I151746483"]},{"raw_affiliation_string":"Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada","institution_ids":["https://openalex.org/I151746483"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084666411","display_name":"D. Joshua Liao","orcid":"https://orcid.org/0000-0003-3904-349X"},"institutions":[{"id":"https://openalex.org/I151746483","display_name":"University of Waterloo","ror":"https://ror.org/01aff2v68","country_code":"CA","type":"education","lineage":["https://openalex.org/I151746483"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Disen Liao","raw_affiliation_strings":["Cheriton School of Computer Science, University of Waterloo , Waterloo, ON, N2L 3G1,","Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada"],"affiliations":[{"raw_affiliation_string":"Cheriton School of Computer Science, University of Waterloo , Waterloo, ON, N2L 3G1,","institution_ids":["https://openalex.org/I151746483"]},{"raw_affiliation_string":"Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada","institution_ids":["https://openalex.org/I151746483"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064767131","display_name":"Qiyun Zhu","orcid":"https://orcid.org/0000-0002-3568-6271"},"institutions":[{"id":"https://openalex.org/I55732556","display_name":"Arizona State University","ror":"https://ror.org/03efmqc40","country_code":"US","type":"education","lineage":["https://openalex.org/I55732556"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qiyun Zhu","raw_affiliation_strings":["School of Life Sciences, Arizona State University , Tempe, AZ, 85281,","School of Life Sciences, Arizona State University, Tempe, Arizona, USA"],"affiliations":[{"raw_affiliation_string":"School of Life Sciences, Arizona State University , Tempe, AZ, 85281,","institution_ids":["https://openalex.org/I55732556"]},{"raw_affiliation_string":"School of Life Sciences, Arizona State University, Tempe, Arizona, USA","institution_ids":["https://openalex.org/I55732556"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101935781","display_name":"Yang Young Lu","orcid":"https://orcid.org/0000-0003-1686-5917"},"institutions":[{"id":"https://openalex.org/I151746483","display_name":"University of Waterloo","ror":"https://ror.org/01aff2v68","country_code":"CA","type":"education","lineage":["https://openalex.org/I151746483"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Yang Young Lu","raw_affiliation_strings":["Cheriton School of Computer Science, University of Waterloo , Waterloo, ON, N2L 3G1,","Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada"],"affiliations":[{"raw_affiliation_string":"Cheriton School of Computer Science, University of Waterloo , Waterloo, ON, N2L 3G1,","institution_ids":["https://openalex.org/I151746483"]},{"raw_affiliation_string":"Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada","institution_ids":["https://openalex.org/I151746483"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5101505105"],"corresponding_institution_ids":["https://openalex.org/I151746483"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.2495,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.85541199,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"41","issue":"2","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":0.9993000030517578,"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":0.9993000030517578,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9958000183105469,"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":0.9904999732971191,"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/microbiome","display_name":"Microbiome","score":0.8063444495201111},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6268630623817444},{"id":"https://openalex.org/keywords/trait","display_name":"Trait","score":0.6246285438537598},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.5560690760612488},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5161508321762085},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5086058378219604},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.4790973961353302},{"id":"https://openalex.org/keywords/raw-data","display_name":"Raw data","score":0.4465489387512207},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4339224398136139},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.419106662273407},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35549822449684143},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.31734877824783325},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.22964248061180115}],"concepts":[{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.8063444495201111},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6268630623817444},{"id":"https://openalex.org/C106934330","wikidata":"https://www.wikidata.org/wiki/Q1971873","display_name":"Trait","level":2,"score":0.6246285438537598},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.5560690760612488},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5161508321762085},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5086058378219604},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.4790973961353302},{"id":"https://openalex.org/C132964779","wikidata":"https://www.wikidata.org/wiki/Q2110223","display_name":"Raw data","level":2,"score":0.4465489387512207},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4339224398136139},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.419106662273407},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35549822449684143},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31734877824783325},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.22964248061180115},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","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":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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":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":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf014","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf014","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf014/61416299/btaf014.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:39799515","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39799515","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:11849959","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11849959","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11849959/pdf/btaf014.pdf","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/btaf014","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf014","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf014/61416299/btaf014.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":[{"id":"https://openalex.org/G1597412403","display_name":null,"funder_award_id":"RGPIN-","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G6221715925","display_name":null,"funder_award_id":"RGPIN","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"}],"funders":[{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4406292104.pdf","grobid_xml":"https://content.openalex.org/works/W4406292104.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W1976526581","https://openalex.org/W1993784588","https://openalex.org/W2071841602","https://openalex.org/W2074405982","https://openalex.org/W2101234009","https://openalex.org/W2110235509","https://openalex.org/W2125826054","https://openalex.org/W2148143831","https://openalex.org/W2163922914","https://openalex.org/W2167062509","https://openalex.org/W2170024099","https://openalex.org/W2624135745","https://openalex.org/W2761210275","https://openalex.org/W2765407302","https://openalex.org/W2769542288","https://openalex.org/W2805009121","https://openalex.org/W2810671429","https://openalex.org/W2892206041","https://openalex.org/W2904250115","https://openalex.org/W2947189704","https://openalex.org/W2953073956","https://openalex.org/W2953710982","https://openalex.org/W2963702053","https://openalex.org/W2990925943","https://openalex.org/W3005680577","https://openalex.org/W3016963629","https://openalex.org/W3024771599","https://openalex.org/W3028383715","https://openalex.org/W3108417339","https://openalex.org/W3128236819","https://openalex.org/W3128912982","https://openalex.org/W3159499196","https://openalex.org/W3164235949","https://openalex.org/W3173196825","https://openalex.org/W4213182271","https://openalex.org/W4224295733","https://openalex.org/W4224943843","https://openalex.org/W4287854464","https://openalex.org/W4293030232","https://openalex.org/W4299542564","https://openalex.org/W4302426080","https://openalex.org/W4309028162","https://openalex.org/W4312107756","https://openalex.org/W4317830385","https://openalex.org/W4320813886","https://openalex.org/W4360943977","https://openalex.org/W4388398414","https://openalex.org/W4394759342","https://openalex.org/W4400893242","https://openalex.org/W6675354045","https://openalex.org/W6754669440","https://openalex.org/W6779738646","https://openalex.org/W6849815238"],"related_works":["https://openalex.org/W2174809885","https://openalex.org/W2057191541","https://openalex.org/W2883025420","https://openalex.org/W1992658754","https://openalex.org/W2111939425","https://openalex.org/W2065083790","https://openalex.org/W2375383082","https://openalex.org/W2604174992","https://openalex.org/W1974895455","https://openalex.org/W3023641210"],"abstract_inverted_index":{"The":[0],"Apache-licensed":[1],"source":[2],"code":[3],"is":[4],"available":[5],"at":[6],"(https://github.com/batmen-lab/phylomix).":[7]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2}],"updated_date":"2026-04-14T08:04:32.555800","created_date":"2025-10-10T00:00:00"}