{"id":"https://openalex.org/W3033594250","doi":"https://doi.org/10.1093/bioinformatics/btaa564","title":"Tropical principal component analysis on the space of phylogenetic trees","display_name":"Tropical principal component analysis on the space of phylogenetic trees","publication_year":2020,"publication_date":"2020-06-03","ids":{"openalex":"https://openalex.org/W3033594250","doi":"https://doi.org/10.1093/bioinformatics/btaa564","mag":"3033594250","pmid":"https://pubmed.ncbi.nlm.nih.gov/32516398"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa564","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa564","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/17/4590/34220689/btaa564.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/17/4590/34220689/btaa564.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045391356","display_name":"R.W. Page","orcid":null},"institutions":[{"id":"https://openalex.org/I35364215","display_name":"Naval Postgraduate School","ror":"https://ror.org/033yfkj90","country_code":"US","type":"education","lineage":["https://openalex.org/I1330347796","https://openalex.org/I3130687028","https://openalex.org/I35364215"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert Page","raw_affiliation_strings":["Department of Operations Research, Naval Postgraduate School , Monterey, CA 93943, USA"],"affiliations":[{"raw_affiliation_string":"Department of Operations Research, Naval Postgraduate School , Monterey, CA 93943, USA","institution_ids":["https://openalex.org/I35364215"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079338715","display_name":"Ruriko Yoshida","orcid":"https://orcid.org/0000-0003-0995-2553"},"institutions":[{"id":"https://openalex.org/I35364215","display_name":"Naval Postgraduate School","ror":"https://ror.org/033yfkj90","country_code":"US","type":"education","lineage":["https://openalex.org/I1330347796","https://openalex.org/I3130687028","https://openalex.org/I35364215"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ruriko Yoshida","raw_affiliation_strings":["Department of Operations Research, Naval Postgraduate School , Monterey, CA 93943, USA"],"affiliations":[{"raw_affiliation_string":"Department of Operations Research, Naval Postgraduate School , Monterey, CA 93943, USA","institution_ids":["https://openalex.org/I35364215"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008912634","display_name":"Leon Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Leon Zhang","raw_affiliation_strings":["Department of Mathematics, University of California , Berkeley, Berkeley, CA 94720, USA"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics, University of California , Berkeley, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5079338715"],"corresponding_institution_ids":["https://openalex.org/I35364215"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.8387,"has_fulltext":true,"cited_by_count":32,"citation_normalized_percentile":{"value":0.85777388,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"36","issue":"17","first_page":"4590","last_page":"4598"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9962999820709229,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.972599983215332,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant 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"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.741996705532074},{"id":"https://openalex.org/keywords/principal-component-analysis","display_name":"Principal component analysis","score":0.5752294063568115},{"id":"https://openalex.org/keywords/polytope","display_name":"Polytope","score":0.5603957176208496},{"id":"https://openalex.org/keywords/markov-chain-monte-carlo","display_name":"Markov chain Monte Carlo","score":0.4854326844215393},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.45423147082328796},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.44492650032043457},{"id":"https://openalex.org/keywords/tree-rearrangement","display_name":"Tree rearrangement","score":0.419981986284256},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.4196649193763733},{"id":"https://openalex.org/keywords/dimensionality-reduction","display_name":"Dimensionality reduction","score":0.4192694425582886},{"id":"https://openalex.org/keywords/tropical-geometry","display_name":"Tropical geometry","score":0.41216155886650085},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.35945066809654236},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.32157379388809204},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2701091170310974},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.15221115946769714},{"id":"https://openalex.org/keywords/monte-carlo-method","display_name":"Monte Carlo method","score":0.13957864046096802},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11330705881118774}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.741996705532074},{"id":"https://openalex.org/C27438332","wikidata":"https://www.wikidata.org/wiki/Q2873","display_name":"Principal component analysis","level":2,"score":0.5752294063568115},{"id":"https://openalex.org/C145691206","wikidata":"https://www.wikidata.org/wiki/Q747980","display_name":"Polytope","level":2,"score":0.5603957176208496},{"id":"https://openalex.org/C111350023","wikidata":"https://www.wikidata.org/wiki/Q1191869","display_name":"Markov chain Monte Carlo","level":3,"score":0.4854326844215393},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.45423147082328796},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.44492650032043457},{"id":"https://openalex.org/C53208351","wikidata":"https://www.wikidata.org/wiki/Q7837630","display_name":"Tree rearrangement","level":4,"score":0.419981986284256},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.4196649193763733},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.4192694425582886},{"id":"https://openalex.org/C202652594","wikidata":"https://www.wikidata.org/wiki/Q2982669","display_name":"Tropical geometry","level":2,"score":0.41216155886650085},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.35945066809654236},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32157379388809204},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2701091170310974},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.15221115946769714},{"id":"https://openalex.org/C19499675","wikidata":"https://www.wikidata.org/wiki/Q232207","display_name":"Monte Carlo method","level":2,"score":0.13957864046096802},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11330705881118774},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","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":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa564","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa564","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/17/4590/34220689/btaa564.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32516398","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32516398","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:calhoun.nps.edu:10945/69320","is_oa":false,"landing_page_url":"https://hdl.handle.net/10945/69320","pdf_url":null,"source":{"id":"https://openalex.org/S4306400952","display_name":"Calhoun: The Naval Postgraduate School Institutional Archive (Naval Postgraduate School)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I35364215","host_organization_name":"Naval Postgraduate School","host_organization_lineage":["https://openalex.org/I35364215"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa564","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa564","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/17/4590/34220689/btaa564.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5074388257","display_name":null,"funder_award_id":"DMS 1916037","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3033594250.pdf","grobid_xml":"https://content.openalex.org/works/W3033594250.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W622812032","https://openalex.org/W1819566779","https://openalex.org/W1973011883","https://openalex.org/W2003064123","https://openalex.org/W2021636827","https://openalex.org/W2043228814","https://openalex.org/W2075118512","https://openalex.org/W2097706568","https://openalex.org/W2129682166","https://openalex.org/W2132926880","https://openalex.org/W2139086629","https://openalex.org/W2339614597","https://openalex.org/W2963626893","https://openalex.org/W2963866845","https://openalex.org/W3010934897","https://openalex.org/W3100255922","https://openalex.org/W3100433469","https://openalex.org/W3104688568","https://openalex.org/W4210681352","https://openalex.org/W6619594806","https://openalex.org/W6674647444"],"related_works":["https://openalex.org/W4280529077","https://openalex.org/W1493684871","https://openalex.org/W2964260221","https://openalex.org/W4298849132","https://openalex.org/W286253376","https://openalex.org/W2028961295","https://openalex.org/W2979973530","https://openalex.org/W4206048385","https://openalex.org/W3153154543","https://openalex.org/W2884974867"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":6}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
