{"id":"https://openalex.org/W3129189990","doi":"https://doi.org/10.1093/bioinformatics/btab100","title":"PPIT: an R package for inferring microbial taxonomy from <i>nifH</i> sequences","display_name":"PPIT: an R package for inferring microbial taxonomy from <i>nifH</i> sequences","publication_year":2021,"publication_date":"2021-02-12","ids":{"openalex":"https://openalex.org/W3129189990","doi":"https://doi.org/10.1093/bioinformatics/btab100","mag":"3129189990","pmid":"https://pubmed.ncbi.nlm.nih.gov/33580675"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab100","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab100","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053891143","display_name":"Bennett J. Kapili","orcid":"https://orcid.org/0000-0003-3205-4137"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bennett J Kapili","raw_affiliation_strings":["Department of Earth System Science, Stanford University , Stanford, CA 94305, USA"],"affiliations":[{"raw_affiliation_string":"Department of Earth System Science, Stanford University , Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000544031","display_name":"Anne Dekas","orcid":"https://orcid.org/0000-0001-9548-8413"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anne E Dekas","raw_affiliation_strings":["Department of Earth System Science, Stanford University , Stanford, CA 94305, USA"],"affiliations":[{"raw_affiliation_string":"Department of Earth System Science, Stanford University , Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5053891143"],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.2871,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.79275963,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"37","issue":"16","first_page":"2289","last_page":"2298"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12640","display_name":"Environmental DNA in Biodiversity Studies","score":0.9829000234603882,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"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/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.7210758328437805},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6609928011894226},{"id":"https://openalex.org/keywords/taxonomy","display_name":"Taxonomy (biology)","score":0.6577919721603394},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.591090202331543},{"id":"https://openalex.org/keywords/amplicon","display_name":"Amplicon","score":0.5642600059509277},{"id":"https://openalex.org/keywords/horizontal-gene-transfer","display_name":"Horizontal gene transfer","score":0.5429257750511169},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.4903852939605713},{"id":"https://openalex.org/keywords/bacterial-taxonomy","display_name":"Bacterial taxonomy","score":0.4358904957771301},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.37529587745666504},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3417198061943054},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.29100310802459717},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.2731362581253052},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.25485745072364807},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2392807900905609},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.23222562670707703}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7210758328437805},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6609928011894226},{"id":"https://openalex.org/C58642233","wikidata":"https://www.wikidata.org/wiki/Q8269924","display_name":"Taxonomy (biology)","level":2,"score":0.6577919721603394},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.591090202331543},{"id":"https://openalex.org/C8185291","wikidata":"https://www.wikidata.org/wiki/Q2844457","display_name":"Amplicon","level":4,"score":0.5642600059509277},{"id":"https://openalex.org/C92938381","wikidata":"https://www.wikidata.org/wiki/Q83185","display_name":"Horizontal gene transfer","level":4,"score":0.5429257750511169},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.4903852939605713},{"id":"https://openalex.org/C124104306","wikidata":"https://www.wikidata.org/wiki/Q4840005","display_name":"Bacterial taxonomy","level":4,"score":0.4358904957771301},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.37529587745666504},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3417198061943054},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.29100310802459717},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.2731362581253052},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.25485745072364807},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2392807900905609},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.23222562670707703},{"id":"https://openalex.org/C42062724","wikidata":"https://www.wikidata.org/wiki/Q1209205","display_name":"16S ribosomal RNA","level":3,"score":0.0},{"id":"https://openalex.org/C49105822","wikidata":"https://www.wikidata.org/wiki/Q176996","display_name":"Polymerase chain reaction","level":3,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btab100","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab100","pdf_url":null,"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:33580675","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33580675","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}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Life below water","score":0.8700000047683716,"id":"https://metadata.un.org/sdg/14"}],"awards":[{"id":"https://openalex.org/G200853206","display_name":null,"funder_award_id":"OCE-1634297","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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":68,"referenced_works":["https://openalex.org/W1137788491","https://openalex.org/W1529156136","https://openalex.org/W1534233155","https://openalex.org/W1580609970","https://openalex.org/W1878020421","https://openalex.org/W1879581702","https://openalex.org/W1932864695","https://openalex.org/W1937431683","https://openalex.org/W2003437633","https://openalex.org/W2008559554","https://openalex.org/W2022456551","https://openalex.org/W2028302194","https://openalex.org/W2031611770","https://openalex.org/W2033900229","https://openalex.org/W2036897871","https://openalex.org/W2045083208","https://openalex.org/W2046183549","https://openalex.org/W2049046940","https://openalex.org/W2052639391","https://openalex.org/W2056279562","https://openalex.org/W2073416134","https://openalex.org/W2103528628","https://openalex.org/W2103901746","https://openalex.org/W2108949308","https://openalex.org/W2110994797","https://openalex.org/W2111647009","https://openalex.org/W2113153253","https://openalex.org/W2121710598","https://openalex.org/W2127303481","https://openalex.org/W2127536995","https://openalex.org/W2134136881","https://openalex.org/W2141052558","https://openalex.org/W2160378127","https://openalex.org/W2163677638","https://openalex.org/W2169750458","https://openalex.org/W2181731080","https://openalex.org/W2341722547","https://openalex.org/W2401404581","https://openalex.org/W2434665494","https://openalex.org/W2509381699","https://openalex.org/W2532482941","https://openalex.org/W2537307944","https://openalex.org/W2555218062","https://openalex.org/W2589779285","https://openalex.org/W2593591803","https://openalex.org/W2769258721","https://openalex.org/W2791465597","https://openalex.org/W2793664844","https://openalex.org/W2794501139","https://openalex.org/W2798209956","https://openalex.org/W2800461749","https://openalex.org/W2889019390","https://openalex.org/W2910117231","https://openalex.org/W2927961455","https://openalex.org/W2944021648","https://openalex.org/W2944850954","https://openalex.org/W2952921381","https://openalex.org/W2972679514","https://openalex.org/W2998382010","https://openalex.org/W3038126106","https://openalex.org/W3143110774","https://openalex.org/W4293278156","https://openalex.org/W6634604597","https://openalex.org/W6657345447","https://openalex.org/W6658825153","https://openalex.org/W6685426375","https://openalex.org/W6734427261","https://openalex.org/W6762319404"],"related_works":["https://openalex.org/W2995118009","https://openalex.org/W2487162673","https://openalex.org/W2786748503","https://openalex.org/W2942366970","https://openalex.org/W2793211469","https://openalex.org/W2949152769","https://openalex.org/W2086569686","https://openalex.org/W147961746","https://openalex.org/W3012252241","https://openalex.org/W3153538568"],"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":1},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2021-02-15T00:00:00"}
