{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T05:46:40Z","timestamp":1775800000086,"version":"3.50.1"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2021,1,20]],"date-time":"2021-01-20T00:00:00Z","timestamp":1611100800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"US National Science Foundation","doi-asserted-by":"crossref","award":["1513629"],"award-info":[{"award-number":["1513629"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000001","name":"US National Science Foundation","doi-asserted-by":"crossref","award":["1513615"],"award-info":[{"award-number":["1513615"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Illinois Campus Cluster and the Blue Waters supercomputer"},{"name":"UIUC in conjunction with the National Center for Supercomputing Applications"},{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["OCI-0725070"],"award-info":[{"award-number":["OCI-0725070"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["ACI-1238993"],"award-info":[{"award-number":["ACI-1238993"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"name":"State of Illinois"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Metagenomics has revolutionized microbiome research by enabling researchers to characterize the composition of complex microbial communities. Taxonomic profiling is one of the critical steps in metagenomic analyses. Marker genes, which are single-copy and universally found across Bacteria and Archaea, can provide accurate estimates of taxon abundances in the sample.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present TIPP2, a marker gene-based abundance profiling method, which combines phylogenetic placement with statistical techniques to control classification precision and recall. TIPP2 includes an updated set of reference packages and several algorithmic improvements over the original TIPP method. We find that TIPP2 provides comparable or better estimates of abundance than other profiling methods (including Bracken, mOTUsv2 and MetaPhlAn2), and strictly dominates other methods when there are under-represented (novel) genomes present in the dataset.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The code for our method is freely available in open-source form at https:\/\/github.com\/smirarab\/sepp\/blob\/tipp2\/README.TIPP.md. The code and procedure to create new reference packages for TIPP2 are available at https:\/\/github.com\/shahnidhi\/TIPP_reference_package.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab023","type":"journal-article","created":{"date-parts":[[2021,1,10]],"date-time":"2021-01-10T04:59:25Z","timestamp":1610254765000},"page":"1839-1845","source":"Crossref","is-referenced-by-count":30,"title":["TIPP2: metagenomic taxonomic profiling using phylogenetic markers"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7832-1264","authenticated-orcid":false,"given":"Nidhi","family":"Shah","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of Maryland College Park , College Park, MD 02740, USA"}]},{"given":"Erin K","family":"Molloy","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of California Los Angeles , CA 90095, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9617-5304","authenticated-orcid":false,"given":"Mihai","family":"Pop","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Maryland College Park , College Park, MD 02740, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7717-3514","authenticated-orcid":false,"given":"Tandy","family":"Warnow","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Illinois Urbana-Champaign , Urbana, IL 61801, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,1,20]]},"reference":[{"key":"2023051611461238900_btab023-B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. 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