{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:13Z","timestamp":1740185113921,"version":"3.37.3"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2017,5,4]],"date-time":"2017-05-04T00:00:00Z","timestamp":1493856000000},"content-version":"vor","delay-in-days":30,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R37AI054165","UM1AI068635","UM1AI068618"],"award-info":[{"award-number":["R37AI054165","UM1AI068635","UM1AI068618"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000005","name":"U.S. Department of Defense","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000005","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007812","name":"University of Washington","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007812","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000936","name":"Gordon and Betty Moore Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000936","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Analysis of HIV-1 virions from participants infected in a randomized controlled preventive HIV-1 vaccine efficacy trial can help elucidate mechanisms of partial protection. By comparing the genetic sequence of viruses from vaccine and placebo recipients to the sequence of the vaccine itself, a technique called \u2018sieve analysis\u2019, one can identify functional specificities of vaccine-induced immune responses. We have created an interactive web-based visualization and data access tool for exploring the results of sieve analyses performed on four major preventive HIV-1 vaccine efficacy trials: (i) the HIV Vaccine Trial Network (HVTN) 502\/Step trial, (ii) the RV144\/Thai trial, (iii) the HVTN 503\/Phambili trial and (iv) the HVTN 505 trial. The tool acts simultaneously as a platform for rapid reinterpretation of sieve effects and as a portal for organizing and sharing the viral sequence data. Access to these valuable datasets also enables the development of novel methodology for future sieve analyses.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>Visualization: http:\/\/sieve.fredhutch.org\/viz. Source code: https:\/\/github.com\/nkullman\/SIEVE. Data API: http:\/\/sieve.fredhutch.org\/data.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx168","type":"journal-article","created":{"date-parts":[[2017,3,22]],"date-time":"2017-03-22T00:55:07Z","timestamp":1490144107000},"page":"2386-2388","source":"Crossref","is-referenced-by-count":3,"title":["SieveSifter: a web-based tool for visualizing the sieve analyses of HIV-1 vaccine efficacy trials"],"prefix":"10.1093","volume":"33","author":[{"given":"Andrew","family":"Fiore-Gartland","sequence":"first","affiliation":[{"name":"Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA"},{"name":"eScience Institute, University of Washington, Seattle, WA, USA"}]},{"given":"Nicholas","family":"Kullman","sequence":"additional","affiliation":[{"name":"eScience Institute, University of Washington, Seattle, WA, USA"}]},{"given":"Allan C","family":"deCamp","sequence":"additional","affiliation":[{"name":"Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA"}]},{"given":"Graham","family":"Clenaghan","sequence":"additional","affiliation":[{"name":"eScience Institute, University of Washington, Seattle, WA, USA"}]},{"given":"Wayne","family":"Yang","sequence":"additional","affiliation":[{"name":"eScience Institute, University of Washington, Seattle, WA, USA"}]},{"given":"Craig A","family":"Magaret","sequence":"additional","affiliation":[{"name":"Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA"}]},{"given":"Paul T","family":"Edlefsen","sequence":"additional","affiliation":[{"name":"Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA"}]},{"given":"Peter B","family":"Gilbert","sequence":"additional","affiliation":[{"name":"Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA"},{"name":"Department of Biostatistics, University of Washington, Seattle, WA, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,4,4]]},"reference":[{"key":"2023063012501588500_btx168-B1","doi-asserted-by":"crossref","first-page":"1881","DOI":"10.1016\/S0140-6736(08)61591-3","article-title":"Efficacy assessment of a cell-mediated immunity HIV-1 vaccine (the Step Study): a double-blind, randomised, placebo-controlled, test-of-concept trial","volume":"372","author":"Buchbinder","year":"2008","journal-title":"Lancet"},{"key":"2023063012501588500_btx168-B2","doi-asserted-by":"crossref","first-page":"432","DOI":"10.1097\/COH.0b013e328362db2b","article-title":"Sieve analysis in HIV-1 vaccine efficacy trials","volume":"8","author":"Edlefsen","year":"2013","journal-title":"Curr. 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