{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T06:22:45Z","timestamp":1774333365166,"version":"3.50.1"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2021,5,22]],"date-time":"2021-05-22T00:00:00Z","timestamp":1621641600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"National Institute of Allergy"},{"name":"National Institute of Health","award":["UM1AI068635"],"award-info":[{"award-number":["UM1AI068635"]}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["S10OD028685"],"award-info":[{"award-number":["S10OD028685"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,18]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>A single monoclonal broadly neutralizing antibody (bnAb) regimen was recently evaluated in two randomized trials for prevention efficacy against HIV-1 infection. Subsequent trials will evaluate combination bnAb regimens (e.g. cocktails, multi-specific antibodies), which demonstrate higher potency and breadth in vitro compared to single bnAbs. Given the large number of potential regimens, methods for down-selecting these regimens into efficacy trials are of great interest.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We developed Super LeArner Prediction of NAb Panels (SLAPNAP), a software tool for training and evaluating machine learning models that predict in vitro neutralization sensitivity of HIV Envelope (Env) pseudoviruses to a given single or combination bnAb regimen, based on Env amino acid sequence features. SLAPNAP also provides measures of variable importance of sequence features. By predicting bnAb coverage of circulating sequences, SLAPNAP can improve ranking of bnAb regimens by their potential prevention efficacy. In addition, SLAPNAP can improve sieve analysis by defining sequence features that impact bnAb prevention efficacy.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availabilityand implementation<\/jats:title>\n                    <jats:p>SLAPNAP is a freely available docker image that can be downloaded from DockerHub (https:\/\/hub.docker.com\/r\/slapnap\/slapnap). Source code and documentation are available at GitHub (https:\/\/github.com\/benkeser\/slapnap and https:\/\/benkeser.github.io\/slapnap\/).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab398","type":"journal-article","created":{"date-parts":[[2021,5,21]],"date-time":"2021-05-21T15:13:55Z","timestamp":1621610035000},"page":"4187-4192","source":"Crossref","is-referenced-by-count":22,"title":["Super LeArner Prediction of NAb Panels (SLAPNAP): a containerized tool for predicting combination monoclonal broadly neutralizing antibody sensitivity"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7024-548X","authenticated-orcid":false,"given":"Brian D","family":"Williamson","sequence":"first","affiliation":[{"name":"Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center , Seattle, WA 98109, USA"}]},{"given":"Craig A","family":"Magaret","sequence":"additional","affiliation":[{"name":"Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center , Seattle, WA 98109, USA"}]},{"given":"Peter B","family":"Gilbert","sequence":"additional","affiliation":[{"name":"Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center , Seattle, WA 98109, USA"},{"name":"Department of Biostatistics, University of Washington , Seattle, WA 98195, USA"}]},{"given":"Sohail","family":"Nizam","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University , Atlanta, GA 30322, USA"}]},{"given":"Courtney","family":"Simmons","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University , Atlanta, GA 30322, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1019-8343","authenticated-orcid":false,"given":"David","family":"Benkeser","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University , Atlanta, GA 30322, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,5,22]]},"reference":[{"key":"2023051607110012800_btab398-B1","doi-asserted-by":"crossref","first-page":"1701","DOI":"10.1038\/s41591-018-0186-4","article-title":"Safety and antiviral activity of combination HIV-1 broadly neutralizing antibodies in viremic individuals","volume":"24","author":"Bar-On","year":"2018","journal-title":"Nat. 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