{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,5,4]],"date-time":"2024-05-04T14:10:03Z","timestamp":1714831803067},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: To define V3 genetic elements and structural features underlying different HIV-1 co-receptor usage in vivo.<\/jats:p><jats:p>Results: By probabilistically modeling mutations in the viruses isolated from HIV-1 B subtype patients, we present a unique statistical procedure that would first identify V3 determinants associated with the usage of different co-receptors cooperatively or independently, and then delineate the complicated interactions among mutations functioning cooperatively. We built a model based on dual usage of CXCR4 and CCR5 co-receptors. The molecular basis of our statistical predictions is further confirmed by phenotypic and molecular modeling analyses. Our results provide new insights on molecular basis of different HIV-1 co-receptor usage. This is critical to optimize the use of genotypic tropism testing in clinical practice and to obtain molecular-implication for design of vaccine and new entry-inhibitors.<\/jats:p><jats:p>Contact: \u00a0jing.zhang.jz349@yale.edu or cf.perno@uniroma2.it<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt002","type":"journal-article","created":{"date-parts":[[2013,1,8]],"date-time":"2013-01-08T23:12:01Z","timestamp":1357686721000},"page":"451-460","source":"Crossref","is-referenced-by-count":13,"title":["Detecting and understanding genetic and structural features in HIV-1 B subtype V3 underlying HIV-1 co-receptor usage"],"prefix":"10.1093","volume":"29","author":[{"given":"Mengjie","family":"Chen","sequence":"first","affiliation":[{"name":"1 Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 2Department of Experimental Medicine and Surgery, University of Tor Vergata, Rome, 3Department of Health Sciences, University \u201cMagna Gr\u00e6ia\u201d of Catanzaro, Campus \u201cS. Venuta\u201d, Viale Europa, 88100, Catanzaro (CZ), Italy and 4Department of Statistics, Yale University, New Haven, CT 06511, USA"}]},{"given":"Valentina","family":"Svicher","sequence":"additional","affiliation":[{"name":"1 Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 2Department of Experimental Medicine and Surgery, University of Tor Vergata, Rome, 3Department of Health Sciences, University \u201cMagna Gr\u00e6ia\u201d of Catanzaro, Campus \u201cS. Venuta\u201d, Viale Europa, 88100, Catanzaro (CZ), Italy and 4Department of Statistics, Yale University, New Haven, CT 06511, USA"}]},{"given":"Anna","family":"Artese","sequence":"additional","affiliation":[{"name":"1 Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 2Department of Experimental Medicine and Surgery, University of Tor Vergata, Rome, 3Department of Health Sciences, University \u201cMagna Gr\u00e6ia\u201d of Catanzaro, Campus \u201cS. Venuta\u201d, Viale Europa, 88100, Catanzaro (CZ), Italy and 4Department of Statistics, Yale University, New Haven, CT 06511, USA"}]},{"given":"Giosu\u00e8","family":"Costa","sequence":"additional","affiliation":[{"name":"1 Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 2Department of Experimental Medicine and Surgery, University of Tor Vergata, Rome, 3Department of Health Sciences, University \u201cMagna Gr\u00e6ia\u201d of Catanzaro, Campus \u201cS. Venuta\u201d, Viale Europa, 88100, Catanzaro (CZ), Italy and 4Department of Statistics, Yale University, New Haven, CT 06511, USA"}]},{"given":"Claudia","family":"Alteri","sequence":"additional","affiliation":[{"name":"1 Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 2Department of Experimental Medicine and Surgery, University of Tor Vergata, Rome, 3Department of Health Sciences, University \u201cMagna Gr\u00e6ia\u201d of Catanzaro, Campus \u201cS. Venuta\u201d, Viale Europa, 88100, Catanzaro (CZ), Italy and 4Department of Statistics, Yale University, New Haven, CT 06511, USA"}]},{"given":"Francesco","family":"Ortuso","sequence":"additional","affiliation":[{"name":"1 Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 2Department of Experimental Medicine and Surgery, University of Tor Vergata, Rome, 3Department of Health Sciences, University \u201cMagna Gr\u00e6ia\u201d of Catanzaro, Campus \u201cS. Venuta\u201d, Viale Europa, 88100, Catanzaro (CZ), Italy and 4Department of Statistics, Yale University, New Haven, CT 06511, USA"}]},{"given":"Lucia","family":"Parrotta","sequence":"additional","affiliation":[{"name":"1 Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 2Department of Experimental Medicine and Surgery, University of Tor Vergata, Rome, 3Department of Health Sciences, University \u201cMagna Gr\u00e6ia\u201d of Catanzaro, Campus \u201cS. Venuta\u201d, Viale Europa, 88100, Catanzaro (CZ), Italy and 4Department of Statistics, Yale University, New Haven, CT 06511, USA"}]},{"given":"Yang","family":"Liu","sequence":"additional","affiliation":[{"name":"1 Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 2Department of Experimental Medicine and Surgery, University of Tor Vergata, Rome, 3Department of Health Sciences, University \u201cMagna Gr\u00e6ia\u201d of Catanzaro, Campus \u201cS. Venuta\u201d, Viale Europa, 88100, Catanzaro (CZ), Italy and 4Department of Statistics, Yale University, New Haven, CT 06511, USA"}]},{"given":"Chang","family":"Liu","sequence":"additional","affiliation":[{"name":"1 Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 2Department of Experimental Medicine and Surgery, University of Tor Vergata, Rome, 3Department of Health Sciences, University \u201cMagna Gr\u00e6ia\u201d of Catanzaro, Campus \u201cS. Venuta\u201d, Viale Europa, 88100, Catanzaro (CZ), Italy and 4Department of Statistics, Yale University, New Haven, CT 06511, USA"}]},{"given":"Carlo Federico","family":"Perno","sequence":"additional","affiliation":[{"name":"1 Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 2Department of Experimental Medicine and Surgery, University of Tor Vergata, Rome, 3Department of Health Sciences, University \u201cMagna Gr\u00e6ia\u201d of Catanzaro, Campus \u201cS. Venuta\u201d, Viale Europa, 88100, Catanzaro (CZ), Italy and 4Department of Statistics, Yale University, New Haven, CT 06511, USA"}]},{"given":"Stefano","family":"Alcaro","sequence":"additional","affiliation":[{"name":"1 Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 2Department of Experimental Medicine and Surgery, University of Tor Vergata, Rome, 3Department of Health Sciences, University \u201cMagna Gr\u00e6ia\u201d of Catanzaro, Campus \u201cS. Venuta\u201d, Viale Europa, 88100, Catanzaro (CZ), Italy and 4Department of Statistics, Yale University, New Haven, CT 06511, USA"}]},{"given":"Jing","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 2Department of Experimental Medicine and Surgery, University of Tor Vergata, Rome, 3Department of Health Sciences, University \u201cMagna Gr\u00e6ia\u201d of Catanzaro, Campus \u201cS. Venuta\u201d, Viale Europa, 88100, Catanzaro (CZ), Italy and 4Department of Statistics, Yale University, New Haven, CT 06511, USA"},{"name":"1 Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA, 2Department of Experimental Medicine and Surgery, University of Tor Vergata, Rome, 3Department of Health Sciences, University \u201cMagna Gr\u00e6ia\u201d of Catanzaro, Campus \u201cS. 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