{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,10]],"date-time":"2026-02-10T19:04:46Z","timestamp":1770750286374,"version":"3.50.0"},"reference-count":24,"publisher":"Springer Science and Business Media LLC","issue":"S8","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2016,8]]},"DOI":"10.1186\/s12859-016-1114-6","type":"journal-article","created":{"date-parts":[[2016,8,31]],"date-time":"2016-08-31T03:23:57Z","timestamp":1472613837000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":31,"title":["Automated prediction of HIV drug resistance from genotype data"],"prefix":"10.1186","volume":"17","author":[{"given":"ChenHsiang","family":"Shen","sequence":"first","affiliation":[]},{"given":"Xiaxia","family":"Yu","sequence":"additional","affiliation":[]},{"given":"Robert W.","family":"Harrison","sequence":"additional","affiliation":[]},{"given":"Irene T.","family":"Weber","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2016,8,31]]},"reference":[{"issue":"1","key":"1114_CR1","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/j.antiviral.2013.01.007","volume":"98","author":"L Menendez-Arias","year":"2013","unstructured":"Menendez-Arias L. Molecular basis of human immunodeficiency virus type 1 drug resistance: overview and recent developments. Antiviral Res. 2013;98(1):93\u2013120.","journal-title":"Antiviral Res"},{"issue":"5","key":"1114_CR2","doi-asserted-by":"crossref","first-page":"1587","DOI":"10.1097\/00126334-200412150-00011","volume":"37","author":"A Saracino","year":"2004","unstructured":"Saracino A, Monno L, Locaputo S, Torti C, Scudeller L, Ladisa N, Antinori A, Sighinolfi L, Chirianni A, Mazzotta F, et al. Selection of antiretroviral therapy guided by genotypic or phenotypic resistance testing: an open-label, randomized, multicenter study (PhenGen). J Acquir Immune Defic Syndr. 2004;37(5):1587\u201398.","journal-title":"J Acquir Immune Defic Syndr"},{"key":"1114_CR3","volume-title":"Benefits of resistance testing","author":"D Descamps","year":"2006","unstructured":"Descamps D, Brun-Vezinet F. In: Geretti AM, editor. Benefits of resistance testing. London: Antiretroviral Resistance in Clinical Practice; 2006."},{"issue":"9171","key":"1114_CR4","doi-asserted-by":"crossref","first-page":"2195","DOI":"10.1016\/S0140-6736(98)12291-2","volume":"353","author":"J Durant","year":"1999","unstructured":"Durant J, Clevenbergh P, Halfon P, Delgiudice P, Porsin S, Simonet P, Montagne N, Boucher CA, Schapiro JM, Dellamonica P. Drug-resistance genotyping in HIV-1 therapy: the VIRADAPT randomised controlled trial. Lancet. 1999;353(9171):2195\u20139.","journal-title":"Lancet"},{"issue":"4","key":"1114_CR5","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1097\/00002030-200203080-00009","volume":"16","author":"CJ Cohen","year":"2002","unstructured":"Cohen CJ, Hunt S, Sension M, Farthing C, Conant M, Jacobson S, Nadler J, Verbiest W, Hertogs K, Ames M, et al. A randomized trial assessing the impact of phenotypic resistance testing on antiretroviral therapy. AIDS. 2002;16(4):579\u201388.","journal-title":"AIDS"},{"key":"1114_CR6","volume-title":"Resistance assays","author":"M Schutten","year":"2006","unstructured":"Schutten M. In: Geretti AM, editor. Resistance assays. London: Antiretroviral Resistance in Clinical Practice; 2006."},{"key":"1114_CR7","first-page":"S1","volume":"15 Suppl 5","author":"X Yu","year":"2014","unstructured":"Yu X, Weber IT, Harrison RW. Prediction of HIV drug resistance from genotype with encoded three-dimensional protein structure. BMC Genomics. 2014;15 Suppl 5:S1.","journal-title":"BMC Genomics"},{"issue":"12","key":"1114_CR8","doi-asserted-by":"crossref","first-page":"8271","DOI":"10.1073\/pnas.112177799","volume":"99","author":"N Beerenwinkel","year":"2002","unstructured":"Beerenwinkel N, Schmidt B, Walter H, Kaiser R, Lengauer T, Hoffmann D, Korn K, Selbig J. Diversity and complexity of HIV-1 drug resistance: a bioinformatics approach to predicting phenotype from genotype. Proc Natl Acad Sci U S A. 2002;99(12):8271\u20136.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"5","key":"1114_CR9","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1086\/377453","volume":"188","author":"D Wang","year":"2003","unstructured":"Wang D, Larder B. Enhanced prediction of lopinavir resistance from genotype by use of artificial neural networks. J Infect Dis. 2003;188(5):653\u201360.","journal-title":"J Infect Dis"},{"issue":"13","key":"1114_CR10","doi-asserted-by":"crossref","first-page":"3850","DOI":"10.1093\/nar\/gkg575","volume":"31","author":"N Beerenwinkel","year":"2003","unstructured":"Beerenwinkel N, Daumer M, Oette M, Korn K, Hoffmann D, Kaiser R, Lengauer T, Selbig J, Walter H. Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes. Nucleic Acids Res. 2003;31(13):3850\u20135.","journal-title":"Nucleic Acids Res"},{"issue":"24","key":"1114_CR11","doi-asserted-by":"crossref","first-page":"2975","DOI":"10.1093\/bioinformatics\/btl508","volume":"22","author":"K Deforche","year":"2006","unstructured":"Deforche K, Silander T, Camacho R, Grossman Z, Soares MA, Van Laethem K, Kantor R, Moreau Y, Vandamme AM, non BW. Analysis of HIV-1 pol sequences using Bayesian Networks: implications for drug resistance. Bioinformatics. 2006;22(24):2975\u20139.","journal-title":"Bioinformatics"},{"issue":"11","key":"1114_CR12","doi-asserted-by":"crossref","first-page":"1608","DOI":"10.1086\/503914","volume":"42","author":"TF Liu","year":"2006","unstructured":"Liu TF, Shafer RW. Web resources for HIV type 1 genotypic-resistance test interpretation. Clin Infect Dis. 2006;42(11):1608\u201318.","journal-title":"Clin Infect Dis"},{"issue":"2","key":"1114_CR13","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1159\/000331999","volume":"55","author":"M Obermeier","year":"2012","unstructured":"Obermeier M, Pironti A, Berg T, Braun P, Daumer M, Eberle J, Ehret R, Kaiser R, Kleinkauf N, Korn K, et al. HIV-GRADE: a publicly available, rules-based drug resistance interpretation algorithm integrating bioinformatic knowledge. Intervirology. 2012;55(2):102\u20137.","journal-title":"Intervirology"},{"issue":"12","key":"1114_CR14","doi-asserted-by":"crossref","first-page":"1795","DOI":"10.1097\/00002030-200308150-00008","volume":"17","author":"F Brun-Vezinet","year":"2003","unstructured":"Brun-Vezinet F, Descamps D, Ruffault A, Masquelier B, Calvez V, Peytavin G, Telles F, Morand-Joubert L, Meynard JL, Vray M, et al. Clinically relevant interpretation of genotype for resistance to abacavir. AIDS. 2003;17(12):1795\u2013802.","journal-title":"AIDS"},{"issue":"8","key":"1114_CR15","doi-asserted-by":"crossref","first-page":"e1002639","DOI":"10.1371\/journal.pcbi.1002639","volume":"8","author":"E Humphris-Narayanan","year":"2012","unstructured":"Humphris-Narayanan E, Akiva E, Varela R, \u00d3 Conch\u00fair S, Kortemme T. Prediction of mutational tolerance in HIV-1 protease and reverse transcriptase using flexible backbone protein design. PLoS Comput Biol. 2012;8(8):e1002639.","journal-title":"PLoS Comput Biol"},{"key":"1114_CR16","first-page":"342","volume":"2013","author":"X Yu","year":"2013","unstructured":"Yu X, Weber IT, Harrison RW. Sparse representation for prediction of HIV-1 protease drug resistance. Proc SIAM Int Conf Data Min. 2013;2013:342\u20139.","journal-title":"Proc SIAM Int Conf Data Min"},{"issue":"1","key":"1114_CR17","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1093\/nar\/gkg100","volume":"31","author":"SY Rhee","year":"2003","unstructured":"Rhee SY, Gonzales MJ, Kantor R, Betts BJ, Ravela J, Shafer RW. Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Res. 2003;31(1):298\u2013303.","journal-title":"Nucleic Acids Res"},{"issue":"10","key":"1114_CR18","doi-asserted-by":"crossref","first-page":"4253","DOI":"10.1128\/AAC.00574-10","volume":"54","author":"SY Rhee","year":"2010","unstructured":"Rhee SY, Taylor J, Fessel WJ, Kaufman D, Towner W, Troia P, Ruane P, Hellinger J, Shirvani V, Zolopa A, et al. HIV-1 protease mutations and protease inhibitor cross-resistance. Antimicrob Agents Chemother. 2010;54(10):4253\u201361.","journal-title":"Antimicrob Agents Chemother"},{"issue":"5","key":"1114_CR19","doi-asserted-by":"crossref","first-page":"2305","DOI":"10.1128\/AAC.05487-11","volume":"56","author":"GL Melikian","year":"2012","unstructured":"Melikian GL, Rhee SY, Taylor J, Fessel WJ, Kaufman D, Towner W, Troia-Cancio PV, Zolopa A, Robbins GK, Kagan R, et al. Standardized comparison of the relative impacts of HIV-1 reverse transcriptase (RT) mutations on nucleoside RT inhibitor susceptibility. Antimicrob Agents Chemother. 2012;56(5):2305\u201313.","journal-title":"Antimicrob Agents Chemother"},{"issue":"8","key":"1114_CR20","doi-asserted-by":"crossref","first-page":"3122","DOI":"10.1128\/AAC.48.8.3122-3126.2004","volume":"48","author":"SY Rhee","year":"2004","unstructured":"Rhee SY, Liu T, Ravela J, Gonzales MJ, Shafer RW. Distribution of human immunodeficiency virus type 1 protease and reverse transcriptase mutation patterns in 4,183 persons undergoing genotypic resistance testing. Antimicrob Agents Chemother. 2004;48(8):3122\u20136.","journal-title":"Antimicrob Agents Chemother"},{"key":"1114_CR21","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1109\/BIBMW.2011.6112396","volume-title":"Bioinformatics and Biomedicine Workshops (BIBMW), 2011 IEEE International Conference on: 12\u201315 Nov. 2011","author":"P Bose","year":"2011","unstructured":"Bose P, Xiaxia Y, Harrison RW. Encoding protein structure with functions on graphs. In: Bioinformatics and Biomedicine Workshops (BIBMW), 2011 IEEE International Conference on: 12\u201315 Nov. 2011. 2011. p. 338\u201344."},{"key":"1114_CR22","doi-asserted-by":"crossref","unstructured":"Adeniyi DA, Wei Z, Yongquan Y. Automated web usage data mining and recommendation system using K-Nearest Neighbor (KNN) classification method. Applied Computing and Informatics. 2015. http:\/\/dx.doi.org\/10.1016\/j.aci.2014.10.001 .","DOI":"10.1016\/j.aci.2014.10.001"},{"issue":"8","key":"1114_CR23","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.4155\/fmc.15.44","volume":"7","author":"IT Weber","year":"2015","unstructured":"Weber IT, Kneller DW, Wong-Sam A. Highly resistant HIV-1 proteases and strategies for their inhibition. Future medicinal chemistry. 2015;7(8):1023\u201338.","journal-title":"Future medicinal chemistry"},{"key":"1114_CR24","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1186\/1756-0500-4-94","volume":"4","author":"D Heider","year":"2011","unstructured":"Heider D, Verheyen J, Hoffmann D. Machine learning on normalized protein sequences. BMC research notes. 2011;4:94.","journal-title":"BMC research notes"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1114-6","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,6,24]],"date-time":"2017-06-24T17:43:13Z","timestamp":1498326193000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-016-1114-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,8]]},"references-count":24,"journal-issue":{"issue":"S8","published-print":{"date-parts":[[2016,8]]}},"alternative-id":["1114"],"URL":"https:\/\/doi.org\/10.1186\/s12859-016-1114-6","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,8]]},"article-number":"278"}}