{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,13]],"date-time":"2025-09-13T16:36:54Z","timestamp":1757781414979},"reference-count":81,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2014,11,6]],"date-time":"2014-11-06T00:00:00Z","timestamp":1415232000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1003886","type":"journal-article","created":{"date-parts":[[2014,11,6]],"date-time":"2014-11-06T19:06:40Z","timestamp":1415300800000},"page":"e1003886","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":3,"title":["Estimating HIV-1 Fitness Characteristics from Cross-Sectional Genotype Data"],"prefix":"10.1371","volume":"10","author":[{"given":"Sathej","family":"Gopalakrishnan","sequence":"first","affiliation":[]},{"given":"Hesam","family":"Montazeri","sequence":"additional","affiliation":[]},{"given":"Stephan","family":"Menz","sequence":"additional","affiliation":[]},{"given":"Niko","family":"Beerenwinkel","sequence":"additional","affiliation":[]},{"given":"Wilhelm","family":"Huisinga","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2014,11,6]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.1056\/NEJMra025195","article-title":"HIV drug resistance","volume":"350","author":"F Clavel","year":"2004","journal-title":"N Engl J Med"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"995","DOI":"10.1038\/35073673","article-title":"HIV chemotherapy","volume":"410","author":"DD Richman","year":"2001","journal-title":"Nature"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1038\/373123a0","article-title":"Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection","volume":"373","author":"DD Ho","year":"1995","journal-title":"Nature"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1038\/387188a0","article-title":"Decay characteristics of HIV-1-infected compartments during combination therapy","volume":"387","author":"AS Perelson","year":"1997","journal-title":"Nature"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"4832","DOI":"10.1073\/pnas.0711372105","article-title":"Decay dynamics of HIV-1 depend on the inhibited stages of the viral life cycle","volume":"105","author":"AR Sedaghat","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"e1000720","DOI":"10.1371\/journal.pcbi.1000720","article-title":"Drug-class specific impact of antivirals on the reproductive capacity of HIV","volume":"6","author":"M von Kleist","year":"2010","journal-title":"PLoS Comput Biol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"6971","DOI":"10.1073\/pnas.94.13.6971","article-title":"Virus dynamics and drug therapy","volume":"94","author":"S Bonhoeffer","year":"1997","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"5037","DOI":"10.1128\/JVI.77.8.5037-5038.2003","article-title":"A novel antiviral intervention results in more accurate assessment of human immunodeficiency virus type 1 replication dynamics and T-cell decay in vivo","volume":"77","author":"M Markowitz","year":"2003","journal-title":"J Virol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1097\/00002030-199805000-00006","article-title":"The frequency of resistant mutant virus before antiviral therapy","volume":"12","author":"RM Ribeiro","year":"1998","journal-title":"AIDS"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"2027","DOI":"10.1007\/s11538-007-9203-3","article-title":"Emergence of HIV-1 drug resistance during antiretroviral treatment","volume":"69","author":"L Rong","year":"2007","journal-title":"Bull Math Biol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1128\/JVI.71.1.161-168.1997","article-title":"Clinical data sets of human immunodeficiency virus type 1 reverse transcriptase-resistant mutants explained by a mathematical model","volume":"71","author":"NI Stilianakis","year":"1997","journal-title":"J Virol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"8271","DOI":"10.1073\/pnas.112177799","article-title":"Diversity and complexity of HIV-1 drug resistance: a bioinformatics approach to predicting phenotype from genotype","volume":"99","author":"N Beerenwinkel","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1186\/1742-6405-8-26","article-title":"HIV-1 mutational pathways under multidrug therapy","volume":"8","author":"G Lawyer","year":"2011","journal-title":"AIDS Res Ther"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/1471-2105-12-5","article-title":"Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing","volume":"12","author":"MCF Prosperi","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"1321","DOI":"10.1073\/pnas.0907304107","article-title":"Detecting and understanding combinatorial mutation patterns responsible for HIV drug resistance","volume":"107","author":"J Zhang","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1","DOI":"10.2202\/1544-6115.1603","article-title":"Learning monotonic genotype-phenotype maps","volume":"10","author":"N Beerenwinkel","year":"2011","journal-title":"Stat Appl Genet Molec Biol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1186\/1471-2105-11-409","article-title":"Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape","volume":"11","author":"K Theys","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"e1003203","DOI":"10.1371\/journal.pcbi.1003203","article-title":"The individualized genetic barrier predicts treatment response in a large cohort of HIV-1 infected patients","volume":"9","author":"N Beerenwinkel","year":"2013","journal-title":"PLoS Comput Biol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"i16","DOI":"10.1093\/bioinformatics\/btg1001","article-title":"Methods for optimizing antiviral combination therapies","volume":"19","author":"N Beerenwinkel","year":"2003","journal-title":"Bioinformatics"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1137\/040603024","article-title":"Human immunodeficiency virus: quasispecies and drug resistance","volume":"3","author":"JM Murray","year":"2005","journal-title":"Multiscale Model Simul"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1126\/science.7824947","article-title":"HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy","volume":"267","author":"JM Coffin","year":"1995","journal-title":"Science"},{"key":"ref22","doi-asserted-by":"crossref","unstructured":"Goudsmit J (2004) Viral Fitness: The next SARS and West Nile in the making. Oxford University Press.","DOI":"10.1093\/acprof:oso\/9780195130348.001.0001"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"4440","DOI":"10.1103\/PhysRevLett.76.4440","article-title":"RNA virus evolution via a fitness-space model","volume":"76","author":"LS Tsimring","year":"1996","journal-title":"Phys Rev Lett"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"1031","DOI":"10.2202\/1544-6115.1031","article-title":"Relating HIV-1 sequence variation to replication capacity via trees and forests","volume":"3","author":"MR Segal","year":"2004","journal-title":"Stat Appl Genet Molec Biol"},{"key":"ref25","first-page":"1317","article-title":"Epistasis and shapes of fitness landscapes","volume":"17","author":"N Beerenwinkel","year":"2007","journal-title":"Stat Sinica"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"e1002551","DOI":"10.1371\/journal.pgen.1002551","article-title":"Exploring the complexity of the HIV-1 fitness landscape","volume":"8","author":"RD Kouyos","year":"2012","journal-title":"PLoS Genetics"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1016\/S1368-7646(02)00123-1","article-title":"Fitness of drug resistant HIV-1: methodology and clinical implications","volume":"5","author":"ME Qui\u00f1ones-Mateu","year":"2002","journal-title":"Drug Resist Update"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1038\/ng.795","article-title":"A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase","volume":"43","author":"T Hinkley","year":"2011","journal-title":"Nat Gen"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1128\/CMR.00017-07","article-title":"Clinical significance of human immunodeficiency virus type 1 replication fitness","volume":"20","author":"C Dykes","year":"2007","journal-title":"Clin Microbiol Rev"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"11067","DOI":"10.1128\/JVI.74.23.11067-11072.2000","article-title":"Estimating relative fitness in viral competition experiments","volume":"74","author":"AFM Mar\u00e9e","year":"2000","journal-title":"J Virol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"1887","DOI":"10.1098\/rspb.2002.2097","article-title":"Procedures for reliable estimation of viral fitness from time-series data","volume":"269","author":"S Bonhoeffer","year":"2002","journal-title":"Proc R Soc Lond B"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"6262","DOI":"10.1128\/JVI.74.14.6262-6268.2000","article-title":"Evolution of lamivudine resistance in human immunodeficiency virus type 1 - infected individuals: the relative roles of drift and selection","volume":"74","author":"SDW Frost","year":"2000","journal-title":"J Virol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"e1001012","DOI":"10.1371\/journal.pcbi.1001012","article-title":"Treatment-mediated alterations in HIV fitness preserve CD4+ T cell counts but have minimal effects on viral load","volume":"6","author":"NK Vaidya","year":"2010","journal-title":"PLoS Comput Biol"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"e18204","DOI":"10.1371\/journal.pone.0018204","article-title":"HIV quasispecies dynamics during pro-active treatment switching: impact on multi-drug resistance and resistance archiving in latent reservoirs","volume":"8","author":"M von Kleist","year":"2011","journal-title":"PLoS One"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"1378","DOI":"10.1038\/nm.2892","article-title":"Antiretroviral dynamics determines HIV evolution and predicts therapy outcome","volume":"18","author":"DI Rosenbloom","year":"2012","journal-title":"Nat Med"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1093\/nar\/gkg100","article-title":"Human immunodeficiency virus reverse transcriptase and protease sequence database","volume":"31","author":"SY Rhee","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"4099","DOI":"10.1128\/JCM.37.12.4099-4106.1999","article-title":"Mutation patterns of the reverse transcriptase and protease genes in human immunodeficiency virus type 1-infected patients undergoing combination therapy: survey of 787 sequences","volume":"37","author":"N Yahi","year":"1999","journal-title":"J Clin Microbiol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"904","DOI":"10.1086\/315329","article-title":"Patterns of resistance mutations selected by treatment of human immunodeficiency virus type 1 infection with zidovudine, didanosine, and nevirapine","volume":"181","author":"GJ Hanna","year":"2000","journal-title":"J Infect Dis"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"791","DOI":"10.1177\/135965350501000705","article-title":"Thymidine analogue mutation profiles: factors associated with acquiring specific profiles and their impact on the virological response to therapy","volume":"10","author":"A Cozzi-Lepri","year":"2005","journal-title":"Antivir Ther"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1093\/biomet\/asp023","article-title":"Markov models for accumulating mutations","volume":"96","author":"N Beerenwinkel","year":"2009","journal-title":"Biometrika"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"820","DOI":"10.1016\/S0140-6736(95)92963-0","article-title":"HIV-1 RNA serum-load and resistant viral genotypes during early zidovudine therapy","volume":"345","author":"C Loveday","year":"1995","journal-title":"The Lancet"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1016\/j.epidem.2012.10.001","article-title":"Pre-existence and emergence of drug resistance in a generalized model of intra-host viral dynamics","volume":"4","author":"HK Alexander","year":"2012","journal-title":"Epidemics"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"3773","DOI":"10.1128\/JVI.72.5.3773-3778.1998","article-title":"Relative replicative fitness of zidovudine-resistant human immunodeficiency virus type 1 isolates in vitro","volume":"72","author":"PR Harrigan","year":"1998","journal-title":"J Virol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"3744","DOI":"10.1128\/JVI.73.5.3744-3752.1999","article-title":"Replicative fitness of protease inhibitor-resistant mutants of human immunodeficiency virus type 1","volume":"73","author":"J Martinez-Picado","year":"1999","journal-title":"J Virol"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"5930","DOI":"10.1128\/JVI.70.9.5930-5934.1996","article-title":"Significance of amino acid variation at human immunodeficiency virus type 1 reverse transcriptase residue 210 for zidovudine susceptibility","volume":"70","author":"PR Harrigan","year":"1996","journal-title":"J Virol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"7020","DOI":"10.1128\/JVI.02747-05","article-title":"Fitness comparison of thymidine analog resistance pathways in human immunodeficiency virus type 1","volume":"80","author":"Z Hu","year":"2006","journal-title":"J Virol"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1002\/jmv.10550","article-title":"Thymidine analogue reverse transcriptase inhibitors resistance mutations profiles and association to other nucleoside reverse transcriptase inhibitors resistance mutations observed in the context of virological failure","volume":"72","author":"AG Marcelin","year":"2004","journal-title":"J Med Virol"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"1172","DOI":"10.1093\/infdis\/171.5.1172","article-title":"Prevalence and clinical significance of zidovudine resistance mutations in human immunodeficiency virus isolated from patients after longterm zidovudine treatment","volume":"171","author":"AJ Japour","year":"1995","journal-title":"J Infect Dis"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"3037","DOI":"10.1128\/JVI.02712-06","article-title":"The fitness cost of mutations associated with human immunodeficiency virus type 1 drug resistance is modulated by mutational interactions","volume":"81","author":"M Cong","year":"2007","journal-title":"J Virol"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"5501","DOI":"10.1073\/pnas.93.11.5501","article-title":"Host-parasite dynamics and outgrowth of virus containing a single K70R amino acid change in reverse transcriptase are responsible for the loss of human immunodeficiency virus type 1 RNA load suppression by zidovudine","volume":"93","author":"MD De Jong","year":"1996","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1056\/NEJM199709113371102","article-title":"Treatment with indinavir, zidovudine, and lamivudine in adults with human immunodeficiency virus infection and prior antiretroviral therapy","volume":"337","author":"RM Gulick","year":"1997","journal-title":"N Engl J Med"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"35","DOI":"10.7326\/0003-4819-133-1-200007040-00007","article-title":"3-year suppression of HIV viremia with indinavir, zidovudine, and lamivudine","volume":"133","author":"RM Gulick","year":"2000","journal-title":"Ann Intern Med"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"2349","DOI":"10.1097\/00002030-199912030-00006","article-title":"Increased fitness of drug resistant HIV-1 protease as a result of acquisition of compensatory mutations during suboptimal therapy","volume":"13","author":"M Nijhuis","year":"1999","journal-title":"AIDS"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1007\/BF02253518","article-title":"HIV-1 evolution under pressure of protease inhibitors: climbing the stairs of viral fitness","volume":"6","author":"B Berkhout","year":"1999","journal-title":"J Biomed Sci"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1086\/510533","article-title":"Persistence of HIV-1 variants with multiple protease inhibitor resistance mutations in the absence of PI therapy can be explained by compensatory fixation","volume":"195","author":"NM van Maarseveen","year":"2007","journal-title":"J Infect Dis"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"8524","DOI":"10.1128\/JVI.74.18.8524-8531.2000","article-title":"Retracing the evolutionary pathways of human immunodeficiency virus type 1 resistance to protease inhibitors: virus fitness in the absence and in the presence of drug","volume":"74","author":"F Mammano","year":"2000","journal-title":"J Virol"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1128\/AAC.05549-11","article-title":"Interplay between single resistance-associated mutations in the HIV-1 protease and viral infectivity, protease activity and inhibitor sensitivity","volume":"56","author":"GJ Henderson","year":"2012","journal-title":"Antimicrob Agents Chemother"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1177\/135965350400900312","article-title":"Infrequent transmission of HIV-1 drug-resistant variants","volume":"9","author":"S Yerly","year":"2004","journal-title":"Antivir Ther"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1086\/380098","article-title":"Strong cell-mediated immune responses are associated with the maintenance of low-level viremia in antiretroviral-treated individuals with drug-resistant human immunodeficiency virus type 1","volume":"189","author":"SG Deeks","year":"2004","journal-title":"J Infect Dis"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1056\/NEJM200102153440702","article-title":"Virologic and immunologic consequences of discontinuing combination antiretroviral-drug therapy in HIV-infected patients with detectable viremia","volume":"344","author":"SG Deeks","year":"2001","journal-title":"N Engl J Med"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"e1002321","DOI":"10.1371\/journal.ppat.1002321","article-title":"Assessing predicted HIV-1 replicative capacity in a clinical setting","volume":"7","author":"RD Kouyos","year":"2011","journal-title":"PLoS Pathogens"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1001\/jama.283.2.229","article-title":"Drug susceptibility in HIV infection after viral rebound in patients receiving indinavir-containing regimens","volume":"283","author":"DV Havlir","year":"2000","journal-title":"JAMA"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"1167","DOI":"10.1089\/aid.2011.0256","article-title":"No evidence for evolution of protease inhibitor resistance from standard genotyping, after three years of treatment with darunavir\/ritonavir, with or without nucleoside analogues","volume":"28","author":"F Pulido","year":"2012","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1146\/annurev.pharmtox.40.1.67","article-title":"Pharmacokinetic\/pharmacodynamic modeling in drug development","volume":"40","author":"LB Sheiner","year":"2000","journal-title":"Annu Rev Pharmacol Toxicol"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1137\/S0036144598335107","article-title":"Mathematical analysis of HIV-1 dynamics in vivo","volume":"41","author":"AS Perelson","year":"1999","journal-title":"SIAM Review"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1051\/proc:2005001","article-title":"Exact simulation of hybrid stochastic and deterministic models for biochemical systems","volume":"14","author":"A Alfonsi","year":"2005","journal-title":"ESAIM Proc"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"e1000305","DOI":"10.1371\/journal.pcbi.1000305","article-title":"Timing the emergence of resistance to anti-HIV drugs with large genetic barriers","volume":"5","author":"P Arora","year":"2009","journal-title":"PLoS Computational Biology"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"6662","DOI":"10.1128\/JVI.71.9.6662-6670.1997","article-title":"Drug resistance during indinavir therapy is caused by mutations in the protease gene and in its Gag substrate cleavage sites","volume":"71","author":"YM Zhang","year":"1997","journal-title":"J Virol"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"6146","DOI":"10.1128\/JVI.72.7.6146-6150.1998","article-title":"Novel Gag-Pol frameshift site in human immunodeficiency virus type 1 variants resistant to protease inhibitors","volume":"72","author":"L Doyon","year":"1998","journal-title":"J Virol"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"5087","DOI":"10.1128\/JVI.69.8.5087-5094.1995","article-title":"Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase","volume":"69","author":"LM Mansky","year":"1995","journal-title":"J Virol"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"1271","DOI":"10.1016\/j.cell.2012.02.021","article-title":"Outwitting evolution: fighting drug resistant TB, malaria and HIV","volume":"148","author":"D Goldberg","year":"2012","journal-title":"Cell"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"e1002359","DOI":"10.1371\/journal.pcbi.1002359","article-title":"HIV-1 polymerase inhibition by nucleoside analogs: cellular- and kinetic parameters of efficacy, susceptibility and resistance selection","volume":"6","author":"M von Kleist","year":"2012","journal-title":"PLoS Comput Biol"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"e36494","DOI":"10.1371\/journal.pone.0036494","article-title":"Low-cost ultra-wide genotyping using Roche\/454 pyrosequencing for surveillance of HIV drug resistance","volume":"7","author":"DM Dudley","year":"2012","journal-title":"PLoS One"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"7895","DOI":"10.1128\/JVI.71.10.7895-7902.1997","article-title":"Neutralization sensitivity of cell culture-passaged simian immunodeficiency virus","volume":"71","author":"RE Means","year":"1997","journal-title":"J Virol"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"920","DOI":"10.1128\/AAC.44.4.920-928.2000","article-title":"A novel phenotypic drug susceptibility assay for human immunodeficiency virus type 1","volume":"44","author":"CJ Petropoulos","year":"2000","journal-title":"Antimicrob Agents Chemother"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1128\/AAC.42.2.269","article-title":"A rapid method for simultaneous detection of phenotypic resistance to inhibitors of protease and reverse transcriptase in recombinant human immunodeficiency virus type 1 isolates from patients treated with antiretroviral drugs","volume":"42","author":"K Hertogs","year":"1998","journal-title":"Antimicrob Agents Chemother"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"3559","DOI":"10.1128\/JCM.41.8.3559-3565.2003","article-title":"Quality control trial for human immunodeficiency virus type 1 drug resistance testing using clinical samples reveals problems with detecting minority species and interpretation of test results","volume":"41","author":"K Korn","year":"2003","journal-title":"J Clin Microbiol"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1093\/comjnl\/7.4.308","article-title":"A simplex method for function minimization","volume":"7","author":"J Nelder","year":"1965","journal-title":"The Computer Journal"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"e189","DOI":"10.1371\/journal.pcbi.0030189","article-title":"Universally sloppy parameter sensitivities in systems biology models","volume":"3","author":"RN Gutenkunst","year":"2007","journal-title":"PLoS Comput Biol"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"e27755","DOI":"10.1371\/journal.pone.0027755","article-title":"Structural identifiability of systems biology models: A critical comparison of methods","volume":"6","author":"OT Chis","year":"2011","journal-title":"PLoS One"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1038\/msb.2008.74","article-title":"Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data","volume":"5","author":"WW Chen","year":"2009","journal-title":"Mol Syst Biol"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003886","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,4,21]],"date-time":"2022-04-21T15:51:19Z","timestamp":1650556279000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003886"}},"subtitle":[],"editor":[{"given":"Sergei L kosakovsky.","family":"Pond","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2014,11,6]]},"references-count":81,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2014,11,6]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1003886","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,11,6]]}}}