{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,3,31]],"date-time":"2022-03-31T13:57:27Z","timestamp":1648735047259},"reference-count":62,"publisher":"Springer Science and Business Media LLC","issue":"4","license":[{"start":{"date-parts":[[2010,10,14]],"date-time":"2010-10-14T00:00:00Z","timestamp":1287014400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Swarm Intell"],"published-print":{"date-parts":[[2010,12]]},"DOI":"10.1007\/s11721-010-0046-4","type":"journal-article","created":{"date-parts":[[2010,10,14]],"date-time":"2010-10-14T07:45:44Z","timestamp":1287042344000},"page":"319-340","source":"Crossref","is-referenced-by-count":0,"title":["An integrated modelling approach for R5\u2013X4 mutation and HAART therapy assessment"],"prefix":"10.1007","volume":"4","author":[{"given":"Anil","family":"Sorathiya","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrea","family":"Bracciali","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pietro","family":"Li\u00f2","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2010,10,14]]},"reference":[{"issue":"5","key":"46_CR1","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1000390","volume":"5","author":"S. Agrawal","year":"2009","unstructured":"Agrawal, S., Archer, C., & Schaffer, D. V. (2009). Computational models of the notch network elucidate mechanisms of context-dependent signalling. PLoS Computational Biology, 5(5), e1000390.","journal-title":"PLoS Computational Biology"},{"issue":"7","key":"46_CR2","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1000103","volume":"4","author":"C. L. Althaus","year":"2008","unstructured":"Althaus, C. L., & De Boer, R. J. (2008). Dynamics of immune escape during HIV\/SIV infection. PLOS Computational Biology, 4(7), e1000103.","journal-title":"PLOS Computational Biology"},{"issue":"4","key":"46_CR3","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.0040090","volume":"4","author":"B. Asquith","year":"2006","unstructured":"Asquith, B., Edwards, C. T. T., Lipsitch, M., & McLean, A. R. (2006). Inefficient cytotoxic T lymphocyte mediated killing of HIV-1 infected cells in vivo. PLOS Biology, 4(4), e90.","journal-title":"PLOS Biology"},{"issue":"1","key":"46_CR4","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1145\/343369.343402","volume":"1","author":"A. Aziz","year":"2000","unstructured":"Aziz, A., Sanwal, K., Singhal, V., & Brayton, R. (2000). Model checking continuous time Markov chains. ACM Transactions on Computational Logic, 1(1), 162\u2013170.","journal-title":"ACM Transactions on Computational Logic"},{"issue":"6","key":"46_CR5","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1109\/TSE.2003.1205180","volume":"29","author":"C. Baier","year":"2003","unstructured":"Baier, C., Haverkort, B., Hermanns, H., & Katoen, J. P. (2003). Model-checking algorithms for continuous-time Markov chains. IEEE Transaction on Software Engineering, 29(6), 524\u2013541.","journal-title":"IEEE Transaction on Software Engineering"},{"key":"46_CR6","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1038\/nm0297-205","volume":"3","author":"P. Borrow","year":"1997","unstructured":"Borrow, P., Lewicki, H., Wei, X., Horwitz, M. S., Peffer, N., Meyers, H., Nelson, J. A., Gairin, J. E., Hahn, B.\u00a0H., Oldstone, M. B. A., & Shaw, G. M. (1997). Antiviral pressure exerted by HIV-1 specific cytotoxic T lymphocytes (CTLs) during primary infection demonstrated by rapid selection of CTL escape virus. Nature Medicine, 3, 205\u2013211.","journal-title":"Nature Medicine"},{"key":"46_CR7","doi-asserted-by":"crossref","first-page":"1163","DOI":"10.1084\/jem.168.3.1163","volume":"168","author":"M. J. Cannon","year":"1988","unstructured":"Cannon, M. J., Openshaw, P. J., & Askonas, B. A. (1988). Cytotoxic T cells clear virus but augment lung pathology in mice infected with respiratory syncytial virus. The Journal of Experimental Medicine, 168, 1163\u20131168.","journal-title":"The Journal of Experimental Medicine"},{"key":"46_CR8","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1146\/annurev.med.54.101601.152346","volume":"54","author":"M. Carrington","year":"2003","unstructured":"Carrington, M., & OBrien, S. J. (2003). The influence of HLA genotype on AIDS. Annual Review of Medicine, 54, 535\u2013551.","journal-title":"Annual Review of Medicine"},{"key":"46_CR9","doi-asserted-by":"crossref","first-page":"6508","DOI":"10.1128\/JVI.75.14.6508-6516.2001","volume":"75","author":"J. Casazza","year":"2001","unstructured":"Casazza, J., Betts, M., Picker, L., & Koup, R. (2001). Decay kinetics of human immunodeficiency virus-specific CD8+ T cells in peripheral blood after initiation of highly active antiretroviral therapy. Journal of Virology, 75, 6508\u20136516.","journal-title":"Journal of Virology"},{"key":"46_CR10","first-page":"1350","volume":"26","author":"F. Celada","year":"1996","unstructured":"Celada, F., & Seiden, P. E. (1996). Affinity maturation and hypermutation in a simulation of the humoral immune response. Journal of Immunology, 26, 1350\u20131358.","journal-title":"Journal of Immunology"},{"key":"46_CR11","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1016\/j.jtbi.2003.12.011","volume":"228","author":"L. Chao","year":"2004","unstructured":"Chao, L., Davenport, M. P., Forrest, S., & Perelson, A. S. (2004). A stochastic model of cytotoxic T cell responses. Theoretical Biology, 228, 227\u2013240.","journal-title":"Theoretical Biology"},{"issue":"33","key":"46_CR12","doi-asserted-by":"crossref","first-page":"3065","DOI":"10.1016\/j.tcs.2009.02.037","volume":"410","author":"F. Ciocchetta","year":"2009","unstructured":"Ciocchetta, F., & Hillston, J. (2009). Bio-PEPA: a framework for the modelling and analysis of biochemical networks. Theoretical Computer Science, 410(33), 3065\u20133084.","journal-title":"Theoretical Computer Science"},{"key":"46_CR13","volume-title":"Model checking","author":"E. M. Clarke","year":"1999","unstructured":"Clarke, E. M., Grumberg, O., & Peled, D. A. (1999). Model checking. Cambridge: MIT Press."},{"key":"46_CR14","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1006\/jtbi.1995.0165","volume":"175","author":"R. J. Boer De","year":"1995","unstructured":"De Boer, R. J., & Perelson, A. S. (1995). Towards a general function describing T-cell proliferation. Journal of Theoretical Biology, 175, 657\u2013576.","journal-title":"Journal of Theoretical Biology"},{"issue":"2","key":"46_CR15","doi-asserted-by":"crossref","first-page":"381","DOI":"10.7326\/0003-4819-137-5_Part_2-200209031-00001","volume":"137","author":"M. Dybul","year":"2002","unstructured":"Dybul, M., Fauci, A. S., Bartlett, J. G., Kaplan, J. E., & Pau, A. K. (2002). Panel on clinical practices for treatment of HIV (September 2002): guidelines for using antiretroviral agents among HIV-infected adults and adolescents. Annals of Internal Medicine, 137(2), 381\u2013433.","journal-title":"Annals of Internal Medicine"},{"key":"46_CR16","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1038\/8394","volume":"5","author":"D. Finzi","year":"1999","unstructured":"Finzi, D., Blankson, J., Siliciano, J. D., Margolick, J. B., Chadwick, K., et al. (1999). Latent infection of CD4+ T cells provides a mechanism for lifelong persistence of HIV-1, even in patients on effective combination therapy. Nature Medicine, 5, 512\u2013517.","journal-title":"Nature Medicine"},{"issue":"5","key":"46_CR17","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.0030092","volume":"3","author":"J. Fisher","year":"2007","unstructured":"Fisher, J., Piterman, N., Hajnal, A., & Henzinger, T. A. (2007). Predictive modeling of signalling crosstalk during C. elegans vulval development. PLoS Computational Biology, 3(5), e92.","journal-title":"PLoS Computational Biology"},{"key":"46_CR18","first-page":"4595","volume-title":"The 29th annual international conference of the IEEE EMBS","author":"J. Fromentin","year":"2007","unstructured":"Fromentin, J., Comet, J. P., Le Gall, P., & Roux, O. (2007). Analysing gene regulatory networks by both constraint programming and model-checking. In The 29th annual international conference of the IEEE EMBS (pp. 4595\u20134598). Washington: IEEE Press."},{"issue":"1677","key":"46_CR19","doi-asserted-by":"crossref","first-page":"4389","DOI":"10.1098\/rspb.2009.1232","volume":"276","author":"H. R. Fryer","year":"2009","unstructured":"Fryer, H. R., Scherer, A., Oxenius, A., Phillips, R., & McLean, A. R. (2009). No evidence for competition between cytotoxic T-lymphocyte responses in HIV-1 infection. Proceeding of Royal Society of Biosciences, 276(1677), 4389\u20134397.","journal-title":"Proceeding of Royal Society of Biosciences"},{"issue":"3","key":"46_CR20","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.0020024","volume":"2","author":"V. V. Ganusov","year":"2005","unstructured":"Ganusov, V. V., & De Boer, R. J. (2005). Estimating costs and benefits of CTL escape mutations in SIV\/HIV infection. PLoS Computational Biology, 2(3), e24.","journal-title":"PLoS Computational Biology"},{"key":"46_CR21","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1016\/j.virol.2005.04.034","volume":"337","author":"L. Gray","year":"2005","unstructured":"Gray, L., Sterjovski, J., Churchill, M., Ellery, P., Nasr, N., Lewin, S. R., Crowe, S. M., Wesselingh, S. L., Cunningham, A. L., & Gorry, P. R. (2005). Uncoupling coreceptor usage of human immunodeficiency virus type 1 (HIV-1) from macrophage tropism reveals biological properties of CCR5-restricted HIV-1 isolates from patients with acquired immunodeficiency syndrome. Virology, 337, 384\u2013398.","journal-title":"Virology"},{"key":"46_CR22","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1146\/annurev.immunol.20.100301.064828","volume":"20","author":"P. Guermonprez","year":"2002","unstructured":"Guermonprez, P., Valladeau, J., Zitvogel, L., Thery, C., & Amigorena, S. (2002). Antigen presentation and T cell stimulation by dendritic cells. Annual Review of Immunology, 20, 621\u2013667.","journal-title":"Annual Review of Immunology"},{"key":"46_CR23","doi-asserted-by":"crossref","first-page":"625","DOI":"10.1146\/annurev.immunol.17.1.625","volume":"17","author":"A. T. Haase","year":"1999","unstructured":"Haase, A. T. (1999). Population biology of HIV-1 infection: viral and CD4+ T cell demography and dynamics in lymphatic tissues. Annual Review of Immunology, 17, 625\u2013656.","journal-title":"Annual Review of Immunology"},{"key":"46_CR24","doi-asserted-by":"crossref","first-page":"13974","DOI":"10.1073\/pnas.0505251102","volume":"102","author":"J. P. Herbeuval","year":"2005","unstructured":"Herbeuval, J. P., Hardy, A. W., Boasso, A., Anderson, S. A., Dolan, M. J., Dy, M., & Shearer, G. M. (2005). Regulation of TNF-related apoptosis-inducing ligand on primary CD4+ T cells by HIV-1: role of type I IFN-producing plasmacytoid dendritic cells. Proceedings of the National Academy of Sciences of the United States of America, 102, 13974\u201313979.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"46_CR25","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1038\/373123a0","volume":"373","author":"D. Ho","year":"1995","unstructured":"Ho, D., Neumann, A. U., Perelson, A. S., Chen, W., Leonard, J. M., & Markowitz, M. (1995). Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection. Nature, 373, 123\u2013126.","journal-title":"Nature"},{"key":"46_CR26","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1084\/jem.189.6.991","volume":"189","author":"X. Jin","year":"1999","unstructured":"Jin, X., Bauer, D. E., Tuttleton, S. E., Lewin, S., Gettie, A., Blanchard, J., Irwin, C. E., Safrit, J. T., Mittler, J., Weinberger, L., Kostrikis, L. G., Zhang, L., Perelson, A. S., & Ho, D. D. (1999). Dramatic rise in plasma viremia after CD8+ T cell depletion in simian immunodeficiency virusinfected macaques. The\u00a0Journal of Experimental Medicine, 189, 991\u2013998.","journal-title":"The\u00a0Journal of Experimental Medicine"},{"key":"46_CR27","doi-asserted-by":"crossref","first-page":"6721","DOI":"10.1128\/JVI.73.8.6721-6728.1999","volume":"73","author":"S. A. Kalams","year":"1999","unstructured":"Kalams, S. A., Goulder, P. J., Shea, A. K., Jones, N. G., Trocha, A. K., Ogg, G. S., & Walker, B. D. (1999). Levels of human immunodeficiency virus type 1-specific cytotoxic T-lymphocyte effector and memory responses decline after suppression of viremia with highly active antiretroviral therapy. Journal of Virology, 73, 6721\u20136728.","journal-title":"Journal of Virology"},{"key":"46_CR28","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1038\/nm0496-405","volume":"2","author":"R. Kaslow","year":"1996","unstructured":"Kaslow, R., Carrington, M., Apple, R., Park, L., Munoz, A., Saah, A. J., Goedert, J. J., Winkler, C., O\u2019Brien, S. J., Rinaldo, C., Detels, R., Blattner, W., Phair, J., Erlich, H., & Mann, D. L. (1996). Influence of combinations of human major histocompatibility complex genes on the course of HIV-1 infection. Nature Medicine, 2, 405\u2013411.","journal-title":"Nature Medicine"},{"key":"46_CR29","first-page":"391","volume-title":"Natural computing series","author":"M. Kwiatkowska","year":"2009","unstructured":"Kwiatkowska, M., Norman, G., & Parker, D. (2009). Algorithmic bioprocesses: quantitative verification techniques for biological processes. In A. Condon, D. Harel, J. Kok, A. Salomaa, & E. Winfree (Eds.), Natural computing series (pp. 391\u2013409). Berlin: Springer."},{"key":"46_CR30","unstructured":"Kwiatkowska, The PRISM model checker. Internet Engineering Task Force. http:\/\/www.prismmodelchecker.org ."},{"key":"46_CR31","doi-asserted-by":"crossref","first-page":"4644","DOI":"10.1073\/pnas.86.12.4644","volume":"86","author":"S. P. Layne","year":"1998","unstructured":"Layne, S. P., Spouge, J. L., & Dembo, M. (1998). Quantifying the infectivity of human immunodeficiency virus. Proceedings of the National Academy of Sciences of the United States of America, 86, 4644\u20134648.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"1","key":"46_CR32","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1021\/bp070255h","volume":"24","author":"H. Li","year":"2008","unstructured":"Li, H., Cao, Y., Petzold, L. R., & Gillespie, D. T. (2008). Algorithms and software for stochastic simulation of biochemical reacting systems. Biotechnology Progress, 24(1), 56\u201361.","journal-title":"Biotechnology Progress"},{"key":"46_CR33","doi-asserted-by":"crossref","first-page":"5087","DOI":"10.1128\/JVI.69.8.5087-5094.1995","volume":"69","author":"L. Mansky","year":"1995","unstructured":"Mansky, L., & Temin, H. (1995). Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. Journal of Virology, 69, 5087\u20135094.","journal-title":"Journal of Virology"},{"issue":"2B","key":"46_CR34","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1142\/S0219720007002850","volume":"5","author":"D. Mateus","year":"2007","unstructured":"Mateus, D., Gallois, J. P., Comet, J. P., & Le\u00a0Gall, P. (2007). Symbolic modeling of genetic regulatory networks. Journal of Bioinformatics and Computational Biology, 5(2B), 627\u2013640.","journal-title":"Journal of Bioinformatics and Computational Biology"},{"issue":"12","key":"46_CR35","doi-asserted-by":"crossref","first-page":"1405","DOI":"10.1097\/00002030-199112000-00001","volume":"5","author":"T. Matsuyama","year":"1991","unstructured":"Matsuyama, T., Kobayashi, N., & Yamamoto, N. (1991). Cytokines and HIV infection: is AIDS a tumor necrosis factor disease? AIDS, 5(12), 1405\u20131417.","journal-title":"AIDS"},{"key":"46_CR36","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1038\/360264a0","volume":"360","author":"C. A. Michie","year":"1992","unstructured":"Michie, C. A., McLean, A., Alcock, C., & Beverly, P. C. L. (1992). Lifespan of human lymphocyte subsets defined by CD45 isoforms. Nature, 360, 264.","journal-title":"Nature"},{"issue":"11","key":"46_CR37","doi-asserted-by":"crossref","first-page":"1415","DOI":"10.1097\/00002030-199907300-00023","volume":"13","author":"J. E. Mittler","year":"1999","unstructured":"Mittler, J. E., Markowitz, M., Ho, D. D., & Perelson, A. S. (1999). Improved estimates for HIV-1 clearance rate and intracellular delay. AIDS, 13(11), 1415\u20131417.","journal-title":"AIDS"},{"issue":"5","key":"46_CR38","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/S0025-5564(98)10046-9","volume":"154","author":"J. M. Murray","year":"1998","unstructured":"Murray, J. M., Kaufmann, G., Kelleher, A. D., & Cooper, D. A. (1998). A model of primary HIV infection. Mathematical Biosciences, 154(5), 57\u201385.","journal-title":"Mathematical Biosciences"},{"key":"46_CR39","doi-asserted-by":"crossref","first-page":"797","DOI":"10.1128\/JVI.73.1.797-800.1999","volume":"73","author":"G. Ogg","year":"1999","unstructured":"Ogg, G., Jin, X., Bonhoeffer, S., Moss, P., Nowak, M., Monard, S., Segal, J. P., Cao, Y., Rowland-Jones, S. L., Hurley, A., Markowitz, M., Ho, D. D., McMichael, A. J., & Nixon, D. F. (1999). Decay kinetics of human immunodeficiency virus-specific effector cytotoxic T lymphocytes after combination antiretroviral therapy. Journal of Virology, 73, 797\u2013800.","journal-title":"Journal of Virology"},{"key":"46_CR40","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1056\/NEJM199302043280508","volume":"328","author":"G. Pantaleo","year":"1993","unstructured":"Pantaleo, G., Graziosi, C., & Fauci, A. S. (1993). The immunopathogenesis of human immunodeficiency virus infection. The New England Journal of Medicine, 328, 327\u2013335.","journal-title":"The New England Journal of Medicine"},{"key":"46_CR41","volume-title":"Differential effects of TNF on HIV-1 expression: R5 inhibition and implications for viral evolution","author":"G. N. Pavlakis","year":"2004","unstructured":"Pavlakis, G. N., Valentin, A., Morrow, M., & Yarchoan, R. (2004). Differential effects of TNF on HIV-1 expression: R5 inhibition and implications for viral evolution. Frederick: International Conference AIDS."},{"key":"46_CR42","doi-asserted-by":"crossref","first-page":"1582","DOI":"10.1126\/science.271.5255.1582","volume":"271","author":"A. S. Perelson","year":"1996","unstructured":"Perelson, A. S., Neumann, A. U., Markowitz, M., Leonard, J. M., & Ho, D. D. (1996). HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time. Science, 271, 1582\u20131586.","journal-title":"Science"},{"issue":"5248","key":"46_CR43","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1126\/science.271.5248.497","volume":"271","author":"B. N. Phillips","year":"1996","unstructured":"Phillips, B. N. (1996). Reduction of HIV concentration during acute infection: independence from a specific immune response. Science, 271(5248), 497\u2013499.","journal-title":"Science"},{"key":"46_CR44","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1038\/354453a0","volume":"354","author":"R. E. Phillips","year":"1991","unstructured":"Phillips, R. E., Rowland-Jones, S., Nixon, D. F., Gotch, F. M., Edwards, J. P., et al. (1991). Human immunodeficiency virus genetic variation that can escape cytotoxic T cell recognition. Nature, 354, 453\u2013459.","journal-title":"Nature"},{"key":"46_CR45","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1038\/71577","volume":"6","author":"B. Ramratnam","year":"2000","unstructured":"Ramratnam, B., Mittler, J. E., Zhang, L., Boden, D., Hurley, A., Fang, F., Macken, C. A., Perelson, A. S., Markowitz, M., & Ho, D. D. (2000). The decay of the latent reservoir of replication-competent HIV-1 is inversely correlated with the extent of residual viral replication during prolonged anti-retroviral therapy. Nature Medicine, 6, 82\u201385.","journal-title":"Nature Medicine"},{"key":"46_CR46","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1097\/00126334-200401010-00004","volume":"35","author":"B. Ramratnam","year":"2004","unstructured":"Ramratnam, B., Ribeiro, R., He, T., Chung, C., Simon, V., Vanderhoeven, J., Hurley, A., Zhang, L., Perelson, A. S., Ho, D. D., & Markowitz, M. (2004). Intensification of antiretroviral therapy accelerates the decay of the HIV-1 latent reservoir and decreases, but does not eliminate, ongoing virus replication. Journal of Acquired Immune Deficiency Syndrome, 35, 33\u201337.","journal-title":"Journal of Acquired Immune Deficiency Syndrome"},{"key":"46_CR47","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1038\/419343a","volume":"419","author":"A. Regev","year":"2002","unstructured":"Regev, A., & Shapiro, E. (2002). Cellular abstractions: cells as computation. Nature, 419, 343.","journal-title":"Nature"},{"issue":"2","key":"46_CR48","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1006\/bulm.2001.0282","volume":"64","author":"R. M. Ribeiro","year":"2002","unstructured":"Ribeiro, R. M., Mohri, H., Ho, D. D., & Perelson, A. S. (2002a). Modeling deuterated glucose labeling of T-lymphocytes. Bulletin of Mathematical Biology, 64(2), 385\u2013405.","journal-title":"Bulletin of Mathematical Biology"},{"issue":"24","key":"46_CR49","doi-asserted-by":"crossref","first-page":"15572","DOI":"10.1073\/pnas.242358099","volume":"99","author":"R. M. Ribeiro","year":"2002","unstructured":"Ribeiro, R. M., Mohri, H., Ho, D. D., & Perelson, A. S. (2002b). In vivo dynamics of T cell activation, proliferation, and death in HIV-1 infection: why are CD4+ but not CD8+ T cells depleted? Proceedings of the National Academy of Sciences of the United States of America, 99(24), 15572\u201315577.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"46_CR50","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1126\/science.1352912","volume":"257","author":"S. R. Riddell","year":"1992","unstructured":"Riddell, S. R., Watanabe, K. S., Goodrich, J. M., Li, C. R., Agha, M. E., & Greenberg, P. D. (1992). Restoration of viral immunity in immunodeficient humans by the adoptive transfer of T cell clones. Science, 257, 238\u2013241.","journal-title":"Science"},{"key":"46_CR51","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1126\/science.283.5403.857","volume":"283","author":"J. Schmitz","year":"1999","unstructured":"Schmitz, J., Kuroda, M., Santra, S., Sasseville, V., Simon, M., et al. (1999). Control of viremia in simian immunodeficiency virus infection by CD8+ lymphocytes. Science, 283, 857\u2013860.","journal-title":"Science"},{"issue":"2","key":"46_CR52","volume":"7","author":"L. Sguanci","year":"2007","unstructured":"Sguanci, L., Bagnoli, F., & Li\u00f3, P. (2007). Modeling HIV quasispecies evolutionary dynamics. BMC Evolutionary Biology, 7(2), S5.","journal-title":"BMC Evolutionary Biology"},{"key":"46_CR53","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1038\/nm880","volume":"9","author":"J. D. Siliciano","year":"2003","unstructured":"Siliciano, J. D., Kajdas, J., Finzi, D., Quinn, T. C., Chadwick, K., et al. (2003). Long-term follow-up studies confirm the stability of the latent reservoir for HIV-1 in resting CD4(+) T cells. Nature Medicine, 9, 727\u2013728.","journal-title":"Nature Medicine"},{"issue":"1","key":"46_CR54","volume":"11","author":"A. Sorathiya","year":"2010","unstructured":"Sorathiya, A., Bracciali, A., & Li\u00f3, P. (2010). Formal reasoning on qualitative models of coinfection of HIV and tuberculosis and HAART therapy. BMC Bioinformatics, 11(1), S67.","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"46_CR55","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1006\/jtbi.2000.1076","volume":"203","author":"M. A. Stafford","year":"2000","unstructured":"Stafford, M. A., Corey, L., Cao, Y., Daar, E. S., Ho, D. D., & Perelson, A. S. (2000). Modeling plasma virus concentration during primary HIV infection. Journal of Theoretical Biology, 203(3), 285\u2013301.","journal-title":"Journal of Theoretical Biology"},{"key":"46_CR56","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1038\/373117a0","volume":"373","author":"X. Wei","year":"1995","unstructured":"Wei, X., Ghosh, S. K., Taylor, M. E., Johnson, V. A., Emini, E. A., Deutsch, P., Lifson, J. D., Bonhoeffer, S., Nowak, M. A., Hahn, B. H., Saag, M. S., & Shaw, G. M. (1995). Viral dynamics in human immunodeficiency virus type 1 infection. Nature, 373, 117\u2013122.","journal-title":"Nature"},{"key":"46_CR57","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.0050009","volume":"5","author":"L. Weinberger","year":"2007","unstructured":"Weinberger, L., & Shenk, T. (2007). An HIV feedback resistor: auto-regulatory circuit deactivator and noise buffer. PLoS Biology, 5, e9.","journal-title":"PLoS Biology"},{"issue":"8","key":"46_CR58","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1000467","volume":"5","author":"A. D. Weinberger","year":"2009","unstructured":"Weinberger, A. D., Perelson, A. S., Ribeiro, R. M., & Weinberger, L. S. (2009). Accelerated immunodeficiency by anti-CCR5 treatment in HIV infection. PLoS Computational Biology, 5(8), e1000467.","journal-title":"PLoS Computational Biology"},{"key":"46_CR59","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1046\/j.0818-9641.2004.01229.x","volume":"82","author":"F. W. Wiegel","year":"2004","unstructured":"Wiegel, F. W., & Perelson, A. S. (2004). Some scaling principles for the immune system. Immunology and Cell Biology, 82, 127\u2013131.","journal-title":"Immunology and Cell Biology"},{"key":"46_CR60","doi-asserted-by":"crossref","first-page":"1178","DOI":"10.1002\/bies.10196","volume":"24","author":"D. Wodarz","year":"2002","unstructured":"Wodarz, D., & Nowak, M. A. (2002). HIV dynamics and evolution. BioEssays, 24, 1178\u20131187.","journal-title":"BioEssays"},{"issue":"1","key":"46_CR61","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1128\/JVI.73.1.855-860.1999","volume":"73","author":"L. Zhang","year":"1999","unstructured":"Zhang, L., Dailey, P. J., He, T., Gettie, A., Bonhoeffer, S., Perelson, A. S., & Ho, D. D. (1999a). Rapid clearance of simian immunodeficiency virus particles from plasma of rhesus macaques. Journal of Virology, 73(1), 855\u2013860.","journal-title":"Journal of Virology"},{"key":"46_CR62","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1056\/NEJM199905273402101","volume":"340","author":"L. Zhang","year":"1999","unstructured":"Zhang, L., Ramratnam, B., Tenner-Racz, K., He, Y., Vesanen, M., et al. (1999b). Quantifying residual HIV-1 replication in patients receiving combination antiretroviral therapy. New England Journal of Medicine, 340, 1605\u20131613.","journal-title":"New England Journal of Medicine"}],"container-title":["Swarm Intelligence"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s11721-010-0046-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s11721-010-0046-4\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s11721-010-0046-4","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,6,12]],"date-time":"2020-06-12T21:58:53Z","timestamp":1591999133000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s11721-010-0046-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,10,14]]},"references-count":62,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2010,12]]}},"alternative-id":["46"],"URL":"https:\/\/doi.org\/10.1007\/s11721-010-0046-4","relation":{},"ISSN":["1935-3812","1935-3820"],"issn-type":[{"value":"1935-3812","type":"print"},{"value":"1935-3820","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,10,14]]}}}