ALAN PERELSON

Summary

Affiliation: Los Alamos National Laboratory
Country: USA

Publications

  1. pmc Modeling latently infected cell activation: viral and latent reservoir persistence, and viral blips in HIV-infected patients on potent therapy
    Libin Rong
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
    PLoS Comput Biol 5:e1000533. 2009
  2. pmc Stochastic theory of early viral infection: continuous versus burst production of virions
    John E Pearson
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
    PLoS Comput Biol 7:e1001058. 2011
  3. pmc Quantifying the diversification of hepatitis C virus (HCV) during primary infection: estimates of the in vivo mutation rate
    Ruy M Ribeiro
    Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
    PLoS Pathog 8:e1002881. 2012
  4. pmc Treatment-mediated alterations in HIV fitness preserve CD4+ T cell counts but have minimal effects on viral load
    Naveen K Vaidya
    Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
    PLoS Comput Biol 6:e1001012. 2010
  5. pmc Analysis of hepatitis C virus decline during treatment with the protease inhibitor danoprevir using a multiscale model
    Libin Rong
    Department of Mathematics and Statistics and Center for Biomedical Research, Oakland University, Rochester, Michigan, USA
    PLoS Comput Biol 9:e1002959. 2013
  6. pmc Effect of 1918 PB1-F2 expression on influenza A virus infection kinetics
    Amber M Smith
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
    PLoS Comput Biol 7:e1001081. 2011
  7. pmc Modeling the within-host dynamics of HIV infection
    Alan S Perelson
    MS K710, Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    BMC Biol 11:96. 2013
  8. pmc Impact of immune escape mutations on HIV-1 fitness in the context of the cognate transmitted/founder genome
    Hongshuo Song
    Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
    Retrovirology 9:89. 2012
  9. pmc Combination antiviral therapy for influenza: predictions from modeling of human infections
    Alan S Perelson
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
    J Infect Dis 205:1642-5. 2012
  10. pmc Kinetics of acute hepatitis B virus infection in humans
    S A Whalley
    Centre for Hepatology, Department of Medicine, Royal Free Campus, United Kingdom
    J Exp Med 193:847-54. 2001

Research Grants

  1. MODELING HIV AND T LYMPHOCYTE DYNAMICS
    ALAN PERELSON; Fiscal Year: 2000
  2. MODELING VIRAL AND T LYMPHOCYTE DYNAMICS
    ALAN PERELSON; Fiscal Year: 2004
  3. MODELING VIRAL AND T LYMPHOCYTE DYNAMICS
    ALAN PERELSON; Fiscal Year: 2003
  4. MODELING VIRAL AND T LYMPHOCYTE DYNAMICS
    ALAN PERELSON; Fiscal Year: 2005
  5. MODELING VIRAL AND T LYMPHOCYTE DYNAMICS
    ALAN PERELSON; Fiscal Year: 2006
  6. Immune System Modeling/HIV
    ALAN PERELSON; Fiscal Year: 2007
  7. MODELING VIRAL AND T LYMPHOCYTE DYNAMICS
    ALAN PERELSON; Fiscal Year: 2009
  8. MODELING VIRAL AND T LYMPHOCYTE DYNAMICS
    ALAN PERELSON; Fiscal Year: 2003
  9. MODELING VIRAL AND T LYMPHOCYTE DYNAMICS
    ALAN PERELSON; Fiscal Year: 2002
  10. MODELING VIRAL AND T LYMPHOCYTE DYNAMICS
    ALAN PERELSON; Fiscal Year: 2001

Detail Information

Publications101 found, 100 shown here

  1. pmc Modeling latently infected cell activation: viral and latent reservoir persistence, and viral blips in HIV-infected patients on potent therapy
    Libin Rong
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
    PLoS Comput Biol 5:e1000533. 2009
    ..Using these models, we provide a quantitative and integrated prospective into the long-term dynamics of HIV-1 and the latent reservoir in the setting of potent antiretroviral therapy...
  2. pmc Stochastic theory of early viral infection: continuous versus burst production of virions
    John E Pearson
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
    PLoS Comput Biol 7:e1001058. 2011
    ..We also compute the distributions of times to establish infection as well as the distribution of times to extinction starting from both a single virion as well as from a single infected cell for both modes of virion production...
  3. pmc Quantifying the diversification of hepatitis C virus (HCV) during primary infection: estimates of the in vivo mutation rate
    Ruy M Ribeiro
    Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
    PLoS Pathog 8:e1002881. 2012
    ..Our model identifies the relevant processes (long-lived cells and slow turnover of replication complexes) and parameters involved in determining the rate of HCV diversification...
  4. pmc Treatment-mediated alterations in HIV fitness preserve CD4+ T cell counts but have minimal effects on viral load
    Naveen K Vaidya
    Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
    PLoS Comput Biol 6:e1001012. 2010
    ..This study provides a framework to investigate HIV and T cell dynamics in patients who develop drug resistance to other antiretroviral agents and may help to develop more effective strategies for treatment...
  5. pmc Analysis of hepatitis C virus decline during treatment with the protease inhibitor danoprevir using a multiscale model
    Libin Rong
    Department of Mathematics and Statistics and Center for Biomedical Research, Oakland University, Rochester, Michigan, USA
    PLoS Comput Biol 9:e1002959. 2013
    ..The multiscale model can be used to study viral dynamics in patients treated with other DAAs and explore their mechanisms of action in treatment of hepatitis C...
  6. pmc Effect of 1918 PB1-F2 expression on influenza A virus infection kinetics
    Amber M Smith
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
    PLoS Comput Biol 7:e1001081. 2011
    ..We discuss the implications these mechanisms have during an infection with a virus expressing a virulent PB1-F2 on the possibility of a pandemic and on the importance of antiviral treatments...
  7. pmc Modeling the within-host dynamics of HIV infection
    Alan S Perelson
    MS K710, Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    BMC Biol 11:96. 2013
    ..We show how modeling has revealed many dynamical features of HIV infection and how it may provide insight into the ultimate cure for this infection. ..
  8. pmc Impact of immune escape mutations on HIV-1 fitness in the context of the cognate transmitted/founder genome
    Hongshuo Song
    Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
    Retrovirology 9:89. 2012
    ....
  9. pmc Combination antiviral therapy for influenza: predictions from modeling of human infections
    Alan S Perelson
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
    J Infect Dis 205:1642-5. 2012
    ..We argue that a triple combination regimen would markedly reduce the risk of antiviral resistance emergence in seasonal and pandemic influenza viruses, especially in seriously ill or immunocompromised hosts...
  10. pmc Kinetics of acute hepatitis B virus infection in humans
    S A Whalley
    Centre for Hepatology, Department of Medicine, Royal Free Campus, United Kingdom
    J Exp Med 193:847-54. 2001
    ..At this peak rate of virion production we estimate that every possible single and most double mutations would be created each day...
  11. pmc Estimating time since infection in early homogeneous HIV-1 samples using a poisson model
    Elena E Giorgi
    Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    BMC Bioinformatics 11:532. 2010
    ..g., BEAST), which are instead based on the simulation of genealogies...
  12. ncbi request reprint Hepatitis B virus kinetics and mathematical modeling
    Alan S Perelson
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
    Semin Liver Dis 24:11-6. 2004
    ....
  13. ncbi request reprint Estimating drug efficacy and viral dynamic parameters: HIV and HCV
    Alan S Perelson
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Stat Med 27:4647-57. 2008
    ..Published in 2007 by John Wiley & Sons, Ltd...
  14. ncbi request reprint Modeling T cell proliferation and death in vitro based on labeling data: generalizations of the Smith-Martin cell cycle model
    Ha Youn Lee
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
    Bull Math Biol 70:21-44. 2008
    ..We also find that if the average cell cycle time increases with division class then the qualify of our fit to the data improves...
  15. ncbi request reprint Modelling viral and immune system dynamics
    Alan S Perelson
    Theoretical Division, Los Alamos National Laboratory, New Mexico 87545, USA
    Nat Rev Immunol 2:28-36. 2002
    ..Mathematical modelling is also improving our understanding of T-cell dynamics and the quantitative events that underlie the immune response to pathogens...
  16. ncbi request reprint New kinetic models for the hepatitis C virus
    Alan S Perelson
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87525, USA
    Hepatology 42:749-54. 2005
    ....
  17. pmc Scaling aspects of lymphocyte trafficking
    Alan S Perelson
    Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    J Theor Biol 257:9-16. 2009
    ..Mass-dependent aspects of immune learning and of the immunological self are shown to be not very significant. Our treatment is somewhat heuristic and aims at combining immunological data with recent progress in biological scaling...
  18. pmc Drug effectiveness explained: the mathematics of antiviral agents for HIV
    Alan S Perelson
    Los Alamos National Laboratory, Los Alamos, NM 87501, USA
    Sci Transl Med 3:91ps30. 2011
    ....
  19. pmc Naïve and memory cell turnover as drivers of CCR5-to-CXCR4 tropism switch in human immunodeficiency virus type 1: implications for therapy
    Ruy M Ribeiro
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    J Virol 80:802-9. 2006
    ..We also investigate the effects of different antiviral strategies. Surprisingly, these results suggest that both conventional antiretroviral regimens and CCR5 receptor-blocking drugs will promote R5 virus over X4 virus...
  20. ncbi request reprint Complex patterns of viral load decay under antiretroviral therapy: influence of pharmacokinetics and intracellular delay
    Narendra M Dixit
    Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, MS K710, Los Alamos, NM 87545, USA
    J Theor Biol 226:95-109. 2004
    ..However, uncertainties in measurement and the low sampling frequencies employed in present clinical studies preclude the identification of these patterns from existing clinical viral load data...
  21. pmc Modeling HIV persistence, the latent reservoir, and viral blips
    Libin Rong
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    J Theor Biol 260:308-31. 2009
    ..We also discuss treatment implications related to these studies...
  22. doi request reprint Mathematical modeling of HCV infection and treatment
    Harel Dahari
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
    Methods Mol Biol 510:439-53. 2009
    ..Here, we describe our current understanding of the kinetics of HCV infection and treatment...
  23. ncbi request reprint Duration of an intermittent episode of viremia
    Michele Di Mascio
    Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Bull Math Biol 67:885-900. 2005
    ..e., a so-called transient episode of viremia. By analyzing time series of blips from a large number of patients, we conclude that transient episodes of viremia exist and that on average they extend for a period of about 3 weeks...
  24. pmc Asymmetric division of activated latently infected cells may explain the decay kinetics of the HIV-1 latent reservoir and intermittent viral blips
    Libin Rong
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Math Biosci 217:77-87. 2009
    ....
  25. pmc Dynamics of intermittent viremia during highly active antiretroviral therapy in patients who initiate therapy during chronic versus acute and early human immunodeficiency virus type 1 infection
    Michele Di Mascio
    Theoretical Division, Los Alamos National Laboratory, New Mexico, USA
    J Virol 78:10566-73. 2004
    ..Finally, in PHI patients the VL set point was a significant predictor of blip frequency during treatment...
  26. pmc Viral and latent reservoir persistence in HIV-1-infected patients on therapy
    Hwijin Kim
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
    PLoS Comput Biol 2:e135. 2006
    ....
  27. ncbi request reprint Optimal viral production
    Daniel Coombs
    Theoretical Biology and Biophysics Group, Theoretical Division, MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Bull Math Biol 65:1003-23. 2003
    ..We present a general mathematical framework for studying problems of this type, which may be adapted to many host-parasite systems, and use it to examine the optimal virus production scheduling problem from the perspective of the virus...
  28. ncbi request reprint Retention of antigen on follicular dendritic cells and B lymphocytes through complement-mediated multivalent ligand-receptor interactions: theory and application to HIV treatment
    William S Hlavacek
    Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Math Biosci 176:185-202. 2002
    ..We also consider the possibility that HIV is retained on B cells during therapy, which like FDCs also interact with HIV. We find that virus associated with B cells is unlikely to persist during therapy...
  29. ncbi request reprint Modeling deuterated glucose labeling of T-lymphocytes
    Ruy M Ribeiro
    Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, MS K710, Los Alamos, New Mexico 87545, USA
    Bull Math Biol 64:385-405. 2002
    ..The use of these models in the interpretation of the experimental data will increase our knowledge of T cell dynamics in the context of HIV infection...
  30. pmc In vivo dynamics of T cell activation, proliferation, and death in HIV-1 infection: why are CD4+ but not CD8+ T cells depleted?
    Ruy M Ribeiro
    Theoretical Division, Los Alamos National Laboratory, NM 87545, USA
    Proc Natl Acad Sci U S A 99:15572-7. 2002
    ..Our results also explain why telomeres shorten in CD8(+) cells, but not in CD4(+) cells of HIV-1-infected patients, compared with age-matched controls...
  31. pmc Hepatitis B virus kinetics under antiviral therapy sheds light on differences in hepatitis B e antigen positive and negative infections
    Ruy M Ribeiro
    Los Alamos National Laboratory, Los Alamos, New Mexico, USA
    J Infect Dis 202:1309-18. 2010
    ..The former usually presents with lower viral levels but faster progression to liver disease. We sought to better understand the balance between replication and the immune response against hepatitis B virus (HBV)...
  32. ncbi request reprint Dynamics of hepatitis B virus infection
    Ruy M Ribeiro
    Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Microbes Infect 4:829-35. 2002
    ..Here, we review the state of the art in modeling and interpreting data obtained from hepatitis B virus infected patients treated with antiviral agents...
  33. pmc HIV dynamics with multiple infections of target cells
    Narendra M Dixit
    Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Proc Natl Acad Sci U S A 102:8198-203. 2005
    ..Inhibiting CD4 down-modulation increases the average number of infections per cell. Consequently, altering CD4 down-modulation may allow for an experimental determination of whether viral or cellular factors limit viral production...
  34. pmc Treatment of hepatitis C virus infection with interferon and small molecule direct antivirals: viral kinetics and modeling
    Libin Rong
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
    Crit Rev Immunol 30:131-48. 2010
    ....
  35. ncbi request reprint Triphasic decline of hepatitis C virus RNA during antiviral therapy
    Harel Dahari
    Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Hepatology 46:16-21. 2007
    ..Finally, the enhanced third phase in patients treated with IFN-alpha in combination with RBV versus patients treated with IFN-alpha alone can be explained by a mutagenic effect of RBV against HCV...
  36. pmc In a subset of subjects on highly active antiretroviral therapy, human immunodeficiency virus type 1 RNA in plasma decays from 50 to <5 copies per milliliter, with a half-life of 6 months
    Michele Di Mascio
    Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
    J Virol 77:2271-5. 2003
    ..This range of half-lives is consistent with the estimated half-life of the latent HIV-1 reservoir in the peripheral blood. Those patients without decay of viral load in plasma may have significant cryptic HIV-1 residual replication...
  37. ncbi request reprint A hepatitis C viral kinetic model that allows for time-varying drug effectiveness
    Emi Shudo
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
    Antivir Ther 13:919-26. 2008
    ..However, for treatment with pegylated (PEG)-IFN-alpha2b dosed weekly, drug levels fall substantially and viral load rebounds have been observed toward the end of the weekly dosing interval, implying non-constant drug efficacy...
  38. ncbi request reprint Modeling the long-term control of viremia in HIV-1 infected patients treated with antiretroviral therapy
    Michele Di Mascio
    Theoretical Division, Los Alamos National Laboratory, 1 Los Alamos Lab, Los Alamos, NM 87545 0001, USA
    Math Biosci 188:47-62. 2004
    ....
  39. ncbi request reprint Dynamics of alanine aminotransferase during hepatitis C virus treatment
    Ruy M Ribeiro
    Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Hepatology 38:509-17. 2003
    ..02). The week-4 ALT decline correlated with the HCV log drop (P =.006) and the efficacy of therapy (P =.025). In conclusion, our results suggest the use of ALT as a surrogate marker for treatment effect in patients with elevated ALT...
  40. pmc Early ribavirin pharmacokinetics, HCV RNA and alanine aminotransferase kinetics in HIV/HCV co-infected patients during treatment with pegylated interferon and ribavirin
    Harel Dahari
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
    J Hepatol 47:23-30. 2007
    ..We evaluated whether early ribavirin pharmacokinetics differ comparing hepatitis C/human immunodeficiency virus coinfected sustained virological responders and nonresponders...
  41. ncbi request reprint Characterizing T cell movement within lymph nodes in the absence of antigen
    Catherine Beauchemin
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    J Immunol 178:5505-12. 2007
    ..Although the calibrated model appears to offer an accurate representation of T cell movement, it has also uncovered inconsistencies across different experimental data sets...
  42. pmc Estimation of the initial viral growth rate and basic reproductive number during acute HIV-1 infection
    Ruy M Ribeiro
    Theoretical Biology and Biophysics Group, MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    J Virol 84:6096-102. 2010
    ..They also better define the challenge that the immune response (or therapeutic intervention) has to overcome to defeat HIV at this early stage...
  43. pmc The effect of early versus delayed challenge after vaccination in controlling SHIV 89.6P infection
    Leslie L Chavez
    Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Virology 381:75-80. 2008
    ..45, p=0.029), suggesting that the kinetics of early viral load may have a role in virus specific CD8+ T cell generation, although these early differences did not lead to different clinical outcomes within the vaccinated animals...
  44. pmc Rapid emergence of protease inhibitor resistance in hepatitis C virus
    Libin Rong
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Sci Transl Med 2:30ra32. 2010
    ....
  45. pmc Modeling HCV kinetics under therapy using PK and PD information
    Emi Shudo
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, MS K710, New Mexico 87545, USA
    Expert Opin Drug Metab Toxicol 5:321-32. 2009
    ..Mathematical models have proven helpful in analyzing the virological response to antiviral therapy in hepatitis C virus (HCV) infected subjects...
  46. pmc Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing
    Will Fischer
    Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
    PLoS ONE 5:e12303. 2010
    ..Dramatic shifts in the frequencies of epitope variants during the first weeks of infection revealed a complex interplay between viral fitness and immune escape...
  47. ncbi request reprint Estimates of intracellular delay and average drug efficacy from viral load data of HIV-infected individuals under antiretroviral therapy
    Narendra M Dixit
    Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
    Antivir Ther 9:237-46. 2004
    ....
  48. ncbi request reprint Modelling how ribavirin improves interferon response rates in hepatitis C virus infection
    Narendra M Dixit
    Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
    Nature 432:922-4. 2004
    ....
  49. pmc Viral blip dynamics during highly active antiretroviral therapy
    Michele Di Mascio
    Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
    J Virol 77:12165-72. 2003
    ....
  50. ncbi request reprint Modeling viral and drug kinetics: hepatitis C virus treatment with pegylated interferon alfa-2b
    Kimberly A Powers
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
    Semin Liver Dis 23:13-8. 2003
    ..Models incorporating pharmacokinetics are needed to correctly interpret viral load changes and estimate drug effectiveness in treatment protocols using peginterferon alfa-2b...
  51. ncbi request reprint Dynamics of HIV Infection. Interview by Vicki Glaser
    Alan S Perelson
    Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
    AIDS Patient Care STDS 17:317-20. 2003
  52. pmc Mathematical modeling of subgenomic hepatitis C virus replication in Huh-7 cells
    Harel Dahari
    Theoretical Biology and Biophysics, MS K710, Los Alamos National Laboratory, NM 87545, USA
    J Virol 81:750-60. 2007
    ..Moreover, the model can serve as an important tool in understanding HCV replication mechanisms and should prove useful in designing and evaluating new antivirals against HCV...
  53. pmc Modeling hepatitis C virus dynamics: liver regeneration and critical drug efficacy
    Harel Dahari
    Theoretical Biology and Biophysics, MS K710, Los Alamos National Laboratory, NM 87545, USA
    J Theor Biol 247:371-81. 2007
    ..Further, we define and characterize a critical drug efficacy, such that for efficacies above the critical value HCV is ultimately cleared, while for efficacies below it, a new chronically infected viral steady-state level is reached...
  54. ncbi request reprint Determining thymic output quantitatively: using models to interpret experimental T-cell receptor excision circle (TREC) data
    Ruy M Ribeiro
    Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Immunol Rev 216:21-34. 2007
    ..We show that mathematical models are not only useful but absolutely necessary for these analyses. As such, they should be taken as just another tool in the immunologist's arsenal...
  55. pmc Multiplicity of human immunodeficiency virus infections in lymphoid tissue
    Narendra M Dixit
    MS K710, T 10, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    J Virol 78:8942-5. 2004
    ..The two mechanisms imply different genetic diversities of proviruses within an infected cell and therefore different rates of emergence of drug resistance via recombination...
  56. pmc Kinetics of influenza A virus infection in humans
    Prasith Baccam
    Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    J Virol 80:7590-9. 2006
    ....
  57. ncbi request reprint Kinetics of hepatitis C virus reinfection after liver transplantation
    Kimberly A Powers
    Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Liver Transpl 12:207-16. 2006
    ..In conclusion, we have quantified liver reinfection dynamics in the absence of posttransplantation antiviral therapy. Our findings support the notion that early antiviral therapy may delay or prevent reinfection...
  58. pmc Backward bifurcations and multiple equilibria in epidemic models with structured immunity
    Timothy C Reluga
    Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    J Theor Biol 252:155-65. 2008
    ..Neutralizing antibody titer data for measles are used to demonstrate the biological application of our theory...
  59. pmc Viral dynamics during primary simian immunodeficiency virus infection: effect of time-dependent virus infectivity
    Naveen K Vaidya
    Theoretical Biology and Biophysics Group, MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    J Virol 84:4302-10. 2010
    ..These results show that the infectivity depends upon the source of viral infection...
  60. ncbi request reprint Different dynamics of CD4+ and CD8+ T cell responses during and after acute lymphocytic choriomeningitis virus infection
    Rob J de Boer
    Theoretical Biology, Utrecht University, Utrecht, The Netherlands
    J Immunol 171:3928-35. 2003
    ....
  61. ncbi request reprint Determining the antiviral activity of tenofovir disoproxil fumarate in treatment-naive chronically HIV-1-infected individuals
    Michael Louie
    Aaron Diamond AIDS Research Center, Rockefeller University, New York, NY 10016, USA
    AIDS 17:1151-6. 2003
    ..To assess the efficacy of tenofovir disoproxil fumarate (TDF) monotherapy by following the initial rate of decline in plasma viral load, which is a measure of the efficacy of therapy in blocking viral replication...
  62. ncbi request reprint Hepatitis C virus (HCV) and human immunodeficiency virus (HIV) dynamics during HCV treatment in HCV/HIV coinfection
    Francesca J Torriani
    Department of Medicine, Division of Infectious Diseases, University of California, San Diego, California 92103, USA
    J Infect Dis 188:1498-507. 2003
    ..Although the early viral kinetics of coinfected subjects treated with PEG-IFN or IFN differ from those of singly infected subjects, the treatment response seems unaffected...
  63. ncbi request reprint Viral dynamics and response differences in HCV-infected African American and white patients treated with IFN and ribavirin
    Jennifer E Layden-Almer
    University of Illinois at Chicago, Chicago, IL, USA
    Hepatology 37:1343-50. 2003
    ..In conclusion, the failure of IFN response in African American patients infected with genotype 1 HCV is in part due to an impaired ability to inhibit viral production...
  64. pmc Estimating average cellular turnover from 5-bromo-2'-deoxyuridine (BrdU) measurements
    Rob J de Boer
    Department of Theoretical Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
    Proc Biol Sci 270:849-58. 2003
    ..2% day(-1) in SIV-infected monkeys. Thus, we show that one can use BrdU data from a possibly heterogeneous population of cells to estimate the average turnover rate of that population in a robust manner...
  65. ncbi request reprint Pharmacodynamics of PEG-IFN alpha differentiate HIV/HCV coinfected sustained virological responders from nonresponders
    Andrew H Talal
    Department of Medicine and the Center for the Study of Hepatitis C, Weill Medical College of Cornell University, New York, NY 10021, USA
    Hepatology 43:943-53. 2006
    ..In contrast, pharmacodynamic measurements-namely EC50, the therapeutic quotient, and C(7)/EC50--are different in coinfected SVRs and NRs. These parameters might be useful predictors of treatment outcome during the first month of therapy...
  66. ncbi request reprint Mathematical modeling of viral kinetics: a tool to understand and optimize therapy
    Thomas J Layden
    Department of Medicine, College of Medicine, University of Illinois at Chicago, 840 South Wood Mail Code 787, Chicago, IL 60612, USA
    Clin Liver Dis 7:163-78. 2003
    ..Pawlotsky and Rosen). If the past is any indication of the usefulness of mathematical modeling and kinetics in the study of viruses, continued employment of these tools will only prove beneficial...
  67. pmc Modeling and estimation of kinetic parameters and replicative fitness of HIV-1 from flow-cytometry-based growth competition experiments
    Hongyu Miao
    Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Box 630, Rochester, NY, 14642, USA
    Bull Math Biol 70:1749-71. 2008
    ..Practical identifiability was investigated via Monte Carlo simulations...
  68. ncbi request reprint Effect of target cell availability on HIV-1 production in vitro
    Elissa J Schwartz
    Division of Nephrology, Mount Sinai Medical Center, One Gustave L Levy Place, New York, NY 10029, USA
    AIDS 16:341-5. 2002
    ..To address this hypothesis, we directly examined whether the CD4 target cell number increases viral production in the presence of suboptimal therapy...
  69. ncbi request reprint HIV-1 infection and low steady state viral loads
    Duncan S Callaway
    Department of Theoretical and Applied Mechanics, Cornell University, Ithaca, NY 14853, USA
    Bull Math Biol 64:29-64. 2002
    ....
  70. ncbi request reprint Mathematical analysis of delay differential equation models of HIV-1 infection
    Patrick W Nelson
    Department of Mathematics, The University of Michigan, 525 E University, 3071 E Hall, Ann Arbor, MI 48109 1109, USA
    Math Biosci 179:73-94. 2002
    ..We provide a mathematical justification for this increased value of delta. We also provide some general results on the stability of non-linear delay differential equation infection models...
  71. ncbi request reprint Early hepatitis C viral kinetics correlate with long-term outcome in patients receiving high dose induction followed by combination interferon and ribavirin therapy
    Hugo R Rosen
    Division of Gastroenterology and Hepatology, Portland Veterans Affairs Medical Center, Portland, OR 97207, USA
    J Hepatol 37:124-30. 2002
    ..The majority of patients with genotype 1 do not respond to interferon (IFN) plus ribavirin. Limited data exist on the use of induction followed by combination therapy...
  72. ncbi request reprint Dynamics of T cells and TCR excision circles differ after treatment of acute and chronic HIV infection
    Sharon R Lewin
    Department of Microbiology and Immunology, University of Melbourne, Royal Melbourne Hospital, Parkville, Victoria 3052, Australia
    J Immunol 169:4657-66. 2002
    ....
  73. ncbi request reprint Modeling the effects of vaccination on chronically infected HIV-positive patients
    Laura E Jones
    Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
    J Acquir Immune Defic Syndr 31:369-77. 2002
    ....
  74. ncbi request reprint Turnover rates of B cells, T cells, and NK cells in simian immunodeficiency virus-infected and uninfected rhesus macaques
    Rob J de Boer
    Theoretical Biology, Utrecht University, Utrecht, The Netherlands
    J Immunol 170:2479-87. 2003
    ..Because the viral load and the CD4 T cell count are negatively correlated we cannot determine which of the two plays the most important role in this generalized immune activation...
  75. ncbi request reprint Determining the relative efficacy of highly active antiretroviral therapy
    Michael Louie
    Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York, NY 10016, USA
    J Infect Dis 187:896-900. 2003
    ..Nevertheless, we believe that optimal treatment regimens for HIV-1 have yet to be identified and that continued research to achieve this goal is warranted...
  76. pmc A novel antiviral intervention results in more accurate assessment of human immunodeficiency virus type 1 replication dynamics and T-cell decay in vivo
    Martin Markowitz
    Aaron Diamond AIDS Research Center, Rockefeller University, New York, New York 10016, USA
    J Virol 77:5037-8. 2003
    ..7 day, and the generation time of HIV-1 in vivo, approximately 2 days, confirming the dynamic nature of HIV-1 replication...
  77. ncbi request reprint The distribution of viral blips observed in HIV-1 infected patients treated with combination antiretroviral therapy
    Jerome K Percus
    Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
    Bull Math Biol 65:263-77. 2003
    ....
  78. ncbi request reprint Intensification of antiretroviral therapy accelerates the decay of the HIV-1 latent reservoir and decreases, but does not eliminate, ongoing virus replication
    Bharat Ramratnam
    Aaron Diamond AIDS Research Center, The Rockefeller University, New York, NY, USA
    J Acquir Immune Defic Syndr 35:33-7. 2004
    ..Additional studies are needed to understand the host- and pathogen-related determinants of incomplete pharmacologic control of HIV-1 replication...
  79. ncbi request reprint Virus dynamics and immune responses during treatment in patients coinfected with hepatitis C and HIV
    Andrew H Talal
    Department of Medicine, Weill Medical College of Cornell University, New York City, NY, USA
    J Acquir Immune Defic Syndr 35:103-13. 2004
    ....
  80. pmc Modeling the mechanisms of acute hepatitis B virus infection
    Stanca M Ciupe
    Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87507, USA
    J Theor Biol 247:23-35. 2007
    ..In particular, we find that a cell-mediated immune response plays an important role in controlling the virus after the peak in viral load...
  81. ncbi request reprint Mathematical modeling of primary hepatitis C infection: noncytolytic clearance and early blockage of virion production
    Harel Dahari
    Faculty of Life Science, Bar Ilan University, Ramat Gan 52900, Israel
    Gastroenterology 128:1056-66. 2005
    ..Although hepatitis C virus kinetics and immune determinants during primary infection have been described, the virus-host interplay is not fully understood. We used mathematical modeling to elucidate and quantify virus-host dynamics...
  82. pmc Polyspecificity of T cell and B cell receptor recognition
    Kai W Wucherpfennig
    Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
    Semin Immunol 19:216-24. 2007
    ..This review summarizes the relevance of polyspecificity for lymphocyte development, activation and disease processes...
  83. ncbi request reprint Understanding the mechanisms and limitations of immune control of HIV
    Miles P Davenport
    Department of Haematology, Prince of Wales Hospital and Centre for Vascular Research, University of New South Wales, Kensington, NSW, Australia
    Immunol Rev 216:164-75. 2007
    ..However, important questions remain as to whether differences in pathogenesis in HIV will lead to different 'rules of engagement' for immune control of virus...
  84. pmc The role of cells refractory to productive infection in acute hepatitis B viral dynamics
    Stanca M Ciupe
    Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87507, USA
    Proc Natl Acad Sci U S A 104:5050-5. 2007
    ..Without this assumption, viral resurgence is observed as uninfected cells are regenerated. Such protection, possibly mediated by cytokines, may also be important in resolving other acute viral infections...
  85. ncbi request reprint Viral decay dynamics in HIV-infected patients receiving ritonavir-boosted saquinavir and efavirenz with or without enfuvirtide: a randomized, controlled trial (HIV-NAT 012)
    Mark A Boyd
    HIV Netherlands Australia Thailand Research Collaboration, Thai Red Cross AIDS Research Centre, Bangkok, Thailand
    J Infect Dis 194:1319-22. 2006
    ..62+/-0.34 per day and -0.51+/-0.16 per day; P>.1). Antiretroviral therapy that inhibits HIV reverse transcriptase and protease exerts potent antiviral effects that might not be augmented by the addition of an HIV fusion inhibitor...
  86. pmc High-potency human immunodeficiency virus vaccination leads to delayed and reduced CD8+ T-cell expansion but improved virus control
    Miles P Davenport
    Department of Haematology, Prince of Wales Hospital and Centre for Vascular Research, University of New South Wales, Kensington, Australia
    J Virol 79:10059-62. 2005
    ..Nevertheless, higher initial CD8(+) T-cell numbers were associated with reduced peak and chronic viral loads and reduced CD4(+) T-cell depletion...
  87. ncbi request reprint Opportunistic infection as a cause of transient viremia in chronically infected HIV patients under treatment with HAART
    Laura E Jones
    Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
    Bull Math Biol 67:1227-51. 2005
    ..Using these models we show that viral blips with realistic duration and amplitude can be generated by intercurrent infections in HAART treated patients...
  88. ncbi request reprint Pharmacodynamics of antiretroviral agents in HIV-1 infected patients: using viral dynamic models that incorporate drug susceptibility and adherence
    Hulin Wu
    Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, NY 14642, USA
    J Pharmacokinet Pharmacodyn 33:399-419. 2006
    ..But their combinations in viral dynamic modeling significantly predicted virologic response. The HIV dynamic modeling can appropriately capture complicated nonlinear relationships and interactions among multiple covariates...
  89. pmc Analysis of human immunodeficiency virus cytopathicity by using a new method for quantitating viral dynamics in cell culture
    Christina Speirs
    Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 1892, USA
    J Virol 79:4025-32. 2005
    ..Our approach provides a general method for estimating time-dependent death rates that can be applied to study the dynamics of other viruses...
  90. ncbi request reprint Ribavirin: is it a mutagen for hepatitis C virus?
    Alan S Perelson
    Gastroenterology 132:2050-2. 2007
  91. pmc Transient viremia, plasma viral load, and reservoir replenishment in HIV-infected patients on antiretroviral therapy
    Laura E Jones
    Ecology and Evolutionary Biology, Comell University, Ithaca, NY, USA
    J Acquir Immune Defic Syndr 45:483-93. 2007
    ....
  92. pmc Treatment response in acute/early infection versus advanced AIDS: equivalent first and second phases of HIV RNA decline
    J Michael Kilby
    Division of Infectious Diseases and 1917 HIV Research Clinic, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama 35294 2050, USA
    AIDS 22:957-62. 2008
    ..Compare the initial phases of virologic decay when acute/early and advanced HIV-infected adults are administered the same treatment regimen...
  93. pmc Why are there different dynamics in the selection of drug resistance in HIV and hepatitis B and C viruses?
    Vincent Soriano
    Department of Infectious Diseases, Hospital Carlos III, Sinesio Delgado 10, 28029 Madrid, Spain
    J Antimicrob Chemother 62:1-4. 2008
    ....
  94. ncbi request reprint Hepatitis C virus genotype 1a NS5A pretreatment sequence variation and viral kinetics in African American and white patients
    Jennifer E Layden-Almer
    Department of Medicine, University of Illinois at Chicago, 60612, USA
    J Infect Dis 192:1078-87. 2005
    ..The results of this study, in conjunction with those of a previous study illustrating the impaired IFN effectiveness in African Americans, suggest a role for host-related factors...
  95. pmc Dynamics of T- and B-lymphocyte turnover in a natural host of simian immunodeficiency virus
    Amitinder Kaur
    Division of Immunology, New England Primate Research Center, Harvard Medical School, One Pine Hill Drive, P O Box 9102, Southborough, MA 01772 9102, USA
    J Virol 82:1084-93. 2008
    ....
  96. ncbi request reprint Hepatitis C virus kinetics in chimeric mice during antiviral therapy
    Harel Dahari
    Hepatology 46:2048-9; author reply 2049-50. 2007
  97. ncbi request reprint Impact of early viral kinetics on T-cell reactivity during antiviral therapy in chronic hepatitis B
    George K K Lau
    Department of Medicine, Queen Mary Hospital, Hong Kong SAR, China
    Antivir Ther 12:705-18. 2007
    ..The patterns of hepatitis B viral dynamics during different antiviral therapies and the associated changes in HBV-specific T-cell reactivity are not well defined...
  98. pmc Kinetics of virus-specific CD8+ T cells and the control of human immunodeficiency virus infection
    Miles P Davenport
    Department of Haematology, Prince of Wales Hospital, Kensington, New South Wales, Australia
    J Virol 78:10096-103. 2004
    ..However, this response is too little too late to prevent establishment of persistent infection...
  99. ncbi request reprint Hepatitis C virus RNA kinetics: drug efficacy and the rate of HCV-infected cells loss
    Harel Dahari
    World J Gastroenterol 13:3020-1. 2007
  100. pmc Modeling within-host HIV-1 dynamics and the evolution of drug resistance: trade-offs between viral enzyme function and drug susceptibility
    Libin Rong
    Department of Mathematics, Purdue University, West Lafayette, IN 47907, USA
    J Theor Biol 247:804-18. 2007
    ..We show that the window of opportunity for invasion of drug resistant strains is widened for a higher level of drug efficacy provided that the treatment is not potent enough to eradicate both the sensitive and resistant virus...
  101. ncbi request reprint Influence of peak viral load on the extent of CD4+ T-cell depletion in simian HIV infection
    Miles P Davenport
    Department of Haematology, Prince of Wales Hospital and Centre for Vascular Research, University of New South Wales, Kensington, New South Wales, Australia
    J Acquir Immune Defic Syndr 41:259-65. 2006
    ..Whether such a simple relation also holds for HIV or simian immunodeficiency virus infections remains to be determined, particularly in the gut and other anatomic sites in which most early T-cell depletion occurs...

Research Grants21

  1. MODELING HIV AND T LYMPHOCYTE DYNAMICS
    ALAN PERELSON; Fiscal Year: 2000
    ..In addition to gaining basic understanding the Investigator proposes putting this information into a practical setting, and to interact with clinical groups in the design and evaluation of new treatment protocols. ..
  2. MODELING VIRAL AND T LYMPHOCYTE DYNAMICS
    ALAN PERELSON; Fiscal Year: 2004
    ..In addition to gaining basic understanding, this approach aims to put information into a practical setting, and the applicants hope to interact with clinical groups in the design and evaluation of new treatment protocols. ..
  3. MODELING VIRAL AND T LYMPHOCYTE DYNAMICS
    ALAN PERELSON; Fiscal Year: 2003
    ..Our goal in all of these analyses is to gain basic understanding and help move that understanding into new treatments. ..
  4. MODELING VIRAL AND T LYMPHOCYTE DYNAMICS
    ALAN PERELSON; Fiscal Year: 2005
    ..Our goal in all of these analyses is to gain basic understanding and help move that understanding into new treatments. ..
  5. MODELING VIRAL AND T LYMPHOCYTE DYNAMICS
    ALAN PERELSON; Fiscal Year: 2006
    ..abstract_text> ..
  6. Immune System Modeling/HIV
    ALAN PERELSON; Fiscal Year: 2007
    ..Other areas also will be explored such as Infection of gut associated lymphoid tissue, the possibility of cells being multiply infected, and issues of the stability of the latent reservoir. ..
  7. MODELING VIRAL AND T LYMPHOCYTE DYNAMICS
    ALAN PERELSON; Fiscal Year: 2009
    ..By developing mathematical models of these infections and their treatment we aim to improve our basic understanding of disease pathogenesis and improve protocols for antiviral therapy. ..
  8. MODELING VIRAL AND T LYMPHOCYTE DYNAMICS
    ALAN PERELSON; Fiscal Year: 2003
    ..In addition to gaining basic understanding, this approach aims to put information into a practical setting, and the applicants hope to interact with clinical groups in the design and evaluation of new treatment protocols. ..
  9. MODELING VIRAL AND T LYMPHOCYTE DYNAMICS
    ALAN PERELSON; Fiscal Year: 2002
    ..In addition to gaining basic understanding, this approach aims to put information into a practical setting, and the applicants hope to interact with clinical groups in the design and evaluation of new treatment protocols. ..
  10. MODELING VIRAL AND T LYMPHOCYTE DYNAMICS
    ALAN PERELSON; Fiscal Year: 2001
    ..In addition to gaining basic understanding, this approach aims to put information into a practical setting, and the applicants hope to interact with clinical groups in the design and evaluation of new treatment protocols. ..
  11. MODELING HIV AND T LYMPHOCYTE DYNAMICS
    ALAN PERELSON; Fiscal Year: 1999
    ..In addition to gaining basic understanding the Investigator proposes putting this information into a practical setting, and to interact with clinical groups in the design and evaluation of new treatment protocols. ..
  12. MATHEMATICAL MODELS OF IMMUNE NETWORKS
    ALAN PERELSON; Fiscal Year: 1991
    ..We think that it is due to our lack of understanding, and not necessarily a lack of knowledge, that we have generally failed to develop adequate therapies for autoimmune disease, allergies and other immune system disorders...
  13. MATHEMATICAL MODELS OF IMMUNE NETWORKS
    ALAN PERELSON; Fiscal Year: 1992
    ..We think that it is due to our lack of understanding, and not necessarily a lack of knowledge, that we have generally failed to develop adequate therapies for autoimmune disease, allergies and other immune system disorders...
  14. MATHEMATICAL MODELS OF IMMUNE NETWORKS
    ALAN PERELSON; Fiscal Year: 1993
    ..We think that it is due to our lack of understanding, and not necessarily a lack of knowledge, that we have generally failed to develop adequate therapies for autoimmune disease, allergies and other immune system disorders...
  15. MODELING VIRAL AND T LYMPHOCYTE DYNAMICS
    Alan S Perelson; Fiscal Year: 2010
    ..By developing mathematical models of these infections and their treatment we aim to improve our basic understanding of disease pathogenesis and improve protocols for antiviral therapy. ..