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List of works by Ruy M. Ribeiro

A mathematical model of hepatitis C virus dynamics in patients with high baseline viral loads or advanced liver disease

scientific article

A stochastic model for primary HIV infection: optimal timing of therapy.

scientific article

Accelerated immunodeficiency by anti-CCR5 treatment in HIV infection

scientific article

Acute loss of intestinal CD4+ T cells is not predictive of simian immunodeficiency virus virulence

scientific article published on September 2007

Agent-based and phylogenetic analyses reveal how HIV-1 moves between risk groups: injecting drug users sustain the heterosexual epidemic in Latvia

scientific article

Analysis of hepatitis B viral load decline under potent therapy: complex decay profiles observed.

scientific article published in November 2001

Antibiotic and Antiinflammatory Therapy Transiently Reduces Inflammation and Hypercoagulation in Acutely SIV-Infected Pigtailed Macaques

scientific article

Antibody responses during hepatitis B viral infection

scientific article

CD8+ lymphocytes control viral replication in SIVmac239-infected rhesus macaques without decreasing the lifespan of productively infected cells

scientific article

Coagulation biomarkers predict disease progression in SIV-infected nonhuman primates

scientific article

Current estimates for HIV-1 production imply rapid viral clearance in lymphoid tissues

scientific article

Cutting edge: Experimentally induced immune activation in natural hosts of simian immunodeficiency virus induces significant increases in viral replication and CD4+ T cell depletion

scientific article

Determining thymic output quantitatively: using models to interpret experimental T-cell receptor excision circle (TREC) data

scientific article

Division-linked differentiation can account for CD8+ T-cell phenotype in vivo

scientific article published in January 2009

Dynamics of CD4+ T cells in HIV-1 infection

scientific article published on 27 March 2007

Dynamics of T- and B-lymphocyte turnover in a natural host of simian immunodeficiency virus

scientific article

Dynamics of alanine aminotransferase during hepatitis C virus treatment

scientific article published in August 2003

Dynamics of hepatitis B virus infection

scientific article

Early HIV RNA decay during raltegravir-containing regimens exhibits two distinct subphases (1a and 1b).

scientific article

Early hepatitis C viral kinetics correlate with long-term outcome in patients receiving high dose induction followed by combination interferon and ribavirin therapy

scientific article published in July 2002

Early microbial translocation blockade reduces SIV-mediated inflammation and viral replication

scientific article

Early ribavirin pharmacokinetics, HCV RNA and alanine aminotransferase kinetics in HIV/HCV co-infected patients during treatment with pegylated interferon and ribavirin

scientific article

Effect of 1918 PB1-F2 expression on influenza A virus infection kinetics

scientific article

Effect of B-cell depletion on viral replication and clinical outcome of simian immunodeficiency virus infection in a natural host

scientific article published on 05 August 2009

Effects of antibody on viral kinetics in simian/human immunodeficiency virus infection: implications for vaccination

scientific article published on May 2004

Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing

scientific article

Estimating biologically relevant parameters under uncertainty for experimental within-host murine West Nile virus infection.

scientific article published on 13 April 2016

Estimating drug efficacy and viral dynamic parameters: HIV and HCV

scientific article

Estimating the impact of vaccination on acute simian-human immunodeficiency virus/simian immunodeficiency virus infections

scientific article published on 17 September 2008

Estimation of the initial viral growth rate and basic reproductive number during acute HIV-1 infection

scientific article

Evolution of drug-resistant viral populations during interruption of antiretroviral therapy

scientific article

Experimental depletion of CD8+ cells in acutely SIVagm-infected African Green Monkeys results in increased viral replication

scientific article

Functional cure of SIVagm infection in rhesus macaques results in complete recovery of CD4+ T cells and is reverted by CD8+ cell depletion

scientific article

HIV influences clustering and intracellular replication of hepatitis C virus

scientific article published on 30 October 2020

HIV persistence in tissue macrophages of humanized myeloid-only mice during antiretroviral therapy

scientific article published on 17 April 2017

Hepatitis B virus kinetics and mathematical modeling

scientific article published on January 2004

Hepatitis B virus kinetics under antiviral therapy sheds light on differences in hepatitis B e antigen positive and negative infections

scientific article

Hepatitis B virus viral dynamics: effects of drug dose and baseline alanine aminotransferase

scientific article

Hepatitis C virus (HCV) and human immunodeficiency virus (HIV) dynamics during HCV treatment in HCV/HIV coinfection

scientific article published on 13 November 2003

Hepatitis C virus genotype 1a NS5A pretreatment sequence variation and viral kinetics in African American and white patients

scientific article published on 12 August 2005

High-potency human immunodeficiency virus vaccination leads to delayed and reduced CD8+ T-cell expansion but improved virus control

scientific article

Human systems immunology: hypothesis-based modeling and unbiased data-driven approaches

scientific article

Immunovirological analyses of chronically simian immunodeficiency virus SIVmnd-1- and SIVmnd-2-infected mandrills (Mandrillus sphinx).

scientific article published on 28 September 2011

Impact of thymectomy on the peripheral T cell pool in rhesus macaques before and after infection with simian immunodeficiency virus

scientific article published in January 2005

In vivo dynamics of T cell activation, proliferation, and death in HIV-1 infection: why are CD4+ but not CD8+ T cells depleted?

scientific article

Increased turnover of T lymphocytes in HIV-1 infection and its reduction by antiretroviral therapy

scientific article

Inferring viral dynamics in chronically HCV infected patients from the spatial distribution of infected hepatocytes

scientific article

Inflammatory monocytes expressing tissue factor drive SIV and HIV coagulopathy.

scientific article published on August 2017

Influence of peak viral load on the extent of CD4+ T-cell depletion in simian HIV infection

scientific article published on March 2006

Intensification of antiretroviral therapy accelerates the decay of the HIV-1 latent reservoir and decreases, but does not eliminate, ongoing virus replication

scientific article published on January 2004

Introduction to modeling viral infections and immunity

scientific article published on 01 September 2018

Kinetics of coinfection with influenza A virus and Streptococcus pneumoniae

scientific article

Kinetics of hepatitis C virus reinfection after liver transplantation

scientific article published in February 2006

Kinetics of myeloid dendritic cell trafficking and activation: impact on progressive, nonprogressive and controlled SIV infections

scientific article

Kinetics of virus-specific CD8+ T cells and the control of human immunodeficiency virus infection

scientific article published on September 2004

Limited ability of humoral immune responses in control of viremia during infection with SIVsmmD215 strain ⬇️

scientific article published on 23 January 2009

Mathematical Modeling of Subgenomic Hepatitis C Virus Replication in Huh-7 Cells

scientific article

Mathematical modeling of viral kinetics: a tool to understand and optimize therapy

scientific article

Mathematics in modern immunology ⬇️

scientific article

Mechanisms Underlying CD4+ Treg Immune Regulation in the Adult: From Experiments to Models

scientific article

Modeling HCV kinetics under therapy using PK and PD information

article

Modeling amantadine treatment of influenza A virus in vitro.

scientific article published on 23 July 2008

Modeling complex decay profiles of hepatitis B virus during antiviral therapy

scientific article published on January 2009

Modeling deuterated glucose labeling of T-lymphocytes

scientific article

Modeling hepatitis C virus dynamics: Liver regeneration and critical drug efficacy

scientific article

Modeling quasispecies and drug resistance in hepatitis C patients treated with a protease inhibitor

scientific article

Modeling the Effects of Morphine on Simian Immunodeficiency Virus Dynamics

scientific article

Modeling the long-term control of viremia in HIV-1 infected patients treated with antiretroviral therapy

scientific article published in March 2004

Modeling the mechanisms of acute hepatitis B virus infection

scientific article

Modeling the viral dynamics of influenza A virus infection

scientific article published on January 2010

Modeling the within-host dynamics of HIV infection

scientific article

Modelling deuterium labelling of lymphocytes with temporal and/or kinetic heterogeneity

scientific article

Modelling the kinetics of hepatitis C virus RNA decline over 4 weeks of treatment with pegylated interferon α-2b

scientific article

Multi-dose Romidepsin Reactivates Replication Competent SIV in Post-antiretroviral Rhesus Macaque Controllers

scientific article (publication date: September 2016)

Mutagenic effects of ribavirin in vivo

scientific article published in October 2005

Naïve and memory cell turnover as drivers of CCR5-to-CXCR4 tropism switch in human immunodeficiency virus type 1: implications for therapy

scientific article

Pharmacodynamics of PEG-IFN alpha differentiate HIV/HCV coinfected sustained virological responders from nonresponders

scientific article published in May 2006

Predicting the impact of a nonsterilizing vaccine against human immunodeficiency virus

scientific article published on October 2004

Probabilistic control of HIV latency and transactivation by the Tat gene circuit

scientific article published on 19 November 2018

Production of resistant HIV mutants during antiretroviral therapy

scientific article

Quantifying the activity of anti-HIV treatment in silico ⬇️

scientific article published on March 6, 2012

Quantifying the diversification of hepatitis C virus (HCV) during primary infection: estimates of the in vivo mutation rate

scientific article

Rapid emergence of protease inhibitor resistance in hepatitis C virus

scientific article

Real time bayesian estimation of the epidemic potential of emerging infectious diseases

scientific article

Response network analysis of differential gene expression in human epithelial lung cells during avian influenza infections

scientific article

Simian immunodeficiency virus SIVagm dynamics in African green monkeys

scientific article

Single hepatocytes show persistence and transcriptional inactivity of hepatitis B

scientific article published on 02 October 2020

Single-Genome Sequencing of Hepatitis C Virus in Donor-Recipient Pairs Distinguishes Modes and Models of Virus Transmission and Early Diversification

scientific article

Superinfection and cure of infected cells as mechanisms for hepatitis C virus adaptation and persistence

article published in the Proceedings of the National Academy of Sciences of the United States of America

Th-1-type cytotoxic CD8+ T-lymphocyte responses to simian immunodeficiency virus (SIV) are a consistent feature of natural SIV infection in sooty mangabeys

scientific article

The Role of Infected Cell Proliferation in the Clearance of Acute HBV Infection in Humans

scientific article published on 18 November 2017

The contribution of the thymus to the recovery of peripheral naive T-cell numbers during antiretroviral treatment for HIV infection

scientific article

The effect of early versus delayed challenge after vaccination in controlling SHIV 89.6P infection

scientific article published on 14 September 2008

The evolutionary rate dynamically tracks changes in HIV-1 epidemics: application of a simple method for optimizing the evolutionary rate in phylogenetic trees with longitudinal data

scientific article (publication date: December 2009)

The fate of CD4+ T cells under tolerance-inducing stimulation: a modeling perspective

scientific article published on 22 October 2013

The frequency of resistant mutant virus before antiviral therapy

scientific article published in March 1998

The level of monocyte turnover predicts disease progression in the macaque model of AIDS.

scientific article published on 21 April 2009

The life span of ganglionic glia in murine sensory ganglia estimated by uptake of bromodeoxyuridine.

scientific article published in March 2004

The maths of memory

scientific article published on 28 April 2017

The race between infection and immunity: how do pathogens set the pace?

scientific article published on 8 January 2009

The race between initial T-helper expansion and virus growth upon HIV infection influences polyclonality of the response and viral set-point.

scientific article published in July 2003

The reproduction number and its probability distribution for stochastic viral dynamics

scientific article published in January 2024

The role of cells refractory to productive infection in acute hepatitis B viral dynamics

scholarly article

Transmitted virus fitness and host T cell responses collectively define divergent infection outcomes in two HIV-1 recipients

scientific article

Treatment with integrase inhibitor suggests a new interpretation of HIV RNA decay curves that reveals a subset of cells with slow integration.

scientific article published on 5 July 2017

Triphasic decline of hepatitis C virus RNA during antiviral therapy

scientific article published in July 2007

Trypanosoma brucei Parasites Occupy and Functionally Adapt to the Adipose Tissue in Mice

scientific article published on 26 May 2016

Understanding the mechanisms and limitations of immune control of HIV.

scientific article published on April 2007

Unequal evolutionary rates in the human immunodeficiency virus type 1 (HIV-1) pandemic: the evolutionary rate of HIV-1 slows down when the epidemic rate increases

scientific article

Untangling the immune basis of disease susceptibility

scientific article published on 14 May 2020

Use of laser capture microdissection to map hepatitis C virus-positive hepatocytes in human liver

scientific article

Viral dynamics and response differences in HCV-infected African American and white patients treated with IFN and ribavirin

scientific article published in June 2003

Viral dynamics during primary simian immunodeficiency virus infection: effect of time-dependent virus infectivity

scientific article

Virus dynamics and immune responses during treatment in patients coinfected with hepatitis C and HIV.

scientific article published on February 2004

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