Mathematical Analysis of Viral Replication Dynamics and Antiviral Treatment Strategies: From Basic Models to Age-Based Multi-Scale Modeling

Efficacy and effectiveness of an rVSV-vectored vaccine in preventing Ebola virus disease: final results from the Guinea ring vaccination, open-label, cluster-randomised trial (Ebola Ça Suffit!)

(2017) Ana Maria Henao-Restrepo et al.   LANCET

Zika plasma viral dynamics in nonhuman primates provides insights into early infection and antiviral strategies

(2017) Katharine Best et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NS5A inhibitors unmask differences in functional replicase complex half-life between different hepatitis C virus strains

(2017) Tiffany Benzine et al.   PLoS Pathogens

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

(2017) E. Fabian Cardozo et al.   PLoS Pathogens

In silico Analyses of Subtype Specific HIV-1 Tat-TAR RNA Interaction Reveals the Structural Determinants for Viral Activity

(2017) Larance Ronsard et al.   Frontiers in Microbiology

Impact of Genetic Variations in HIV-1 Tat on LTR-Mediated Transcription via TAR RNA Interaction

(2017) Larance Ronsard et al.   Frontiers in Microbiology

Modelling Ebola virus dynamics: Implications for therapy

(2016) Alexey Martyushev et al.   ANTIVIRAL RESEARCH

Multiscale modeling of virus replication and spread

(2016) Peter Kumberger et al.   FEBS LETTERS

Hepatitis C Virus Resistance to Direct-Acting Antiviral Drugs in Interferon-Free Regimens

(2016) Jean-Michel Pawlotsky   GASTROENTEROLOGY

HCV kinetic and modeling analyses indicate similar time to cure among sofosbuvir combination regimens with daclatasvir, simeprevir or ledipasvir

(2016) Harel Dahari et al.   JOURNAL OF HEPATOLOGY

Late Ebola virus relapse causing meningoencephalitis: a case report

(2016) Michael Jacobs et al.   LANCET

The global economic burden of dengue: a systematic analysis

(2016) Donald S Shepard et al.   LANCET INFECTIOUS DISEASES

Direct-acting antivirals for the treatment of hepatitis C virus infection: optimizing current IFN-free treatment and future perspectives

(2016) Tarik Asselah et al.   LIVER INTERNATIONAL

Zika viral dynamics and shedding in rhesus and cynomolgus macaques

(2016) Christa E Osuna et al.   NATURE MEDICINE

Evidence of Sexual Transmission of Zika Virus

(2016) Eric D’Ortenzio et al.   NEW ENGLAND JOURNAL OF MEDICINE

Multi-scale model for hepatitis C viral load kinetics under treatment with direct acting antivirals

(2016) Diana Clausznitzer et al.   VIRUS RESEARCH

Zika virus outbreak in Brazil

(2016) Jorg Heukelbach et al.   Journal of Infection in Developing Countries

Approaches to preventative and therapeutic HIV vaccines

(2016) Glenda E Gray et al.   Current Opinion in Virology

Modelling Virus and Antibody Dynamics during Dengue Virus Infection Suggests a Role for Antibody in Virus Clearance

(2016) Hannah E Clapham et al.   PLoS Computational Biology

Viral RNA Degradation and Diffusion Act as a Bottleneck for the Influenza A Virus Infection Efficiency

(2016) Max Schelker et al.   PLoS Computational Biology

Drivers of Inter-individual Variation in Dengue Viral Load Dynamics

(2016) Rotem Ben-Shachar et al.   PLoS Computational Biology

Modeling Viral Spread

(2016) Frederik Graw et al.   Annual Review of Virology

Mathematical Model Reveals the Role of Memory CD8 T Cell Populations in Recall Responses to Influenza

(2016) Veronika I. Zarnitsyna et al.   Frontiers in Immunology

On the Role of CD8+ T Cells in Determining Recovery Time from Influenza Virus Infection

(2016) Pengxing Cao et al.   Frontiers in Immunology

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

(2015) Adriana Andrade et al.   AIDS

A Drug-Disease Model Describing the Effect of Oseltamivir Neuraminidase Inhibition on Influenza Virus Progression

(2015) Mohamed A. Kamal et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Ebola virus dynamics in mice treated with favipiravir

(2015) Vincent Madelain et al.   ANTIVIRAL RESEARCH

Clearance of persistent hepatitis C virus infection in humanized mice using a claudin-1-targeting monoclonal antibody

(2015) Laurent Mailly et al.   NATURE BIOTECHNOLOGY

Modelling hepatitis C therapy—predicting effects of treatment

(2015) Alan S. Perelson et al.   Nature Reviews Gastroenterology & Hepatology

Efficacy of a Tetravalent Dengue Vaccine in Children in Latin America

(2015) Luis Villar et al.   NEW ENGLAND JOURNAL OF MEDICINE

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

Post-treatment control of HIV infection

(2015) Jessica M. Conway et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modeling Influenza Virus Infection: A Roadmap for Influenza Research

(2015) Alessandro Boianelli et al.   Viruses-Basel

Live Cell Analysis and Mathematical Modeling Identify Determinants of Attenuation of Dengue Virus 2’-O-Methylation Mutant

(2015) Bianca Schmid et al.   PLoS Pathogens

Modeling the Effects of Vorinostat In Vivo Reveals both Transient and Delayed HIV Transcriptional Activation and Minimal Killing of Latently Infected Cells

(2015) Ruian Ke et al.   PLoS Pathogens

Ebola virus infection modeling and identifiability problems

(2015) Van Kinh Nguyen et al.   Frontiers in Microbiology

Update on hepatitis C virus resistance to direct-acting antiviral agents

(2014) Eva Poveda et al.   ANTIVIRAL RESEARCH

Analysis of the hepatitis C viral kinetics during administration of two nucleotide analogues: sofosbuvir (GS-7977) and GS-0938

(2014) Jeremie Guedj et al.   ANTIVIRAL THERAPY

Within-host influenza dynamics: A small-scale mathematical modeling approach

(2014) Himanshu Manchanda et al.   BIOSYSTEMS

Emerging and Reemerging Neglected Tropical Diseases: a Review of Key Characteristics, Risk Factors, and the Policy and Innovation Environment

(2014) Tim K. Mackey et al.   CLINICAL MICROBIOLOGY REVIEWS

Viral kinetic modeling: state of the art

(2014) Laetitia Canini et al.   JOURNAL OF PHARMACOKINETICS AND PHARMACODYNAMICS

Minimal within-host dengue models highlight the specific roles of the immune response in primary and secondary dengue infections

(2014) R. Ben-Shachar et al.   Journal of the Royal Society Interface

Within-host viral dynamics of dengue serotype 1 infection

(2014) H. E. Clapham et al.   Journal of the Royal Society Interface

Effects of Aging on Influenza Virus Infection Dynamics

(2014) E. A. Hernandez-Vargas et al.   JOURNAL OF VIROLOGY

HIV infection: epidemiology, pathogenesis, treatment, and prevention

(2014) Gary Maartens et al.   LANCET

Ledipasvir and Sofosbuvir for Untreated HCV Genotype 1 Infection

(2014) Nezam Afdhal et al.   NEW ENGLAND JOURNAL OF MEDICINE

Ledipasvir and Sofosbuvir for Previously Treated HCV Genotype 1 Infection

(2014) Nezam Afdhal et al.   NEW ENGLAND JOURNAL OF MEDICINE

Ledipasvir and Sofosbuvir for 8 or 12 Weeks for Chronic HCV without Cirrhosis

(2014) Kris V. Kowdley et al.   NEW ENGLAND JOURNAL OF MEDICINE

Molecular and Genetic Characterization of Natural HIV-1 Tat Exon-1 Variants from North India and Their Functional Implications

(2014) Larance Ronsard et al.   PLoS One

Impact of Different Oseltamivir Regimens on Treating Influenza A Virus Infection and Resistance Emergence: Insights from a Modelling Study

(2014) Laetitia Canini et al.   PLoS Computational Biology

Modeling antiretroviral drug responses for HIV-1 infected patients using differential equation models

(2013) Yanni Xiao et al.   ADVANCED DRUG DELIVERY REVIEWS

Favipiravir (T-705), a novel viral RNA polymerase inhibitor

(2013) Yousuke Furuta et al.   ANTIVIRAL RESEARCH

Modeling the within-host dynamics of HIV infection

(2013) Alan S Perelson et al.   BMC BIOLOGY

Understanding the hepatitis C virus life cycle paves the way for highly effective therapies

(2013) Troels K H Scheel et al.   NATURE MEDICINE

Modeling shows that the NS5A inhibitor daclatasvir has two modes of action and yields a shorter estimate of the hepatitis C virus half-life

(2013) J. Guedj et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Profile of alisporivir and its potential in the treatment of hepatitis C

(2013) Philippe Gallay et al.   Drug Design Development and Therapy

Transcriptional and Posttranscriptional Regulation of HIV-1 Gene Expression

(2013) J. Karn et al.   Cold Spring Harbor Perspectives in Medicine

Analysis of Hepatitis C Virus Decline during Treatment with the Protease Inhibitor Danoprevir Using a Multiscale Model

(2013) Libin Rong et al.   PLoS Computational Biology

Multiscale Modeling of Influenza A Virus Infection Supports the Development of Direct-Acting Antivirals

(2013) Frank S. Heldt et al.   PLoS Computational Biology

Replication Vesicles are Load- and Choke-Points in the Hepatitis C Virus Lifecycle

(2013) Marco Binder et al.   PLoS Pathogens

Post-Treatment HIV-1 Controllers with a Long-Term Virological Remission after the Interruption of Early Initiated Antiretroviral Therapy ANRS VISCONTI Study

(2013) Asier Sáez-Cirión et al.   PLoS Pathogens

HIV-1 control after transient antiretroviral treatment initiated in primary infection: role of patient characteristics and effect of therapy

(2012) Cécile Goujard et al.   ANTIVIRAL THERAPY

Prospects for Treatment of Latent HIV

(2012) K M Barton et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

The cyclophilin inhibitor SCY-635 suppresses viral replication and induces endogenous interferons in patients with chronic HCV genotype 1 infection

(2012) Sam Hopkins et al.   JOURNAL OF HEPATOLOGY

Host-targeting agents for prevention and treatment of chronic hepatitis C – Perspectives and challenges

(2012) Mirjam B. Zeisel et al.   JOURNAL OF HEPATOLOGY

The H275Y Neuraminidase Mutation of the Pandemic A/H1N1 Influenza Virus Lengthens the Eclipse Phase and Reduces Viral Output of Infected Cells, Potentially Compromising Fitness in Ferrets

(2012) L. T. Pinilla et al.   JOURNAL OF VIROLOGY

Administration of vorinostat disrupts HIV-1 latency in patients on antiretroviral therapy

(2012) N. M. Archin et al.   NATURE

Modelling the Course of an HIV Infection: Insights from Ecology and Evolution

(2012) Samuel Alizon et al.   Viruses-Basel

Modeling Within-Host Dynamics of Influenza Virus Infection Including Immune Responses

(2012) Kasia A. Pawelek et al.   PLoS Computational Biology

Effect of therapeutic HIV recombinant poxvirus vaccines on the size of the resting CD4+ T-cell latent HIV reservoir

(2011) Deborah Persaud et al.   AIDS

Safety, pharmacokinetics, and antiviral activity of the cyclophilin inhibitor NIM811 alone or in combination with pegylated interferon in HCV-infected patients receiving 14 days of therapy

(2011) Eric Lawitz et al.   ANTIVIRAL RESEARCH

A review of mathematical models of influenza A infections within a host or cell culture: lessons learned and challenges ahead

(2011) Catherine AA Beauchemin et al.   BMC PUBLIC HEALTH

Second-phase hepatitis C virus RNA decline during telaprevir-based therapy increases with drug effectiveness: Implications for treatment duration

(2011) Jeremie Guedj et al.   HEPATOLOGY

Hepatitis C viral kinetics with the nucleoside polymerase inhibitor mericitabine (RG7128)

(2011) Jeremie Guedj et al.   HEPATOLOGY

Telaprevir for Previously Untreated Chronic Hepatitis C Virus Infection

(2011) Ira M. Jacobson et al.   NEW ENGLAND JOURNAL OF MEDICINE

Assessing the In Vitro Fitness of an Oseltamivir-Resistant Seasonal A/H1N1 Influenza Strain Using a Mathematical Model

(2011) Benjamin P. Holder et al.   PLoS One

Prolonged control of replication-competent dual- tropic human immunodeficiency virus-1 following cessation of highly active antiretroviral therapy

(2011) Maria Salgado et al.   Retrovirology

A perspective on modelling hepatitis C virus infection

(2010) J. Guedj et al.   JOURNAL OF VIRAL HEPATITIS

Estimation of the Initial Viral Growth Rate and Basic Reproductive Number during Acute HIV-1 Infection

(2010) R. M. Ribeiro et al.   JOURNAL OF VIROLOGY

Quantifying the Early Immune Response and Adaptive Immune Response Kinetics in Mice Infected with Influenza A Virus

(2010) H. Miao et al.   JOURNAL OF VIROLOGY

Dynamics of Influenza Virus Infection and Pathology

(2010) R. A. Saenz et al.   JOURNAL OF VIROLOGY

Chemical genetics strategy identifies an HCV NS5A inhibitor with a potent clinical effect

(2010) Min Gao et al.   NATURE

Assembly of infectious hepatitis C virus particles

(2010) Ralf Bartenschlager et al.   TRENDS IN MICROBIOLOGY

Human Fatal Zaire Ebola Virus Infection Is Associated with an Aberrant Innate Immunity and with Massive Lymphocyte Apoptosis

(2010) Nadia Wauquier et al.   PLoS Neglected Tropical Diseases

Towards a quantitative understanding of the within-host dynamics of influenza A infections

(2009) A. Handel et al.   Journal of the Royal Society Interface

Modeling HIV persistence, the latent reservoir, and viral blips

(2009) Libin Rong et al.   JOURNAL OF THEORETICAL BIOLOGY

Critical Role of Cyclophilin A and Its Prolyl-Peptidyl Isomerase Activity in the Structure and Function of the Hepatitis C Virus Replication Complex

(2009) Z. Liu et al.   JOURNAL OF VIROLOGY

HIV reservoir size and persistence are driven by T cell survival and homeostatic proliferation

(2009) Nicolas Chomont et al.   NATURE MEDICINE

Elucidating the elite: mechanisms of control in HIV-1 infection

(2009) Karen A. O’Connell et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Agent-based modeling of host–pathogen systems: The successes and challenges

(2008) Amy L. Bauer et al.   INFORMATION SCIENCES

Modeling amantadine treatment of influenza A virus in vitro

(2008) Catherine A.A. Beauchemin et al.   JOURNAL OF THEORETICAL BIOLOGY

Raltegravir with Optimized Background Therapy for Resistant HIV-1 Infection

(2008) Roy T. Steigbigel et al.   NEW ENGLAND JOURNAL OF MEDICINE

Low-level viremia persists for at least 7 years in patients on suppressive antiretroviral therapy

(2008) S. Palmer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA