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List of works by Christophe Fraser

27 years of the HIV epidemic amongst men having sex with men in the Netherlands: an in depth mathematical model-based analysis

scientific article

A new framework and software to estimate time-varying reproduction numbers during epidemics

scientific article published on 15 September 2013

A simple approach to measure transmissibility and forecast incidence

scientific article published on 24 February 2017

A strong case for viral genetic factors in HIV virulence

scientific article

A systematic review of reported reassortant viral lineages of influenza A

scientific article published in 2016

A transmission-virulence evolutionary trade-off explains attenuation of HIV-1 in Uganda

scientific article

Adherence to antiretroviral therapy and its impact on clinical outcome in HIV-infected patients

scientific article published in September 2005

After Ebola in West Africa — Unpredictable Risks, Preventable Epidemics

scientific article (publication date: 11 August 2016)

An evolutionary model to predict the frequency of antibiotic resistance under seasonal antibiotic use, and an application to Streptococcus pneumoniae.

scientific article published in May 2017

Antigen-driven CD4+ T cell and HIV-1 dynamics: residual viral replication under highly active antiretroviral therapy

scientific article published on December 1999

Antigen-driven T-cell turnover

scientific article published in November 2002

Assessing the reliability of eBURST using simulated populations with known ancestry

scientific article published on 12 April 2007

Assessing the severity of the novel influenza A/H1N1 pandemic.

scientific article

Assessment of epidemic projections using recent HIV survey data in South Africa: a validation analysis of ten mathematical models of HIV epidemiology in the antiretroviral therapy era.

scientific article published in October 2015

Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data

scientific article

CD4 Cell Counts of 800 Cells/mm3 or Greater After 7 Years of Highly Active Antiretroviral Therapy Are Feasible in Most Patients Starting With 350 Cells/mm3 or Greater

scientific article published on 01 June 2007

CD4+ cell dynamics in untreated HIV-1 infection: overall rates, and effects of age, viral load, sex and calendar time

scientific article published in November 2015

Clinical and public health implications of acute and early HIV detection and treatment: a scoping review

scientific article published on June 2017

Coalescent models for populations with time-varying population sizes and arbitrary offspring distributions

Comparison of cluster-based and source-attribution methods for estimating transmission risk using large HIV sequence databases.

scientific article

Convergent evolution and topologically disruptive polymorphisms among multidrug-resistant tuberculosis in Peru.

scientific article

Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis

scientific article

Distinguishing Between Reservoir Exposure and Human-to-Human Transmission for Emerging Pathogens Using Case Onset Data

scientific article

Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.

scientific article published in January 2018

Ebola Virus Disease among Male and Female Persons in West Africa

scientific article published on January 2016

Ebola virus disease among children in West Africa

scientific article

Effect of Universal Testing and Treatment on HIV Incidence - HPTN 071 (PopART)

scientific article published on 01 July 2019

Effect of the Latent Reservoir on the Evolution of HIV at the Within- and Between-Host Levels

scientific article

Epidemic growth rate and household reproduction number in communities of households, schools and workplaces ⬇️

scientific article published on December 1, 2010

Epidemiological and genetic analysis of severe acute respiratory syndrome

scientific article

Epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in Hong Kong

scientific article

Epidemiological impacts of the NHS COVID-19 app in England and Wales throughout its first year ⬇️

Epidemiology, transmission dynamics and control of SARS: the 2002-2003 epidemic

scientific article

Essential epidemiological mechanisms underpinning the transmission dynamics of seasonal influenza

scientific article published on 29 June 2011

Estimating HIV Incidence, Time to Diagnosis, and the Undiagnosed HIV Epidemic Using Routine Surveillance Data

scientific article

Estimating SARS-CoV-2 variant fitness and the impact of interventions in England using statistical and geo-spatial agent-based models

scientific article published on 3 October 2022

Estimating individual and household reproduction numbers in an emerging epidemic

scientific article

Estimating the public health impact of the effect of herpes simplex virus suppressive therapy on plasma HIV-1 viral load

scientific article published on May 2009

Ethical considerations in global HIV phylogenetic research

article

Evaluation of phylogenetic methods for inferring the direction of HIV transmission: HPTN 052

scientific article published on 10 January 2020

Evidence that pneumococcal serotype replacement in Massachusetts following conjugate vaccination is now complete

scientific article

Evolution of HIV virulence in response to widespread scale up of antiretroviral therapy: a modeling study

scientific article published in July 2016

Evolution of HIV-1 within untreated individuals and at the population scale in Uganda

article

Evolution of antibiotic resistance is linked to any genetic mechanism affecting bacterial duration of carriage

scientific article published on 17 January 2017

Evolutionary epidemiology: preparing for an age of genomic plenty

scientific article published on 4 February 2013

Exploring Genetic Relatedness, Patterns of Evolutionary Descent, and the Population Genetics of Bacterial Pathogens Using Multilocus Sequence Typing

article

Exposure Patterns Driving Ebola Transmission in West Africa: A Retrospective Observational Study

scientific article

Factors that make an infectious disease outbreak controllable

scientific article published on 20 April 2004

Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae

scientific article published on 22 October 2020

Frequency-dependent selection in vaccine-associated pneumococcal population dynamics

scientific article published on 16 October 2017

Frequent recombination of pneumococcal capsule highlights future risks of emergence of novel serotypes

article

From clinical sample to complete genome: Comparing methods for the extraction of HIV-1 RNA for high-throughput deep sequencing

scientific article published on 4 August 2016

Fuzzy species among recombinogenic bacteria

scientific article

Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting

scientific article published on 9 December 2014

Genomic Infectious Disease Epidemiology in Partially Sampled and Ongoing Outbreaks

scientific article published on 18 January 2017

Genomic analysis of emerging pathogens: methods, application and future trends

scientific article

Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1

scientific article published on 20 July 2023

HIV recombination: what is the impact on antiretroviral therapy? ⬇️

scientific article published on December 2005

HIV treatment as prevention: debate and commentary--will early infection compromise treatment-as-prevention strategies?

scientific article

HIV treatment as prevention: optimising the impact of expanded HIV treatment programmes

scientific article published on 10 July 2012

HIV treatment as prevention: systematic comparison of mathematical models of the potential impact of antiretroviral therapy on HIV incidence in South Africa

scientific article

HIV treatment-as-prevention research: taking the right road at the crossroads

scientific article

HIV-1 Sequence Data Coverage in Central East Africa from 1959 to 2013.

scientific article

HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences

scientific article published on 25 May 2017

HIV-1 transmitting couples have similar viral load set-points in Rakai, Uganda

scientific article

HPTN 071 (PopART): a cluster-randomized trial of the population impact of an HIV combination prevention intervention including universal testing and treatment: mathematical model

scientific article published on 15 January 2014

HPTN 071 (PopART): rationale and design of a cluster-randomised trial of the population impact of an HIV combination prevention intervention including universal testing and treatment - a study protocol for a cluster randomised trial

scientific article published on 13 February 2014

Has the rate of CD4 cell count decline before initiation of antiretroviral therapy changed over the course of the Dutch HIV epidemic among MSM?

scientific article

Health benefits, costs, and cost-effectiveness of earlier eligibility for adult antiretroviral therapy and expanded treatment coverage: a combined analysis of 12 mathematical models

scientific article published in December 2013

Heterogeneities in the case fatality ratio in the West African Ebola outbreak 2013–2016

scientific article (publication date: 10 April 2017)

Heterogeneity in the frequency and characteristics of homologous recombination in pneumococcal evolution

scientific article

High Transmissibility During Early HIV Infection Among Men Who Have Sex With Men-San Francisco, California

scientific article published on 26 December 2014

High heritability is compatible with the broad distribution of set point viral load in HIV carriers

scientific article published on 6 February 2015

Historical zoonoses and other changes in host tropism of Staphylococcus aureus, identified by phylogenetic analysis of a population dataset

scientific article

Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict.

scientific article

Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae

scientific article published on 20 May 2020

Host immunity and synchronized epidemics of syphilis across the United States

scientific article

Host population structure and treatment frequency maintain balancing selection on drug resistance

scientific article

Household transmission of 2009 pandemic influenza A (H1N1) virus in the United States.

scientific article

How the dynamics and structure of sexual contact networks shape pathogen phylogenies

scientific article

Hyper-recombination, diversity, and antibiotic resistance in pneumococcus

scientific article published in June 2009

Identifying currents in the gene pool for bacterial populations using an integrative approach

scientific article

Impact and Cost-Effectiveness of Point-Of-Care CD4 Testing on the HIV Epidemic in South Africa

scientific article published on 8 July 2016

Increasing sexual risk behaviour among Dutch men who have sex with men: mathematical models versus prospective cohort data

scientific article published in September 2012

Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis

article

Inferring pandemic growth rates from sequence data ⬇️

scientific article published on February 15, 2012

Influenza pandemic vaccines: spread them thin?

scientific article

Influenza transmission in households during the 1918 pandemic

scientific article

Instantons, three dimensional gauge theories, and monopole moduli spaces

scholarly article

Integrating phylodynamics and epidemiology to estimate transmission diversity in viral epidemics

scientific article

Interpretation of correlations in setpoint viral load in transmitting couples ⬇️

scientific article published on October 23, 2010

Is HIV short-sighted? Insights from a multistrain nested model

scientific article published on 13 June 2013

Key data for outbreak evaluation: building on the Ebola experience

scientific article

Large Variations in HIV-1 Viral Load Explained by Shifting-Mosaic Metapopulation Dynamics

scientific article published on 5 October 2016

Let it be sexual - selection, aggregation and distortion used to construct a case against sexual transmission

article

Link between the numbers of particles and variants founding new HIV-1 infections depends on the timing of transmission

article

Mathematical models of infectious disease transmission

scientific article

Methods for estimating the case fatality ratio for a novel, emerging infectious disease

scientific article

Mixing patterns of HIV transmission among men who have sex with men in the United Kingdom

article

Modeling the effect of exposure notification and non-pharmaceutical interventions on COVID-19 transmission in Washington state

scientific article published on 12 March 2021

Modeling the long-term antibody response of a human papillomavirus (HPV) virus-like particle (VLP) type 16 prophylactic vaccine

scientific article

Modelling bacterial speciation

scientific article

Modelling sexual transmission of HIV: testing the assumptions, validating the predictions

scientific article

Molecular Epidemiology of HIV-1 Subtype B Reveals Heterogeneous Transmission Risk: Implications for Intervention and Control

article

Neutral microepidemic evolution of bacterial pathogens

scientific article

New insights into the evolutionary rate of HIV-1 at the within-host and epidemiological levels ⬇️

scientific article published on 22 August 2012

New strategies for the elimination of polio from India

scientific article

No coexistence for free: neutral null models for multistrain pathogens

scientific article

On the evolutionary ecology of multidrug resistance in bacteria

scientific article published on 13 May 2019

OpenABM-Covid19-An agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing

scholarly article by Robert Hinch published in 2021

Optimizing the precision of case fatality ratio estimates under the surveillance pyramid approach.

scientific article

OutbreakTools: a new platform for disease outbreak analysis using the R software

scientific article (publication date: June 2014)

PANGEA-HIV 2: Phylogenetics And Networks for Generalised Epidemics in Africa

article

PANGEA-HIV: phylogenetics for generalised epidemics in Africa

scientific article published on March 2015

PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity.

scientific article published on 23 November 2017

Pandemic potential of a strain of influenza A (H1N1): early findings

scientific article

Phylodynamic inference and model assessment with approximate bayesian computation: influenza as a case study

scientific article

Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.

scientific article published on 07 October 2016

Phylogenetic and Demographic Characterization of Directed HIV-1 Transmission Using Deep Sequences from High-Risk and General Population Cohorts/Groups in Uganda

scientific article published on 18 March 2020

Phylogenetic methods inconsistently predict direction of HIV transmission among heterosexual pairs in the HPTN052 cohort

article

Phylogenetic studies of transmission dynamics in generalized HIV epidemics: an essential tool where the burden is greatest?

scientific article

Pneumococcal capsule synthesis locus cps as evolutionary hotspot with potential to generate novel serotypes by recombination.

scientific article published on 08 June 2017

PopART-IBM, a highly efficient stochastic individual-based simulation model of generalised HIV epidemics developed in the context of the HPTN 071 (PopART) trial

scientific article published in September 2021

PopART-IBM, a highly efficient stochastic individual-based simulation model of generalised HIV epidemics developed in the context of the HPTN 071 (PopART) trial

preprint

Potential Biases in Estimating Absolute and Relative Case-Fatality Risks during Outbreaks

scientific article

Prediction of post-vaccine population structure of Streptococcus pneumoniae using accessory gene frequencies

article

Public health. Public health risk from the avian H5N1 influenza epidemic

scientific article published in May 2004

Quantification of intrinsic residual viral replication in treated HIV-infected patients

scientific article

Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda

scientific article published on 14 January 2020

Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing

scientific article published on 31 March 2020

Quantifying Transmission Heterogeneity Using Both Pathogen Phylogenies and Incidence Time Series

scientific article published on 11 July 2017

Quantifying the transmissibility of human influenza and its seasonal variation in temperate regions.

scientific article

Rapid Pneumococcal Evolution in Response to Clinical Interventions ⬇️

scientific article (publication date: 28 January 2011)

Recombination and the nature of bacterial speciation

scientific article published on January 2007

Reducing the impact of the next influenza pandemic using household-based public health interventions

scientific article (publication date: September 2006)

Reduction of the HIV-1-infected T-cell reservoir by immune activation treatment is dose-dependent and restricted by the potency of antiretroviral drugs

scientific article published in April 2000

Reproductive numbers, epidemic spread and control in a community of households.

scientific article

Response--Influenza

scientific article published in Science

Resurgence of HIV infection among men who have sex with men in Switzerland: mathematical modelling study

scientific article

S-duality in N = 4 supersymmetric gauge theories with arbitrary gauge group

SARS-CoV antibody prevalence in all Hong Kong patient contacts

scientific article published in September 2004

Seasonal infectious disease epidemiology

scientific article published in October 2006

Sequences, sequence clusters and bacterial species

scientific article published on November 2006

Seroprevalence of IgG antibodies to SARS-coronavirus in asymptomatic or subclinical population groups

scientific article published on 01 April 2006

Sources of HIV infection among men having sex with men and implications for prevention

scientific article

Strategies for containing an emerging influenza pandemic in Southeast Asia

scientific article (publication date: 8 September 2005)

Strategies for mitigating an influenza pandemic

scientific article (publication date: 27 July 2006)

Studies needed to address public health challenges of the 2009 H1N1 influenza pandemic: insights from modeling

article

Synergistic Activity of Mobile Genetic Element Defences in Streptococcus pneumoniae

scientific article published on 13 September 2019

Systematic selection between age and household structure for models aimed at emerging epidemic predictions

scientific article published on 14 February 2020

The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity

scientific article

The Early Transmission Dynamics of H1N1pdm Influenza in the United Kingdom

scientific article

The effect on treatment comparisons of different measurement frequencies in human immunodeficiency virus observational databases

scientific article published on 16 February 2006

The effectiveness of contact tracing in emerging epidemics ⬇️

scientific article published on 20 December 2006

The epidemiology of severe acute respiratory syndrome in the 2003 Hong Kong epidemic: an analysis of all 1755 patients

scientific article published in November 2004

The evolution of antibiotic resistance in a structured host population

scholarly article by François Blanquart et al published June 2018 in Journal of the Royal Society Interface

The evolution of subtype B HIV-1 tat in the Netherlands during 1985-2012.

scientific article

The impact of homologous recombination on the generation of diversity in bacteria

scientific article published on 19 October 2005

The potential effects of changing HIV treatment policy on tuberculosis outcomes in South Africa: results from three tuberculosis-HIV transmission models.

scientific article

The relationship between real-time and discrete-generation models of epidemic spread

scientific article published in November 2008

The role of antigenic stimulation and cytotoxic T cell activity in regulating the long-term immunopathogenesis of HIV: mechanisms and clinical implications

scientific article published in October 2001

The role of rapid diagnostics in managing Ebola epidemics

scientific article published on December 2015

Threshold parameters for a model of epidemic spread among households and workplaces

scientific article published on 25 February 2009

Time to evaluate COVID-19 contact-tracing apps

scientific article published on 15 February 2021

Transformation asymmetry and the evolution of the bacterial accessory genome.

scientific article published in December 2017

Transmission Dynamics and Control of the Viral Aetiological Agent of SARS

article

Transmission characteristics of the 2009 H1N1 influenza pandemic: comparison of 8 Southern hemisphere countries

scientific article

Transmission dynamics of the etiological agent of SARS in Hong Kong: impact of public health interventions

scientific article

Transmission selects for HIV-1 strains of intermediate virulence: a modelling approach

scientific article published on 13 October 2011

Unraveling the drivers of MERS-CoV transmission

scientific article published on 25 July 2016

Variation in HIV-1 set-point viral load: epidemiological analysis and an evolutionary hypothesis

scientific article

Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe

scientific article

Viral load levels measured at set-point have risen over the last decade of the HIV epidemic in the Netherlands

scientific article

Viral replication under combination antiretroviral therapy: a comparison of four different regimens

scientific article published in June 2002

Virulence and pathogenesis of HIV-1 infection: an evolutionary perspective

scientific article

Virus genomes reveal factors that spread and sustained the Ebola epidemic

scientific article (publication date: 12 April 2017)

West African Ebola epidemic after one year--slowing but not yet under control

scientific article

What is the mechanism for persistent coexistence of drug-susceptible and drug-resistant strains of Streptococcus pneumoniae?

scientific article

Within-host and between-host evolutionary rates across the HIV-1 genome ⬇️

scientific article published on 02 May 2013

Workup of Human Blood Samples for Deep Sequencing of HIV-1 Genomes

scientific article published in January 2018

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