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List of works by Roger Kouyos

A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland

scientific article published on 19 September 2016

A Method to Estimate the Size and Characteristics of HIV-positive Populations Using an Individual-based Stochastic Simulation Model

scientific article published on 24 November 2015

A Systematic Phylogenetic Approach to Study the Interaction of HIV-1 With Coinfections, Noncommunicable Diseases, and Opportunistic Diseases

scientific article published on 01 June 2019

A novel Acute Retroviral Syndrome Severity Score predicts the key surrogate markers for HIV-1 disease progression

scientific article

Ambiguous nucleotide calls from population-based sequencing of HIV-1 are a marker for viral diversity and the age of infection

scientific article published on 10 January 2011

An integrated approach to identifying international foodborne norovirus outbreaks

scientific article

Assessing efficacy of different nucleos(t)ide backbones in NNRTI-containing regimens in the Swiss HIV Cohort Study

scientific article published on 11 September 2015

Assessing predicted HIV-1 replicative capacity in a clinical setting

scientific article published in November 2011

Assessing the Paradox Between Transmitted and Acquired HIV Type 1 Drug Resistance Mutations in the Swiss HIV Cohort Study From 1998 to 2012.

scientific article published on 9 January 2015

Assessing the danger of self-sustained HIV epidemics in heterosexuals by population based phylogenetic cluster analysis

scientific article published on 12 September 2017

Assessing the impact of adherence to anti-retroviral therapy on treatment failure and resistance evolution in HIV.

scientific article published on 14 March 2012

Assessment of Overlap of Phylogenetic Transmission Clusters and Communities in Simple Sexual Contact Networks: Applications to HIV-1.

scientific article published on 10 February 2016

Bottleneck-induced transitions in a minimal model for intracellular transport

article

Bridging the gap between HIV epidemiology and antiretroviral resistance evolution: Modelling the spread of resistance in South Africa

scientific article published on 24 June 2019

Can Directionality of HIV Transmission be Predicted by Next-Generation Sequencing Data?

scientific article published on 01 September 2019

Can we believe the DAGs? A comment on the relationship between causal DAGs and mechanisms

scientific article published on 28 March 2014

Changing Trends in International Versus Domestic HCV Transmission in HIV-Positive Men Who Have Sex With Men: A Perspective for the Direct-Acting Antiviral Scale-Up Era

scientific article published on 01 June 2019

Chemsex drugs on the rise: a longitudinal analysis of the Swiss HIV Cohort Study from 2007 to 2017

scientific article published on 18 December 2019

Clustering of HCV coinfections on HIV phylogeny indicates domestic and sexual transmission of HCV.

scientific article published on 22 January 2014

Clusters of Sexual Behavior in Human Immunodeficiency Virus-positive Men Who Have Sex With Men Reveal Highly Dissimilar Time Trends

scientific article published on 01 January 2020

Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C

scientific article published on 07 September 2021

Contribution of APOBEC3G/F activity to the development of low-abundance drug-resistant human immunodeficiency virus type 1 variants.

scientific article published on 16 October 2015

Contribution of a mutational bias in hepatitis C virus replication to the genetic barrier in the development of drug resistance

scientific article published on December 2011

Corrigendum to: Impact of the M184V/I Mutation on the Efficacy of Abacavir/Lamivudine/Dolutegravir Therapy in HIV Treatment-Experienced Patients

scientific article published on 08 December 2019

Cycling empirical antibiotic therapy in hospitals: meta-analysis and models

scientific article

Determinants of HIV-1 broadly neutralizing antibody induction.

scientific article

Determinants of HIV-1 reservoir size and long-term dynamics during suppressive ART

scientific article published on 19 July 2019

Development of a high-throughput bead based assay system to measure HIV-1 specific immune signatures in clinical samples

scientific article published on 22 December 2017

Diagnosis of latent tuberculosis infection is associated with reduced HIV viral load and lower risk for opportunistic infections in people living with HIV

scientific article published on 07 December 2020

Distinct conformations of the HIV-1 V3 loop crown are targetable for broad neutralization

scientific article published on 18 November 2021

Distinct, IgG1-driven antibody response landscapes demarcate individuals with broadly HIV-1 neutralizing activity

scientific article published on 24 May 2018

Dually Active HIV/HBV Antiretrovirals as Protection Against Incident Hepatitis B Infections: Potential for Prophylaxis

scientific article

Editorial Commentary: The Irreversibility of HIV Drug Resistance

scientific article published on 19 May 2015

Effect of varying epistasis on the evolution of recombination

scientific article

Emergence of Acquired HIV-1 Drug Resistance Almost Stopped in Switzerland: A 15-Year Prospective Cohort Analysis

scientific article published on 8 March 2016

Epistasis between deleterious mutations and the evolution of recombination

scientific article published on 6 March 2007

Estimating the basic reproductive number from viral sequence data.

scientific article

Estimating the dynamics and dependencies of accumulating mutations with applications to HIV drug resistance

scientific article published on 14 May 2015

Estimating the fitness cost of escape from HLA presentation in HIV-1 protease and reverse transcriptase.

scientific article

Exploring the complexity of the HIV-1 fitness landscape

scientific article

Factors associated with syphilis incidence in the HIV-infected in the era of highly active antiretrovirals

scientific article published on January 2017

Five challenges in evolution and infectious diseases

scientific article published on 18 December 2014

Frequency and Spectrum of Unexpected Clinical Manifestations of Primary HIV-1 Infection

scientific article published on 19 May 2015

From Intracellular Traffic to a Novel Class of Driven Lattice Gas Models

Genotypic Resistance Tests Sequences Reveal the Role of Marginalized Populations in HIV-1 Transmission in Switzerland

scientific article published on 14 June 2016

HIV Transmission Chains Exhibit Greater HLA-B Homogeneity Than Randomly Expected

scientific article published on 01 August 2019

HIV-1 Transmission During Recent Infection and During Treatment Interruptions as Major Drivers of New Infections in the Swiss HIV Cohort Study

scientific article published on 19 September 2015

Hepatitis C Infection and the Risk of Non-Liver-Related Morbidity and Mortality in HIV-Infected Persons in the Swiss HIV Cohort Study

scientific article published on February 2017

Hepatitis C virus transmission among human immunodeficiency virus-infected men who have sex with men: Modeling the effect of behavioral and treatment interventions

scientific article published on 17 August 2016

Heritability of the HIV-1 reservoir size and decay under long-term suppressive ART

scientific article published on 02 November 2020

High Cure Rates With Grazoprevir-Elbasvir With or Without Ribavirin Guided by Genotypic Resistance Testing Among Human Immunodeficiency Virus/Hepatitis C Virus-coinfected Men Who Have Sex With Men

scientific article published on 01 February 2019

High Number of Potential Transmitters Revealed in a Population-based Systematic Hepatitis C Virus RNA Screening Among Human Immunodeficiency Virus-infected Men Who Have Sex With Men

scientific article published on 01 February 2019

High hepatic and extrahepatic mortality and low treatment uptake in HCV-coinfected persons in the Swiss HIV cohort study between 2001 and 2013.

scientific article published on 30 April 2015

Higher risk of incident hepatitis C virus coinfection among men who have sex with men, in whom the HIV genetic bottleneck at transmission was wide

scientific article

Hospital-Community Interactions Foster Coexistence between Methicillin-Resistant Strains of Staphylococcus aureus ⬇️

scientific article published on February 28, 2013

Impact of scaling up dolutegravir on antiretroviral resistance in South Africa: A modeling study

scientific article published on 14 December 2020

Impact of screening and antiretroviral therapy on anal cancer incidence in HIV-positive MSM.

scientific article

Impact of the M184V/I Mutation on the Efficacy of Abacavir/Lamivudine/Dolutegravir Therapy in HIV Treatment-Experienced Patients

scientific article published on 12 July 2019

Increases in Condomless Sex in the Swiss HIV Cohort Study

scientific article published in April 2015

Inferring epidemic contact structure from phylogenetic trees

scientific article published on 8 March 2012

Informed switching strongly decreases the prevalence of antibiotic resistance in hospital wards

scientific article

Large-scale inference of conjunctive Bayesian networks

scientific article

Low-frequency drug-resistant HIV-1 and risk of virological failure to first-line NNRTI-based ART: a multicohort European case-control study using centralized ultrasensitive 454 pyrosequencing

scientific article

Lower Broadly Neutralizing Antibody Responses in Female Versus Male HIV-1 Infected Injecting Drug Users. ⬇️

scientific article published on 25 April 2019

Mining for pairs: shared clinic visit dates identify steady HIV-positive partnerships.

scientific article published on 4 April 2017

Modeling the effect of HIV coinfection on clearance and sustained virologic response during treatment for hepatitis C virus

scientific article published on 27 April 2015

Modeling the measles paradox reveals the importance of cellular immunity in regulating viral clearance

scientific article published on 28 December 2018

Modelling the impact of deferring HCV treatment on liver-related complications in HIV coinfected men who have sex with men.

scientific article

Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland

scientific article published in May 2010

Monocyte-derived macrophages exhibit distinct and more restricted HIV-1 integration site repertoire than CD4(+) T cells

scientific article published on 12 April 2016

Multifactorial seroprofiling dissects the contribution of pre-existing human coronaviruses responses to SARS-CoV-2 immunity

scientific article published on 18 November 2021

Noninferiority of Simplified Dolutegravir Monotherapy Compared to Continued Combination Antiretroviral Therapy That Was Initiated During Primary Human Immunodeficiency Virus Infection: A Randomized, Controlled, Multisite, Open-label, Noninferiority

scientific article published on 01 October 2019

On being the right size: the impact of population size and stochastic effects on the evolution of drug resistance in hospitals and the community

scientific article

On the causes of selection for recombination underlying the red queen hypothesis

scientific article

On the evolution of sexual reproduction in hosts coevolving with multiple parasites

scientific article published on 20 January 2010

On the role of resonance in drug failure under HIV treatment interruption

scientific article published on 11 July 2013

Parent-offspring regression to estimate the heritability of an HIV-1 trait in a realistic setup

scientific article

Persistence of transmitted HIV-1 drug resistance mutations associated with fitness costs and viral genetic backgrounds

scientific article (publication date: March 2015)

Phylodynamics on local sexual contact networks

scientific article

Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load

scientific article published on 30 September 2010

Population biological principles of drug-resistance evolution in infectious diseases

scientific article published on March 2011

Postnatal retention in HIV care: insight from the Swiss HIV Cohort Study over a 15-year observational period

scientific article

Predicting the evolution of sex on complex fitness landscapes

scientific article

Prescription of Postexposure Prophylaxis for HIV-1 in the Emergency Room: Correct Transmission Risk Assessment Remains Challenging

scientific article published on 30 November 2016

Prevalence and risk factors of late presentation for HIV diagnosis and care in a tertiary referral centre in Switzerland

scientific article published on 10 April 2014

Prolonged persistence of measles virus RNA is characteristic of primary infection dynamics

scientific article

Quantifying the drivers of HIV transmission and prevention in men who have sex with men: a population model-based analysis in Switzerland

article

Quantifying the fitness cost of HIV-1 drug resistance mutations through phylodynamics

scientific article published on 20 February 2018

Quantifying the impact of treatment history on plasmid-mediated resistance evolution in human gut microbiota

scientific article published on 30 October 2019

Rapid parasite adaptation drives selection for high recombination rates

scientific article published on 26 November 2007

Rational design of HIV-1 fluorescent hydrolysis probes considering phylogenetic variation and probe performance

scientific article published on 29 January 2010

Reasons for late presentation to HIV care in Switzerland

scientific article

Recombination accelerates adaptation on a large-scale empirical fitness landscape in HIV-1

scientific article (publication date: June 2014)

Recombination and drug resistance in HIV: Population dynamics and stochasticity

article

Reply to correspondence 'Conserved signatures indicate HIV-1 transmission is under strong selection and thus is not a "stochastic" process' by Gonzalez et al., Retrovirology 2017.

scientific article published on 24 February 2017

Rotating antibiotics does not minimize selection for resistance

scientific article published in October 2010

Sex and gender in infection and immunity: addressing the bottlenecks from basic science to public health and clinical applications

scientific article published in 2023

Similar impact of CD8+ T cell responses on early virus dynamics during SIV infections of rhesus macaques and sooty mangabeys

scientific article

Social meets molecular: Combining phylogenetic and latent class analyses to understand HIV-1 transmission in Switzerland

scientific article published on 12 May 2014

Stochastic or deterministic: what is the effective population size of HIV-1?

scientific article published on 16 October 2006

Successful Prevention of Transmission of Integrase Resistance in the Swiss HIV Cohort Study

scientific article published on 29 April 2016

The Red Queen and the persistence of linkage-disequilibrium oscillations in finite and infinite populations

scientific article

The Role of Adherence and Retreatment in De Novo Emergence of MDR-TB

scientific article

The TransFLUas influenza transmission study in acute healthcare - recruitment rates and protocol adherence in healthcare workers and inpatients

article

The impact of HCV therapy in a high HIV-HCV prevalence population: A modeling study on people who inject drugs in Ho Chi Minh City, Vietnam

scientific article

The impact of vaccination on the breadth and magnitude of the antibody response to influenza A viruses in HIV-infected individuals

scientific article published on September 2015

The path of least resistance: aggressive or moderate treatment?

scientific article published in November 2014

The potential impact of coinfection on antimicrobial chemotherapy and drug resistance

scientific article

The role of epistasis on the evolution of recombination in host-parasite coevolution

scientific article published on 14 October 2008

The role of migration and domestic transmission in the spread of HIV-1 non-B subtypes in Switzerland

scientific article published in October 2011

The role of recombination for the coevolutionary dynamics of HIV and the immune response

scientific article

The state of affairs in the kingdom of the Red Queen

scientific article

Tracing HIV-1 transmission: envelope traits of HIV-1 transmitter and recipient pairs

scientific article published on 05 September 2016

Treatment-naive individuals are the major source of transmitted HIV-1 drug resistance in men who have sex with men in the Swiss HIV Cohort Study

scientific article published on 21 October 2013

Viral Diversity Based on Next-Generation Sequencing of HIV-1 Provides Precise Estimates of Infection Recency and Time Since Infection

scientific article published on 01 June 2019

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

scientific article

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