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List of works by Sebastian Bonhoeffer

A combined within-host and between-hosts modelling framework for the evolution of resistance to antimalarial drugs

scientific article published on 13 April 2016

A random walk from the cello to the lab

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

scientific article

A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase

article

African descent is associated with slower CD4 cell count decline in treatment-naive patients of the Swiss HIV Cohort Study

scientific article published in June 2009

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 antigenic threshold for maintaining human immunodeficiency virus type 1-specific cytotoxic T lymphocytes.

scientific article

An evolutionary perspective on the systems of adaptive immunity.

scientific article published on 26 July 2017

An evolutionary scenario for the transition to undifferentiated multicellularity

scientific article

Analysis of total human immunodeficiency virus (HIV)-specific CD4(+) and CD8(+) T-cell responses: relationship to viral load in untreated HIV infection

scientific article

Antagonism between bacteriostatic and bactericidal antibiotics is prevalent

scientific article

Anti-viral drug treatment: dynamics of resistance in free virus and infected cell populations

scientific article published in January 1997

Antibacterial effects of antiretrovirals, potential implications for microbiome studies in HIV.

scientific article published on 12 May 2017

Antibiotic Resistance Detection Is Essential For Gonorrhoea Point-Of-Care Testing: A Mathematical Modelling Study

scholarly article published 10 April 2017

Antibiotic-Resistant Neisseria gonorrhoeae Spread Faster with More Treatment, Not More Sexual Partners

scientific article

Antibiotic-resistant Neisseria gonorrhoeae spread faster with more treatment, not more sexual partners

scholarly article published 24 October 2015

Antibiotic-resistant Neisseria gonorrhoeae spread faster with more treatment, not more sexual partners

scholarly article published 24 October 2015

Assessing predicted HIV-1 replicative capacity in a clinical setting

scientific article published in November 2011

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

scientific article published on 14 March 2012

Assessing the public health impact of tolerance-based therapies with mathematical models.

scientific article

Bacterial growth properties at low optical densities.

scientific article published on 24 April 2009

Birth–death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV) ⬇️

scientific article published on December 17, 2012

CCTTT-repeat polymorphism of the inducible nitric oxide synthase is not associated with HIV pathogenesis

article

Can High-Risk Fungicides be Used in Mixtures Without Selecting for Fungicide Resistance?

Can live attenuated virus work as post-exposure treatment?

scientific article

Cancer-Induced Immunosuppression can enable Effectiveness of Immunotherapy through Bistability Generation: a mathematical and computational Examination

Causes of HIV diversity

scientific article published in July 1995

Clonal dominance and transplantation dynamics in hematopoietic stem cell compartments

scientific article

Compensation of fitness costs and reversibility of antibiotic resistance mutations

scientific article published on 22 February 2010

Contribution of peaks of virus load to simian immunodeficiency virus pathogenesis

scientific article

Contribution of recombination to the evolutionary history of HIV.

scientific article published on March 2015

Cooperation and competition in the evolution of ATP-producing pathways

scientific article published on 29 March 2001

Corrigendum to “Weighting for sex acts to understand the spread of STI on networks” [J. Theor. Biol. 311 (2012) 46–53]

scholarly article published in Journal of Theoretical Biology

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

scientific article

Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria

article

Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria.

scientific article

Decay kinetics of human immunodeficiency virus-specific effector cytotoxic T lymphocytes after combination antiretroviral therapy.

scientific article published on January 1999

Decelerating decay of latently infected cells during prolonged therapy for human immunodeficiency virus type 1 infection

scientific article

Detection of antibiotic resistance is essential for gonorrhoea point-of-care testing: a mathematical modelling study

scientific article

Developing smarter host mixtures to control plant disease

article

Dissecting HIV Virulence: Heritability of Setpoint Viral Load, CD4+ T-Cell Decline, and Per-Parasite Pathogenicity

scientific article published in January 2018

Dose-dependent infection rates of parasites produce the Allee effect in epidemiology

scientific article (publication date: 7 February 2002)

Dynamic variation in cycling of hematopoietic stem cells in steady state and inflammation

scientific article (publication date: 14 February 2011)

Ecological effects of stress drive bacterial evolvability under sub-inhibitory antibiotic treatments

scientific article published in 2022

Effect of varying epistasis on the evolution of recombination

scientific article

Effective polyploidy causes phenotypic delay and influences bacterial evolvability

Effective polyploidy causes phenotypic delay and influences bacterial evolvability.

scientific article

Eight challenges in phylodynamic inference.

scientific article

Emergence of Resistance to Fungicides: The Role of Fungicide Dose

scientific article published on 12 January 2017

Emergence of drug-resistant influenza virus: population dynamical considerations.

scientific article

Emergence of minor populations of human immunodeficiency virus type 1 carrying the M184V and L90M mutations in subjects undergoing structured treatment interruptions

scientific article published on 3 November 2003

Entry and transcription as key determinants of differences in CD4 T-cell permissiveness to human immunodeficiency virus type 1 infection.

scientific article published on October 2004

Epistasis and Pleiotropy Affect the Modularity of the Genotype-Phenotype Map of Cross-Resistance in HIV-1

scientific article published on 27 September 2016

Epistasis between deleterious mutations and the evolution of recombination

scientific article published on 6 March 2007

Epitope down-modulation as a mechanism for the coexistence of competing T-cells

scientific article

Error Thresholds on Correlated Fitness Landscapes

Estimating seroprevalence with imperfect serological tests: exploiting cutoff-free approaches

scientific article published on 01 May 2020

Estimating the basic reproductive number from viral sequence data.

scientific article

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

scientific article

Estimating the stoichiometry of human immunodeficiency virus entry

scientific article

Evaluating treatment protocols to prevent antibiotic resistance

scientific article published on October 1997

Evidence for Positive Epistasis in HIV-1

scientific article

Evolution and emergence of infectious diseases in theoretical and real-world networks

scientific article

Evolution of complexity in signaling pathways

scholarly article

Evolution of cooperation by generalized reciprocity

article

Evolution of cross-feeding in microbial populations

scientific article

Evolution of drug resistance in malaria parasites

scholarly article by Mathieu Legros & Sebastian Bonhoeffer published 2012 in Malaria Journal

Evolution of stress response in the face of unreliable environmental signals

scientific article

Evolution of virulence in a heterogeneous host population

scientific article published on 01 February 2000

Evolutionary rescue: linking theory for conservation and medicine

scientific article

Experimental tests for an evolutionary trade-off between growth rate and yield in E. coli.

scientific article

Explaining "linguistic features" of noncoding DNA.

scientific article published in January 1996

Exploring the complexity of the HIV-1 fitness landscape

scientific article

Fixation probability of mobile genetic elements such as plasmids

article

From "What Is?" to "What Isn't?" Computational Biology

scientific article

Glancing behind virus load variation in HIV-1 infection

scientific article published on November 2003

Global trends in antimicrobial resistance in animals in low- and middle-income countries

scientific article published on 01 September 2019

Guanine-adenine bias: a general property of retroid viruses that is unrelated to host-induced hypermutation

scientific article published in May 2005

HIV coreceptor usage and drug treatment

scientific article published in August 2002

HIV replication elicits little cytopathic effects in vivo: analysis of surrogate markers for virus production, cytotoxic T cell response and infected cell death

scientific article published in September 2006

HIV results in the frame

scientific article published in Nature

HIV-1 antigen-specific and -nonspecific B cell responses are sensitive to combination antiretroviral therapy

scientific article

HIV-1 evolution and disease progression.

scientific article published in November 1996

HIV-1-specific immune responses in subjects who temporarily contain virus replication after discontinuation of highly active antiretroviral therapy

scientific article

High Frequency of Cytomegalovirus‐Specific Cytotoxic T‐Effector Cells in HLA‐A*0201–Positive Subjects during Multiple Viral Coinfections

article

High epitope expression levels increase competition between T cells

scientific article

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

scientific article published on 6 February 2015

Host population structure impedes reversion to drug sensitivity after discontinuation of treatment

scientific article published on 21 August 2017

How Good Are Statistical Models at Approximating Complex Fitness Landscapes?

scientific article published on 14 May 2016

Human immunodeficiency virus drug therapy and virus load.

scientific article published in April 1997

Human immunodeficiency virus type 1 fitness is a determining factor in viral rebound and set point in chronic infection

scientific article

Humoral immunity to HIV-1: kinetics of antibody responses in chronic infection reflects capacity of immune system to improve viral set point

scientific article published on 8 June 2004

Increase in antimicrobial resistance in <i>Escherichia coli</i> in food animals between 1980 and 2018 assessed using genomes from public databases

scientific article published in 2021

Inference of epidemiological dynamics based on simulated phylogenies using birth-death and coalescent models

scientific article

Inferring epidemic contact structure from phylogenetic trees

scientific article published on 8 March 2012

Influence of recombination on acquisition and reversion of immune escape and compensatory mutations in HIV-1.

scientific article published on 18 October 2015

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

scientific article

Interchromatid and interhomolog recombination in Arabidopsis thaliana

scientific article

Intra-host versus inter-host selection: viral strategies of immune function impairment

scientific article published on August 1994

Invasiveness of plant pathogens depends on the spatial scale of host distribution

article

Is antimicrobial resistance evolution accelerating?

scientific article published on 22 October 2020

Long-term trends of HIV type 1 drug resistance prevalence among antiretroviral treatment-experienced patients in Switzerland

scientific article published in April 2009

Mathematical approaches in the study of viral kinetics and drug resistance in HIV-1 infection

scientific article published on December 2003

Metabolically cohesive microbial consortia and ecosystem functioning

scientific article published on 23 March 2020

Modeling antibiotic treatment in hospitals: A systematic approach shows benefits of combination therapy over cycling, mixing, and mono-drug therapies

scientific article published on 15 September 2017

Modeling antimicrobial cycling and mixing: Differences arising from an individual-based versus a population-based perspective

scientific article published on 26 September 2017

Modelling cytomegalovirus replication patterns in the human host: factors important for pathogenesis

scientific article published in August 2006

Models of viral kinetics and drug resistance in HIV-1 infection

scientific article

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

scientific article published in May 2010

Molecular tracking of an Human Immunodeficiency Virus nef specific cytotoxic T-cell clone shows persistence of clone-specific T-cell receptor DNA but not mRNA following early combination antiretroviral therapy

scientific article published in March 1999

Mutation accumulation in space and the maintenance of sexual reproduction

scientific article published in 2006

Nested model reveals potential amplification of an HIV epidemic due to drug resistance.

scientific article published on 17 November 2012

Neutral drift and polymorphism in gene-for-gene systems

article

No Signs of Hidden Language in Noncoding DNA

scientific article published in Physical Review Letters

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

Passive infusion of immune serum into simian immunodeficiency virus-infected rhesus macaques undergoing a rapid disease course has minimal effect on plasma viremia

scientific article published in April 2000

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

scientific article (publication date: March 2015)

Phenotypic changes in drug susceptibility associated with failure of human immunodeficiency virus type 1 (HIV-1) triple combination therapy

scientific article published on September 1999

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

scientific article published on 30 September 2010

Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo

scientific article published on 04 November 2020

Plasmids and evolutionary rescue by drug resistance

scientific article published on 21 May 2014

Population Biology, Evolution, and Infectious Disease: Convergence and Synthesis

scientific article published in Science

Population Heterogeneity in Mutation Rate Increases the Frequency of Higher-Order Mutants and Reduces Long-Term Mutational Load.

scientific article published on 11 November 2016

Population biological principles of drug-resistance evolution in infectious diseases

scientific article published on March 2011

Population heterogeneity in mutation rate increases mean fitness and the frequency of higher order mutants

Potential Pitfalls in Estimating Viral Load Heritability

scientific article published on 12 May 2016

Potential pitfalls in estimating viral load heritability

article

Practical considerations for measuring the effective reproductive number, Rt

scientific article published on 20 June 2020

Pre-existence and emergence of drug resistance in HIV-1 infection

scientific article published in May 1997

Pre-existence and emergence of drug resistance in a generalized model of intra-host viral dynamics.

scientific article published on 24 October 2012

Predicting the evolution of sex on complex fitness landscapes

scientific article

Principal component analysis of general patterns of HIV-1 replicative fitness in different drug environments.

scientific article published on 31 March 2010

Procedures for reliable estimation of viral fitness from time-series data.

scientific article published in September 2002

Production of resistant HIV mutants during antiretroviral therapy

scientific article

Quantification of cell turnover kinetics using 5-bromo-2'-deoxyuridine

scientific article published in May 2000

Quantification of in vivo replicative capacity of HIV-1 in different compartments of infected cells

article

Quantification of infectious HIV-1 plasma viral load using a boosted in vitro infection protocol

scientific article

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

scientific article published on 20 February 2018

Quantitation of HIV-1-Specific Cytotoxic T Lymphocytes and Plasma Load of Viral RNA

scientific article published in Science

Quantitative constraints on the scope of negative selection

scientific article

RNA multi-structure landscapes. A study based on temperature dependent partition functions

scientific article published in January 1993

Rapid clearance of simian immunodeficiency virus particles from plasma of rhesus macaques

scientific article

Rapid parasite adaptation drives selection for high recombination rates

scientific article published on 26 November 2007

Rapid production and clearance of HIV-1 and hepatitis C virus assessed by large volume plasma apheresis

scientific article

Rapid turnover of T lymphocytes in SIV-infected rhesus macaques

scientific article published in February 1998

Rapid viral decay in simian immunodeficiency virus-infected macaques receiving quadruple antiretroviral therapy

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

Recombination in HIV and the evolution of drug resistance: for better or for worse?

scientific article

Red Queen dynamics with non-standard fitness interactions

scientific article

Reducing antimicrobial use in food animals

scientific article published on 28 September 2017

Research on infectious disease dynamics. Introduction

article

Residual viral replication during antiretroviral therapy boosts human immunodeficiency virus type 1-specific CD8+ T-cell responses in subjects treated early after infection

scientific article published in January 2002

Resistance to antimicrobial chemotherapy: a prescription for research and action

scientific article published in February 1998

Response to Bandeira and Faro: Closing the circle of constraints ⬇️

scientific article published on 01 April 2003

Response to Comment on "Evidence for Positive Epistasis in HIV-1"

scientific article published in Science

Reversing resistance: different routes and common themes across pathogens.

scientific article

Risks and benefits of structured antiretroviral drug therapy interruptions in HIV-1 infection.

scientific article published in October 2000

Robustness of cooperation

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

Short Communication: HIV Type 2 Dynamics

article

Short-term activity cycles impede information transmission in ant colonies

scientific article

Signal transduction networks: topology, response and biochemical processes

scientific article

Simulating the evolution of signal transduction pathways

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

scientific article published on 12 May 2014

Spatial games and the maintenance of cooperation

scientific article

Spatial heterogeneity in drug concentrations can facilitate the emergence of resistance to cancer therapy ⬇️

scientific article (publication date: March 2015)

Spatial models of virus-immune dynamics

scientific article published on 14 November 2004

Stable virulence levels in the HIV epidemic of Switzerland over two decades

article

Stochastic interplay between mutation and recombination during the acquisition of drug resistance mutations in human immunodeficiency virus type 1

scientific article

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

scientific article published on 16 October 2006

Structured antiretroviral treatment interruptions in chronically HIV-1-infected subjects

scientific article

Temporal analyses of virus replication, immune responses, and efficacy in rhesus macaques immunized with a live, attenuated simian immunodeficiency virus vaccine.

scientific article

The Effect of Multifunctionality on the Rate of Evolution in Yeast

scientific article published on 27 December 2005

The HIV coreceptor switch: a population dynamical perspective

scientific article

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 curse of the pharaoh: the evolution of virulence in pathogens with long living propagules

scientific article published in June 1996

The effect of opinion clustering on disease outbreaks

scientific article

The effect of population structure on the emergence of drug resistance during influenza pandemics.

scientific article

The evolution of connectivity in metabolic networks

scientific article

The evolution of groups of cooperating bacteria and the growth rate versus yield trade-off

scientific article published on 01 March 2005

The evolution of network topology by selective removal

scientific article published on December 2005

The frequency of resistant mutant virus before antiviral therapy

scientific article published in March 1998

The path of least resistance: aggressive or moderate treatment?

scientific article published in November 2014

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

The virological and immunological consequences of structured treatment interruptions in chronic HIV-1 infection

article

Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods ⬇️

scientific article (publication date: 19 March 2013)

Using an epidemiological model for phylogenetic inference reveals density dependence in HIV transmission

scientific article (publication date: 2014)

Viral dynamics and in vivo fitness of HIV-1 in the presence and absence of enfuvirtide

scientific article published on August 2008

Viral dynamics in hepatitis B virus infection

scientific article published on April 1996

Viral dynamics in human immunodeficiency virus type 1 infection

scientific article (publication date: 12 January 1995)

Viral dynamics in vivo: limitations on estimates of intracellular delay and virus decay

scientific article published on July 1996

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

scientific article

Virus dynamics and drug therapy

scientific article

Virus evolution: the importance of being erroneous

scientific article published in November 2002

Virus load and antigenic diversity

scientific article published in September 1997

Virus-induced target cell activation reconciles set-point viral load heritability and within-host evolution

scientific article published on 23 September 2013

Virus-induced target cell activation reconciles set-point viral load heritability and within-host evolution

scholarly article published by Sebastian Bonhoeffer in 2014

Weighting for sex acts to understand the spread of STI on networks

scientific article published on 3 July 2012

Why There Are No Essential Genes on Plasmids

article

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