Publications de Claudia Bank | EPFL Graph Search

The fitness landscape of the codon space across environments

Jeffrey David Jensen, Claudia Bank, Sebastian Matuszewski

Fitness landscapes map the relationship between genotypes and fitness. However, most fitness landscape studies ignore the genetic architecture imposed by the codon table and thereby neglect the potential role of synonymous mutations. To quantify the fitnes ...

NATURE PUBLISHING GROUP2018

Two sides of the same coin: A population genetics perspective on lethal mutagenesis and mutational meltdown

Jeffrey David Jensen, Claudia Bank, Sebastian Matuszewski, Nicky Louise Ormond

The extinction of RNA virus populations upon application of a mutagenic drug is frequently referred to as evidence for the existence of an error threshold, above which the population cannot sustain the mutational load. To explain the extinction process aft ...

Oxford Univ Press2017

The Combined Effect of Oseltamivir and Favipiravir on Influenza A Virus Evolution

Jeffrey David Jensen, Claudia Bank, Sebastian Matuszewski, Nicky Louise Ormond

Influenza virus inflicts a heavy death toll annually and resistance to existing antiviral drugs has generated interest in the development of agents with novel mechanisms of action. Favipiravir is an antiviral drug that acts by increasing the genome-wide mu ...

Oxford University Press (OUP)2017

An experimental evaluation of drug-induced mutational meltdown as an antiviral treatment strategy

Jeffrey David Jensen, Claudia Bank, Matthieu Foll, Sebastian Matuszewski, Hyunjin Shim

The rapid evolution of drug resistance remains a critical public health concern. The treatment of influenza A virus (IAV) has proven particularly challenging, due to the ability of the virus to develop resistance against current antivirals and vaccines. He ...

Wiley-Blackwell2016

A Balance between Inhibitor Binding and Substrate Processing Confers Influenza Drug Resistance

Jeffrey David Jensen, Claudia Bank, Li Jiang

The therapeutic benefits of the neuraminidase (NA) inhibitor oseltamivir are dampened by the emergence of drug resistance mutations in influenza A virus (IAV). To investigate the mechanistic features that underlie resistance, we developed an approach to qu ...

Academic Press Ltd- Elsevier Science Ltd2016

On the (un) predictability of a large intragenic fitness landscape

Jeffrey David Jensen, Claudia Bank, Sebastian Matuszewski

The study of fitness landscapes, which aims at mapping genotypes to fitness, is receiving ever-increasing attention. Novel experimental approaches combined with next-generation sequencing (NGS) methods enable accurate and extensive studies of the fitness e ...

National Academy of Sciences2016

A Statistical Guide to the Design of Deep Mutational Scanning Experiments

Jeffrey David Jensen, Claudia Bank, Sebastian Matuszewski

The characterization of the distribution of mutational effects is a key goal in evolutionary biology. Recently developed deep-sequencing approaches allow for accurate and simultaneous estimation of the fitness effects of hundreds of engineered mutations by ...

Genetics Society America2016

A Systematic Survey of an Intragenic Epistatic Landscape

Jeffrey David Jensen, Claudia Bank

Mutations are the source of evolutionary variation. The interactions of multiple mutations can have important effects on fitness and evolutionary trajectories. We have recently described the distribution of fitness effects of all single mutations for a nin ...

Oxford Univ Press2015

Influenza Virus Drug Resistance: A Time-Sampled Population Genetics Perspective

Jeffrey David Jensen, Claudia Bank, Matthieu Foll, Hyunjin Shim, Gregory Bruce Ewing, Anna Ferrer Admetlla

Author Summary In recent years, considerable attention has been given to the evolution of drug resistance in the influenza A H1N1 strain. As a major annual cause of morbidity and mortality, combined with the rapid global spread of drug resistance, influenz ...

Public Library of Science2014

Thinking too positive? Revisiting current methods of population genetic selection inference

Jeffrey David Jensen, Claudia Bank, Matthieu Foll, Gregory Bruce Ewing

In the age of next-generation sequencing, the availability of increasing amounts and improved quality of data at decreasing cost ought to allow for a better understanding of how natural selection is shaping the genome than ever before. However, alternative ...

Elsevier Science London2014