Jeffrey David Jensen

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Populations of human cytomegalovirus (HCMV), a large DNA virus, are highly polymorphic in patient samples, which may allow for rapid evolution within human hosts. To understand HCMV evolution, longitudinally sampled genomic populations from the urine and p ...

Influenza A virus (IAV) is a major cause of morbidity and mortality throughout the world. Current antiviral therapies include oseltamivir, a neuraminidase inhibitor that prevents the release of nascent viral particles from infected cells. However, the IAV ...

Waterborne viruses can exhibit resistance to common water disinfectants, yet the mechanisms that allow them to tolerate disinfection are poorly understood. Here, we generated echovirus 11 (E11) with resistance to chlorine dioxide (ClO2) by experimental evo ...

Intrahost and interhost assessments of viral diversity are often treated as measures of separate and distinct evolutionary processes, with numerous investigations reporting seemingly incompatible results between the two. For example, in human cytomegalovir ...

With novel developments in sequencing technologies, time-sampled data are becoming more available and accessible. Naturally, there have been efforts in parallel to infer population genetic parameters from these data sets. Here, we compare and analyse four ...

Helicobacter pylori is an important human pathogen associated with serious gastric diseases. Owing to its medical importance and close relationship with its human host, understanding genomic patterns of global and local adaptation in H. pylori may be of pa ...

To understand how organisms adapt to novel habitats, which involves both demographic and selective events, we require knowledge of the evolutionary history of populations and also selected alleles. There are still few cases in which the precise mutations ( ...

The role of adaptation in molecular evolution has been contentious for decades. Here, we shed light on the adaptive potential in Saccharomyces cerevisiae by presenting systematic fitness measurements for all possible point mutations in a region of Hsp90 un ...

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 ...

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 ...

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 ...

Rice is a staple crop that has undergone substantial phenotypic and physiological changes during domestication. Here we resequenced the genomes of 40 cultivated accessions selected from the major groups of rice and 10 accessions of their wild progenitors ( ...

The recent availability of whole-genome sequencing data affords tremendous power for statistical inference. With this, there has been great interest in the development of polymorphism-based approaches for the estimation of population genetic parameters. Th ...

The role of adaptation in the evolutionary process has been contentious for decades. At the heart of the century-old debate between neutralists and selectionists lies the distribution of fitness effects (DFE)that is, the selective effect of all mutations. ...

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 ...

Uncontrolled transposable element (TE) insertions and excisions can cause chromosome breaks and mutations with dramatic deleterious effects. The PIWI interacting RNA (piRNA) pathway functions as an adaptive TE silencing system during germline development. ...

Developing tools to accurately predict the clinical prevalence of drug-resistant mutations is a key step toward generating more effective therapeutics. Here we describe a high-throughput CRISPR-Cas9-based saturated mutagenesis approach to generate comprehe ...

During his well-known debate with Fisher regarding the phenotypic dataset of Panaxia dominula, Wright suggested fluctuating selection as a potential explanation for the observed change in allele frequencies. This model has since been invoked in a number of ...

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 ...

Levels of nucleotide diversity vary greatly across the genomes of most species owing to multiple factors. These include variation in the underlying mutation rates, as well as the effects of both direct and linked selection. Fundamental to interpreting the ...

Jeffrey David Jensen

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Rapid Intrahost Evolution of Human Cytomegalovirus Is Shaped by Demography and Positive Selection

Evolution of the Influenza A Virus Genome during Development of Oseltamivir Resistance In Vitro

Resistance of echovirus 11 to ClO2 is associated with enhanced host receptor use, altered entry routes and high fitness

On the Analysis of Intrahost and Interhost Viral Populations: Human Cytomegalovirus as a Case Study of Pitfalls and Expectations

WFABC: a Wright-Fisher ABC-based approach for inferring effective population sizes and selection coefficients from time-sampled data

Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

Evidence Of Adaptation From Ancestral Variation In Young Populations Of Beach Mice

Shifting Fitness Landscapes In Response To Altered Environments

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

A Statistical Guide to the Design of Deep Mutational Scanning Experiments

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

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

Recent Progress in Polymorphism-Based Population Genetic Inference

A Bayesian MCMC Approach to Assess the Complete Distribution of Fitness Effects of New Mutations: Uncovering the Potential for Adaptive Walks in Challenging Environments

A Systematic Survey of an Intragenic Epistatic Landscape

RECURRENT AND RECENT SELECTIVE SWEEPS IN THE piRNA PATHWAY

CRISPR-Cas9-mediated saturated mutagenesis screen predicts clinical drug resistance with improved accuracy

Detecting and Quantifying Changing Selection Intensities from Time-Sampled Polymorphism Data

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

The Impact of Linked Selection in Chimpanzees: A Comparative Study