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Jeffrey David Jensen

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Related publications (53)

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The Genomic Signature of Population Reconnection Following Isolation: From Theory to HIV

Jeffrey David Jensen, Séverine Vuilleumier Varisco

Ease of worldwide travel provides increased opportunities for organisms not only to colonize new environments but also to encounter related but diverged populations. Such events of reconnection and secondary contact of previously isolated populations are w ...

Genetics Society of America2015

The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards

Jeffrey David Jensen, Susanne Petra Pfeifer, Stefan Jean Laurent, Nicky Louise Ormond

Understanding the process of adaptation during rapid environmental change remains one of the central focal points of evolutionary biology. The recently formed White Sands system of southern New Mexico offers an outstanding example of rapid adaptation, with ...

Wiley-Blackwell2016

Molecular Basis for Differential Patterns of Drug Resistance in Influenza N1 and N2 Neuraminidase

Jeffrey David Jensen

Neuraminidase (NA) inhibitors are used for the prevention and treatment of influenza A virus infections. Two subtypes of NA, N1 and N2, predominate in viruses that infect humans, but differential patterns of drug resistance have emerged in each subtype des ...

Amer Chemical Soc2016

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

Jeffrey David Jensen

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 ...

Public Library of Science2013

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

Jeffrey David Jensen

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 ...

American Society for Microbiology2014

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

Tamar Kohn, Jeffrey David Jensen, Anna Carratala Ripolles, Virginie Bachmann, Qingxia Zhong, Hyunjin Shim

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 ...

Amer Chemical Soc2017

Antiviral drug resistance as an adaptive process

Kristen Kay Irwin, Jeffrey David Jensen

Antiviral drug resistance is a matter of great clinical importance that, historically, has been investigated mostly from a virological perspective. Although the proximate mechanisms of resistance can be readily uncovered using these methods, larger evoluti ...

Oxford University Press2016

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

Jeffrey David Jensen, Susanne Petra Pfeifer, Sebastian Matuszewski

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 ...

American Society for Microbiology2017

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

Jeffrey David Jensen, Matthieu Foll, Hyunjin Shim

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 ...

Wiley-Blackwell2015

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

Jeffrey David Jensen, Matthieu Foll

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 ...

Genetics Society America2015

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

Jeffrey David Jensen

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 ( ...

Wiley-Blackwell2012

Shifting Fitness Landscapes In Response To Altered Environments

Jeffrey David Jensen, Claudia Bank

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 ...

Wiley-Blackwell2013

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

Jeffrey David Jensen, Claudia Bank

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

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

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

Jeffrey David Jensen, Matthieu Foll, Claudia Bank, 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

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

Jian Wang, Jeffrey David Jensen, Xin Liu, Jun Wang

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 ( ...

Nature Publishing Group2012

Recent Progress in Polymorphism-Based Population Genetic Inference

Jeffrey David Jensen

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 ...

Oxford University Press2012

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

Jeffrey David Jensen, Claudia Bank

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. ...

Genetics Soc Am2014

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

RECURRENT AND RECENT SELECTIVE SWEEPS IN THE piRNA PATHWAY

Jeffrey David Jensen

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. ...

Wiley-Blackwell2013