Jeffrey David Jensen

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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 ...

As one of the most commonly utilized organisms in the study of local adaptation, an accurate characterization of the demographic history of Drosophila melanogaster remains as an important research question. This owes both to the inherent interest in charac ...

Cognitive abilities and disorders unique to humans are thought to result from adaptively driven changes in brain transcriptomes, but little is known about the role of cis-regulatory changes affecting transcription start sites (TSS). Here, we mapped in huma ...

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 ...

The first microRNAs (miRNAs) were identified as essential, conserved regulators of gene expression, targeting the same genes across nearly all bilaterians. However, there are also prominent examples of conserved miRNAs whose functions appear to have shifte ...

Recently, there has been increased awareness of the role of background selection (BGS) in both data analysis and modelling advances. However, BGS is still difficult to take into account because of tractability issues with simulations and difficulty with no ...

Given the strong selective pressures often faced by populations when colonizing a novel habitat, the level of variation present on which selection may act is an important indicator of adaptive potential. While often discussed in an ecological context, this ...

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 ...

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 ...

Human cytomegalovirus (HCMV) exhibits surprisingly high genomic diversity during natural infection although little is known about the limits or patterns of HCMV diversity among humans. To address this deficiency, we analyzed genomic diversity among congeni ...

Estimating the age and strength of beneficial alleles is central to understanding how adaptation proceeds in response to changing environmental conditions. Several haplotype-based estimators exist for inferring the age of segregating beneficial mutations. ...

Characterizing the role of effective population size in dictating the rate of adaptive evolution remains a major challenge in evolutionary biology. Depending on the underlying distribution of fitness effects of new mutations, populations of different sizes ...

The joint and accurate inference of selection and demography from genetic data is considered a particularly challenging question in population genetics, since both process may lead to very similar patterns of genetic diversity. However, additional informat ...

A workshop recently held at the École Polytechnique Fédérale de Lausanne (EPFL, Switzerland) was dedicated to understanding the genetic basis of adaptive change, taking stock of the different approaches developed in theoretical population genetics and land ...

Identifying adaptively important loci in recently bottlenecked populations - be it natural selection acting on a population following the colonization of novel habitats in the wild, or artificial selection during the domestication of a breed - remains a ma ...

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 ...

It remains a central problem in population genetics to infer the past action of natural selection, and these inferences pose a challenge because demographic events will also substantially affect patterns of polymorphism and divergence. Thus it is imperativ ...

In the age of whole-genome population genetics, so-called genomic scan studies often conclude with a long list of putatively selected loci. These lists are then further scrutinized to annotate these regions by gene function, corresponding biological proces ...

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 ...

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 ...

Jeffrey David Jensen

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

The Demographic History of African Drosophila melanogaster

Human-Specific Histone Methylation Signatures at Transcription Start Sites in Prefrontal Neurons

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

Inferring the Evolutionary History of Primate microRNA Binding Sites: Overcoming Motif Counting Biases

The consequences of not accounting for background selection in demographic inference

Characterizing human cytomegalovirus reinfection in congenitally infected infants: an evolutionary perspective

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

The fitness landscape of the codon space across environments

Limits and patterns of cytomegalovirus genomic diversity in humans

Inferring the age of a fixed beneficial allele

Characterizing the Influence of Effective Population Size on the Rate of Adaptation: Gillespie's Darwin Domain

An Approximate Markov Model for the Wright-Fisher Diffusion and Its Application to Time Series Data

Uncovering the genetic basis of adaptive change: on the intersection of landscape genomics and theoretical population genetics

On the Prospect of Identifying Adaptive Loci in Recently Bottlenecked Populations

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

Inferences of Demography and Selection in an African Population of Drosophila melanogaster

A Critical Assessment of Storytelling: Gene Ontology Categories and the Importance of Validating Genomic Scans

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

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