J. D. Jensen

Engineering Memory T Cells as a platform for Long-Term Enzyme Replacement Therapy in Lysosomal Storage Disorders

This study demonstrates that genetically engineered memory T cells can deliver enzyme replacement therapy for mucopolysaccharidosis type I, reducing GAG levels in multiple tissues for up to 22 weeks.

Automated Seminal Root Angle Measurement with Corrective Annotation

The paper introduces an automated method for measuring seminal root angles from images and validates its accuracy against manual measurements.

A simulation framework for modeling the within-patient evolutionary dynamics of SARS-CoV-2

This study develops a simulation framework to model SARS-CoV-2 evolutionary dynamics within patients, identifying plausible models with severe infection bottlenecks and high rates of deleterious mutations.

Developing an evolutionary baseline model for humans: jointly inferring purifying selection with population history

The paper develops a baseline model for the Yoruba population to jointly infer purifying selection and population history, finding recent population growth and a distribution of fitness effects skewed towards neutral mutations.

Protective effect of pre-existing natural immunity in a nonhuman primate reinfection model of congenital cytomegalovirus infection

This study shows that pre-existing CMV immunity in nonhuman primates reduces placental transmission and fetal loss during reinfection compared to primary infection.

Interpreting the pervasive observation of U-shaped Site Frequency Spectra

The paper analyzes site frequency spectra across species and finds U-shaped patterns, suggesting that multiple merger coalescent models better fit the data than the standard neutral model.

Recommendations for improving statistical inference in population genomics

The paper discusses challenges in population genomics due to data abundance and highlights best practices for statistical inference and model fitting.

Revisiting the notion of deleterious sweeps

The paper examines how fixation of mildly deleterious mutations affects polymorphism patterns and divergence between populations, finding minor but measurable impacts on private variants and FST.

Functional immune mapping with deep-learning enabled phenomics applied to immunomodulatory and COVID-19 drug discovery

This paper develops a deep-learning enabled phenomics platform to identify immune-modulating compounds and applies it to study SARS-CoV-2 infection and cytokine storm, identifying clinically relevant compounds and new drug candidates.

The impact of purifying and background selection on the inference of population history: problems and prospects

This paper examines how purifying and background selection affect population history inference, showing biases in demographic estimates and proposing a correction method using the distribution of fitness effects.

Convergent evolution of seasonal camouflage in response to reduced snow cover across the snowshoe hare range

This study investigates how snowshoe hares adapt to reduced snow cover by evolving seasonal camouflage, revealing convergent evolution and the role of allelic dominance in adaptation rates.

Towards an evolutionarily appropriate null model: jointly inferring demography and purifying selection

The paper develops a statistical framework to jointly infer demography and purifying selection, finding slower population growth in Drosophila melanogaster when purifying selection is considered.

The origin and spread of locally adaptive seasonal camouflage in snowshoe hares

The paper investigates the origin and spread of seasonal camouflage in snowshoe hares, finding that hybridization and selection on recessive alleles drove adaptation.

On the unfounded enthusiasm for soft selective sweeps II: examining recent evidence from humans, flies, and viruses

The paper evaluates three recent studies claiming pervasive soft selective sweeps in humans, flies, and viruses, finding high false-positive rates and suggesting rare soft sweeps instead.

The fitness landscape of the codon space across environments

The paper quantifies the fitness effects of synonymous mutations across environments in yeast using Bayesian methods and shows their impact on evolutionary dynamics.

The demographic history of African Drosophila melanogaster

This paper quantitatively models the demographic history of African Drosophila melanogaster populations, including ancestral Zambian and colonized West African populations.

The evolutionary history of Nebraska deer mice: local adaptation in the face of strong gene flow

This study examines the demographic and selective history of deer mice in Nebraska, finding that gene flow homogenizes most of the genome but the Agouti locus shows local adaptation due to cryptic coloration.

Coalescent Processes With Skewed Offspring Distributions And Non-Equilibrium Demography

This paper develops a coalescent model that jointly estimates reproductive skew and population history, showing that ignoring demography can bias coalescent inferences and demonstrating its application to Japanese sardine data.