D. Petrov

Recommendations for Population and Individual Diagnostic SNP Selection in Non-Model Species

This paper develops a SNP selection pipeline, mPCRselect, to design cost-effective SNP panels for population assignment and individual identification in non-model species.

A shift from pleiotropic to modular adaptation revealed by a high-resolution two-step adaptive walk

This study shows that early adaptive mutations in yeast are pleiotropic, while later mutations are modular, focusing on respiration over fermentation.

Efficient and multiplexed somatic genome editing with Cas12a mice

This study develops transgenic Cas12a mice to enable efficient, multiplexed somatic genome editing for studying complex genetic interactions in vivo.

Extreme in Every Way: Exceedingly Low Genetic Diversity in Snow Leopards Due to Persistently Small Population Size

This study uses whole-genome sequencing of 41 snow leopards to show they have the lowest genetic diversity of any big cat species due to long-term small population size, not recent inbreeding.

Improving the accuracy of bulk fitness assays by correcting barcode processing biases

The paper develops a computational method to correct barcode processing biases in bulk fitness assays, improving fitness estimates in yeast variant libraries.

Bayesian inference of relative fitness on high-throughput pooled competition assays

This paper introduces a Bayesian framework to infer microbial fitness from lineage tracking assays, accounting for noise and scaling to large datasets.

Prolonged delays in human microbiota transmission after a controlled antibiotic perturbation

This study investigates gut microbiome colonization dynamics after antibiotic use, finding prolonged delays in microbial transmission and ecological barriers to colonization.

Far From Home: Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments

The paper evolves haploid and diploid yeast populations in different environments and finds common, unpredictable pleiotropic effects of adaptive mutations in non-home environments.

Extreme sensitivity of fitness to environmental conditions; lessons from #1BigBatch

This study identifies environmental variability as a major source of noise in fitness measurements and proposes best practices for improving precision.

Cancers adapt to their mutational load by buffering protein misfolding stress

The paper shows high mutational load tumors upregulate proteostasis machinery to buffer protein misfolding stress, revealing therapeutic vulnerabilities.

Multiplexed identification of RAS paralog imbalance as a driver of lung cancer growth

This study identifies HRAS and NRAS as suppressors of KRASG12D-driven lung cancer using CRISPR screens in mouse models and confirms their role in human cell lines.

Genetic determinants of EGFR-Driven Lung Cancer Growth and Therapeutic Response In Vivo

This study investigates how genetic alterations affect EGFR-driven lung cancer growth and therapy response using a mouse model and CRISPR-Cas9 editing.

Most cancers carry a substantial deleterious load due to Hill-Robertson interference

This study shows that most cancers do not remove deleterious mutations due to Hill-Robertson interference, leading to a 40% average fitness cost per cell.

Broad geographic sampling reveals predictable, pervasive, and strong seasonal adaptation in Drosophila

The paper identifies parallel seasonal allele frequency shifts in Drosophila melanogaster across North America and Europe, linking environmental conditions to genomic responses to selection.

Widespread introgression across a phylogeny of 155 Drosophila genomes

The paper analyzes 155 Drosophila genomes to detect widespread introgression across nine monophyletic radiations, revealing both ancient and recent hybridization events.

Development of Optically-Controlled "Living Electrodes" with Long-Projecting Axon Tracts for a Synaptic Brain-Machine Interface

This paper develops and validates axon-based 'living electrodes' for a synaptic brain-machine interface, demonstrating their fabrication, function, and in vivo integration in rats.

Ancient RNA virus epidemics through the lens of recent adaptation in human genomes

The paper identifies genomic footprints of ancient RNA virus epidemics in human populations over the past 50,000 years, showing RNA viruses drove many adaptive events across diverse populations.

Quantitative in vivo analyses reveal a complex pharmacogenomic landscape in lung adenocarcinoma

The paper uses a quantitative platform and statistical methods to map pharmacogenomic responses in lung cancer, revealing complex genotype-specific therapeutic interactions.

Accurate allele frequencies from ultra-low coverage pool-seq samples in evolve-and-resequence experiments

This paper introduces a method to accurately estimate allele frequencies from low-coverage pool-seq data in evolve-and-resequence experiments using haplotype inference.

Reconsidering the management paradigm of fragmented populations

The paper challenges the 'one migrant per generation' management paradigm for fragmented populations by highlighting trade-offs in genetic diversity and proposing alternative strategies.

Single Nucleotide Mapping of the Locally Accessible Trait Space in Yeast Reveals Pareto Fronts that Constrain Initial Adaptation

The paper samples adaptive mutations in yeast to identify tradeoffs and Pareto fronts between growth cycle traits, finding that no single mutation can circumvent these constraints.

Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations

The paper analyzes mutation rates and patterns in Drosophila melanogaster using mutation accumulation lines and rare polymorphisms, revealing biases in the mutation spectrum and its evolutionary implications.

Pervasive adaptation in Plasmodium-interacting proteins in mammals

This study identifies 410 Plasmodium-interacting proteins in mammals, showing they experience significantly more positive selection than other proteins, linked to immune interactions and pathogen pressure.