Dmitri A. Petrov

Intragenic epistasis in couch potato shapes life history traits and climatic adaptation in Drosophila melanogaster

The paper shows non-additive interactions among three intronic SNPs in the cpo gene affect life history traits and climatic adaptation in Drosophila melanogaster.

Order invariance of fitness makes evolution predictable despite strong history-dependent effects

The paper tests how environmental order affects the fitness of yeast mutants and finds that overall fitness is largely invariant to order due to compensatory history-dependent effects.

Transcriptional Response to Tumor Mutational Burden Is Consistent Across Cancer Types

The paper analyzes ~9,100 tumors across 32 cancer types to determine if the transcriptional response to tumor mutational burden (TMB) is consistent across tissues, finding it to be largely consistent within each cancer type.

Persistent, Multi-Species Outbreaks and Long-Range Transmissions of a Measles-Like Virus

The paper shows CDV persists in Arctic foxes for over a decade and spreads across species and regions, connecting North America to Eurasia.

Tumor suppressor genotype influences the extent and mode of immunosurveillance in lung cancer

This study shows tumor suppressor genotype affects immune cell recruitment and tumor growth in KRAS-driven lung cancer with varying neoantigen expression.

Genetic Diversity and Population Structure of the Black-Footed Cat: Insights into Felis's Deadliest Predator

This study sequenced whole genomes of black-footed cats to analyze their population structure and genetic diversity, finding low diversity but no long runs of homozygosity and evidence of recent population contraction.

Pervasive fitness trade-offs revealed by rapid adaptation in large experimental populations of Drosophila melanogaster

This study uses genomic data from Drosophila melanogaster to show how fitness trade-offs manifest under fluctuating selection, identifying genomic regions linked to reproduction and stress tolerance.

Comparative gene annotation and orthology assignments across 301 species of Drosophilidae

The paper annotates protein-coding genes in 301 Drosophilidae species and analyzes evolutionary patterns in gene number and codon usage.

Learning the Shape of Evolutionary Landscapes: Geometric Deep Learning Reveals Hidden Structure in Phenotype-to-Fitness Maps

This paper introduces a geometric deep learning method to model phenotype-to-fitness maps, showing it outperforms linear methods in capturing nonlinear structure and predicting fitness landscapes.

Community coalescence reveals strong selection and coexistence within species in complex microbial communities

The paper studies intra-species diversity in microbial communities by competing gut strains, finding strong selection and coexistence due to biotic interactions.

High-resolution mapping of a rapidly evolving complex trait reveals genotype-phenotype stability and an unpredictable genetic architecture of adaptation

This study maps the genetic architecture of pigmentation evolution in Drosophila melanogaster and finds that while trait direction can be predicted, the specific loci involved are unpredictable and the genotype-phenotype map is stable across populations.

Aging represses lung tumorigenesis and alters tumor suppression

This study shows aging suppresses lung tumor initiation and growth in mice, with age-dependent effects on tumor suppressor genes like PTEN and persistent age-related transcriptomic changes in tumors.

Adaptive evolution can overwrite initial natural fitness variation only in highest-fitness yeast isolates

This study shows that high initial fitness is necessary but not sufficient for long-term success in yeast, as adaptive mutations can override small fitness differences.

Functional mapping of epigenetic regulators uncovers coordinated tumor suppression by the HBO1 and MLL1 complexes

The paper identifies HBO1 and MLL1 complexes as key tumor suppressors in lung cancer using in vivo functional screens of epigenetic regulators.

EML4-ALK variant-specific genetic interactions shape lung tumorigenesis

The paper investigates functional differences between EML4-ALK variants V1 and V3 in lung cancer using mouse models and human data, showing variant-specific effects on tumorigenesis.

Beneficial reversal of dominance maintains a resistance polymorphism under fluctuating insecticide selection

The paper shows that beneficial reversal of dominance at the Ace locus in Drosophila melanogaster allows resistant alleles to persist under fluctuating insecticide selection.

Variation in Resource Environment Drives Adaptive Divergence in Drosophila melanogaster

This study shows that resource variation in Drosophila melanogaster affects phenotypic and genomic evolution but is secondary to seasonal selective pressures, with adaptation to resource environments being trait-specific.

Footprints of worldwide adaptation in structured populations of D. melanogaster through the expanded DEST 2.0 genomic resource

The paper uses DEST 2.0 to analyze genetic variation in D. melanogaster across continents and time, identifying adaptation patterns and stable spatial genetic structures.

Integrative multiomic approaches reveal ZMAT3 and p21 as conserved hubs in the p53 tumor suppression network

The paper identifies ZMAT3 and CDKN1A as key hubs in the p53 tumor suppression network through integrative multiomic analyses in a mouse model.

Manual validation finds only ultra-long long-read sequencing enables faithful, population-level structural variant calling in Drosophila melanogaster euchromatin

The paper shows ultra-long long-read sequencing is needed for accurate structural variant calling in Drosophila melanogaster.

Drosophila melanogaster pigmentation demonstrates adaptive phenotypic parallelism over multiple timescales

This study shows that Drosophila melanogaster pigmentation adapts rapidly and deterministically to environmental gradients across multiple timescales through distinct genetic components.

Low-dimensional genotype-fitness mapping across divergent environments suggests a limiting functions model of fitness

The paper uses yeast mutants to show that fitness can be predicted by low-dimensional genotype-phenotype-fitness maps across environments, supporting a limiting functions model of fitness.

Parameterizing Pantherinae: de novo mutation rate estimates from Panthera and Neofelis pedigrees

The paper estimates de novo mutation rates in Panthera and Neofelis species using pedigrees, finding rates between 0.5 and 1.4e-08 per generation per base pair.

President Roosevelt's lions reveal a century of population fragmentation in Africa's largest carnivore

The paper uses whole-genome sequencing of historical and recent lion populations to show population fragmentation and genetic diversity loss in East Africa over the past century.

Next-generation snow leopard population assessment tool: multiplex-PCR SNP panel for individual identification from feces

The paper develops a SNP panel for identifying snow leopard individuals from fecal samples, validated with zoo and field samples, showing high accuracy and utility for population assessment.

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 STAG2-PAXIP1/PAGR1 axis suppresses lung tumorigenesis

This study identifies a STAG2-PAXIP1/PAGR1 tumor-suppressive axis in lung cancer by showing their combined role in suppressing oncogenic KRAS-driven tumorigenesis.

Massively parallel interrogation of the fitness of natural variants in ancient signaling pathways reveals pervasive local adaptation

The paper assesses fitness effects of 9,000 natural variants in yeast signaling pathways, finding that many non-neutral variants show signs of local adaptation.

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.