Leonid Kruglyak

Genome-scale base editing reveals the functional effects of variants in yeast

This study uses genome-scale CRISPR base editing in yeast to assess the functional effects of 308,461 variants, identifying 18,009 with significant growth impacts.

Microscale bulk segregant analysis

This paper introduces a 96-well liquid format for high-throughput QTL mapping in yeast, enabling efficient analysis of multiple crosses and environmental conditions.

Large-scale pooled selection enables mapping of modifiers of RNAi gene knockdown effects in C. elegans

The paper develops a pooled selection platform to map modifiers of RNAi gene knockdown effects in C. elegans, identifying two classes of QTL influencing RNAi responses.

The genetics of transcriptional responses to stress in yeast

This study identifies context-specific eQTLs and their dynamic effects on gene expression in yeast under acute environmental stress, linking genetic variation to physiological adaptation.

Regeneration leads to global tissue rejuvenation in aging sexual planarians

Regeneration in aging planarians reverses age-related physiological and molecular changes, restoring youthful gene expression and tissue composition.

Single-cell eQTL mapping in yeast reveals a tradeoff between growth and reproduction

The paper maps eQTLs in yeast using single-cell RNA sequencing, revealing tradeoffs between growth and reproduction through allele-specific effects on gene expression and cell-cycle progression.

Divergent C. elegans toxin alleles are suppressed by distinct mechanisms

The paper identifies a new TA system in C. elegans with divergent toxin alleles suppressed by distinct mechanisms, including piRNA-mediated silencing in the N2 haplotype.

No evidence that synonymous mutations in yeast genes are mostly deleterious

The paper reanalyzes data from Shen et al. to argue that most synonymous mutations in yeast genes are not deleterious, challenging their original conclusions about fitness effects.

Cas9-induced nonhomologous recombination in C. elegans

This paper introduces a method to induce targeted recombination in C. elegans using Cas9, enabling high-resolution genetic mapping in species with low natural recombination rates.

A minimal role for synonymous variation in human disease

The paper cautions against interpreting a yeast study claiming synonymous mutations are as disease-causing as nonsynonymous ones, given existing evidence for their predominant neutrality in humans.

Genome-wide base editor screen identifies regulators of protein abundance in yeast

The paper uses a CRISPR base editor screen in yeast to identify regulators of protein abundance, revealing both specific and broad regulatory relationships.

Genetics of white color and iridophoroma in "Lemon Frost" leopard geckos

The paper identifies a mutation in leopard geckos causing white coloration and tumors, linking it to a tumor suppressor gene.

Island-specific evolution of a sex-primed autosome in the planarian Schmidtea mediterranea

The paper identifies chromosome 1 in Schmidtea mediterranea as a sex-primed autosome through genomic analysis showing restricted recombination and sex-specific gene expression.

Whole-organism eQTL mapping at cellular resolution with single-cell sequencing

The paper maps eQTLs at cellular resolution in C. elegans using single-cell RNA sequencing, revealing cell-type-specific and single-cell-specific eQTL effects.

Ubiquitous selfish toxin-antidote elements in Caenorhabditis species

The paper identifies toxin-antidote elements in Caenorhabditis species, showing they cause developmental delay and are subject to balancing selection.

Massively parallel identification of causal variants underlying gene expression differences in a yeast cross

The paper identifies 451 causal regulatory variants in yeast promoters using a massively parallel reporter assay and finds they show epistasis, conservation, and enrichment in transcription factor binding sites.

Rapid cost-effective viral genome sequencing by V-seq

The paper introduces V-seq, a cost-effective method for viral genome sequencing that uses multiplexed RT primers to improve coverage and reduce costs.

Screening human embryos for polygenic traits has limited utility

This paper evaluates the potential benefits of using polygenic scores to select embryos for traits like height and cognitive function, finding limited gains with current predictors.

Rare variants contribute disproportionately to quantitative trait variation in yeast

This study shows rare DNA variants have a larger impact on quantitative traits in yeast compared to common variants, due to their greater effect sizes and recent evolutionary origins.

Analysis of the genetic basis of height in large Jewish nuclear families

This study identifies genetic loci contributing to height variation in a Jewish population cohort, explaining 6% of the variance through rare variants.

Fast genetic mapping of complex traits in C. elegans using millions of individuals in bulk

This paper introduces ceX-QTL, a method for fast genetic mapping of complex traits in C. elegans using bulk selection on millions of individuals, and demonstrates its application in identifying drug resistance, gene expression, and fitness loci.

The genetic basis of mutation rate variation in yeast

This study identifies genetic variants affecting mutation rates in yeast by analyzing natural isolates and segregant progeny, finding heritability and specific genes involved in mutation rate variation.

Genetics of trans-regulatory variation in gene expression

This study identifies eQTLs in yeast to show that most gene expression variation is driven by distant, trans-acting eQTLs clustered at hotspots.

Highly parallel genome variant engineering with CRISPR/Cas9 in eukaryotic cells

The paper uses CRISPR/Cas9 in yeast to engineer and screen variants, finding most premature termination codons are deleterious except near the C-terminal end.

Accounting for genetic interactions improves modeling of individual quantitative trait phenotypes in yeast

The paper shows that accounting for genetic interactions improves modeling of quantitative trait phenotypes in yeast by considering epistatic networks and allele frequencies.

CRISPR-directed mitotic recombination enables genetic mapping without crosses

This study uses CRISPR to create targeted recombination events in yeast, enabling fine-mapping of trait variation to a single causal polymorphism.

Genetic interactions contribute less than additive effects to quantitative trait variation in yeast

The paper estimates the contribution of genetic interactions to quantitative trait variation in yeast and finds they account for 9% of phenotypic variance, less than additive effects.

Genetics of intra-species variation in avoidance behavior induced by a thermal stimulus in C. elegans

The paper identifies genetic loci influencing thermal avoidance behavior in C. elegans, showing how distinct genetic factors control different components of the response.

Full-genome evolutionary histories of selfing, splitting and selection in Caenorhabditis

This study uses whole-genome sequencing of C. briggsae isolates to infer population history, selection effects, and speciation dynamics across different geographic groups.

Genetic dissection of MAPK-mediated complex traits across S. cerevisiae

This study identifies genetic variants influencing MAPK signaling phenotypes in S. cerevisiae using QTL mapping across diverse strains.