Michael M. Desai

Inferring modularity in genotype-phenotype maps using patterns of epistasis and pleiotropy

This paper introduces two methods, SLED and GTD, to infer modular structure in genotype-phenotype maps by combining epistasis and pleiotropy, showing they yield similar modular architectures in yeast data.

Joint QTL mapping reveals patterns of pleiotropy across structured environments in budding yeast

The paper uses joint QTL mapping to analyze pleiotropy patterns across structured environments in budding yeast, revealing genetic interactions influenced by environmental relationships.

Mutation choice biases the structure of empirical fitness landscapes

The paper examines how mutation selection biases affect fitness landscape statistics in random models and real datasets, showing inflated variance and altered local maxima under adaptive trajectory mutations.

Interactions between epistasis and pleiotropy in generic models of complex traits

This study examines how epistasis and pleiotropy interact in complex traits using generic models and experimental data from yeast, showing that specific mutation patterns emerge under certain conditions.

Amino acid exchangeability and surface accessibility underpin the effects of single substitutions

The paper performs a statistical meta-analysis of single amino acid substitutions using deep mutational scans to quantify physicochemical trends and derive an empirical amino acid exchangeability matrix.

Epistasis and background dependence in the evolution of Omicron variants of the SARS-CoV-2 Spike protein

This study maps epistatic interactions in Omicron SARS-CoV-2 Spike RBD mutations, revealing how mutations interact to affect ACE2 binding and antibody evasion.

Laboratory yeast crosses reveal limited epistasis in the genetic basis of complex traits

The paper uses a broad range of yeast genotypes to assess epistasis in complex traits, finding limited contributions of epistasis to phenotypic variance.

Parallel but distinct adaptive routes in the budding and fission yeasts after 10,000 generations of experimental evolution

This study compares adaptive routes in two yeast species after 10,000 generations, finding parallel but distinct molecular mechanisms of adaptation.

Inferring genotype-phenotype maps using attention models

This paper applies attention-based models to predict phenotype from genotype, showing improved performance in epistatic regimes and enabling transfer learning across environments.

DYNAMICS OF CONTAMINANT MICROBES IN BIOETHANOL PRODUCTION FROM SUGARCANE

The paper investigates microbial contaminants in sugarcane bioethanol production, finding dynamic bacterial communities affect ethanol yield and yeast viability.

Impact of fluctuating environments on the fitness and robustness of evolving laboratory and industrial Saccharomyces cerevisiae strains

This study compares the fitness and robustness of two yeast strains under fluctuating and constant environments, finding that the lab strain improved fitness but not robustness, while the industrial strain became more robust.

Sex decreases the pleiotropic costs of local adaptation

This study shows that sex helps organisms maintain generalist phenotypes by reducing pleiotropic costs of local adaptation in fluctuating environments.

Distinguishing multiple-merger from Kingman coalescence using two-site frequency spectra

This paper introduces a statistical test to detect deviations from the Kingman coalescent model using the two-site frequency spectrum, showing that Drosophila melanogaster genomic data are inconsistent with the model.

Effects of selection stringency on the outcomes of directed evolution

This study examines how selection stringency affects outcomes in directed evolution by analyzing fitness distributions and diversification effects across rounds.

Barcoded bulk QTL mapping reveals highly polygenic and epistatic architecture of complex traits in yeast

The paper introduces BB-QTL mapping to study complex traits in yeast, revealing polygenic, pleiotropic, and epistatic genetic architectures with increased sample size.

Evolution of mutation rates in rapidly adapting asexual populations

The paper calculates the fixation probability of mutator and antimutator alleles in asexual populations, showing how clonal interference and deleterious mutations influence mutation rate evolution.

The fate of a mutation in a fluctuating environment

This study examines how mutations' fates in fluctuating environments depend on environmental dynamics and selective pressures, finding that temporal variation can reduce selection efficiency and increase fixation probabilities for certain mutations.

The evolutionarily stable distribution of fitness effects

The paper derives the evolutionarily stable distribution of fitness effects (DFE) under a constant environment and shows its dependence on population genetic parameters and epistasis.