M. M. Desai

Protein sequence landscapes are not so simple: on reference-free versus reference-based inference

The paper shows that reference-free analysis is equivalent to reference-based methods, leading to identical landscapes but different interpretations of epistasis.

A dynamical limit to evolutionary adaptation

The paper analyzes conditions under which evolutionary adaptation leads to higher or lower fitness, identifying a boundary state where adaptation is balanced by Muller's ratchet and fitness remains stable.

Inferring sparse structure in genotype-phenotype maps

This paper introduces a method to infer sparse structure in genotype-phenotype maps by identifying core processes that influence multiple phenotypes and genetic loci.

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.

Yeast population dynamics in Brazilian bioethanol production

The paper tracks yeast population dynamics in Brazilian bioethanol biorefineries using metagenomic and clonal sequencing data, finding stable process indicators despite population changes.

Hierarchical sequence-affinity landscapes shape the evolution of breadth in an anti-influenza receptor binding site antibody

This study characterizes the hierarchical epistasis between heavy and light chain mutations in an anti-influenza bnAb, showing how such interactions shape the evolution of broad antigen affinity.

The landscape of antibody binding affinity in SARS-CoV-2 Omicron BA.1 evolution

The paper maps how mutations in the SARS-CoV-2 Omicron BA.1 RBD affect antibody binding affinity through systematic analysis of 32,768 genotypes against four monoclonal antibodies.

Compensatory epistasis maintains ACE2 affinity in SARS-CoV-2 Omicron BA.1

This study identifies compensatory epistasis in SARS-CoV-2 Omicron BA.1 that maintains ACE2 affinity despite antibody-escape mutations.

Spatial structure alters the site frequency spectrum produced by hitchhiking

This study shows spatial structure changes the site frequency spectrum from hitchhiking, revealing distinct frequency regimes near and far from a selective sweep.

Mutational robustness changes during long-term adaptation in laboratory budding yeast populations

This study measures how the fitness landscape neighborhood changes during yeast adaptation, finding reduced mutational robustness in one environment but not another.

Idiosyncratic epistasis leads to global fitness-correlated trends

The paper constructs all combinations of 10 missense mutations in budding yeast and shows that global fitness trends arise from specific idiosyncratic epistatic interactions.

Population genetics of polymorphism and divergence in rapidly evolving populations

This paper extends the traveling wave framework to intermediate regimes of mutation fitness effects, deriving new expressions for fixation probabilities and site frequency spectra.

Dynamics and variability in the pleiotropic effects of adaptation in laboratory budding yeast populations

The paper studies how pleiotropic effects of adaptation in yeast change over time and vary across environments, finding increasing variability and overlapping contributions of chance and contingency.

Binding affinity landscapes constrain the evolution of broadly neutralizing anti-influenza antibodies

This study measures binding affinity landscapes of two influenza bnAbs to understand their evolutionary pathways and how they acquire breadth.

Hemodynamic molecular imaging of tumor-associated enzyme activity in the living brain.

This paper develops a molecular sensor to noninvasively map FAP enzyme activity in the brain, demonstrating its utility in rats and nonhuman primates for detecting tumor-associated biomarkers.

The Genetic Basis of Differential Autodiploidization in Evolving Yeast Populations

This study identifies SSD1 gene variants as the genetic determinant of differential autodiploidization rates in yeast strains.

Phenotypic and molecular evolution across 10,000 generations in laboratory budding yeast populations

This study tracks phenotypic and molecular evolution in 205 yeast populations over 10,000 generations, revealing patterns of declining adaptability, mutation accumulation, and genetic parallelism.

Global epistasis emerges from a generic model of a complex trait

The paper shows that global epistasis patterns emerge from microscopic epistasis, confirming a quantitative relationship and introducing a new fitness landscape model.

Chance and Necessity in the Pleiotropic Consequences of Adaptation for Budding Yeast

The paper evolves yeast populations in different environments and finds that pleiotropic effects of mutations are shaped by both deterministic factors and stochastic mutation accumulation.

Higher fitness yeast genotypes are less robust to deleterious mutations

The paper shows that more-fit yeast genotypes are less robust to deleterious mutations, as they exhibit lower mean and higher variance in mutation fitness effects.

Long-term adaptive evolution of genomically recoded Escherichia coli

This paper reports the adaptive evolution of a genomically recoded E. coli strain to improve its fitness and identifies mutations that enhance its growth in defined media.

The effect of strong purifying selection on genetic diversity

This study analyzes the dynamics of neutral and deleterious mutations under strong purifying selection using a forward-time approach, revealing distortions in the site frequency spectrum that can mimic population expansions or positive selection.

Genetic Variation In Adaptability And Pleiotropy In Budding Yeast

The paper quantifies genetic variation in adaptability and pleiotropy in budding yeast offspring, finding that initial genotype affects adaptability and pleiotropy, with heritable differences arising from natural variation.