Michael Lynch

The paper develops a model to predict prey capture performance and growth rate in heliozoans based on axopod characteristics.

The paper shows that ecological interactions can significantly alter fixation probabilities of mutant alleles even in effectively neutral conditions.

The paper analyzes transcription initiation sites in Paramecium species to understand gene expression and sequence architecture.

This study examines regulatory divergence in the Daphnia pulex complex by analyzing promoter architecture and gene expression across developmental stages.

The paper develops a value-of-information framework for microbial predator-prey interactions, showing how sensory information can disproportionately enhance survival benefits during encounters.

This paper develops theory to explain how host-symbiont coevolution leads to either cooperation or exploitation, depending on population-genetic factors.

The paper analyzes the nuclear genomes of Mesodinium rubrum and finds it lacks spliceosomal introns and related machinery, suggesting introns hinder endosymbiotic genomic integration.

The paper quantifies amino acid substitution rates in E. coli, finding no significant differences in overall translation error rates among ribosomal variants but unique mistranslation profiles.

This study sequenced genomes of hundreds of Paramecium isolates worldwide to investigate population-genetic patterns, finding geographic differentiation and speciation driven by genetic isolation.

This study analyzes mitochondrial genomes of Paramecium to explore evolutionary dynamics, revealing cryptic diversity, conserved genes, and patterns of molecular evolution.

The paper identifies a genetic variant in Daphnia pulex that suppresses recombination, leading to the emergence of a mixed-mating system with both genetic and environmental sex determination.

The paper analyzes mutation dynamics in Daphnia obtusa using whole-genome sequencing of mutation accumulation lines, revealing mutation rates, spectra, and selection pressures affecting genome stability.

This study shows that evolving larger cell size reduces internal cellular density, as material accumulation does not keep pace with volume increase, both in experimental evolution and across species.

The paper analyzes gene expression across eight tissues in Daphnia pulex and investigates selection pressures on genes in different tissues, identifying novel evolutionary patterns.

The paper develops a mathematical model to quantify the fitness benefits of phagocytosis in evolutionary contexts and identifies conditions under which it provides an advantage.

This paper introduces DNA circle-sequencing to reduce sequencing errors and identifies ultrasonication as a source of DNA damage in library preparation.

The paper develops a physiological model to explain the scaling of bacterial growth rate with cell size by linking resource allocation to the cell envelope.

This paper uses subcellular proteomics to show that glycolytic and gluconeogenic enzymes are mosaically localized in Paramecium tetraurelia, with some enzymes in mitochondria and others in the cytosol, suggesting a preference for gluconeogenesis.

The paper quantifies evolutionary fitness gains of endomembrane systems through two models: pinocytosis and proto-endoplasmic reticulum, finding the latter provides net fitness gains.

This study experimentally evolved E. coli populations under feast/famine cycles, finding high mutational parallelism and trade-offs between growth and survival traits.

OSPALC provides a one-step PCR method for amplicon library construction, reducing cost and time compared to commercial kits, and includes a QIIME2 analysis pipeline.

The paper estimates transcription fidelity in human cells, identifies factors controlling its accuracy, and links transcription errors to Alzheimer's disease progression.

This study analyzes 13 Paramecium species with a shared ancestral whole-genome duplication to reveal trends in post-duplication gene retention and selective pressures.

The paper examines mutation rate variation in bacterial genomes linked to replication timing, finding periodic patterns in mutation rates across chromosomes.

This study measures mutation rates and spectra in two Vibrio species under minimal selection, finding low mutation rates and AT-biased spectra, with MMR loss causing convergence in mutation patterns.

This study uses CAGE to profile 5′-mRNA ends in Daphnia pulex, revealing promoter architecture and sex-specific gene expression patterns, including novel cis-regulatory elements and insights into cyclical parthenogenesis.

The paper measures the germline base-substitution mutation rate in Tetrahymena thermophila and finds it to be low, similar to Paramecium tetraurelia, but notes fitness decline in exclusion lines suggests other factors contribute to mutational load.

This paper estimates seven pairwise relatedness coefficients from population genomic data and applies them to Daphnia pulex populations to identify related individuals and asexual clones.

This study analyzes the mutation rates and spectra in Burkholderia cenocepacia, revealing non-AT-biased mutations and chromosome-specific variation.