Lucas B. Carey

The paper identifies super compensatory substitutions that restore protein function and confer mutational robustness across diverse genetic backgrounds.

The paper identifies a conserved gene expression signature linked to proliferation rate, showing it predicts growth rates across species and reveals lineage-specific differences in proliferation dynamics.

The paper identifies rapidly reversible mutations in S. pombe that confer drug resistance and subclonal genetic diversity through MTDs, using whole-genome sequencing and machine learning.

The paper shows that overdosage of balanced protein complexes reduces proliferation in aneuploid yeast and human cancer cells.

The paper compares RNA-Seq and Ribo-Seq for gene expression analysis under oxidative stress in baker's yeast, finding Ribo-Seq better correlates with protein abundance.

This study identifies de novo genes in yeast genomes, showing they arise frequently despite compact genomes and some are translated and under selection.

The paper quantifies the fitness effects of gene expression mean and noise in yeast, showing they have equivalent impacts and that noise minimization is promoted by epistatic ratchet mechanisms.

The paper shows that frameshift errors lead to suboptimal codon usage, which may trigger mRNA degradation through codon-usage mediated pathways, alongside NMD.

The paper shows that gene sequences beyond promoters can buffer or amplify TF effects, reducing fitness costs from misregulation.

The paper investigates cell-to-cell variation in yeast by analyzing the impact of gene deletions on mitochondrial state and its effects on proliferation, drug resistance, and mutation outcomes.

The paper shows that DNA curvature affects mutation rates in yeast and human tumors, with lower curvature linked to higher mutation rates.

The paper experimentally assays a fitness landscape on a macroevolutionary scale by analyzing the effects of amino acid substitutions in yeast His3 orthologs.

The paper shows that promoter architecture influences co-translational regulation of mRNA levels, with Dbp2 mediating reduced regulation in inducible promoters and ORF sequence playing a major role in constitutive genes.

The paper identifies a recurrent structure in gene regulatory networks across five organisms, showing it enables dynamical encoding and information integration through a reservoir-computing paradigm.

The paper measures promoter activity in budding yeast under varying TF concentrations and shows that competition between binding sites, not site number, determines gene expression, with a thermodynamic model explaining the results.