D. M. McCandlish

Protein evolvability under rewired genetic codes

This study investigates how rewired genetic codes affect protein evolvability by analyzing adaptive landscapes under various genetic codes.

Mutation and selection induce correlations between selection coefficients and mutation rates

The paper analyzes the joint distribution of selection coefficients and mutation rates under the SSWM regime, showing that correlations can arise even without initial correlations.

Specificity, synergy, and mechanisms of splice-modifying drugs

This study develops quantitative models to understand how splice-modifying drugs work, showing drug-specific mechanisms and revealing widespread drug synergy and cooperativity.

Multiple distinct evolutionary mechanisms govern the dynamics of selfish mitochondrial genomes

The paper investigates evolutionary mechanisms of selfish mitochondrial genomes in C. elegans, revealing diverse strategies for persistence and phenotypic consequences.

Genomic and experimental evidence that alternate transcription initiation of the Anaplastic Lymphoma Kinase (ALK) kinase domain does not predict single agent sensitivity to ALK inhibitors.

The paper reanalyzes ALKATI's role in melanoma using genomic and experimental methods, finding it does not predict single-agent ALK inhibitor sensitivity.

Mutation bias shapes the spectrum of adaptive substitutions

The paper analyzes how mutation bias affects the spectrum of adaptive substitutions in three species using statistical models and simulations.

Higher-order epistasis and phenotypic prediction

This paper introduces a method to model higher-order genetic interactions from partially observed data and applies it to predict phenotypes in antibody-binding domains and splicing efficiency.

The role of mutation bias in adaptive molecular evolution: insights from convergent changes in protein function

The paper examines how mutation bias at CpG dinucleotides influences adaptive molecular evolution by analyzing convergent changes in hemoglobin function across high-altitude birds.

Selection for protein stability enriches for epistatic interactions

The paper shows that small non-additive contributions to folding free energy are essential for protein stability, compatible with observed additive mutation effects.

Inferring the shape of global epistasis

The paper infers the shape of global epistasis in three proteins using high-throughput mutagenesis data and a maximum-likelihood method with monotonic nonlinear functions.

Mutational biases influence parallel adaptation

The paper examines the role of mutational biases in adaptation by analyzing the frequency of transitions versus transversions in parallel adaptive substitutions.