G. Tkacik

Linking Molecular Mechanisms to their Evolutionary Consequences: a primer

The paper develops a mechanistic model of bacterial promoters to explore how molecular complexity affects evolutionary predictions, finding that simplifying mechanisms does not compromise accuracy.

Chromatin enables precise and scalable gene regulation with factors of limited specificity

This paper shows chromatin reduces regulatory errors in gene expression by silencing off-target genes and enabling scalable gene regulation.

Accumulation and maintenance of information in evolution

The paper quantifies how selection accumulates and maintains information in populations, showing bounds on information precision and maintenance costs.

Structure and Evolution of Constitutive Bacterial Promoters

The paper develops a biophysical model to predict constitutive gene expression from bacterial promoter sequences and estimates the prevalence of functional promoters in random sequences.

Minimal biophysical model of combined antibiotic action

This paper develops a minimal biophysical model to predict antibiotic interactions using bacterial growth laws and experimental validation of resistance gene effects.

Normative models of enhancer function

This paper develops minimal non-equilibrium models of enhancer function that achieve low TF residence time, high specificity, and tunable cooperativity by introducing a 'linking rate' parameter.

Molecular noise of innate immunity shapes bacteria-phage ecologies

This study uses mathematical models to show how molecular stochasticity in bacterial immunity affects population-level ecological outcomes and optimal defense strategies against phages.