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Article
Open AccessFacile: a command-line network compiler for systems biology
A goal of systems biology is the quantitative modelling of biochemical networks. Yet for many biochemical systems, parameter values and even the existence of interactions between some chemical species are unkn...
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Article
The scaffold protein Ste5 directly controls a switch-like mating decision in yeast
Before mating, a Saccharomyces cerevisiae yeast cell must detect a partner cell in the vicinity that is expressing large amounts of a sex pheromone. The pheromone detection system involves the MAP kinase signal t...
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Article
Open AccessA Bayesian method for inferring quantitative information from FRET data
Understanding biological networks requires identifying their elementary protein interactions and establishing the timing and strength of those interactions. Fluorescence microscopy and Förster resonance energy...
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Article
Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy
Quantitative single-cell time-lapse microscopy is a powerful method for analyzing gene circuit dynamics and heterogeneous cell behavior. We describe the application of this method to imaging bacteria by using ...
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Article
Open AccessUnmixing of fluorescence spectra to resolve quantitative time-series measurements of gene expression in plate readers
To connect gene expression with cellular physiology, we need to follow levels of proteins over time. Experiments typically use variants of Green Fluorescent Protein (GFP), and time-series measurements require ...
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Article
A geometric analysis of fast-slow models for stochastic gene expression
Stochastic models for gene expression frequently exhibit dynamics on several different scales. One potential time-scale separation is caused by significant differences in the lifetimes of mRNA and protein; the...
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Article
Open AccessInferring time derivatives including cell growth rates using Gaussian processes
Often the time derivative of a measured variable is of as much interest as the variable itself. For a growing population of biological cells, for example, the population’s growth rate is typically more importa...
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Article
Open AccessGeneral calibration of microbial growth in microplate readers
Optical density (OD) measurements of microbial growth are one of the most common techniques used in microbiology, with applications ranging from studies of antibiotic efficacy to investigations of growth under...
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Article
Open AccessPredicting metabolic adaptation from networks of mutational paths
Competition for substrates is a ubiquitous selection pressure faced by microbes, yet intracellular trade-offs can prevent cells from metabolizing every type of available substrate. Adaptive evolution is constr...
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Article
Open AccessEstimating numbers of intracellular molecules through analysing fluctuations in photobleaching
The impact of fluorescence microscopy has been limited by the difficulties of expressing measurements of fluorescent proteins in numbers of molecules. Absolute numbers enable the integration of results from di...
