Software available


Distributed and dynamic intracellular organization of extracellular information
Granados et al., Proc Nat Acad Sci USA 115 (2018) 6088
The code for estimating mutual information for time-series in R and Matlab.

Morphologically constrained and data informed cell segmentation of budding yeast
Bakker et al., Bioinformatics 34 (2018) 88
The analysis code in Matlab.


Inferring time derivatives including growth rates using Gaussian processes
Swain et al., Nat Commun 7 (2016) 13766
The analysis code in Python.


Mechanistic links between cellular trade-offs, gene expression, and growth
Weisse et al., Proc Nat Acad Sci USA 112 (2015) E1038
The model in SBML and Matlab.


Unmixing of fluorescence spectra to resolve quantitative time-series measurements of gene expression in plate readers
Lichten, White, Clark, & Swain, BMC Biotechnol 14 (2014) 11
The analysis code in Python.


A Bayesian method for inferring quantitative information from FRET data
Lichten & Swain, BMC Biophys 4 (2011) 10
A Matlab version of the algorithm.


Scalable rule-based modelling of allosteric proteins and biochemical networks
Ollivier et al., PLoS Comput Biol 6 (2010) e1000975
The Allosteric Network Compiler.


Analytical expressions for stochastic gene expression
Shahrezaei & Swain, Proc Nat Acad Sci USA 105 (2008) 17256
Matlab files for probability distributions.

Colored extrinsic fluctuations and stochastic gene expression
Shahrezaei et al., Mol Syst Biol 4 (2008) 196
The Easystoch stochastic simulator.


Facile: a command-line network compiler for systems biology
Siso-Nadal et al., BMC Syst Biol 1 (2007) 36
Code for the compiler in Perl and Python.


A fluctuation method to quantify in vivo fluorescence
Rosenfeld et al., Biophys J 91 (2006) 759
Matlab implementations of both methods.