Nunchaku: optimally partitioning data into
piece-wise contiguous segments
Huo et al., Bioinformatics 39 (2023) btad688
The nunchaku Python
package.
Analysing and meta-analysing time-series data
of microbial growth and gene expression from plate
readers
Montaño-Gutierrez et al., PLoS Comput Biol 18
(2022) e1010138
The omniplate Python
package.
Multiple nutrient transporters enable cells
to mitigate a rate-affinity tradeoff
Montaño-Gutierrez et al., PLoS Comput Biol 18
(2022) e1010060
The Mathematica notebooks
for facilitative transport and symport.
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 Omniplate Python
package.
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.