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Article
Open AccessA probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways
We present a generative model, Lux, to quantify DNA methylation modifications from any combination of bisulfite sequencing approaches, including reduced, oxidative, TET-assisted, chemical-modification assisted...
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Article
Open AccessIdentification of global regulators of T-helper cell lineage specification
Activation and differentiation of T-helper (Th) cells into Th1 and Th2 types is a complex process orchestrated by distinct gene activation programs engaging a number of genes. This process is crucial for a rob...
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Article
Open AccessIn vivo kinetics of transcription initiation of the lar promoter in Escherichia coli. Evidence for a sequential mechanism with two rate-limiting steps
In Escherichia coli the mean and cell-to-cell diversity in RNA numbers of different genes vary widely. This is likely due to different kinetics of transcription initiation, a complex process with multiple rate-li...
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Article
Open AccessCell-to-cell diversity in protein levels of a gene driven by a tetracycline inducible promoter
Gene expression in Escherichia coli is regulated by several mechanisms. We measured in single cells the expression level of a single copy gene coding for green fluorescent protein (GFP), integrated into the genom...
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Article
Open AccessInference of Kinetic Parameters of Delayed Stochastic Models of Gene Expression Using a Markov Chain Approximation
We propose a Markov chain approximation of the delayed stochastic simulation algorithm to infer properties of the mechanisms in prokaryote transcription from the dynamics of RNA levels. We model transcription ...
