10 Result(s)
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Article
Andre S. Ribeiro
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Open AccessChromosome and plasmid-borne PLacO3O1 promoters differ in sensitivity to critically low temperatures
Temperature shifts trigger genome-wide changes in Escherichia coli’s gene expression. We studied if chromosome integration impacts on a gene’s sensitivity to these shifts, by comparing the single-RNA production k...
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Open AccessRate-limiting steps in transcription dictate sensitivity to variability in cellular components
Cell-to-cell variability in cellular components generates cell-to-cell diversity in RNA and protein production dynamics. As these components are inherited, this should also cause lineage-to-lineage variability...
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Open AccessEffects of multimerization on the temporal variability of protein complex abundance
We explore whether the process of multimerization can be used as a means to regulate noise in the abundance of functional protein complexes. Additionally, we analyze how this process affects the mean level of ...
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Open AccessCell segmentation by multi-resolution analysis and maximum likelihood estimation (MAMLE)
Cell imaging is becoming an indispensable tool for cell and molecular biology research. However, most processes studied are stochastic in nature, and require the observation of many cells and events. Ideally, ...
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Open AccessDetecting sequence dependent transcriptional pauses from RNA and protein number time series
Evidence suggests that in prokaryotes sequence-dependent transcriptional pauses affect the dynamics of transcription and translation, as well as of small genetic circuits. So far, a few pause-prone sequences h...
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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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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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Open AccessStochastic sequence-level model of coupled transcription and translation in prokaryotes
In prokaryotes, transcription and translation are dynamically coupled, as the latter starts before the former is complete. Also, from one transcript, several translation events occur in parallel. To study how ...
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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 ...
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Open AccessInformation propagation within the Genetic Network of Saccharomyces cerevisiae
A gene network's capacity to process information, so as to bind past events to future actions, depends on its structure and logic. From previous and new microarray measurements in Saccharomyces cerevisiae followi...
