12 Result(s)
within
Andre S. Ribeiro
Computational Biology/Bioinformatics
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Chapter and Conference Paper
Modeling and Engineering Promoters with Pre-defined RNA Production Dynamics in Escherichia Coli
Recent developments in live-cell time-lapse microscopy and signal processing methods for single-cell, single-RNA detection now allow characterizing the in vivo dynamics of RNA production of Escherichia coli promo...
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Chapter and Conference Paper
Modelling Polar Retention of Complexes in Escherichia coli
The cytoplasm of Escherichia coli is a crowded, heterogeneous environment. The spatial kinetics and heterogeneities of synthetic RNA-protein complexes have been recently studied using single-cell live imaging. A ...
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Article
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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Article
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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Article
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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Chapter and Conference Paper
Expressive Statistical Model Checking of Genetic Networks with Delayed Stochastic Dynamics
The recently introduced Hybrid Automata Stochastic Logic (HASL) establishes a powerful framework for the analysis of a broad class of stochastic processes, namely Discrete Event Stochastic Processes (DESPs). H...
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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 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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Chapter
Evolutionary Dynamics of a Population of Cells with a Toxin Suppressor Gene
Environmental changes are known to trigger evolutionary changes, e.g. by favoring higher mutation rates. We study the evolutionary dynamics of a delayed stochastic genetic circuit using a simulator developed f...
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Chapter
Information Propagation in the Long-Term Behavior of Gene Regulatory Networks
Gene regulatory networks (GRNs) constantly receive, process and send information. While stochastic in nature, GRNs respond differently to different inputs and similarly to identical inputs. Since cell types st...
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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 ...
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Article
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...
