7 Result(s)
within
Andre S. Ribeiro
Computer Science
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Chapter and Conference Paper
Estimating Effects of Extrinsic Noise on Model Genes and Circuits with Empirically Validated Kinetics
Recent studies of Escherichia coli transcription dynamics using time-lapse confocal microscopy and in vivo single-RNA detection confirmed that transcription initiation has two main rate-limiting steps. Here, we a...
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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
Detecting and Tracking the Tips of Fluorescently Labeled Mitochondria in U2OS Cells
We present a method for automatically detecting the tips of fluorescently labeled mitochondria. The method is based on a Random Forest classifier, which is trained on small patches extracted from confocal micr...
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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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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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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 Flow in Systems of Interacting Agents as a Function of Local and Global Topological Features
Information flow between elements of a system determines the system’s functioning. This flow depends on the topology of the system. This chapter presents the latest results on how a system’s structure, namely,...
