11 Result(s)
within
Chapter
Andre S. Ribeiro
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Chapter
Efficiency and Robustness of Processes Driven by Nucleoid Exclusion in Escherichia coli
The internal spatial organization of prokaryotic organisms, including Escherichia coli, is essential for the proper functioning of processes such as cell division. One source of this organization in E. coli is th...
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Chapter and Conference Paper
A strategy for dissecting the kinetics of transcription repression mechanisms
Promoters in Escherichia coli include an ‘OFF’ state, during which transcription is halted. Here, we propose a novel empirical method for assessing the time-length spent by promoters in this state. It relies on d...
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Chapter and Conference Paper
Generator Platform of Benchmark Time-Lapsed Images Development of Cell Tracking Algorithms: Implementation of New Features Towards a Realistic Simulation of the Cell Spatial and Temporal Organization
Recent developments in live-cell microscopy imaging have led to the emergence of Single Cell Biology. This field has also been supported by the development of cell segmentation and tracking algorithms for dat...
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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 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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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,...
