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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,...
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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...
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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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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 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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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 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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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 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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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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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
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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Article
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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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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Article
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...
