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List of works by Andre S Ribeiro

A general modeling strategy for gene regulatory networks with stochastic dynamics

scientific article

Added value of autoregulation and multi-step kinetics of transcription initiation

scientific article published on 28 November 2018

Analytical kinetic model of native tandem promoters in E. coli

scientific article published on 31 January 2022

Cell segmentation by multi-resolution analysis and maximum likelihood estimation (MAMLE)

scientific article

Cell-to-cell diversity in protein levels of a gene driven by a tetracycline inducible promoter

scientific article

Detecting sequence dependent transcriptional pauses from RNA and protein number time series.

scientific article

Determining noisy attractors of delayed stochastic gene regulatory networks from multiple data sources

scientific article

Dissecting the in vivo dynamics of transcription locking due to positive supercoiling buildup

scientific article published on 27 February 2020

Dissecting the stochastic transcription initiation process in live Escherichia coli.

scientific article published on 28 March 2016

Effects of multimerization on the temporal variability of protein complex abundance

scientific article

Effects of rate-limiting steps in transcription initiation on genetic filter motifs

scientific article

Effects of transcriptional pausing on gene expression dynamics

scientific article

Estimation of GFP-tagged RNA numbers from temporal fluorescence intensity data

scientific article

Estimation of kinetic parameters of transcription from temporal single-RNA measurements

scientific article published on 29 October 2015

In vivo kinetics of segregation and polar retention of MS2-GFP-RNA complexes in Escherichia coli

scientific article

In vivo kinetics of transcription initiation of the lar promoter in Escherichia coli. Evidence for a sequential mechanism with two rate-limiting steps

scientific article

In vivo transcription kinetics of a synthetic gene uninvolved in stress-response pathways in stressed Escherichia coli cells

scientific article (publication date: 2014)

Information propagation within the Genetic Network of Saccharomyces cerevisiae

scientific article

Kinetics of the cellular intake of a gene expression inducer at high concentrations

scientific article published on 30 July 2015

Mytoe: automatic analysis of mitochondrial dynamics.

scientific article

Polar Localization of the Serine Chemoreceptor of Escherichia coli Is Nucleoid Exclusion-Dependent

scientific article published on December 2016

Rate-limiting steps in transcription dictate sensitivity to variability in cellular components

scientific article published on 6 September 2017

Reversible Disruption of Neuronal Mitochondria by Ischemic and Traumatic Injury Revealed by Quantitative Two-Photon Imaging in the Neocortex of Anesthetized Mice

scientific article

Robustness and information propagation in attractors of Random Boolean Networks

scientific article

SCIP: a single-cell image processor toolbox

scientific article published on 01 December 2018

SGN Sim, a stochastic genetic networks simulator

scientific article

Screen for mitochondrial DNA copy number maintenance genes reveals essential role for ATP synthase

scientific article

Single-cell kinetics of a repressilator when implemented in a single-copy plasmid

scientific article (publication date: 2015)

Stochastic sequence-level model of coupled transcription and translation in prokaryotes

scientific article

Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements.

scientific article

ZebIAT, an image analysis tool for registering zebrafish embryos and quantifying cancer metastasis.

scientific article

sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters

scientific article

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