A. Ribeiro

发表

Noisy attractors and ergodic sets in models of gene regulatory networks.

S. Kauffman, A. Ribeiro, 2007, Journal of theoretical biology.

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

Mohamed N. M. Bahrudeen, A. Ribeiro, Vinodh Kandavalli, 2020, Biochimica et biophysica acta. Gene regulatory mechanisms.

Chromosome and plasmid-borne PLacO3O1 promoters differ in sensitivity to critically low temperatures

Samuel M. D. Oliveira, A. Ribeiro, Vinodh Kandavalli, 2019, Scientific Reports.

Regulation of asymmetries in the kinetics and protein numbers of bacterial gene expression.

A. Ribeiro, A. Visa, Vinodh Kandavalli, 2019, Biochimica et biophysica acta. Gene regulatory mechanisms.

Estimating RNA numbers in single cells by RNA fluorescent tagging and flow cytometry.

Mohamed N. M. Bahrudeen, Samuel M. D. Oliveira, A. Ribeiro, 2019, Journal of microbiological methods.

Temperature-dependence of the single-cell variability in the kinetics of transcription activation in Escherichia coli

Mohamed N. M. Bahrudeen, Samuel M. D. Oliveira, A. Ribeiro, 2018, Physical biology.

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

A. Ribeiro, M. Prajapat, 2018, Royal Society Open Science.

MOHAMED NASURUDEEN MOHAMED BAHRUDEEN EXTRINSIC NOISE EFFECTS REGULATION AT THE SINGLE GENE AND SMALL GENE NETWORK LEVELS

A. Ribeiro, 2017 .

A strategy for dissecting the kinetics of transcription repression mechanisms

José Manuel Cantera Fonseca, A. Ribeiro, C. Palma, 2017 .

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

A. Ribeiro, Vinodh Kandavalli, Jarno Mäkelä, 2017, Scientific Reports.

Dissecting the stochastic transcription initiation process in live Escherichia coli

Samuel M. D. Oliveira, Jerome G. Chandraseelan, A. Ribeiro, 2016, DNA research : an international journal for rapid publication of reports on genes and genomes.

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

A. Ribeiro, A. Häkkinen, C. Zimmer, 2016, Mathematical biosciences.

Effects of σ factor competition are promoter initiation kinetics dependent.

A. Ribeiro, Vinodh Kandavalli, Huy Tran, 2016, Biochimica et biophysica acta.

Increased cytoplasm viscosity hampers aggregate polar segregation in Escherichia coli

Samuel M. D. Oliveira, A. Ribeiro, S. M. D. Oliveira, 2016, Molecular microbiology.

MARZIEH ZARE SINGLE CELL ANALYSIS OF Z RING FORMATION IN ESCHE- RICHIA COLI USING MACHINE LEARNING METHODS

S. Peltonen, A. Ribeiro, U. Ruotsalainen, 2016 .

Delays as Regulators of the Dynamics of Genetic Circuits

A. Ribeiro, 2016 .

TEPPO ANNILA DETECTION OF FLUORESCENTLY LABELED PARTICLES IN ESCHERICHIA COLI

A. Ribeiro, 2015 .

ANTTI MARTIKAINEN SEGREGATION OF PROTEIN AGGREGATES IN ESCHERICHIA COLI

A. Ribeiro, 2015 .

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

Samuel M. D. Oliveira, A. Ribeiro, S. M. D. Oliveira, 2015, Molecular bioSystems.

Study of the influence of σ factors on the kinetics of RNA production

A. Ribeiro, J. Fonseca, Grau de Mestre, 2014 .

Robustness of the division symmetry in Escherichia coli and functional consequences of symmetry breaking

Olli Yli-Harja, Abhishekh Gupta, Jason Lloyd-Price, 2014, Physical biology.

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

Abhishekh Gupta, Jason Lloyd-Price, Samuel M. D. Oliveira, 2014, Biophysical journal.

In vivo single-molecule kinetics of activation and subsequent activity of the arabinose promoter

Olli Yli-Harja, Meenakshisundaram Kandhavelu, Andre S. Ribeiro, 2013, Nucleic acids research.

Effects of temperature on the dynamics of the LacI-TetR-CI repressilator.

Antti Häkkinen, Meenakshisundaram Kandhavelu, Samuel M. D. Oliveira, 2013, Molecular bioSystems.

Probabilistic RNA partitioning generates transient increases in the normalized variance of RNA numbers in synchronized populations of Escherichia coli.

Olli Yli-Harja, Meenakshisundaram Kandhavelu, Jason Lloyd-Price, 2012, Molecular bioSystems.

Single-molecule dynamics of transcription of the lar promoter

M Kandhavelu, O. Yli-Harja, A. Ribeiro, 2012, Physical biology.

Asymmetric Disposal of Individual Protein Aggregates in Escherichia coli, One Aggregate at a Time

Antti Häkkinen, Olli Yli-Harja, Meenakshisundaram Kandhavelu, 2012, Journal of bacteriology.

ABHISHEKH GUPTA STOCHASTIC PROCESSES AS A SOURCE OF CELL TO CELL DIVERSITY AND CELLULAR AGEING

A. Ribeiro, I. Hammouda, 2012 .

Regulation of mean and noise of the in vivo kinetics of transcription under the control of the lac/ara‐1 promoter

Olli Yli-Harja, Meenakshisundaram Kandhavelu, Abhishekh Gupta, 2012, FEBS letters.

Dynamics of transcription driven by the tetA promoter, one event at a time, in live Escherichia coli cells

Olli Yli-Harja, Meenakshisundaram Kandhavelu, Andre S. Ribeiro, 2012, Nucleic acids research.

Aggregate at a Time Aggregates in Escherichia coli , One Asymmetric Disposal of Individual Protein

O. Yli-Harja, A. Ribeiro, J. Lloyd-Price, 2012 .

Dynamics of transcription of closely spaced promoters in Escherichia coli, one event at a time.

O. Yli-Harja, A. Ribeiro, Leonardo Martins, 2012, Journal of theoretical biology.

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

Olli Yli-Harja, Meenakshisundaram Kandhavelu, Henrik Mannerström, 2011, BMC Molecular Biology.

Stochastic and delayed stochastic models of gene expression and regulation.

A. Ribeiro, 2010, Mathematical biosciences.

Tuning cell differentiation patterns and single cell dynamics by regulating proteins' functionalities in a toggle switch.

Olli Yli-Harja, Xiaofeng Dai, O. Yli-Harja, 2009, Journal of theoretical biology.

Variability of the distribution of differentiation pathway choices regulated by a multipotent delayed stochastic switch.

O. Yli-Harja, A. Ribeiro, Xiaofeng Dai, 2009, Journal of theoretical biology.

Identification of β-lactam antibiotics using bioluminescent Escherichia coli and a support vector machine classifier algorithm

O. Yli-Harja, A. Ribeiro, Olli-Pekka Smolander, 2009 .

Measuring information propagation and retention in boolean networks and its implications to a model of human organizations

S. Kauffman, A. Ribeiro, J. Lloyd-Price, 2006 .

Effects of codon sequence on the dynamics of genetic networks.

O. Yli-Harja, A. Ribeiro, Jarno Mäkelä, 2012, Journal of theoretical biology.

‘miSimBa’ — A simulator of synthetic time-lapsed microscopy images of bacterial cells

Leonardo Martins, A. Ribeiro, Leonardo Martins, 2015, 2015 IEEE 4th Portuguese Meeting on Bioengineering (ENBENG).

Effects of Rate-Limiting Steps in Transcription Initiation on Genetic Filter Motifs

Antti Häkkinen, Olli Yli-Harja, Andre S. Ribeiro, 2013, PloS one.

JASON LLOYD-PRICE SIMULATING STOCHASTIC CHEMICAL KINETICS WITH DYNAMIC COMPARTMENTALIZATION AT RUNTIME

O. Yli-Harja, A. Ribeiro, Jarno Mäkelä, 2011 .

Dynamics of a two-dimensional model of cell tissues with coupled stochastic gene networks.

A. Ribeiro, 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

Parameter Estimation and Tuning of Firefly Luciferase Pathway Model

O. Yli-Harja, A. Ribeiro, J. Lloyd-Price, 2007, 2007 IEEE International Workshop on Genomic Signal Processing and Statistics.

CellLine , a stochastic cell lineage simulator : Applications

Daniel A. Charlebois, A. Ribeiro, J. Lloyd-Price, 2007 .

Efficiency and Robustness of Processes Driven by Nucleoid Exclusion in Escherichia coli.

A. Ribeiro, Vinodh Kandavalli, Vatsala Chauhan, 2020, Advances in experimental medicine and biology.

The precision of the symmetry in Z-ring placement in Escherichia coli is hampered at critical temperatures

Mohamed N. M. Bahrudeen, Samuel M. D. Oliveira, A. Ribeiro, 2018, Physical biology.

Information Propagation in the Long-Term Behavior of Gene Regulatory Networks

A. Ribeiro, J. Lloyd-Price, 2011 .

Delayed Stochastic Model of Transcription at the Single Nucleotide Level

Antti Häkkinen, Olli Yli-Harja, Andre S. Ribeiro, 2009, J. Comput. Biol..

Dynamics of a genetic toggle switch at the nucleotide and codon levels.

O. Yli-Harja, A. Ribeiro, J. Lloyd-Price, 2011, Physical review. E, Statistical, nonlinear, and soft matter physics.

Genome wide study of NF-Y type CCAAT boxes in unidirectional and bidirectional promoters in human and mouse.

A. Ribeiro, H. Jacobs, A. Häkkinen, 2011, Journal of theoretical biology.

Effects of multimerization on the temporal variability of protein complex abundance

Antti Häkkinen, Olli Yli-Harja, Brian Ingalls, 2013, BMC Systems Biology.

Transcription closed and open complex formation coordinate expression of genes with a shared promoter region

Samuel M. D. Oliveira, A. Ribeiro, S. M. D. Oliveira, 2019, bioRxiv.

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

A. Ribeiro, Ramakanth Neeli-Venkata, S. Startceva, 2016, Biophysical journal.

Automatic quantification of mitochondrial fragmentation from two‐photon microscope images of mouse brain tissue

A. Ribeiro, L. Khiroug, E. Lihavainen, 2015, Journal of microscopy.

Evolutionary Dynamics of a Population of Cells with a Toxin Suppressor Gene

Antti Häkkinen, Olli Yli-Harja, Andre S. Ribeiro, 2011, Trans. Comp. Sys. Biology.

Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli

Mohamed N. M. Bahrudeen, A. Ribeiro, C. Palma, 2022, Nucleic acids research.

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

O. Yli-Harja, A. Ribeiro, X. Dai, 2009 .

Effects of Mg2+ on in vivo transcriptional dynamics of the lar promoter

Meenakshisundaram Kandhavelu, Andre S. Ribeiro, Olli Yli-Harja, 2012, Biosyst..

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

A. Ribeiro, H. Jacobs, E. Dufour, 2014, Molecular systems biology.

Analytical kinetic model of native tandem promoters in E. coli

Mohamed N. M. Bahrudeen, A. Ribeiro, Vinodh Kandavalli, 2021, bioRxiv.

Effects of gene length on the dynamics of gene expression

Antti Häkkinen, Andre S. Ribeiro, Jason Lloyd-Price, 2012, Comput. Biol. Chem..

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

Olli Yli-Harja, Andre S. Ribeiro, Jarno Mäkelä, 2011, BMC Bioinformatics.

The transcription factor network of E. coli steers global responses to shifts in RNAP concentration

Mohamed N. M. Bahrudeen, Samuel M. D. Oliveira, M. Nykter, 2022, bioRxiv.

Positive supercoiling buildup is a trigger of E. coli’s short-term response to cold shock

Mohamed N. M. Bahrudeen, A. Ribeiro, C. Palma, 2021, bioRxiv.

Stochastic models coupling gene expression and partitioning in cell division in Escherichia coli

Andre S Ribeiro, Ines Baptista, A. Ribeiro, 2020, Biosyst..

Effects of inducer intake kinetics on the dynamics of gene expression

Andre S. Ribeiro, Huy Tran, A. Ribeiro, 2013, ECAL.

Chromosome and plasmid-borne PLacO3O1 promoters differ in sensitivity to critically low temperatures

Samuel M. D. Oliveira, A. Ribeiro, Vinodh Kandavalli, 2019, Scientific Reports.

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

Antti Häkkinen, Andre S. Ribeiro, Huy Tran, 2016, PLoS Comput. Biol..

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

Samuel M. D. Oliveira, Jerome G. Chandraseelan, O. Yli-Harja, 2015, Molecular bioSystems.

In Vivo Transcription Kinetics of a Synthetic Gene Uninvolved in Stress-Response Pathways in Stressed Escherichia coli Cells

A. Ribeiro, Ramakanth Neeli-Venkata, Anantha-Barathi Muthukrishnan, 2014, PloS one.

CellAging: a tool to study segregation and partitioning in division in cell lineages of Escherichia coli

José Manuel Fonseca, Antti Häkkinen, Andre S. Ribeiro, 2013, Bioinform..

SGNS2: a compartmentalized stochastic chemical kinetics simulator for dynamic cell populations

Andre S. Ribeiro, Abhishekh Gupta, Jason Lloyd-Price, 2012, Bioinform..

Inference of Kinetic Parameters of Delayed Stochastic Models of Gene Expression Using a Markov Chain Approximation

Olli Yli-Harja, Andre S. Ribeiro, Henrik Mannerström, 2010, EURASIP J. Bioinform. Syst. Biol..

NF-Y influences directionality of transcription from the bidirectional Mrps12/Sarsm promoter in both mouse and human cells.

Bairong Shen, Antti Häkkinen, Gabriel N. Teku, 2009, Biochimica et biophysica acta.

Sequence-dependent model of genes with dual σ factor preference.

Mohamed N. M. Bahrudeen, A. Ribeiro, Vinodh Kandavalli, 2022, Biochimica et biophysica acta. Gene regulatory mechanisms.

Modeling and Engineering Promoters with Pre-defined RNA Production Dynamics in Escherichia Coli

Andre S. Ribeiro, Mohamed N. M. Bahrudeen, Samuel M. D. Oliveira, 2018, CMSB.

Estimating Effects of Extrinsic Noise on Model Genes and Circuits with Empirically Validated Kinetics

Andre S. Ribeiro, Mohamed N. M. Bahrudeen, Samuel M. D. Oliveira, 2017, WIVACE.

Effects of Extrinsic Noise are Promoter Kinetics Dependent

Mohamed N. M. Bahrudeen, A. Ribeiro, S. Startceva, 2017, ICBBT '17.

iCellFusion: Tool for Fusion and Analysis of Live-Cell Images from Time-Lapse Multimodal Microscopy

Antti Häkkinen, Andre S. Ribeiro, Abhishekh Gupta, 2016 .

Characterizing rate limiting steps in transcription from RNA production times in live cells

Antti Häkkinen, Andre S. Ribeiro, A. Ribeiro, 2016, Bioinform..

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

Antti Häkkinen, Andre S. Ribeiro, A. Ribeiro, 2015, Bioinform..

Dynamics of small genetic circuits subject to stochastic partitioning in cell division.

A. Ribeiro, J. Lloyd-Price, Huy Tran, 2014, Journal of theoretical biology.

Estimation of fluorescence-tagged RNA numbers from spot intensities

Antti Häkkinen, Meenakshisundaram Kandhavelu, Stefania Garasto, 2014, Bioinform..

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

O. Yli-Harja, A. Ribeiro, M. Kandhavelu, 2013, BMC Bioinformatics.

HUY TRAN SEQUENCE-DEPENDENT NOISE FILTERING IN SMALL GENETIC MOTIFS

O. Yli-Harja, A. Ribeiro, 2013 .

Sequence Dependent Properties of the Expression Dynamics of Genes and Gene Networks

Olli Yli-Harja, Andre S. Ribeiro, Jarno Mäkelä, 2012, CMSB.

Expressive Statistical Model Checking of Genetic Networks with Delayed Stochastic Dynamics

Paolo Ballarini, Andre S. Ribeiro, Jarno Mäkelä, 2012, CMSB.

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

Antti Häkkinen, Frank Emmert-Streib, Andre S. Ribeiro, 2012, BMC Bioinformatics.

Evolving kinetics of gene expression in stochastic environments

Antti Häkkinen, Andre S. Ribeiro, A. Ribeiro, 2012, Comput. Biol. Chem..

Automatic detection of changes in the dynamics of delayed stochastic gene networks and in vivo production of RNA molecules in Escherichia coli

Heikki Huttunen, Olli Yli-Harja, Meenakshisundaram Kandhavelu, 2011, Bioinform..

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

Antti Häkkinen, Olli Yli-Harja, Meenakshisundaram Kandhavelu, 2011, BMC Systems Biology.

Robustness to Sub-optimal Temperatures of the Processes of Tsr Cluster Formation and Positioning in Escherichia Coli

Andre S. Ribeiro, Teppo Annila, Ramakanth Neeli-Venkata, 2016, BIOINFORMATICS.

Quantitative Estimation of Long-living Fluorescent Molecules from Temporal Fluorescence Intensity Data Corrupted by Nonzero-mean Noise

Ari Visa, Andre S. Ribeiro, Sofia Startceva, 2016, BIOSIGNALS.

Effects of coupling strength and space on the dynamics of coupled toggle switches in stochastic gene networks with multiple-delayed reactions.

A. Ribeiro, Andre S Ribeiro, 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

Dynamics and evolution of stochastic bistable gene networks with sensing in fluctuating environments.

Andre S Ribeiro, A. Ribeiro, 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

Studying genetic regulatory networks at the molecular level: delayed reaction stochastic models.

Andre S Ribeiro, Stuart A Kauffman, Rui Zhu, 2007, Journal of theoretical biology.

SGN Sim, a Stochastic Genetic Networks Simulator

Andre S. Ribeiro, Jason Lloyd-Price, A. Ribeiro, 2007, Bioinform..

A General Modeling Strategy for Gene Regulatory Networks with Stochastic Dynamics

Rui Zhu, Stuart A. Kauffman, Andre Ribeiro, 2006, J. Comput. Biol..

CellLine, a stochastic cell lineage simulator

Andre S. Ribeiro, Jason Lloyd-Price, Daniel A. Charlebois, 2007, Bioinform..

Dynamical effects of transcriptional pause-prone sites

Antti Häkkinen, Olli Yli-Harja, Andre S. Ribeiro, 2010, Comput. Biol. Chem..

Effects of Transcriptional Pausing on Gene Expression Dynamics

Antti Häkkinen, Olli Yli-Harja, Andre S. Ribeiro, 2010, PLoS Comput. Biol..

Effects of the promoter open complex formation on gene expression dynamics.

Antti Häkkinen, Olli Yli-Harja, Henrik Mannerström, 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.

Robustness and Information Propagation in Attractors of Random Boolean Networks

Andre S. Ribeiro, Abhishekh Gupta, Jason Lloyd-Price, 2012, PloS one.

Diversity of temporal correlations between genes in models of noisy and noiseless gene networks

Olli Yli-Harja, Andre S. Ribeiro, Jason Lloyd-Price, 2011, Biosyst..

Information propagation within the Genetic Network of Saccharomyces cerevisiae

Olli Yli-Harja, Andre S. Ribeiro, Timothy R. Hughes, 2010, BMC Systems Biology.

Information Flow in Systems of Interacting Agents as a Function of Local and Global Topological Features

Andre S. Ribeiro, A. Ribeiro, 2010, Computational Social Network Analysis.

In silico analysis of division times of Escherichia coli populations as a function of the partitioning scheme of non-functional proteins

Andre S. Ribeiro, Abhishekh Gupta, Jason Lloyd-Price, 2015, Silico Biol..

Mutual information in random Boolean models of regulatory networks.

Jason Lloyd-Price, Joshua E S Socolar, Björn Samuelsson, 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

In Vivo Single-Molecule Dynamics of Transcription of the Viral T7 Phi 10 Promoter in Escherichia coli

José Manuel Cantera Fonseca, A. Ribeiro, Nadia S. M. Goncalves, 2016 .

An interacting multiple model filter‐based autofocus strategy for confocal time‐lapse microscopy

S Chowdhury, M Kandhavelu, O Yli-Harja, 2012, Journal of microscopy.

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

Olli Yli-Harja, Meenakshisundaram Kandhavelu, Andre S. Ribeiro, 2013, BMC Bioinformatics.

Mytoe: automatic analysis of mitochondrial dynamics

Andre S. Ribeiro, Jarno Mäkelä, Eero Lihavainen, 2012, Bioinform..

A general model of the dynamics of genes with dual σ factor preference

A. Ribeiro, Vinodh Kandavalli, C. Palma, 2021, bioRxiv.

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

Olli Yli-Harja, Andre S. Ribeiro, Teppo Annila, 2013, BMC Bioinformatics.

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

José Manuel Fonseca, Andre S. Ribeiro, Leonardo Martins, 2016, SIMULTECH.

An image generator platform to improve cell tracking algorithms: Simulation of objects of various morphologies, kinetics and clustering

José Manuel Fonseca, Andre S. Ribeiro, Leonardo Martins, 2016, 2016 6th International Conference on Simulation and Modeling Methodologies, Technologies and Applications (SIMULTECH).

Robustness of the Process of Nucleoid Exclusion of Protein Aggregates in Escherichia coli

Andre S. Ribeiro, Abhishekh Gupta, Ramakanth Neeli-Venkata, 2016, Journal of bacteriology.

Short-term and long-term memory deficits in handedness learning in mice with absent corpus callosum and reduced hippocampal commissure

B. A. Eales, A. Ribeiro, F. Biddle, 2013, Behavioural Brain Research.

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

S. Kirov, A. Ribeiro, L. Khiroug, 2017, The Journal of Neuroscience.

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

S. Kirov, A. Ribeiro, L. Khiroug, 2017, The Journal of Neuroscience.

Predictability and randomness of paw choices are critical elements in the behavioural plasticity of mouse paw preference

B. A. Eales, A. Ribeiro, J. Lloyd-Price, 2014, Animal Behaviour.

Title: Short-term and Long-term Memory Deficits in Handedness Learning in Mice with absent Corpus Callosum and Reduced Hippocampal Commissure Short Title: Handedness Learning in Mice with absent Cc/hc

B. A. Eales, A. Ribeiro, F. Biddle, 2013 .