A General Modeling Strategy for Gene Regulatory Networks with Stochastic Dynamics. - Andre S. Ribeiro; Rui Zhu; Stuart A. Kauffman (J. Comput. Biol., 2006)

CellLine, a stochastic cell lineage simulator. - Andre S. Ribeiro; Daniel A. Charlebois; Jason Lloyd-Price (Bioinform., 2007)

SGN Sim, a Stochastic Genetic Networks Simulator. - Andre S. Ribeiro; Jason Lloyd-Price (Bioinform., 2007)

Optimize Observational Time Points to Maximize the Inferability of Gene Networks. - Frank Emmert-Streib; Andre S. Ribeiro (BIOCOMP, 2008)

Determining noisy attractors of delayed stochastic gene regulatory networks from multiple data sources. - Xiaofeng Dai; Olli Yli-Harja; Andre S. Ribeiro (Bioinform., 2009)

Delayed Stochastic Model of Transcription at the Single Nucleotide Level. - Andre S. Ribeiro; Olli-Pekka Smolander; Tiina Rajala; Antti Häkkinen; Olli Yli-Harja (J. Comput. Biol., 2009)

Dynamic Agent-Based Model of Hand-Preference Behavior Patterns in the Mouse. - Andre S. Ribeiro; Jason Lloyd-Price; Brenda A. Eales; Fred G. Biddle (Adapt. Behav., 2010)

Information propagation within the Genetic Network of Saccharomyces cerevisiae. - Sharif Chowdhury; Jason Lloyd-Price; Olli-Pekka Smolander; Wayne C. V. Baici; Timothy R. Hughes; Olli Yli-Harja; Gordon Chua; Andre S. Ribeiro (BMC Syst. Biol., 2010)

Dynamical effects of transcriptional pause-prone sites. - Andre S. Ribeiro; Antti Häkkinen; Shannon Healy; Olli Yli-Harja (Comput. Biol. Chem., 2010)

Effects of Transcriptional Pausing on Gene Expression Dynamics. - Tiina Rajala; Antti Häkkinen; Shannon Healy; Olli Yli-Harja; Andre S. Ribeiro (PLoS Comput. Biol., 2010)

Information Flow in Systems of Interacting Agents as a Function of Local and Global Topological Features. - Andre S. Ribeiro (Computational Social Network Analysis, 2010)

Automatic detection of changes in the dynamics of delayed stochastic gene networks and in vivo production of RNA molecules in Escherichia coli. - Jarno Mäkelä; Heikki Huttunen; Meenakshisundaram Kandhavelu; Olli Yli-Harja; Andre S. Ribeiro (Bioinform., 2011)

Diversity of temporal correlations between genes in models of noisy and noiseless gene networks. - Andre S. Ribeiro; Jason Lloyd-Price; Sharif Chowdhury; Olli Yli-Harja (Biosyst., 2011)

Stochastic sequence-level model of coupled transcription and translation in prokaryotes. - Jarno Mäkelä; Jason Lloyd-Price; Olli Yli-Harja; Andre S. Ribeiro (BMC Bioinform., 2011)

In vivo kinetics of transcription initiation of the lar promoter in Escherichia coli. Evidence for a sequential mechanism with two rate-limiting steps. - Meenakshisundaram Kandhavelu; Henrik Mannerström; Abhishekh Gupta; Antti Häkkinen; Jason Lloyd-Price; Olli Yli-Harja; Andre S. Ribeiro (BMC Syst. Biol., 2011)

Inference of Kinetic Parameters of Delayed Stochastic Models of Gene Expression Using a Markov Chain Approximation. - Henrik Mannerström; Olli Yli-Harja; Andre S. Ribeiro (EURASIP J. Bioinform. Syst. Biol., 2011)

Evolutionary Dynamics of a Population of Cells with a Toxin Suppressor Gene. - Antti Häkkinen; Fred G. Biddle; Olli-Pekka Smolander; Olli Yli-Harja; Andre S. Ribeiro (Trans. Comp. Sys. Biology, 2011)

Expressive Statistical Model Checking of Genetic Networks with Delayed Stochastic Dynamics. - Paolo Ballarini; Jarno Mäkelä; Andre S. Ribeiro (CMSB, 2012)

Sequence Dependent Properties of the Expression Dynamics of Genes and Gene Networks. - Ilya Potapov; Jarno Mäkelä; Olli Yli-Harja; Andre S. Ribeiro (CMSB, 2012)

Mytoe: automatic analysis of mitochondrial dynamics. - Eero Lihavainen; Jarno Mäkelä; Johannes N. Spelbrink; Andre S. Ribeiro (Bioinform., 2012)

SGNS2: a compartmentalized stochastic chemical kinetics simulator for dynamic cell populations. - Jason Lloyd-Price; Abhishekh Gupta; Andre S. Ribeiro (Bioinform., 2012)

Effects of Mg2+ on in vivo transcriptional dynamics of the lar promoter. - Meenakshisundaram Kandhavelu; Eero Lihavainen; Anantha Barathi Muthukrishnan; Olli Yli-Harja; Andre Sanches Ribeiro (Biosyst., 2012)

Detecting sequence dependent transcriptional pauses from RNA and protein number time series. - Frank Emmert-Streib; Antti Häkkinen; Andre S. Ribeiro (BMC Bioinform., 2012)

Evolving kinetics of gene expression in stochastic environments. - Antti Häkkinen; Andre S. Ribeiro (Comput. Biol. Chem., 2012)

Effects of gene length on the dynamics of gene expression. - Andre S. Ribeiro; Antti Häkkinen; Jason Lloyd-Price (Comput. Biol. Chem., 2012)

In silico analysis of division times of Escherichia coli populations as a function of the partitioning scheme of non-functional proteins. - Abhishekh Gupta; Jason Lloyd-Price; Andre S. Ribeiro (Silico Biol., 2012)

Effects of inducer intake kinetics on the dynamics of gene expression. - Huy Tran; Andre S. Ribeiro (ECAL, 2013)

CellAging: a tool to study segregation and partitioning in division in cell lineages of Escherichia coli. - Antti Häkkinen; Anantha Barathi Muthukrishnan; André Mora; José Manuel Fonseca; Andre S. Ribeiro (Bioinform., 2013)

ZebIAT, an image analysis tool for registering zebrafish embryos and quantifying cancer metastasis. - Teppo Annila; Eero Lihavainen; Ines J. Marques; Darren R. Williams; Olli Yli-Harja; Andre S. Ribeiro (BMC Bioinform., 2013)

Cell segmentation by multi-resolution analysis and maximum likelihood estimation (MAMLE). - Sharif Chowdhury; Meenakshisundaram Kandhavelu; Olli Yli-Harja; Andre S. Ribeiro (BMC Bioinform., 2013)

Effects of multimerization on the temporal variability of protein complex abundance. - Antti Häkkinen; Huy Tran; Olli Yli-Harja; Brian P. Ingalls; Andre S. Ribeiro (BMC Syst. Biol., 2013)

Modelling Polar Retention of Complexes in Escherichia coli. - Abhishekh Gupta; Jason Lloyd-Price; Andre S. Ribeiro (CMSB, 2014)

Estimation of fluorescence-tagged RNA numbers from spot intensities. - Antti Häkkinen; Meenakshisundaram Kandhavelu; Stefania Garasto; Andre S. Ribeiro (Bioinform., 2014)

Detecting and Tracking the Tips of Fluorescently Labeled Mitochondria in U2OS Cells. - Eero Lihavainen; Jarno Mäkelä; Johannes N. Spelbrink; Andre S. Ribeiro (ICIAP (2), 2015)

Estimation of GFP-tagged RNA numbers from temporal fluorescence intensity data. - Antti Häkkinen; Andre S. Ribeiro (Bioinform., 2015)

Robustness to Sub-optimal Temperatures of the Processes of Tsr Cluster Formation and Positioning in Escherichia Coli. - Teppo Annila; Ramakanth Neeli-Venkata; Andre S. Ribeiro (BIOINFORMATICS, 2016)

Quantitative Estimation of Long-living Fluorescent Molecules from Temporal Fluorescence Intensity Data Corrupted by Nonzero-mean Noise. - Sofia Startceva; Jerome G. Chandraseelan; Ari Visa; Andre S. Ribeiro (BIOSIGNALS, 2016)

An Image Generator Platform to Improve Cell Tracking Algorithms - Simulation of Objects of Various Morphologies, Kinetics and Clustering. - Pedro Canelas; Leonardo Martins; André Mora; Andre S. Ribeiro; José Manuel Fonseca (SIMULTECH, 2016)

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. - Leonardo Martins; Pedro Canelas; André Mora; Andre S. Ribeiro; José Manuel Fonseca (SIMULTECH (Selected Papers), 2016)

Characterizing rate limiting steps in transcription from RNA production times in live cells. - Antti Häkkinen; Andre S. Ribeiro (Bioinform., 2016)

Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements. - Samuel M. D. Oliveira; Antti Häkkinen; Jason Lloyd-Price; Huy Tran; Vinodh Kandavalli; Andre S. Ribeiro (PLoS Comput. Biol., 2016)

Automatic Classification of Z-ring Formation Stages at the Single Cell Level in Escherichia Coli by Machine Learning. - Marzieh Zare; Ramakanth Neeli-Venkata; Leonardo Martins; Sari Peltonen; Ulla Ruotsalainen; Andre S. Ribeiro (BIOIMAGING, 2017)

Tuning extrinsic noise effects on a small genetic circuit. - Mohamed N. M. Bahrudeen; Andre S. Ribeiro (ECAL, 2017)

Effects of Extrinsic Noise are Promoter Kinetics Dependent. - Mohamed N. M. Bahrudeen; Sofia Startceva; Andre S. Ribeiro (ICBBT, 2017)

Estimating Effects of Extrinsic Noise on Model Genes and Circuits with Empirically Validated Kinetics. - Samuel M. D. Oliveira; Mohamed N. M. Bahrudeen; Sofia Startceva; Andre S. Ribeiro (WIVACE, 2017)

sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters. - Shailesh Tripathi; Jason Lloyd-Price; Andre S. Ribeiro; Olli Yli-Harja; Matthias Dehmer; Frank Emmert-Streib (BMC Bioinform., 2017)

Modeling and Engineering Promoters with Pre-defined RNA Production Dynamics in Escherichia Coli. - Samuel M. D. Oliveira; Mohamed N. M. Bahrudeen; Sofia Startceva; Vinodh Kandavalli; Andre S. Ribeiro (CMSB, 2018)

SCIP: a single-cell image processor toolbox. - Leonardo Martins; Ramakanth Neeli-Venkata; Samuel M. D. Oliveira; Antti Häkkinen; Andre S. Ribeiro; José M. Fonseca 001 (Bioinform., 2018)

Mean and Variability in RNA Polymerase Numbers Are Correlated to the Mean but Not the Variability in Size and Composition of Escherichia Coli Cells. - Bilena Almeida; Vatsala Chauhan; Vinodh Kandavalli; Andre S. Ribeiro (BIOINFORMATICS, 2019)

Stochastic models coupling gene expression and partitioning in cell division in Escherichia coli. - Ines S. C. Baptista; Andre S. Ribeiro (Biosyst., 2020)

Analytical kinetic model of native tandem promoters in E. coli. - Vatsala Chauhan; Mohamed N. M. Bahrudeen; Cristina S. D. Palma; Ines S. C. Baptista; Bilena Almeida; Suchintak Dash; Vinodh Kandavalli; Andre S. Ribeiro (PLoS Comput. Biol., 2022)

Bimodality in E. coli gene expression: Sources and robustness to genome-wide stresses. - Ines S. C. Baptista; Suchintak Dash; Amir M. Arsh; Vinodh Kandavalli; Carlo Maria Scandolo; Barry C. Sanders; Andre S. Ribeiro (PLoS Comput. Biol., 2025)