Andre S. Ribeiro

49 papers C 1Journal 32Unranked 15
YearRankTypeTitle / Venue / Authors
2025 J jnl
Bimodality in E. coli gene expression: Sources and robustness to genome-wide stresses.
PLoS Comput. Biol.
Ines S. C. Baptista, Suchintak Dash, Amir M. Arsh, Vinodh Kandavalli, Carlo Maria Scandolo, Barry C. Sanders, Andre S. Ribeiro
2022 J jnl
Analytical kinetic model of native tandem promoters in E. coli.
PLoS Comput. Biol.
Vatsala Chauhan, Mohamed N. M. Bahrudeen, Cristina S. D. Palma, Ines S. C. Baptista, Bilena Almeida, Suchintak Dash, Vinodh Kandavalli, Andre S. Ribeiro
2020 J jnl
Stochastic models coupling gene expression and partitioning in cell division in
Biosyst.
Ines S. C. Baptista, Andre S. Ribeiro
2019 — conf
Mean and Variability in RNA Polymerase Numbers Are Correlated to the Mean but Not the Variability in Size and Composition of Escherichia Coli Cells.
BIOINFORMATICS
Bilena Almeida, Vatsala Chauhan, Vinodh Kandavalli, Andre S. Ribeiro
2018 — conf
Modeling and Engineering Promoters with Pre-defined RNA Production Dynamics in Escherichia Coli.
CMSB
Samuel M. D. Oliveira, Mohamed N. M. Bahrudeen, Sofia Startceva, Vinodh Kandavalli, Andre S. Ribeiro
2018 J jnl
SCIP: a single-cell image processor toolbox.
Bioinform.
Leonardo Martins, Ramakanth Neeli-Venkata, Samuel M. D. Oliveira, Antti Häkkinen, Andre S. Ribeiro, José M. Fonseca
2017 — conf
Automatic Classification of Z-ring Formation Stages at the Single Cell Level in Escherichia Coli by Machine Learning.
BIOIMAGING
Marzieh Zare, Ramakanth Neeli-Venkata, Leonardo Martins, Sari Peltonen, Ulla Ruotsalainen, Andre S. Ribeiro
2017 — conf
Effects of Extrinsic Noise are Promoter Kinetics Dependent.
ICBBT
Mohamed N. M. Bahrudeen, Sofia Startceva, Andre S. Ribeiro
2017 — conf
Estimating Effects of Extrinsic Noise on Model Genes and Circuits with Empirically Validated Kinetics.
WIVACE
Samuel M. D. Oliveira, Mohamed N. M. Bahrudeen, Sofia Startceva, Andre S. Ribeiro
2017 — conf
Tuning extrinsic noise effects on a small genetic circuit.
ECAL
Mohamed N. M. Bahrudeen, Andre S. Ribeiro
2017 J jnl
sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters.
BMC Bioinform.
Shailesh Tripathi, Jason Lloyd-Price, Andre S. Ribeiro, Olli Yli-Harja, Matthias Dehmer, Frank Emmert-Streib
2016 C conf
An Image Generator Platform to Improve Cell Tracking Algorithms - Simulation of Objects of Various Morphologies, Kinetics and Clustering.
SIMULTECH
Pedro Canelas, Leonardo Martins, André Mora, Andre S. Ribeiro, José Manuel Fonseca
2016 J jnl
Characterizing rate limiting steps in transcription from RNA production times in live cells.
Bioinform.
Antti Häkkinen, Andre S. Ribeiro
2016 — conf
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.
SIMULTECH (Selected Papers)
Leonardo Martins, Pedro Canelas, André Mora, Andre S. Ribeiro, José Manuel Fonseca
2016 — conf
Quantitative Estimation of Long-living Fluorescent Molecules from Temporal Fluorescence Intensity Data Corrupted by Nonzero-mean Noise.
BIOSIGNALS
Sofia Startceva, Jerome G. Chandraseelan, Ari Visa, Andre S. Ribeiro
2016 — conf
Robustness to Sub-optimal Temperatures of the Processes of Tsr Cluster Formation and Positioning in Escherichia Coli.
BIOINFORMATICS
Teppo Annila, Ramakanth Neeli-Venkata, Andre S. Ribeiro
2016 J jnl
Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements.
PLoS Comput. Biol.
Samuel M. D. Oliveira, Antti Häkkinen, Jason Lloyd-Price, Huy Tran, Vinodh Kandavalli, Andre S. Ribeiro
2015 — conf
Detecting and Tracking the Tips of Fluorescently Labeled Mitochondria in U2OS Cells.
ICIAP (2)
Eero Lihavainen, Jarno Mäkelä, Johannes N. Spelbrink, Andre S. Ribeiro
2015 J jnl
Estimation of GFP-tagged RNA numbers from temporal fluorescence intensity data.
Bioinform.
Antti Häkkinen, Andre S. Ribeiro
2014 J jnl
Estimation of fluorescence-tagged RNA numbers from spot intensities.
Bioinform.
Antti Häkkinen, Meenakshisundaram Kandhavelu, Stefania Garasto, Andre S. Ribeiro
2014 — conf
Modelling Polar Retention of Complexes in Escherichia coli.
CMSB
Abhishekh Gupta, Jason Lloyd-Price, Andre S. Ribeiro
2013 J jnl
Cell segmentation by multi-resolution analysis and maximum likelihood estimation (MAMLE).
BMC Bioinform.
Sharif Chowdhury, Meenakshisundaram Kandhavelu, Olli Yli-Harja, Andre S. Ribeiro
2013 J jnl
CellAging: a tool to study segregation and partitioning in division in cell lineages of
Bioinform.
Antti Häkkinen, Anantha Barathi Muthukrishnan, André Mora, José Manuel Fonseca, Andre S. Ribeiro
2013 — conf
Effects of inducer intake kinetics on the dynamics of gene expression.
ECAL
Huy Tran, Andre S. Ribeiro
2013 J jnl
Effects of multimerization on the temporal variability of protein complex abundance.
BMC Syst. Biol.
Antti Häkkinen, Huy Tran, Olli Yli-Harja, Brian P. Ingalls, Andre S. Ribeiro
2013 J jnl
ZebIAT, an image analysis tool for registering zebrafish embryos and quantifying cancer metastasis.
BMC Bioinform.
Teppo Annila, Eero Lihavainen, Ines J. Marques, Darren R. Williams, Olli Yli-Harja, Andre S. Ribeiro
2012 J jnl
Detecting sequence dependent transcriptional pauses from RNA and protein number time series.
BMC Bioinform.
Frank Emmert-Streib, Antti Häkkinen, Andre S. Ribeiro
2012 J jnl
Effects of gene length on the dynamics of gene expression.
Comput. Biol. Chem.
Andre S. Ribeiro, Antti Häkkinen, Jason Lloyd-Price
2012 J jnl
Evolving kinetics of gene expression in stochastic environments.
Comput. Biol. Chem.
Antti Häkkinen, Andre S. Ribeiro
2012 — conf
Expressive Statistical Model Checking of Genetic Networks with Delayed Stochastic Dynamics.
CMSB
Paolo Ballarini, Jarno Mäkelä, Andre S. Ribeiro
2012 J jnl
Mytoe: automatic analysis of mitochondrial dynamics.
Bioinform.
Eero Lihavainen, Jarno Mäkelä, Johannes N. Spelbrink, Andre S. Ribeiro
2012 J jnl
SGNS2: a compartmentalized stochastic chemical kinetics simulator for dynamic cell populations.
Bioinform.
Jason Lloyd-Price, Abhishekh Gupta, Andre S. Ribeiro
2012 — conf
Sequence Dependent Properties of the Expression Dynamics of Genes and Gene Networks.
CMSB
Ilya Potapov, Jarno Mäkelä, Olli Yli-Harja, Andre S. Ribeiro
2011 J jnl
Automatic detection of changes in the dynamics of delayed stochastic gene networks and
Bioinform.
Jarno Mäkelä, Heikki Huttunen, Meenakshisundaram Kandhavelu, Olli Yli-Harja, Andre S. Ribeiro
2011 J jnl
Diversity of temporal correlations between genes in models of noisy and noiseless gene networks.
Biosyst.
Andre S. Ribeiro, Jason Lloyd-Price, Sharif Chowdhury, Olli Yli-Harja
2011 J jnl
Evolutionary Dynamics of a Population of Cells with a Toxin Suppressor Gene.
Trans. Comp. Sys. Biology
Antti Häkkinen, Fred G. Biddle, Olli-Pekka Smolander, Olli Yli-Harja, Andre S. Ribeiro
2011 J jnl
In vivo kinetics of transcription initiation of the lar promoter in Escherichia coli. Evidence for a sequential mechanism with two rate-limiting steps.
BMC Syst. Biol.
Meenakshisundaram Kandhavelu, Henrik Mannerström, Abhishekh Gupta, Antti Häkkinen, Jason Lloyd-Price, Olli Yli-Harja, Andre S. Ribeiro
2011 J jnl
Inference of Kinetic Parameters of Delayed Stochastic Models of Gene Expression Using a Markov Chain Approximation.
EURASIP J. Bioinform. Syst. Biol.
Henrik Mannerström, Olli Yli-Harja, Andre S. Ribeiro
2011 J jnl
Stochastic sequence-level model of coupled transcription and translation in prokaryotes.
BMC Bioinform.
Jarno Mäkelä, Jason Lloyd-Price, Olli Yli-Harja, Andre S. Ribeiro
2010 J jnl
Dynamic Agent-Based Model of Hand-Preference Behavior Patterns in the Mouse.
Adapt. Behav.
Andre S. Ribeiro, Jason Lloyd-Price, Brenda A. Eales, Fred G. Biddle
2010 J jnl
Dynamical effects of transcriptional pause-prone sites.
Comput. Biol. Chem.
Andre S. Ribeiro, Antti Häkkinen, Shannon Healy, Olli Yli-Harja
2010 J jnl
Effects of Transcriptional Pausing on Gene Expression Dynamics.
PLoS Comput. Biol.
Tiina Rajala, Antti Häkkinen, Shannon Healy, Olli Yli-Harja, Andre S. Ribeiro
2010 — ch.
Information Flow in Systems of Interacting Agents as a Function of Local and Global Topological Features.
Computational Social Network Analysis
Andre S. Ribeiro
2010 J jnl
Information propagation within the Genetic Network of Saccharomyces cerevisiae.
BMC Syst. Biol.
Sharif Chowdhury, Jason Lloyd-Price, Olli-Pekka Smolander, Wayne C. V. Baici, Timothy R. Hughes, Olli Yli-Harja, Gordon Chua, Andre S. Ribeiro
2009 J jnl
Delayed Stochastic Model of Transcription at the Single Nucleotide Level.
J. Comput. Biol.
Andre S. Ribeiro, Olli-Pekka Smolander, Tiina Rajala, Antti Häkkinen, Olli Yli-Harja
2009 J jnl
Determining noisy attractors of delayed stochastic gene regulatory networks from multiple data sources.
Bioinform.
Xiaofeng Dai, Olli Yli-Harja, Andre S. Ribeiro
2008 — conf
Optimize Observational Time Points to Maximize the Inferability of Gene Networks.
BIOCOMP
Frank Emmert-Streib, Andre S. Ribeiro
2007 J jnl
SGN Sim, a Stochastic Genetic Networks Simulator.
Bioinform.
Andre S. Ribeiro, Jason Lloyd-Price
2006 J jnl
A General Modeling Strategy for Gene Regulatory Networks with Stochastic Dynamics.
J. Comput. Biol.
Andre S. Ribeiro, Rui Zhu, Stuart A. Kauffman