Andre S. Ribeiro

Publication Activity (10 Years)

Years Active: 2006-2022
Publications (10 Years): 18

Top Topics

Escherichia Coli

Top Venues

Publications

Vatsala Chauhan, Mohamed N. M. Bahrudeen, Cristina S. D. Palma, Ines S. C. Baptista, Bilena Almeida, Suchintak Dash, Vinodh Kandavalli, Andre S. Ribeiro
Analytical kinetic model of native tandem promoters in E. coli. PLoS Comput. Biol. 18 (1) (2022)
Ines S. C. Baptista, Andre S. Ribeiro
. Biosyst. (2020)
Bilena Almeida, Vatsala Chauhan, Vinodh Kandavalli, Andre S. Ribeiro
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 (2019)
Samuel M. D. Oliveira, Mohamed N. M. Bahrudeen, Sofia Startceva, Vinodh Kandavalli, Andre S. Ribeiro
Modeling and Engineering Promoters with Pre-defined RNA Production Dynamics in Escherichia Coli. CMSB (2018)
Leonardo Martins, Ramakanth Neeli-Venkata, Samuel M. D. Oliveira, Antti Häkkinen, Andre S. Ribeiro, José M. Fonseca
SCIP: a single-cell image processor toolbox. Bioinform. 34 (24) (2018)
Marzieh Zare, Ramakanth Neeli-Venkata, Leonardo Martins, Sari Peltonen, Ulla Ruotsalainen, Andre S. Ribeiro
Automatic Classification of Z-ring Formation Stages at the Single Cell Level in Escherichia Coli by Machine Learning. BIOIMAGING (2017)
Mohamed N. M. Bahrudeen, Sofia Startceva, Andre S. Ribeiro
Effects of Extrinsic Noise are Promoter Kinetics Dependent. ICBBT (2017)
Samuel M. D. Oliveira, Mohamed N. M. Bahrudeen, Sofia Startceva, Andre S. Ribeiro
Estimating Effects of Extrinsic Noise on Model Genes and Circuits with Empirically Validated Kinetics. WIVACE (2017)
Mohamed N. M. Bahrudeen, Andre S. Ribeiro
Tuning extrinsic noise effects on a small genetic circuit. ECAL (2017)
Shailesh Tripathi, Jason Lloyd-Price, Andre S. Ribeiro, Olli Yli-Harja, Matthias Dehmer, Frank Emmert-Streib
sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters. BMC Bioinform. 18 (1) (2017)
Teppo Annila, Ramakanth Neeli-Venkata, Andre S. Ribeiro
Robustness to Sub-optimal Temperatures of the Processes of Tsr Cluster Formation and Positioning in Escherichia Coli. BIOINFORMATICS (2016)
Antti Häkkinen, Andre S. Ribeiro
Characterizing rate limiting steps in transcription from RNA production times in live cells. Bioinform. 32 (9) (2016)
Sofia Startceva, Jerome G. Chandraseelan, Ari Visa, Andre S. Ribeiro
Quantitative Estimation of Long-living Fluorescent Molecules from Temporal Fluorescence Intensity Data Corrupted by Nonzero-mean Noise. BIOSIGNALS (2016)
Samuel M. D. Oliveira, Antti Häkkinen, Jason Lloyd-Price, Huy Tran, Vinodh Kandavalli, Andre S. Ribeiro
Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements. PLoS Comput. Biol. 12 (10) (2016)
Pedro Canelas, Leonardo Martins, André Mora, Andre S. Ribeiro, José Manuel Fonseca
An Image Generator Platform to Improve Cell Tracking Algorithms - Simulation of Objects of Various Morphologies, Kinetics and Clustering. SIMULTECH (2016)
Leonardo Martins, Pedro Canelas, André Mora, Andre S. Ribeiro, José Manuel Fonseca
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) (2016)
Eero Lihavainen, Jarno Mäkelä, Johannes N. Spelbrink, Andre S. Ribeiro
Detecting and Tracking the Tips of Fluorescently Labeled Mitochondria in U2OS Cells. ICIAP (2) (2015)
Antti Häkkinen, Andre S. Ribeiro
Estimation of GFP-tagged RNA numbers from temporal fluorescence intensity data. Bioinform. 31 (1) (2015)
Abhishekh Gupta, Jason Lloyd-Price, Andre S. Ribeiro
Modelling Polar Retention of Complexes in Escherichia coli. CMSB (2014)
Antti Häkkinen, Meenakshisundaram Kandhavelu, Stefania Garasto, Andre S. Ribeiro
Estimation of fluorescence-tagged RNA numbers from spot intensities. Bioinform. 30 (8) (2014)
Teppo Annila, Eero Lihavainen, Ines J. Marques, Darren R. Williams, Olli Yli-Harja, Andre S. Ribeiro
ZebIAT, an image analysis tool for registering zebrafish embryos and quantifying cancer metastasis. BMC Bioinform. 14 (S-10) (2013)
Antti Häkkinen, Anantha Barathi Muthukrishnan, André Mora, José Manuel Fonseca, Andre S. Ribeiro
. Bioinform. 29 (13) (2013)
Sharif Chowdhury, Meenakshisundaram Kandhavelu, Olli Yli-Harja, Andre S. Ribeiro
Cell segmentation by multi-resolution analysis and maximum likelihood estimation (MAMLE). BMC Bioinform. 14 (S-10) (2013)
Huy Tran, Andre S. Ribeiro
Effects of inducer intake kinetics on the dynamics of gene expression. ECAL (2013)
Antti Häkkinen, Huy Tran, Olli Yli-Harja, Brian P. Ingalls, Andre S. Ribeiro
Effects of multimerization on the temporal variability of protein complex abundance. BMC Syst. Biol. 7 (S-1) (2013)
Andre S. Ribeiro, Antti Häkkinen, Jason Lloyd-Price
Effects of gene length on the dynamics of gene expression. Comput. Biol. Chem. 41 (2012)
Ilya Potapov, Jarno Mäkelä, Olli Yli-Harja, Andre S. Ribeiro
Sequence Dependent Properties of the Expression Dynamics of Genes and Gene Networks. CMSB (2012)
Jason Lloyd-Price, Abhishekh Gupta, Andre S. Ribeiro
SGNS2: a compartmentalized stochastic chemical kinetics simulator for dynamic cell populations. Bioinform. 28 (22) (2012)
Eero Lihavainen, Jarno Mäkelä, Johannes N. Spelbrink, Andre S. Ribeiro
Mytoe: automatic analysis of mitochondrial dynamics. Bioinform. 28 (7) (2012)
Abhishekh Gupta, Jason Lloyd-Price, Andre S. Ribeiro
populations as a function of the partitioning scheme of non-functional proteins. Silico Biol. 12 (1-2) (2012)
Paolo Ballarini, Jarno Mäkelä, Andre S. Ribeiro
Expressive Statistical Model Checking of Genetic Networks with Delayed Stochastic Dynamics. CMSB (2012)
Antti Häkkinen, Andre S. Ribeiro
Evolving kinetics of gene expression in stochastic environments. Comput. Biol. Chem. 37 (2012)
Frank Emmert-Streib, Antti Häkkinen, Andre S. Ribeiro
Detecting sequence dependent transcriptional pauses from RNA and protein number time series. BMC Bioinform. 13 (2012)
Antti Häkkinen, Fred G. Biddle, Olli-Pekka Smolander, Olli Yli-Harja, Andre S. Ribeiro
Evolutionary Dynamics of a Population of Cells with a Toxin Suppressor Gene. Trans. Comp. Sys. Biology 13 (2011)
Jarno Mäkelä, Heikki Huttunen, Meenakshisundaram Kandhavelu, Olli Yli-Harja, Andre S. Ribeiro
. Bioinform. 27 (19) (2011)
Meenakshisundaram Kandhavelu, Henrik Mannerström, Abhishekh Gupta, Antti Häkkinen, Jason Lloyd-Price, Olli Yli-Harja, Andre S. Ribeiro
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. 5 (2011)
Jarno Mäkelä, Jason Lloyd-Price, Olli Yli-Harja, Andre S. Ribeiro
Stochastic sequence-level model of coupled transcription and translation in prokaryotes. BMC Bioinform. 12 (2011)
Henrik Mannerström, Olli Yli-Harja, Andre S. Ribeiro
Inference of Kinetic Parameters of Delayed Stochastic Models of Gene Expression Using a Markov Chain Approximation. EURASIP J. Bioinform. Syst. Biol. 2011 (2011)
Andre S. Ribeiro, Jason Lloyd-Price, Sharif Chowdhury, Olli Yli-Harja
Diversity of temporal correlations between genes in models of noisy and noiseless gene networks. Biosyst. 104 (2-3) (2011)
Sharif Chowdhury, Jason Lloyd-Price, Olli-Pekka Smolander, Wayne C. V. Baici, Timothy R. Hughes, Olli Yli-Harja, Gordon Chua, Andre S. Ribeiro
Information propagation within the Genetic Network of Saccharomyces cerevisiae. BMC Syst. Biol. 4 (2010)
Andre S. Ribeiro, Jason Lloyd-Price, Brenda A. Eales, Fred G. Biddle
Dynamic Agent-Based Model of Hand-Preference Behavior Patterns in the Mouse. Adapt. Behav. 18 (2) (2010)
Andre S. Ribeiro, Antti Häkkinen, Shannon Healy, Olli Yli-Harja
Dynamical effects of transcriptional pause-prone sites. Comput. Biol. Chem. 34 (3) (2010)
Tiina Rajala, Antti Häkkinen, Shannon Healy, Olli Yli-Harja, Andre S. Ribeiro
Effects of Transcriptional Pausing on Gene Expression Dynamics. PLoS Comput. Biol. 6 (3) (2010)
Andre S. Ribeiro, Olli-Pekka Smolander, Tiina Rajala, Antti Häkkinen, Olli Yli-Harja
Delayed Stochastic Model of Transcription at the Single Nucleotide Level. J. Comput. Biol. 16 (4) (2009)
Xiaofeng Dai, Olli Yli-Harja, Andre S. Ribeiro
Determining noisy attractors of delayed stochastic gene regulatory networks from multiple data sources. Bioinform. 25 (18) (2009)
Frank Emmert-Streib, Andre S. Ribeiro
Optimize Observational Time Points to Maximize the Inferability of Gene Networks. BIOCOMP (2008)
Andre S. Ribeiro, Daniel A. Charlebois, Jason Lloyd-Price
, a stochastic cell lineage simulator. Bioinform. 23 (24) (2007)
Andre S. Ribeiro, Jason Lloyd-Price
SGN Sim, a Stochastic Genetic Networks Simulator. Bioinform. 23 (6) (2007)
Andre S. Ribeiro, Rui Zhu, Stuart A. Kauffman
A General Modeling Strategy for Gene Regulatory Networks with Stochastic Dynamics. J. Comput. Biol. 13 (9) (2006)