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ORCIDAndre S. Ribeiro
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2020 – today
- 2022
[j34]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)- 2020
- [j33]Ines S. C. Baptista, Andre S. Ribeiro:
Stochastic models coupling gene expression and partitioning in cell division in Escherichia coli. Biosyst. 193-194: 104154 (2020)
2010 – 2019
- 2019
- [c16]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: 226-233 - 2018
- [j32]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): 4318-4320 (2018) - [c15]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: 3-20 - 2017
- [j31]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): 325 (2017) - [c14]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: 72-76 - [c13]Mohamed N. M. Bahrudeen, Andre S. Ribeiro:
Tuning extrinsic noise effects on a small genetic circuit. ECAL 2017: 454-459 - [c12]Mohamed N. M. Bahrudeen, Sofia Startceva, Andre S. Ribeiro:
Effects of Extrinsic Noise are Promoter Kinetics Dependent. ICBBT 2017: 44-47 - [c11]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: 181-193 - 2016
- [j30]Antti Häkkinen, Andre S. Ribeiro:
Characterizing rate limiting steps in transcription from RNA production times in live cells. Bioinform. 32(9): 1346-1352 (2016) - [j29]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) - [c10]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: 17-24 - [c9]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: 137-141 - [c8]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: 44-55 - [c7]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: 52-74 - 2015
- [j28]Antti Häkkinen, Andre S. Ribeiro:
Estimation of GFP-tagged RNA numbers from temporal fluorescence intensity data. Bioinform. 31(1): 69-75 (2015) - [c6]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: 363-372 - 2014
- [j27]Antti Häkkinen, Meenakshisundaram Kandhavelu, Stefania Garasto, Andre S. Ribeiro:
Estimation of fluorescence-tagged RNA numbers from spot intensities. Bioinform. 30(8): 1146-1153 (2014) - [c5]Abhishekh Gupta, Jason Lloyd-Price, Andre S. Ribeiro:
Modelling Polar Retention of Complexes in Escherichia coli. CMSB 2014: 239-243 - 2013
- [j26]Antti Häkkinen, Anantha Barathi Muthukrishnan, André Mora, José Manuel Fonseca, Andre S. Ribeiro:
CellAging: a tool to study segregation and partitioning in division in cell lineages of Escherichia coli. Bioinform. 29(13): 1708-1709 (2013) - [j25]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): S5 (2013) - [j24]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): S8 (2013) - [j23]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): S3 (2013) - [c4]Huy Tran, Andre S. Ribeiro:
Effects of inducer intake kinetics on the dynamics of gene expression. ECAL 2013: 1174-1181 - 2012
- [j22]Eero Lihavainen, Jarno Mäkelä, Johannes N. Spelbrink, Andre S. Ribeiro:
Mytoe: automatic analysis of mitochondrial dynamics. Bioinform. 28(7): 1050-1051 (2012) - [j21]Jason Lloyd-Price, Abhishekh Gupta, Andre S. Ribeiro:
SGNS2: a compartmentalized stochastic chemical kinetics simulator for dynamic cell populations. Bioinform. 28(22): 3004-3005 (2012) - [j20]Meenakshisundaram Kandhavelu, Eero Lihavainen, Anantha Barathi Muthukrishnan, Olli Yli-Harja, Andre Sanches Ribeiro:
Effects of Mg2+ on in vivo transcriptional dynamics of the lar promoter. Biosyst. 107(3): 129-134 (2012) - [j19]Frank Emmert-Streib, Antti Häkkinen, Andre S. Ribeiro:
Detecting sequence dependent transcriptional pauses from RNA and protein number time series. BMC Bioinform. 13: 152 (2012) - [j18]Antti Häkkinen, Andre S. Ribeiro:
Evolving kinetics of gene expression in stochastic environments. Comput. Biol. Chem. 37: 11-16 (2012) - [j17]Andre S. Ribeiro, Antti Häkkinen, Jason Lloyd-Price:
Effects of gene length on the dynamics of gene expression. Comput. Biol. Chem. 41: 1-9 (2012) - [j16]Abhishekh Gupta, Jason Lloyd-Price, Andre S. Ribeiro:
In silico analysis of division times of Escherichia coli populations as a function of the partitioning scheme of non-functional proteins. Silico Biol. 12(1-2) (2012) - [c3]Paolo Ballarini, Jarno Mäkelä, Andre S. Ribeiro:
Expressive Statistical Model Checking of Genetic Networks with Delayed Stochastic Dynamics. CMSB 2012: 29-48 - [c2]Ilya Potapov, Jarno Mäkelä, Olli Yli-Harja, Andre S. Ribeiro:
Sequence Dependent Properties of the Expression Dynamics of Genes and Gene Networks. CMSB 2012: 307-321 - 2011
- [j15]Jarno Mäkelä, Heikki Huttunen, Meenakshisundaram Kandhavelu, Olli Yli-Harja, Andre S. Ribeiro:
Automatic detection of changes in the dynamics of delayed stochastic gene networks and in vivo production of RNA molecules in Escherichia coli. Bioinform. 27(19): 2714-2720 (2011) - [j14]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): 136-144 (2011) - [j13]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: 121 (2011) - [j12]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: 149 (2011) - [j11]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) - [j10]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: 1-12 (2011) - 2010
- [j9]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): 116-131 (2010) - [j8]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: 143 (2010) - [j7]Andre S. Ribeiro, Antti Häkkinen, Shannon Healy, Olli Yli-Harja:
Dynamical effects of transcriptional pause-prone sites. Comput. Biol. Chem. 34(3): 143-148 (2010) - [j6]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) - [p1]Andre S. Ribeiro:
Information Flow in Systems of Interacting Agents as a Function of Local and Global Topological Features. Computational Social Network Analysis 2010: 155-187
2000 – 2009
- 2009
- [j5]Xiaofeng Dai, Olli Yli-Harja, Andre S. Ribeiro:
Determining noisy attractors of delayed stochastic gene regulatory networks from multiple data sources. Bioinform. 25(18): 2362-2368 (2009) - [j4]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): 539-553 (2009) - 2008
- [c1]Frank Emmert-Streib, Andre S. Ribeiro:
Optimize Observational Time Points to Maximize the Inferability of Gene Networks. BIOCOMP 2008: 55-60 - 2007
- [j3]Andre S. Ribeiro, Jason Lloyd-Price:
SGN Sim, a Stochastic Genetic Networks Simulator. Bioinform. 23(6): 777-779 (2007) - [j2]Andre S. Ribeiro, Daniel A. Charlebois, Jason Lloyd-Price:
CellLine, a stochastic cell lineage simulator. Bioinform. 23(24): 3409-3411 (2007) - 2006
- [j1]Andre S. Ribeiro, Rui Zhu, Stuart A. Kauffman:
A General Modeling Strategy for Gene Regulatory Networks with Stochastic Dynamics. J. Comput. Biol. 13(9): 1630-1639 (2006)
Coauthor Index
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