Andre S. Ribeiro (andre.ribeiro AxT tut.fi)

Assist Professor, Computational Systems Biology Research Group, Tampere University of Technology, Finland.

Head of Laboratory of Biosystem Dynamics, CSB, Dept. Signal Processing, Tampere Univ. of Technology.

Recent news:

New Laboratory of cell and molecular biology at the Dept. of Signal Processing

Book: Information Processing and Biological Systems, Series: Intelligent Systems Reference Library, Vol. 11
Niiranen, Samuli; Ribeiro, Andre (Eds.). 1st Ed. 2011. ISBN: 978-3-642-19620-1

http://www.springer.com/engineering/mathematical/book/978-3-642-19620-1

Information propagation and processing pervades biological systems. This book includes chapters on how the processing of information in biological processes is currently understood in various topics, ranging from information processing and propagation in gene regulatory networks to information processing in biological olfaction and natural language. We aim at presenting an overview on the state-of-art on how information processing relates to biological systems and the opinion of current leaders in the field on future directions of research.

Courses:

SGN-6236 Modeling Techniques for Stochastic Gene Regulatory Networks period 1, 3 cr

SGN-6237 Techniques in Molecular Biology and Applications to Gene Expression period 4, 3 cr

SGN-6126 Cell culturing, microscopy and cell image analysis period 2, 3 cr

SGN-6906 Seminar on Signal Processing for Systems Biology period 1-4, 2-3 cr

SGN-6186 Mathematical Modelling of Cellular Systems period 1, 5 cr

SGN-6058 Introduction to Biology of the Cell period 3, 3 cr

SGN-6457 Computational Models in Complex Systems period 4, 5 cr

Research Interests

Gene Regulatory Networks, Stochasticity and Phenotypic diversity, Inference of structure and kinetics of underlying processes in gene expression , Information propagation in networks, Adaptability, Mouse Learning and Paw Preference, Cell Aging.

Recent Publications in Peer-reviewed Journals

2012

.E. Lihavainen, J. Mäkelä, J.N. Spelbrink, and A.S. Ribeiro (2012) Mytoe: Automatic analysis of mitochondrial dynamics. Bioinformatics, in press.

.S. Chowdhury, M. Kandhavelu, O. Yli-Harja and A.S. Ribeiro (2012) An interacting multiple model filter based autofocus strategy for confocal time-lapse microscopy. Journal of Microscopy, in press.

.J. Lloyd-Price, M. Lehtivaara, M. Kandhavelu, S. Chowdhury, A.-B. Muthukrishnan, O. Yli-Harja and A.S. Ribeiro (2012) Probabilistic RNA partitioning generates transient increases in the normalized variance of RNA numbers in synchronized populations of Escherichia coli. Mol. BioSyst., 2012, 8(2), 565–571.

.M. Kandhavelu, E. Lihavainen, A.-B. Muthukrishnan, O. Yli-Harja, and A. S. Ribeiro (2012) Effects of Mg2+ on in vivo transcriptional dynamics of the lar Promoter. Biosystems, in press.

.J. Lloyd-Price, A. Häkkinen, M. Kandhavelu, I.J. Marques, S. Chowdhury, E. Lihavainen, O. Yli-Harja, and A.S. Ribeiro (2012) Asymmetric disposal of individual protein aggregates in Escherichia coli, one aggregate at a time. Journal of Bacteriology, in press.

2011

M Kandhavelu, H Mannerstrom, O Yli-Harja, and AS Ribeiro (2011) In vivo kinetics of transcription initiation of the lar promoter in Escherichia coli. Evidence for a sequential mechanism with two rate limiting steps. BMC Systems Biology 5:149

J Mäkelä, H Huttunen, M Kandhavelu, O Yli-Harja and AS Ribeiro (2011) Automatic detection of changes in the dynamics of delayed stochastic gene networks and in vivo production of RNA molecules in Escherichia coli. Bioinformatics, 27: 2714-2720

I Potapov, J Lloyd-Price, O Yli-Harja, and AS Ribeiro (2011). Dynamics of a genetic toggle switch at the nucleotide and codon levels. Phys Rev E. 84(3).

O-P Smolander, M Kandhavelu, H Mannerstrom, E Lihavainen, S. Kalaichelvan, S Healy, O Yli-Harja, M Karp, and AS Ribeiro (2011) Cell-to-cell diversity in protein levels of a gene driven by a tetracycline inducible promoter. BMC Molecular Biology 2011, 12:21

A. Hakkinen, S. Healy, HT Jacobs, and AS Ribeiro (2011) Genome wide study of NF-Y type CCAAT boxes in uni- and bi-directional promoters in human and mouse, J. of Theoretical Biology 281, 74-83.

J. Mäkelä, J. Lloyd-Price, O. Yli-Harja, A.S. Ribeiro (2011) Stochastic sequence-level model of coupled transcription and translation in prokaryotes. BMC Bioinformatics 2011, 12:121 doi:10.1186/1471-2105-12-121.

AS Ribeiro and A Hakkinen (2011) Probing Stochastic Phenotype Switching as a Survival Strategy in Fluctuating Environments, International Journal of Computational Intelligence in Control (IJCIC), Vol3. No. 1, Jan-Jun 2011.

A.S. Ribeiro, J. Lloyd-Price, S. Chowdhury, O. Yli-Harja, (2011) Diversity of temporal correlations between genes in models of noisy and noiseless gene networks. Biosystems, 104, pp. 136-144.

A. Häkkinen, F.G. Biddle, O-P. Smolander, O. Yli-Harja, and A. S. Ribeiro (2011) Evolutionary Dynamics of a Population of Cells with a Toxin Suppressor Gene, Lecture Notes in Computer Science 6575 LNBI, pp. 1-12, Springer 2011.

H. Mannerström, O. Yli-Harja, and A.S. Ribeiro (2011) Inference of kinetic parameters of delayed stochastic models of gene expression using a Markov chain approximation. EURASIP Journal on Bioinformatics and Systems Biology, vol. 2011, Article ID 572876, 5 pages. doi:10.1155/2011/572876.

A. S. Ribeiro, B. A. Eales and F. G. Biddle, (2011) Learning of paw preference in mice is strain dependent, gradual and based on short-term memory of previous reaches, Animal Behavior, 81(1), 249-257.

2010 and before

S. Chowdhury, J. Lloyd-Price, O-P. Smolander, W. Baici, T.R. Hughes, O. Yli-Harja, G. Chua and A. S Ribeiro (2010) Information propagation within the Genetic Network of Saccharomyces cerevisiae. BMC Systems Biology 2010, 4:143.

T Rajala, A Häkkinen, S Healy, O Yli-Harja and AS Ribeiro, (2010) Effects of Transcriptional Pausing upon Gene Expression Dynamics, PLOS Comput Bio 6(3): e1000704.

AS Ribeiro, J Lloyd-Price, B Eales, FG Biddle (2010) Dynamic Agent-Based Model of Hand-Preference Behavior Patterns in the Mouse, Adapt. Beh. 18(2), 116-31.

A. S. Ribeiro, A. Häkkinen, H. Mannerstrom, J. Lloyd-Price, O. Yli-Harja (2010) Effects of the promoter open complex formation on gene expression dynamics, Phys Rev E 81(1), 011912.

AS Ribeiro (2010) Stochastic and delayed stochastic models of gene expression and regulation, Math. Biosciences, 223(1), 1-11 (invited review article).

E Zanotto, A Häkkinen, G Teku, B Shen, AS Ribeiro, and HT Jacobs (2009) NF-Y enforces directionality of transcription from the bidirectional Mrps12/Sarsm promoter in both mouse and human cells. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1789(5), 432-442.

AS Ribeiro, O-P Smolander, T. Rajala, A. Hakkinen, O. Yli-Harja (2009) Delayed stochastic model of transcription at the single nucleotide level, Journal of Computational Biology 16(4), 539-553.

AS Ribeiro, J. Lloyd-Price, J. Kesseli, A. Hakkinen, O. Yli-Harja (2008), Quantifying Local Structure Effects in Network Dynamics, Phys. Rev. E 78(5), 056108.

AS Ribeiro (2008) Dynamics and evolution of stochastic bistable gene networks with sensing in fluctuating environments, Phys. Rev. E 78(6), 061902.

A S. Ribeiro, SA Kauffman, J Lloyd-Price, B Samuelsson, and J Socolar, (2008) Mutual Information in Random Boolean models of regulatory networks, Phys. Rev. E 77(1).

A.S. Ribeiro (2007) Dynamics of a two-dimensional model of cell tissues with coupled stochastic gene networks, Phys. Rev. E 76(5).

A.S. Ribeiro, D Charlebois, J Lloyd-Price (2007) CellLine A cell lineage simulator Bioinformatics 23(24):3409-3411.

A. S. Ribeiro and J. Lloyd-Price, (2007) SGN Sim, a Stochastic Genetic Networks Simulator, Bioinformatics 23(6):777-779.

A.S. Ribeiro (2007), Effects of coupling strength and space on the dynamics of coupled toggle switches in stochastic gene networks with multiple-delayed reactions, Physical Review E 75(6).

A.S. Ribeiro and S.A. Kauffman (2007), Noisy Attractors and Ergodic Sets in Models of Gene Regulatory Networks, J. of Theoretical Biology 247(4), 743-755.

R Zhu, A.S. Ribeiro, D. Salahub, and S.A. Kauffman (2007) Studying genetic regulatory networks at the molecular level: Delayed reaction stochastic models, Journal of Theoretical Biology, 246(4):725-45.

A.S. Ribeiro, R. Zhu, S.A. Kauffman (2006), A General Modeling Strategy for Gene Regulatory Networks with Stochastic Dynamics, J. of Comput Biol 13(9).

Peer-reviewed Book Chapters:

A. Hakkinen, F.G. Biddle, O-P. Smolander, O. Yli-Harja, and A. S. Ribeiro (2011) Evolutionary Dynamics of a Population of Cells with a Toxin Suppressor Gene, Lecture Notes in Computer Science, Vol. 6575, subseries Transactions on Computational Systems Biology. 193 p., ISBN: 978-3-642-19747-5

A.S. Ribeiro and J. Lloyd-Price (2011) Information Propagation in the Long-Term Behavior of Gene Regulatory Networks, in Information Processing and Biological Systems, Editors: Samuli Niiranen and Andre S. Ribeiro, Springer-Verlag. In press.

A.S. Ribeiro (2011) Delayed stochastic models of genetic switches. Noise, coupling, differentiation patterns and evolvability in Advances in Genetics Research., Volume 6, edited by Kevin V. Urbano, Nova Science Publishers. In press. ISBN: 978-1-61209-793-0.

A.S. Ribeiro, (2010) Information Flow in Systems of Interacting Agents as a Function of Local and Global Topological Features, in Computational Social Networks Analysis: Trends, Tools and Research Advance, edited by A.-E. Hassanien, A. Abraham, V. Snášel, edited by Springer-Verlag, 2010, XII, pg. 155-187, ISBN: 978-1-84882-228-3

J. Kesseli, A.S. Ribeiro, M. Nykter (2009) Measuring Information Propagation and Processing in Biological Systems, in Open Information Management: Applications of Interconnectivity and Collaboration, Information Science Publishing 2009-05-31. Editor Samuli Niiranen, ISBN 1605662461.

A.S. Ribeiro, J. Grefenstette, S.A. Kauffman (2009) Modeling Gene Regulatory Networks with Delayed Stochastic Dynamics, in Handbook of Research on Computational Methodologies in Gene Regulatory Networks, Editors: Sanjoy Das, Doina Caragea, W. H. Hsu, Stephen M. Welch, Kansas State University, USA. IGI Global.

A.S. Ribeiro (2007) A Model of Genetic Networks with Delayed Stochastic Dynamics, in Analysis of Microarray Data: Network based Approaches, pages 167-199. Wiley, M. Dehmer and F. Emmert-Streib (Editors).

Supervised Theses:

Bachelors

. A. Häkkinen, DNA-sekvenssien Etmininen ja löydösten merkitysen analysointi, Dept. of Signal Processing, Tampere Univ. of Technology, Finland. April 2008. Supervisor: A. S. Ribeiro.

Masters

. J. Lloyd-Price, Simulating Stochastic Chemical Kinetics with Dynamics Compartmentalization at Runtime, Dept. of Signal Processing, Tampere University of Technology, Finland. May, 2011. Supervisors: A. S. Ribeiro and O. Yli-Harja.

. J. Mäkelä Dynamics of stochastic sequence-level models of transcription and translation in prokaryotes, Dept. of Signal Processing, Tampere University of Technology, Finland. May, 2011. Supervisors: A. S. Ribeiro and O. Yli-Harja.

. E. Lihavainen, Msc Thesis, Analysis of Mitochondrial motion and structure in confocal time-lapse microscopy. Dept. of Signal Processing, Tampere University of Technology, Finland. May, 2011. Supervisors: A. S. Ribeiro and O. Yli-Harja.

. A. Häkkinen, Msc Thesis, Simulating Evolutionary Processes of Stochastic Genetic Networks in Volatile Environments. Dept. of Signal Processing, Tampere University of Technology, Finland. Nov., 2011. Supervisors: A.S. Ribeiro and O. Yli-Harja.

. L. P. V. Martins, Msc Thesis, Stochastic model of transcription initiation at the nucleotide level of Escherichia coli bidirectional promoters. Universidade Nova de Lisboa, Portugal. Dec. 2011. Supervisors: Jose Manuel Fonseca and Andre S. Ribeiro.

PhD

. X. Dai, PhD Thesis, Data Fusion Methods and Applications on Exploration of Gene Regulatory Mechanisms Dept. of Signal Processing, Tampere University of Technology, Finland. January 12th, 2010. Supervisor: O. Yli-Harja, Co-supervisors: H. Lähdesmäki and A. S. Ribeiro.

. O.-P. Smolander, PhD Thesis, Data Fusion Methods and Applications on Exploration of Gene Regulatory Mechanisms Dept. of Signal Processing, Tampere University of Technology, Finland. June 30th, 2011. Supervisors: O. Yli-Harja, Co-supervisors: M. Karp and A.S. Ribeiro.

Ongoing collaborations:

Fred Biddle, Univ Calgary, Canada. Howard Jacobs, IBT, UTA, Finland.

Hans Spelbrink, IBT, UTA, Finland. Matti Karp, TUT, Finland.

Frank Emmert-Streib, Univ. Belfast, UK, Jose Fonseca (FCT/UNL), Portugal.

Links:

http://www.cs.tut.fi/~sanchesr/CellLine/CellLine.html(CellLine)

http://www.cs.tut.fi/~sanchesr/SGN/SGNSim.html (SGN Sim)

Jan 12, 2012.