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

Associate Professor (tenure track) and Docent,
Head of Laboratory of Biosystem Dynamics,
Department of Signal Processing,
Tampere University of Technology, Finland Office TC338, Department of Signal Processing, Tampere University of Technology,
P.O Box 553, 33101 Tampere, FINLAND.


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Andre Sanches Ribeiro (CV here) graduated in Physics, University of Lisbon, Portugal in 1999. He has a PhD from IST, University Tecnica de Lisboa, Portugal (2004), where he studied information propagation in networks. From 2004 to 2007, he was a Postdoc at the University of Calgary, Canada, where he developed dynamic models of genetic circuits. Currently, he is the PI of the Laboratory of Biosystem Dynamics (LBD) and an Associate Professor at the Department of Signal Processing, Tampere University of Technology, Finland.

The LBD was established in January 2009. At first, we performed studies on computational and theoretical biology. In 2011, we setup a Cell and Molecular Biology Laboratory, specialized in live single cell imaging, and now we combine theory and measurements in our studies. In particular, we conduct live single-cell, single-molecule microscopy measurements in order to study gene expression and genetic circuits as well as other intracellular processes, for which we perform image and data analysis using methods from Signal Processing, and develop detailed stochastic models and simulators. To achieve this, we have assembled a highly multi-disciplinary group that includes backgrounds in physics, theoretical biology, molecular and cell biology, biotechnology, signal processing, and computer science.


Team


Laboratory of Biosystem Dynamics

Left to right: (1st row) Samuel Oliveira, Andre Ribeiro (PI), Sofia Startceva, Jarno Mäkelä, and Lingyu Zhu. (2nd row) Eero Lihavainen, Ramakanth Neeli, Vinodh Kandavalli, Nadia Goncalves, and Leonardo Martins.

The Laboratory of Biosystem Dynamics (LBD) is an inter-disciplinary research group that employs stochastic modelling of biological systems, in vivo single-cell single-molecule measurements, and signal processing techniques to study cellular processes ranging from transcription, to genetic circuits, to cellular aging.

We work towards characterizing the dynamics of these processes at a quantitative level, identifying the regulatory mechanisms that cells use to achieve it, and understanding their selective advantage. From live, time-lapse, single-cell measurements, we extract empirical data on these processes dynamics by employing tailor-made signal processing techniques and software. Based on the data, we produce stochastic, detailed models of the regulatory mechanisms of the processes that are able to not only match this data, but also allow exploring other possible behaviours of these biological systems, so as to study possible beneficial applications of mimicking synthetic systems.

At present, using Escherichia coli as a model organism, we focus on the regulatory mechanisms of transcription initiation, on the spatial distribution and partitioning in cell division of unwanted protein aggregates linked to cellular aging, on the dynamics of genetic clocks and switches, and on how network structures both constrain and add complexity to the activity of the component genes.


Laboratory


Laboratory of Cell and Molecular Biology at the Department of Signal Processing, Tampere University of Technology

Every cell is an individual, with unique behaviour. Thus, to study cellular processes, we need to observe many live cells. With this aim, new measurement techniques are rapidly emerging. We use methods from Signal Processing to process this information.

A laboratory of cell and molecular biology has been built in 2011 at the Dept. of Signal Processing at Tampere University of Technology. The production of biological data in-house, gives our researchers direct access to new biological measurements for their projects and hands-on experience on Molecular Biology techniques ranging from microscopy to qPCR. Meanwhile, the laboratory also allow us to have courses where students are given access to in-house data as well as the possibility to observe how the data is collected. Thus, aside from studying cellular processes, the lab is also used to boost the development of signal processing methods, such as image analysis, and of models and simulation tools to study biological phenomena.

In vivo detection of RNA molecules, one molecule at a time, in live E. coli cells using the MS2-GFP RNA detection system generously provided by Professor Ido Golding.


Courses


The LBD is presently responsible for the following courses at TUT:

SGN-53206, Cell Culturing, Microscopy and Cell Image Analysis, Period 2, 3 cr

SGN-52406, Models of Gene Networks, Period 1, 3 cr

SGN-53807, Methods in Single Cell Biology, Period 4, 3 cr

SGN-99906, Information Processing and Biological Systems, 4 cr

SGN-99906, The Origins of Order: Self-Organization and Selection in Evolution, 6 cr


Software



Publications


Recent Publications:

    2016

  • C Zimmer, A Häkkinen and AS Ribeiro (2016) Estimation of kinetic parameters of transcription from temporal single-RNA measurements. Math Biosciences. 271, 146–153. DOI: 10.1016/j.mbs.2015.10.001.
  • SMD Oliveira, R Neeli-Venkata, N Goncalves, JA Santinha, L Martins, H Tran, J Mäkelä, A Gupta, M Barandas, A Häkkinen, J Lloyd-Price, JM Fonseca, and AS Ribeiro (2016) Increased cytoplasm viscosity hampers aggregate polar segregation in Escherichia coli. Mol. Microbiol. 99(4), 686–699. DOI: 10.1111/mmi.13257
  • A Häkkinen and AS Ribeiro (2016) Identifying Rate Limiting Steps in Transcription from RNA Production Times in Live Cells. Bioinformatics. 32(9): 1346-1352. DOI: 10.1093/bioinformatics/btv744.
  • R Neeli-Venkata, A Martikainen*, A Gupta*, N Gonçalves*, J Fonseca, and AS Ribeiro (2016) Robustness of the process of nucleoid exclusion of protein aggregates in Escherichia coli. Journal of Bacteriology. 198(6), 898-906. DOI: 10.1128/JB.00848-15
  • J Lloyd-Price, S Startceva, V Kandavalli, JG Chandraseelan, N Goncalves, SMD Oliveira, A Häkkinen and AS Ribeiro (2016) Dissecting the stochastic transcription initiation process in live Escherichia coli. DNA Research. 23 (3): 203-214. DOI: 10.1093/dnares/dsw009
  • VK Kandavalli, H Tran, and AS Ribeiro (2016) Effects of sigma factor competition on the in vivo kinetics of transcription initiation in Escherichia coli. BBA Gene Regulatory Mechanisms. In press.
  • 2015

  • A Gupta, J Lloyd-Price, and AS Ribeiro (2015) In silico analysis of division times of Escherichia coli populations as a function of the partitioning scheme of non-functional proteins. In Silico Biology 1(2), 9-21. DOI: 10.3233/ISB-140462
  • A Häkkinen and AS Ribeiro (2015) Estimation of GFP-tagged RNA numbers from temporal fluorescence intensity data. Bioinformatics 31(1), 69-75. DOI: 10.1093/bioinformatics/btu592.
  • SMD Oliveira*, JG Chandraseelan*, A Häkkinen, NSM Goncalves, Olli Yli-Harja, Sofia Startceva, and AS Ribeiro (2015) Single-cell kinetics of the Repressilator when inserted into a single-copy plasmid. Mol. BioSyst. 11, 1939-1945. *Equal contributions. DOI: 10.1039/C5MB00012B
  • E Lihavainen, M Kislin, D Toptunov, L Khiroug, AS Ribeiro (2015) Automatic quantification of mitochondrial fragmentation from two-photon microscope images of mouse brain tissue. Journal of Microscopy. 260(3), 338-51. DOI: 10.1111/jmi.12301.
  • H Tran, SMD Oliveira, N Goncalves, and AS Ribeiro (2015) Kinetics of the cellular intake of a gene expression inducer at high concentrations. Molecular BioSystems, 11, 2579-2587. DOI: 10.1039/C5MB00244C.
  • 2014

  • A Häkkinen, M Kandhavelu, S Garasto, and AS Ribeiro (2014) Estimation of fluorescence-tagged RNA numbers from spot intensities. Bioinformatics (30(8), 1146-1153.
  • A Gupta, J Lloyd-Price, SMD Oliveira, RN Venkata, and AS Ribeiro (2014) In vivo kinetics of segregation and polar retention of MS2-GFP-RNA complexes in Escherichia coli. Biophysical Journal, 106(9), 1928-1937.
  • J Lloyd-Price, H Tran, and AS Ribeiro (2014) Dynamics of small genetic circuits subject to stochastic partitioning in cell division. J. Theo. Biol. 356, 11-19.
  • A Fukuoh*, G Cannino*, M Gerards, S Buckley, S Kazancioglu, F Scialo, E Lihavainen, AS Ribeiro, E Dufour and HT Jacobs (2014) Screen for mitochondrial DNA copy-number maintenance genes reveals essential role for ATP synthase. Mol. Syst. Biol. 10, 734.
  • A-B Muthukrishnan, A Martikainen, R Neeli-Venkata, and AS Ribeiro (2014) In vivo Transcription Kinetics of a Synthetic Gene Uninvolved in Stress-Response Pathways in Stressed Escherichia coli cells. PLoS ONE 9(9): e109005.
  • AS Ribeiro, BA Eales, J Lloyd-Price, and FG Biddle (2014) Predictability and randomness of paw choices are critical elements in the behavioural plasticity of mouse paw preference. Animal Behavior 98, 167-176.
  • A Gupta, J Lloyd-Price, SMD Oliveira, O Yli-Harja, A-B Muthukrishnan and AS Ribeiro (2014) Robustness of the division symmetry in Escherichia coli and functional consequences of symmetry breaking. Physical Biology 11(6):066005.
  • 2013

  • A.S. Ribeiro (2013) Kinetics of gene expression in live bacteria: from models to measurements, and back again. Canadian Journal of Chemistry, 91(7): 487-494.
  • A.S. Ribeiro, B.A. Eales, and F.G. Biddle (2013) Short-term and long-term memory deficits in handedness learning in mice with absent corpus callosum and reduced hippocampal commissure. Behavioural Brain Research 245, 145–151. Link PDF
  • . Mäkelä, M. Kandhavelu, S.M.D. Oliveira, J.G. Chandraseelan, J. Lloyd-Price, J. Peltonen, O. Yli-Harja and A.S. Ribeiro (2013) In vivo single-molecule kinetics of activation and subsequent activity of the arabinose promoter. Nucleic Acids Res 41(13):6544-52. Link PDF
  • A. Häkkinen, A.-B. Muthukrishnan, A. Mora, J.M. Fonseca, and A.S. Ribeiro (2013) CellAging: A tool to study segregation and partitioning in division in cell lineages of Escherichia coli. Bioinformatics 29 (13): 1708-1709.Link
  • A Häkkinen, H Tran, B Ingalls, and AS Ribeiro (2013) Effects of multimerization on the temporal variability of protein complex abundance. BMC Systems Biology 7 (Sup. 1).Link
  • S Chowdhury, M Kandhavelu, O Yli-Harja, and AS Ribeiro (2013) Cell Segmentation by Multi-resolution Analysis and Maximum Likelihood Estimation (MAMLE). BMC Bioinformatics 14 (Sup. 10), S8.Link
  • T Annila, E Lihavainen, IJ Marques, DR Williams, O Yli-Harja and AS Ribeiro (2013) ZebIAT, an image analysis tool for registering zebra fish embryos and quantifying cancer metastasis. BMC Bioinformatics 14 (Sup. 10), S5.Link
  • A Häkkinen, H Tran, O Yli-Harja, and AS Ribeiro (2013) Effects of rate-limiting steps in transcription initiation on genetic filter motifs, PLoS ONE 8(8): e70439. Link
  • J Lloyd-Price and AS Ribeiro (2013) Bistability in a stochastic RNA-mediated gene network. Phys. Rev. E 88(3): 032714. Link
  • JG Chandraseelan, SMD Oliveira, I Potapov, A Häkkinen, M Kandhavelu, and AS Ribeiro (2013) Temperature dependence of the LacI-TetR-CI Repressilator. Mol. BioSyst. 9(12), 3117-23.

Previous, Selected Publications:

  • A. S. Ribeiro, R. Zhu, and S. A. Kauffman (2006) A General Modeling Strategy for Gene Regulatory Networks with Stochastic Dynamics. Journal of Computational Biology 13(9): 1630-1639. Link
    PDF: This is a copy of an article published in the Journal of Computational Biology © 2006 Mary Ann Liebert, Inc.; Journal of Computational Biology is available online at: http://online.liebertpub.com.
  • A. S. Ribeiro and J. Lloyd-Price, (2007) SGN Sim, a Stochastic Genetic Networks Simulator. Bioinformatics 23(6): 777-779. Link PDF
  • A. S. Ribeiro and S. A. Kauffman (2007) Noisy Attractors and Ergodic Sets in Models of Gene Regulatory Networks. Journal of Theoretical Biology 247(4): 743-755. Link PDF
  • 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): 061903. Link PDF
  • A. S. Ribeiro, D. Charlebois, J. Lloyd-Price (2007) CellLine, a stochastic cell lineage simulator. Bioinformatics 23(24): 3409-3411. Link PDF
  • A. S. Ribeiro, S. A. Kauffman, J. Lloyd-Price, B. Samuelsson, and J.E.S. Socolar (2008), Mutual Information in Random Boolean models of regulatory networks. Physical Review E 77(1): 011901. Link PDF
  • A. S. Ribeiro, J. Lloyd-Price, J. Kesseli, A. Häkkinen, and O. Yli-Harja (2008), Quantifying Local Structure Effects in Network Dynamics. Physical Review E 78(5): 056108. Link PDF
  • A. S. Ribeiro (2008) Dynamics and evolution of stochastic bistable gene networks with sensing in fluctuating environments. Physical Review E 78(6): 061902. Link PDF
  • A. S. Ribeiro, O.-P. Smolander, T. Rajala, A. Häkkinen and O. Yli-Harja (2009) Delayed stochastic model of transcription at the single nucleotide level. Journal of Computational Biology 16(4): 539-553. Link
    PDF: This is a copy of an article published in the Journal of Computational Biology © 2009 Mary Ann Liebert, Inc.; Journal of Computational Biology is available online at: http://online.liebertpub.com.
  • A. S. Ribeiro (2010) Stochastic and delayed stochastic models of gene expression and regulation. Mathematical Biosciences 223(1): 1-11. Link PDF
  • A. S. Ribeiro, A. Häkkinen, H. Mannerström, J. Lloyd-Price, and O. Yli-Harja (2010) Effects of the promoter open complex formation on gene expression dynamics. Physical Review E 81(1): 011912. Link PDF
  • A. S. Ribeiro, J. Lloyd-Price, B. Eales, and F. G. Biddle (2010) Dynamic Agent-Based Model of Hand-Preference Behavior Patterns in the Mouse. Adaptive Behavior 18(2): 116-131. Link PDF
  • T. Rajala, A. Häkkinen, S. Healy, O. Yli-Harja, and A. S. Ribeiro (2010) Effects of Transcriptional Pausing on Gene Expression Dynamics. PLoS Computational Biology 6(3): e1000704. Link PDF
  • 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. Link PDF
  • J. Mäkelä, J. Lloyd-Price, O. Yli-Harja, and A. S. Ribeiro (2011) Stochastic sequence-level model of coupled transcription and translation in prokaryotes. BMC Bioinformatics 12: 121. Link PDF
  • O.-P. Smolander, M. Kandhavelu, H. Mannerström, E. Lihavainen, S. Kalaichelvan, S. Healy, O. Yli-Harja, M. Karp, and A. S. Ribeiro (2011) Cell-to-cell diversity in protein levels of a gene driven by a tetracycline inducible promoter. BMC Molecular Biology 12: 21. Link PDF
  • J. Mäkelä, H. Huttunen, M. Kandhavelu, O. Yli-Harja, and A. S. 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. Link PDF
  • M. Kandhavelu, H. Mannerström, A. Gupta, A. Häkkinen, J. Lloyd-Price, O. Yli-Harja, and A. S. 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. Link PDF
  • 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. Molecular BioSystems 8(2): 565–571. Link PDF
  • 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 194(7): 1747–1752. Link PDF
  • E. Lihavainen, J. Mäkelä, J. N. Spelbrink, and A. S. Ribeiro (2012) Mytoe: Automatic analysis of mitochondrial dynamics. Bioinformatics 7(28): 1050-1051. Link PDF
  • M. Kandhavelu, A. Häkkinen, O. Yli-Harja, and A. S. Ribeiro (2012) Single-molecule dynamics of transcription of the lar promoter. Physical Biology 9(2), 026004. Link PDF
  • A.-B. Muthukrishnan, M. Kandhavelu, J. Lloyd-Price, F. Kudasov, S. Chowdhury, O. Yli-Harja, and A. S. Ribeiro (2012) Dynamics of transcription driven by the tetA promoter, one event at a time, in live Escherichia coli cells. Nucleic Acids Research 40(17): 8472-8483. Link PDF
  • F. Emmert-Streib, A. Häkkinen, and A. S. Ribeiro (2012) Detecting sequence dependent trandivional pauses from RNA and protein number time series. BMC Bioinformatics 13: 152. Link PDF
  • J. Lloyd-Price, A. Gupta, and A. S. Ribeiro (2012) Robustness and Information Propagation in Attractors of Random Boolean Networks. PLoS ONE 7(7): e42018. Link PDF
  • M. Kandhavelu, J. Lloyd-Price, A. Gupta, A.-B. Muthukrishnan, O. Yli-Harja, and A. S. Ribeiro (2012) Regulation of mean and noise of the in vivo kinetics of transcription under the control of the lac/ara-1 promoter. FEBS Letters 586: 3870-3875. Link PDF

Supervised Theses


Alumni

PhD

  1. 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.
  2. O.-P. Smolander, PhD Thesis, Studies on Regulatory Mechanisms of Stochastic Gene Expression and Gene Network Dynamics. Dept. of Signal Processing, Tampere University of Technology, Finland. June 30th, 2011. Supervisors: O. Yli-Harja, Co-supervisors: M. Karp and A.S. Ribeiro.
  3. I. Potapov, PhD Thesis, Switching and Oscillatory Dynamics of Genetic Networks. Dept. of Signal Processing, Tampere University of Technology, Finland. January, 2013. Supervisor: A.S. Ribeiro.
  4. A.-B. Muthukrishnan, PhD Thesis, Studies of the plasticity of trandivion in Escherichia coli using single-molecule, in vivo detection techniques. Dept. of Signal Processing, Tampere University of Technology, Finland. September 2014. Supervisor: A.S. Ribeiro.
  5. J. Lloyd-Price, PhD Thesis, Dynamics of Genetic Circuits with Molecule Partitioning Errors in Cell Division and RNA-RNA Interactions. Dept. of Signal Processing, Tampere University of Technology, Finland. August 2015. Supervisor: A.S. Ribeiro.
  6. J. G. Chandraseelan, PhD Thesis, Synthetic Genetic Circuits: Plasticity and Robustness. Dept. of Signal Processing, Tampere University of Technology, Finland. September, 2015. Supervisor: A.S. Ribeiro.
  7. A. Gupta, PhD Thesis, Effects of intracellular and partitioning asymmetries in Escherichia coli, Dept. of Signal Processing, Tampere University of Technology, Finland. Nov., 2015. Supervisor: A.S. Ribeiro.
  8. H. Tran, PhD Thesis, Environment-sensing Mechanisms of Gene Expression and their Effects on the Dynamics of Genetic Circuits across Cell Generations, Dept. of Signal Processing, Tampere University of Technology, Finland. Jan., 2016. Supervisor: A.S. Ribeiro.
  9. A. Hakkinen, PhD Thesis, Quantifying Transcriptional Dynamics and Their Effects on Genetic Motifs from Live Cell Fluorescence Microscopy, Dept. of Signal Processing, Tampere University of Technology, Finland. Feb., 2016. Supervisor: A.S. Ribeiro.
  10. S Chowdhury, PhD Thesis, Image analysis algorithms for single-cell study in systems biology, Dept. of Signal Processing, Tampere University of Technology, Finland. May, 2016. Supervisor: O Yli-Harja. Co-supervisor: AS Ribeiro.

Masters

  1. 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. Approved with maximum grade.
  2. J. Mäkelä, Dynamics of stochastic sequence-level models of trandivion and translation in prokaryotes, Dept. of Signal Processing, Tampere University of Technology, Finland. May, 2011. Supervisors: A. S. Ribeiro and O. Yli-Harja. Approved with maximum grade.
  3. 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. Approved with maximum grade.
  4. L. P. V. Martins, Msc Thesis, Stochastic model of trandivion 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. Approved, grade 18/20.
  5. A. Häkkinen, Msc Thesis, Simulating Evolutionary Processes of Stochastic Genetic Networks in Volatile Environments. Dept. of Signal Processing, Tampere University of Technology, Finland. June. 2012. Supervisors: A. S. Ribeiro and O. Yli-Harja. Approved with maximum grade.
  6. A. Gupta, Msc Thesis, Stochastic processes as a source of cell to cell diversity and cellular ageing. Faculty of Computing and Electrical Engineering, Tampere University of Technology, Finland. June 2012. Supervisors: A. S. Ribeiro and I Hammouda. Approved with maximum grade.
  7. C.C.A. Queimadelas, Msc Thesis, Automated segmentation, tracking and evaluation of bacteria in microscopy images. Supervisor: J.M. Fonseca. Co-supervisors: A. Mora, A.S. Ribeiro, University Nova de Lisboa, Portugal, Nov. 2012. Approved, grade 18/20.
  8. S Garasto, Msc Thesis, A Mixture Model to Estimate Numbers of Fluorescence-tagged Molecules Using Their Intensity Distributions. Supervisor: G. Oriolo. Co-supervisor: A.S. Ribeiro. University of Rome, Italy. Aug. 2013. Approved with maximum grade.
  9. H. Tran, Msc Thesis, Sequence-dependent noise filtering in small genetic motifs, Supervisor: A.S. Ribeiro. Tampere University of Technology, Finland. September 2013. Approved, grade 4/5.
  10. SMD Oliveira, Msc Thesis, In vivo single-cell kinetics of the repressilator as a function of its intracellular copy numbers. Tampere University of Technology, Finland. October, 2014. Supervisor: A. S. Ribeiro. Approved with maximum grade.
  11. C Ferreira, MSc thesis, Study of the influence of sigma factors on the kinetics of RNA production. Supervisor: J.M. Fonseca. Co-supervisor: A.S. Ribeiro, University Nova de Lisboa, Portugal, Nov. 2013. Approved, grade 18/20.
  12. A Martikainen, MSc thesis, Segregation of protein aggregates in Escherichia coli. Supervisors: A. S. Ribeiro and R. Ritala. Approved with maximum grade.
  13. T Annila, MSc Thesis, “Detection of Fluorescently Labeled Particles in Escherichia coli”. Tampere University of Technology, Finland. November, 2015. Supervisor: A. S. Ribeiro. Approved with maximum grade.

Post Doctoral Fellows

  1. S Healy, post-doctoral fellow, Dept. of Signal Processing, Tampere Univ. of Technology, Finland. July 2009-June 2010.
  2. M Kandhavelu, post-doctoral fellow, Dept. of Signal Processing, Tampere Univ. of Technology, Finland. Jan 2010 to Nov 2012.

Bachelors

  1. D. Charlesboi, Bsc. thesis, Modeling the P53 network. Supervisor: A. S. Ribeiro, IBI, Univ. of Calgary. May 2007. Approved with maximum grade.
  2. A. Häkkinen, Bsc. thesis, "DNA-sekvenssien etsiminen ja löydösten merkityksen analysointi" (engl. inf. "Searching DNA sequences and analyzing significance of the findings"), Dept. of Signal Processing, Tampere Univ. of Technology, Finland. April 2008. Supervisor: AS Ribeiro. Approved with maximum grade.
  3. E. Moradi, Bsc. thesis, Analysis of the Dynamics of Trandivion of the Arabinose promoter in Escherichia coli. Dept. of Signal Processing, Tampere Univ. of Technology, Finland. Dec. 2011. Supervisors: AS Ribeiro and J. Mäkelä.
  4. SMD Oliveira, Bsc. thesis, Single-Molecule Dynamics of the Bidirectional Arabinose Promoter, Universidade Estadual Paulista, April 2012. Supervisors: DA Palmieri and AS Ribeiro.
  5. T Annila, Bsc. thesis, Registration of zebrafish images using thin plate splines, Dept. of Signal Processing, Tampere Univ. of Technology, Finland. Dec. 2012. Supervisors: AS Ribeiro and E. Lihavainen.
  6. J Smolander, Bsc. thesis "Lambda-Phage PRM Promoter Dynamics" Dept. of Signal Processing, Tampere Univ. of Technology, Finland. May 2013. Supervisors: AS Ribeiro and H. Tran.

Present Funding


Projects Ongoing:

Academy of Finland General research grants. Research Council for Biosciences and Environment. PI: A.S. Ribeiro. Site of research: Tampere University of Technology. Funding period 01.09.2012 - 31.08.2016.

TUT’s Roadmap for infrastructures. PI: Andre S. Ribeiro. Funding Period: 01.01.2014-31.12.2016.

TUT Rector’s Strategy Salaries Funds. PI: Andre S. Ribeiro. Funding Period: 01.01.2014-31.12.2016.

TUT Rector’s grant. Project: “DENIS: Doctoral Education Network on Intelligent Systems”: 01.01.2014-31.12.2016.

PhD studies

Doctoral Programme of TUT's President, Suomalaisen Tiedeakatemian, FCT Portugal.

    To start soon:

Jane and Aatos Erkko Foundation. PI: Andre S. Ribeiro. Period: 01.09.2016-31.08.2018.

Academy of Finland General research grants. Research Council for Biosciences and Environment. PI: AS Ribeiro. Funding period 01.09.2016 - 31.08.2020.



Alumni


PhD

  1. Xiaofeng Dai: Post-doctoral Fellow at University of Helsinki, Finland.
  2. Olli-Pekka Smolander: Post-doctoral Fellow at University of Helsinki, Finland.
  3. Ilya Potapov: Post-doctoral Fellow at Tampere University of Technology, Finland.
  4. Anantha-Barathi Muthukrishnan: Post-doctoral Fellow at Indian Institute of Technology, Madras, India.
  5. Jason Lloyd-Price: Post-doctoral Fellow at Harvard University, U.S.A.
  6. Jerome Chandraseelan
  7. Abhishekh Gupta: Post-doctoral Fellow at Helsinki University, Finland
  8. Huy Tran: Post-doctoral Fellow at Ecole Normale Supérieure, Paris, France.
  9. Antti Hakkinen: Post-doctoral Fellow at Helsinki University, Finland

Post Doctoral Fellows

  1. Shannon Healy: Post-doctoral Fellow at University of British Columbia, Canada.
  2. Meenakshisundaram Kandhavelu: Assistant Lecturer at Tampere University of Technology, Finland.

MultiBAM


The Multi-scaled biodata analysis and modelling (MultiBAM) is a recently formed research community composed of the Laboratory of Biosystem Dynamics (LBD) of the DSP (TUT) led by Andre Ribeiro (chair of MultiBAM), the Biological Physics and Soft Matter (BIO) Group led by Ilpo Vattulainen (TUT), the Computational Biology Group (CB) of BioMediTech (UTA) led by Matti Nykter, and the Protein Dynamics Group (PD) (UTA) led by Vesa Hytönen. All these groups study, at different scales, how cells sense and respond to the environment and how information flows and is processed inside them.

The new community for multi-scaled biodata analysis and modelling (MultiBAM) will combine knowledge, methods, and tools used by its groups to handle biodata at different scales of observation and from different phenomena. The goal is to study and understand dynamical processes in cells in a broad sense and to produce new computational tools and models that, by being applicable to multiple scales, can provide new comprehensive understanding of biological systems.

News and Open Positions


Interested students are always encouraged to apply. To apply please send your CV, your studies record, and a letter of application to Andre Ribeiro (Email: firstname.lastname@tut.fi). While not strictly necessary, adding to your application a short project proposal (1 page maximum) or the reasons why you selected our group is an important plus.

Postdoc candidates are encouraged to apply for their own funding. If your research aims are in line with our laboratory, we would galdly help writing and submitting an application.

A new funded position for a post doctoral fellowship will open in mid August!


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