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. However, in 2011 we established 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, perform image and data analysis using methods from Signal
Processing, and develop detailed stochastic models and simulators.
For this, we have a highly multi-disciplinary group that includes backgrounds in physics,
theoretical biology, molecular and cell biology, biotechnology, signal
processing, and computer science.
Laboratory of Biosystem Dynamics
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 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 explore 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 of Cell and Molecular
Biology at the Department of Signal Processing, Tampere University of
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, open to all research groups and
students. 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.
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
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-53806, Techniques in Molecular Biology and Applications to Gene Expression, Period 4, 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
- SGNSim (Simulator of delayed
stochastic genetic circuits)
- SGNS2 (Simulator of delayed
stochastic genetic circuits. Version 2, which includes transient
compartmentalization of reactions)
- CellLine (Simulator of genetic circuits within cell lineages)
- Mytoe (Software for image analysis
- CellAging (Software to study
segregation and partitioning in division in cell lineages of Escherichia coli)
- Cell Segmentation Tool (Tool for image analysis of E. coli and other bacteria)
- ZebIAT (Tool for image analysis of zebrafish embryos)
- 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
- 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 12, 9–21.
- 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.
- 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.
- 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
- . 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
- 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):
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
- 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
- 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, D. Charlebois, J. Lloyd-Price (2007)
CellLine, a stochastic cell lineage simulator. Bioinformatics
23(24): 3409-3411. Link
- 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
- 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):
- A. S. Ribeiro (2008) Dynamics and evolution of stochastic
bistable gene networks with sensing in fluctuating environments. Physical
Review E 78(6): 061902. Link
- 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
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
- 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):
- 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):
- 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):
- 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
- 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:
- 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
- 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
- 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:
- 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):
- 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
- E. Lihavainen, J. Mäkelä, J. N. Spelbrink, and A. S.
Ribeiro (2012) Mytoe: Automatic analysis of mitochondrial dynamics. Bioinformatics
7(28): 1050-1051. Link
- 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),
- 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
- 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:
- J. Lloyd-Price, A. Gupta, and A. S. Ribeiro (2012)
Robustness and Information Propagation in Attractors of Random Boolean
Networks. PLoS ONE 7(7):
- 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:
- 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.
- 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
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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
- 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.
- 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
- 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,
- 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
- 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
- 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.
- 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.
- 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.
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.
- 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.
- A Martikainen, MSc thesis, Segregation of protein aggregates in Escherichia coli. Supervisors: A. S.
Ribeiro and R. Ritala. Approved with maximum grade.
- 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
- Shannon Healy, post-doctoral fellow, Dept. of Signal
Processing, Tampere Univ. of Technology, Finland. July 2009-June 2010.
- Meenakshisundaram Kandhavelu, post-doctoral fellow, Dept.
of Signal Processing, Tampere Univ. of Technology, Finland. Jan 2010 to
- D. Charlesboi, Bsc. thesis, Modeling the P53 network.
Supervisor: A. S. Ribeiro, IBI, Univ. of Calgary. May 2007. Approved
with maximum grade.
- 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.
- 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.
- SMD Oliveira, Bsc. thesis, Single-Molecule Dynamics
of the Bidirectional Arabinose Promoter, Universidade Estadual
Paulista, April 2012. Supervisors: DA Palmieri and AS Ribeiro.
- 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.
- 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.
Academy of Finland General research grants.
Research Council for Biosciences and Environment.Project: Study of the
in vivo transcription and translation dynamics in Escherichia
coli, one event at a time, with computational and
experimental tools. PI: A.S. Ribeiro. Site of research: Tampere
University of Technology. Funding period 01.09.2012 - 31.08.2016.
For PhD studies: Doctoral Programme of TUT's President, Finnish Cultural Foundation, Tampere Science Foundation, Alfred Kordelinin Foundation, Suomalaisen Tiedeakatemian Vilho, Yrjö ja Kalle Väisälän rahasto, FCT
- Xiaofeng Dai: Post-doctoral Researcher at University of Helsinki, Finland.
- Olli-Pekka Smolander: Post-doctoral Researcher at University of Helsinki, Finland.
- Ilya Potapov: Post-doctoral Researcher at Tampere University of Technology, Finland.
- Anantha-Barathi Muthukrishnan: Postdoctoral Fellow at Indian Institute of Technology, Madras, India.
- Jason Lloyd-Price: Post-doctoral Researcher at Harvard University, U.S.A.
- Jerome G. Chandraseelan
- Abhishekh Gupta: Post-doctoral Researcher at Helsinki University, Finland
- Huy Tran: Post-doctoral Researcher at Ecole Normale Supérieure, Paris, France.
- Antti Hakkinen: Post-doctoral Researcher at Helsinki University, Finland
Post Doctoral Fellows
- Shannon Healy: Post doctoral fellow at The University of British Columbia, Canada.
- Meenakshisundaram Kandhavelu: Assistant Professor at Tampere University of Technology, Finland.
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: email@example.com). While not strictly necessary, adding to your application a short project proposal (1 page maximum) or the reasons why you selected our group is a plus.
A new position for a post doctoral fellowship will open in mid June!