Laboratory of Biosystem Dynamics (LBD), led by Professor Andre S. Ribeiro of the Biomeditech Institute at Tampere University of
Technology (TUT), studies
the in vivo
dynamics and regulatory mechanisms of bacterial
gene expression and genetic circuits at the single-cell,
using time-lapse microscopy, stochastic models, single-cell signal
and synthetic gene engineering. This research aims to understand how
genes and genetic circuits are regulated and unravel their
range of functionalities, thereby assisting in the
of synthetic circuits for regulating cellular processes.
Our team in March 2018
- June 2018: We are happy to announce that the Bioinformatics Journal
accepted our new software, SCIP, a Single-Cell Image Processor toolbox.
- June 2018: We welcome Carolina to our group.
- April 2018: We are happy to announce that the Physical Biology Journal
accepted our work on the effects of low temperatures in the symmetry in cell division in E. coli.
- March 2018: We received our new Flow-cytometer (see the "Laboratory" webpage for a description).
- March 2018: Inaugural lecture of the full professorship (see audioslides section)
- January 2018: Our laboratory in the Sähkötalo Building, BMT-TUT is now fully operational!
- January 2018: We welcome our new PhD student Bilena Almeida!
- November 2017: We are starting to move our laboratory to the Sähkötalo Building, where BMT-TUT is located!
2017: We are happy to announce that the Physical Biology Journal
accepted our work on the effects of high and low temperatures on the
kinetics of intake of inducers of transcription in E. coli.
2017: Mohamed Bahrudeen obtained a grant for PhD studies from Tampere Universisty of Technology! Congrats to him!
2017: Cristina Palma has obtained a grant for PhD studies from the
Finnish Academy of Science and Letters! Congrats to her!
- November 2017 We congratulate Ramakanth Neeli-Venkata for completing his PhD studies at the LBD.
- November 2017: We thank EDUFI for a fellowship for PhD studies of V Chauhan.
- November 2017: We thank the Vilho, Yrjö and Kalle Väisälä Rahasto for renewing SMD Oliveira PhD studies grant.
- November 2017: We thank TUT-BMT funding for Funds for Laboratory restructuring.
- November 2017: We thank TUT-BMT funding for purchasing a Spectrophotometer (BMT - Faculty's funding opportunities).
- November 2017: We thank TUT-BMT strategic funding for purchasing a state-of-the-art Flow Cytometer (TUT Strategic Funding 2017).
2017: Our team is very happy to announce that Scientific Reports has
accepted our study on the ability of promoters in E.coli to
regulate and evolve the level of extrinsic noise to which their RNA and
proteins are subject to: J. Mäkelä, V. Kandavalli and A.S. Ribeiro
(2017) Scientific Reports 7:10588. [J. Mäkelä is currently a Post-doc in Oxford University, U.K.]
Tran, PhD, a former PhD student at the LBD and currently a Post-doc in
Paris, France, has given a wonderful Seminar at BMT-TUT.
2017: BMT-TUT has decided to fund our request for a Spectrometer
with internal temperature control! We thank for the support.
- August 2017: N
Goncalves, our PhD student, received a short-term funding to complete the PhD studies by Biomeditech-TUT.
- August 2017: BMT-TUT has decided to fund the moving of our laboratory to the BMT-TUT building! We thank for the support.
2017: BMC Bioinformatics published a work by F Emmert-Streib's
team to which we contributed to. We thank Frank for the opportunity.
- August 2017: Two new members, Vatsala Chauhan and Mahendra Prajapat, PhD. have joined our group! Welcome.
- July 2017: A. Ribeiro becomes a tenured Professor.
- June 2017 *We have moved to the Sähkötalo Building, where BMT-TUT is located, at Korkeakoulunkatu 3 (33720 Tampere) *
2017: Mahendra Prajapat has obtained a 1 year grant for Post Doctoral
studies from the Finnish Foundation for Technology Promotion!
2017: Vinodh Kandavalli has obtained a 1 year grant for PhD studies
from the Finnish Cultural Foundation Pirkanmaa Regional
2017: Marco Minoia, PhD, has joined our group as a Posdoc, to bring new
knowledge and contribute to the team's improvement.
2017: The Journal of Neuroscience has published a work by Leonard
Khiroug and Sergei Kirov's teams to which we contributed to.
- The Biophysical Journal has accepted our study on the role of the nucleoid in the polar localization of the Serine Chemoreceptors of
E. coli. (pre-print here)
- We published a paper (review) on stochastic models of genetic circuits: AS Ribeiro (2016) Delays as regulators of the dynamics of genetic circuits. Markov Processes and Related Fields 22, 573-594. PDF
- Our work on the dissection of the dynamics of RNA production at various temperatures in E. coli
has been published in PLOS Computational Biology. Warm
thanks to our former team member and now collaborator Antti Hakkinen. PDF
LBD has been granted the "Key project funding: Forging ahead with
research" grant by the Academy of Finland (01.10.2016 - 30.09.2018) for
more research and applications of ongoing research results in gene
expression and genetic circuits!
Mohamed Bahrudeen has joined our group!
- Eero Lihavainen has completed his PhD at the LBD and will now pursue new adventures! Best wishes to him from all of us!
- Jarno Mäkelä has completed his PhD at the LBD and will now work as a Post-Doctoral Fellow at Oxford! Best wishes from all of us!
- We published a work on σ factor competition effects on in vivo kinetics of
transcription initiation in E. coli:
VK Kandavalli, H Tran, and AS Ribeiro (2016) Effects of σ factor
competition on the in vivo kinetics of transcription initiation
in Escherichia coli. BBA Gene Regulatory Mechanisms 1859
(2016) 1281–8. PDF
- The Academy of Finland has granted the LBD with a new grant (01.09.2016 - 31.08.2020) for a project on studies of
- Huy Tran and Antti Häkkinen
have completed their PhD studies at the LBD, and have now move forward
for Post-doctoral positions in Paris and Helsinki, respectively. We wish them all the best in their new
LBD was established in 2009, as part of the Computational
Systems Biology Research Group of the DSP. In 2015, it became an independent research group
of the Department of Signal Processing, TUT. In 2016, it joined Biomeditech
(Institute of Biosciences and Medical Technologies of Tampere,
Finland). In 2017, the group physically moved its offices to the building where the Biomeditech Institute is located (Sähkötalo Building).
Initially, our studies used computational and theoretical biology methods alone.
In 2011, we setup a Cell and Molecular Biology Laboratory, specialized
in live, single-cell, single-molecule imaging. This allowed us to combine theory and
measurements. Currently, we conduct live single-cell, single-molecule
microscopy measurements to study gene expression and genetic
circuits dynamics, as well as other intracellular processes. For this,
we also perform and develop methods in image and data analysis, and design detailed
stochastic models and simulators of genetic circuits dynamics. This is made possible by having a
highly multi-disciplinary group that includes backgrounds in physics,
theoretical biology, molecular and cell biology, biotechnology, biomedical engineering, signal
processing, and computer science.
description of some of our recent projects is available here.
movies produced in our lab, by microscopy, which we make use
of to study cellular processes ranging from transcription dynamics
to segregation of protein aggregates to the cell poles. (Left) Here, we
image nucleoids (red) and FtsZ proteins (green) associated with the
formation of the cell wall in cell division. (Center)
Here we observe RNAs production, one at a time (bright
a single cell. (Right) Here, we observe the spatial distribution of
MS2-GFP-RNA spots in live cells at 10 oC, to assess how
lower temperatures affect the dynamics of polar segregation of protein
image illustrates a methodology used in several of our studies, which
consists of measurements of RNA
production dynamics processed by state-of-the-art signal and image
processing techniques, from which we design and test novel models of
the processes responsible for RNA production regulation.
- Multi-scaled biodata analysis and
modelling Research Community
Multi-scaled biodata analysis and
modelling (MultiBAM) is a recently formed (2016) research community
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
Nykter, and the Protein Dynamics Group (PD) (UTA) led by Vesa
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. The first and most recent external evaluation
process of RC's conducted by TUT (2017) placed us as the top graded new
RC at TUT.