Our aim is to understand the in vivo dynamics and regulatory mechanisms of bacterial gene networks. We combine measurements (RNA-seq, flow-cytometry, time-lapse microscopy, etc.) and new dynamic models from the nucleotide level, up to circuits with thousands of genes and interactions. We apply tailored methods of single-cell image and signal processing, stochastic and analytical models, RNA-seq data analysis, and synthetic gene engineering.

A little history

The LBD was founded in 2009, at the former Department of Signal Processing of Tampere University of Technology. Nowadays, we are fully established in the Arvo building of the Faculty of Medicine and Health Technology of Tampere University. Initially, we used only computational methods, such as stochastic models and simulators of genetic circuits. In 2011, we setup a laboratory to perform live single-cell microscopy. Nowadays, we also use flow-cytometry and RNA-seq, among other techniques. This is made possible by a multi-disciplinary group of students with backgrounds in biophysics, cell and molecular biology, biomedical engineering, and signal processing. A description of some of our past and current projects is available in Research.

Recent highlights

2024

• 31.5.2024. Our newest paper is now available in mSystems: https://doi.org/10.1128/msystems.00065-24! Produced by S Dash et al, the paper presents a library of fluorescent reporters of the global regulators of gene expression of E. coli. These reporters are not available in the largest strain libraries. Thus, we believe that the new strains will be useful to many researchers using E. coli.

• 2.4.2024. Today, a new student, Miguel Azevedo, has join our group. Welcome!!

• 15.1.2024 We thank the Finnish Cultural Foundation for a 1 year grant for PhD studies for Suchintak Dash.

• 10.1.2024. We thank EDUFI for a 1 year grant for PhD studies for Amir Arsh.

2023

• 10.11.2023 We thank the Yrjö and Kalle Väisälä Fund for renewing for another year the grant for Ph.D. studies of Rahul Jagadeesan. Few deserve more. Thank you.

• 7.11.2023. It is with immense happiness that we announce that Vatsala Chauhan has completed her Ph.D. in our group and will now travel to Uppsala University in Sweden to continue her scientific journey as a Post-doctoral fellow! It was wonderful to have her in our group, and we are sure that we will continue to collaborate closely in the future! We wish the best to her.

• 15.09.2023. Today, a new student, Arsh Amir, has join our group. Welcome!!

• 30.8.2023. Today ends our 3-year grant from the Aatos Erkko Foundation. We are deeply thankful for the support, and very happy with the outcomes. We hope that the Foundation will continue to support us in the future.

• 2.8.2023. We are happy to confirm that we will be responsible for the course of Functional Genomics (BBT.MB.602) of the Faculty of Medicine and Health Technology.

• 1.8.2023. We thank the Finnish Cultural Foundation for confirming the final year (out of 4) of the grant for Ph.D. studies of Ines Baptista.

• 16.3.2023. The Sigrid Jusélius Foundation has funded a 3-years project. We are very thankful to the Foundation's for the support.

• 16.2.2023. We have published another video in YouTube describing our work on the role of E. coli's gene network (logic and topology) in the response to genome wide stresses (https://youtu.be/y9xCNG6B2Hs)

• 3.2.2023. Mohamed B. has completed his Ph.D. studies! Congratulations and best wishes for your new projects.

• 10.1.2023. We have published a video in YouTube describing our recent work on sigma factors (https://www.youtube.com/watch?v=NLVmPHD7TaY)

2022

• 2.12.2022. The 4th LBD Webinar on Biosystems has arrived! We are very happy to see our former students and listen what everyone is working! Wonderful talks and new science! Thank you all!

• Our student and colleague, Cristina Palma, just moved to Rice University to join the group of Oleg Igoshin. We are very proud and we wish her ALL the best! She also received a grant from the Jenny and Antti Wihuri Foundation for post-doctoral research abroad. Very well deserved! We are sure that her future group will benefit from her knowledge and that she will help Finland to further develop scientifically.

• Our study on the genome wide response to cold shock received an honorary mention for best publications of the year of our Faculty of Medicine and Health Technology. We are very thankful to our colleagues for this honor.

• We just published a new video in YouTube about our work on cold shock responses (https://www.youtube.com/watch?v=dHFMum0QMO4)

• We are very thankful to the The Vilho, Yrjö and Kalle Väisälä fund of the Finnish Academy of Science and Letters for supporting two of our Ph.D. students (Rahul J. and Suchintak D.)!

• Aug 2022: Nucleic Acids Research has now also published an in-house work about genes' supercoiling sensitivity as a trigger for genome-wide cold-shock responses by E. coli. DOI: 10.1093/nar/gkac643. We also made two contributions to Wikipedia based on this work.

This is our 3rd study using our new methodology of combining RNA-seq, flow-cytometry, databases, and stochastic models to discover natural response mechanisms to genome-wide stresses. We also explored the conservation of responsive genes and their DNA sequences.

• June 2022: We are thrilled to announce that Nucleic Acids Research has just published one of our studies with several collaborators. 

This study provides direct empirical evidence that global topological and logic features of the gene network of E. coli affect its response to a genome wide stress. Our findings could contribute in the design of new models of complex transcriptional programs in large GRNs: DOI:10.1093/nar/gkac540. We also made a short contribution to Wikipedia.

• June 2022: We all happily welcome Sneha Prakash Y, who just joined our group for a M.Sc. thesis project.

• May 2022: We are thankful to the Finnish Foundation for Technology for their grant supporting the PhD studies of C. Palma! 

• April, 2022: We wish the best to M. Bahrudeen, as he joins a new research group following the submission of his Ph.D. thesis.

• April 01, 2022 (and not because it's April Fool's day): Our new work on sigma factors regulation is out! A great work by I. Baptista, V. Kandavalli and all colleagues. We proposed a new model of gene expression using promoters with dual preference for two sigma factors! Interestingly, unlike most other promoters, the dynamics of these  promoters can be easily predicted from their sequence. Because of it, they could become a 'toolbox' for synthetic gene engineering. DOI: 10.1016/j.bbagrm.2022.194812. 

• March 2022: We have added a small contribution in Wikipedia describing our findings about closely spaced promoters to the general public.

• February 2022:  Our paper on tandem promoters dynamics is now in PLOS Computational Biology! This is our first work where we measure many natural genes by RNA-seq and flow-cytometry, and then produce analytical and stochastic models and explore how to produce libraries of synthetic constructs, based on the models. See the "data (open access)" section for links for the data. Audioslides are now in the YouTube channel! 📽️

• January 2022: We are very thankful to the Finnish National Agency for Education for funding the Ph.D. studies of our new team member, Rahul Jagadeesan! 

2021

• November 2021: We are equally happy to announce the publication (pre-print) of a work on promoters with dual σ factor preference. We propose a sequence dependent kinetic model applicable to both the exponential as well as the stationary growth phase. This and the publication below are the first ones where we relate gene dynamics (flow-cytometry and RNA-seq data) with their ontology, evolutionary conservation, sequence, transcription factor interactions, etc. www.biorxiv.org/content/10.1101/2021.11.17.468920v1

• November 2021: With great joy we announce the publication (pre-print) of our study of tandem promoters of E. coli. We propose a model based on RNA-seq and single-cell flow-cytometry. The results encourage the use of these promoters in synthetic constructs, due to how their dynamics relate with their structure. www.biorxiv.org/content/10.1101/2021.11.19.468961v1

• August 2021: We welcome our new team member, Rahul Jagadeesan, that has joined us for Ph.D. studies!

• August 2021: The work of Jonathan Massera's team and collaborators, which we had the pleasure to participate in as just been published! We thank Jonathan for the opportunity. https://pubs.acs.org/doi/abs/10.1021/acsbiomaterials.1c00735  

• August 2021: We have made available data on transcription dynamics at the single-cell, single-RNA level https://sites.google.com/view/andreribeirolab/home/data-open-access for easy OPEN ACCESS.

• March 2021: We have made a new contribution to Wikipedia (page: "DNA Supercoiling", section "Stochastic Models") to disseminate results in this  area from us and from other groups to the general public.

• February 2021: The Maili Autio fund of the Finnish Cultural Foundation has awarded a 1-year grant for the Ph.D. studies of Cristina Palma. This grant will allow Cristina to fully complete her research on gene-gene interactions in both small- and large-scale genetic circuits. We thank the continuous support provided by the Finnish Cultural Foundation to our research.  The Maili Autio fund supports the promotion of science and economic development, as well as other creative work.

• January 2021: Our Faculty of Medicine and Health Technology has granted funds for a NovoSampler for our Flow Cytometer, which significantly increases our capability of collecting important information for our studies.

2020

• December 2020: We have shared with the scientific community all data (microscopy and flow-cytometry) to produce publication: DOI: 10.1016/j.bbagrm.2020.194515 in Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. Check our section "Data (open access)".

• October 2020: We have made a new contribution to Wikipedia (section "Stochastic Gene Networks") to disseminate results in this  area from us and from other groups to the general public.

• June 2020: We have opened a Twitter account to improve how we inform both the scientific community and the public about our results, and for promoting open science in general. 

• June 2020: We are very happy to announce that the Jane and Aatos Erkko foundation will be supporting one of our projects for the next two years. We are very thankful for the support provided by J&AE!

• May 2020: We congratulate Vinodh Kandavalli for completing his PhD studies at the LBD! We are also happy to announce that he will move for post-doctoral studies at Uppsala University (Sweden). We thank his wonderful dedication and contributions during his Ph.D., which have really helped our group. We wish him all the best.

• May 2020: BioSystems has published our review about stochastic models of cell-to-cell diversity in RNA and proteins that account for both noise in gene expression and noise in partitioning during cell division. DOI: 10.1016/j.biosystems.2020.104154. 

• April 2020: S. Dash has been granted funds for Ph.D. studies by the Finnish Cultural Foundation (Pirkanmaa Regional Fund). We thank the Foundation for this opportunity. 

• Mar 2020: BBA Gene Regulatory Mechanisms has published our recent findings on the effects of positive supercoiling buildup on the dynamics of gene expression in E. coli. DOI: 10.1016/j.bbagrm.2020.194515. 

• Feb 2020: We are happy to announce that Sofia Startceva has completed her Ph.D. on stochastic genetic circuits and will now proceed for post-doctoral studies. Sofia will move to the Technische Universität Darmstadt, Germany, where she will join the group of Heinz Koeppl for post-doctoral studies. We are very happy for her, and wish her all the best! 

• Jan 2020: Ines Baptista has been accepted for Ph.D. studies by our Faculty! She has also obtained a grant for Ph.D. studies from the Finnish Cultural Foundation (Paavo Koskinen Foundation). We thank the Foundation for this opportunity. 

• Jan 2020: We have created a YouTube channel to promote open science and disseminate knowledge produced by our group's research.

2019

• Dec 2019: Samuel Oliveira's Ph.D. was awarded the title of Best Ph.D. thesis of 2018-19 of the Faculty of Medicine and Health Technology (Doctoral Program in Biomedical Sciences and Engineering) of Tampere University!

• Dec 2019: The Journal of the Royal Society Interface has published Antti Häkkinen's work in which we participated, which focuses on how the kinetics of the rate-limiting steps in transcription initiation can shape the RNA production dynamics of gene-pairs sharing promoter elements.

• Nov 2019: The Journal of Microbiological Methods has published our work where we propose a new method to estimate the statistics of single-cell RNA distributions from flow-cytometry data. This will eliminate the limitations caused by cell segmentation on the number of cells that can be measured.

• Oct 2019: Congratulations to Ines Baptista for completing her Masters degree!

• May 2019: We move our offices and laboratory to the Arvo building of Tampere University! We will now work towards sharing knowledge with our new colleagues so as to improve research capabilities.

• We congratulate S. Dash for obtaining a EDUFI Fellowship for starting Ph.D. studies.

• April 2019: We have a new team member, Suchintak Dash, which has join our group to conduct PhD studies.

• Mar 2019: Our former MSc and PhD student, Jason Lloyd-Price, following a post-doc at Harvard, U.S.A., has joined Google in N.Y. We wish him all the best.

• Mar 2019: Scientific Reports has published our work on the effects of low temperatures on the dynamics of a chromosome integrated gene.

• Jan 2019: We congratulate Samuel Oliveira for completing his PhD studies at the LBD! (1st PhD of the new Tampere University). Samuel will now move to Boston University for post-doctoral studies. We sincerely express our gratitude and admiration for his dedication and contributions. We wish him all the best possible and beyond!