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StoNets - Controlling and exploiting stochasticity in gene regulatory networks
Third-party funded project |
Project title |
StoNets - Controlling and exploiting stochasticity in gene regulatory networks |
Principal Investigator(s) |
Zavolan, Mihaela
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Co-Investigator(s) |
Becskei, Attila van Nimwegen, Erik
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Project Members |
Mittal, Nitish Gruber, Andreas Martin, Georges Vina Vilaseca, Arnau Kaiser, Matthias Blank, Diana Lazzari, Gianrocco Bellement-Théroué, Gwendoline Grandy, William Aaron Rzepiela, Andrzej Breda, Jeremie Baudrimont, Antoine Rodak, Christoph Crippa, Alessandro Wolf, Luise Silander, Olin Galbusera, Luca Vögeli, Sylvia Hsu, Chieh Hansen, Marie Mi Bonde Jaquet, Vincent Syed, Afzal Pasha Jedlinski, Dominik Julou, Thomas Gencoglu, Mümün Calero Viloria, Eduardo Katsantoni, Maria
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Organisation / Research unit |
Departement Biozentrum / Bioinformatics (van Nimwegen), Departement Biozentrum / Bioinformatics (Zavolan), Departement Biozentrum / Synthetic Microbiology (Becskei) |
Project Website |
http://www.systemsx.ch/projects/research-technology-and-development-projects/stonets/ |
Project start |
01.03.2013 |
Probable end |
28.02.2017 |
Status |
Completed |
Abstract |
The precision with which cells undergo differentiation programs or respond to external stimuli is remarkable, especially when considering the inherently "noisy" molecular interactions underlying these processes. StoNets aims to understand how stochasticity is controlled - and even exploited - to allow the development of robust behaviors of genetic networks, cells and cellular systems.
Although all cells within an organism carry the same genetic information, regulatory mechanisms that operate at essentially all steps of gene expression lead to a large variety of cell types and behaviors. Progress in measurement technologies has enabled the precise and high-throughput probing of molecules and cells. This in turn has revealed that stochasticity is pervasive in all gene expression regulatory systems. The central question we will address in this StoNets project is how robust and reproducible cellular behaviors can emerge in spite of these noisy molecular interactions.
A "slice" across the levels of gene expression organization
We will undertake a systematic investigation into the mechanisms that have emerged to control noise at different organizational scales of gene expression regulation, from transcription of individual genes to cell fate switching. Each of the example systems that we selected is interesting in its own right and exhibits important stochastic aspects.
Questions motivated by modeling
With the continuous progress in understanding the basic mechanisms of gene regulation, many key molecular players have been identified and numerous direct regulatory interactions have been mapped. Theoreticians have started to model the way in which specific behaviors emerge from the underlying interactions. These efforts have led to a large number of new, inherently quantitative questions regarding the biological systems. Through a very tight integration of experimental and computational approaches StoNets aims to answer such questions ultimately contributing to an improved, quantitative understanding and thereby controllability of cellular behaviors. |
Financed by |
Swiss Government (Research Cooperations)
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Published results () |
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ID |
Autor(en) |
Titel |
ISSN / ISBN |
Erschienen in |
Art der Publikation |
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3208056 |
Breda, Jeremie; Rzepiela, Andrzej J; Gumienny, Rafal; van Nimwegen, Erik; Zavolan, Mihaela |
Quantifying the strength of miRNA-target interactions |
1046-2023 |
Methods |
Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) |
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2637564 |
Baresic, Mario; Salatino, Silvia; Kupr, Barbara; van Nimwegen, Erik; Handschin, Christoph |
Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene program |
1098-5549 |
Molecular and cellular biology |
Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) |
|
4234977 |
Kaiser, Matthias; Jug, Florian; Julou, Thomas; Deshpande, Siddharth; Pfohl, Thomas; Silander, Olin K.; Myers, Gene; van Nimwegen, Erik |
Monitoring single-cell gene regulation under dynamically controllable conditions with integrated microfluidics and software |
2041-1723 |
Nature Communications |
Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) |
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4487357 |
Rzepiela, Andrzej J.; Ghosh, Souvik; Breda, Jeremie; Vina-Vilaseca, Arnau; Syed, Afzal P.; Gruber, Andreas J.; Eschbach, Katja; Beisel, Christian; van Nimwegen, Erik; Zavolan, Mihaela |
Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction |
1744-4292 |
Molecular systems biology |
Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) |
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4639778 |
Urchueguía, Arantxa; Galbusera, Luca; Chauvin, Dany; Bellement, Gwendoline; Julou, Thomas; van Nimwegen, Erik |
Genome-wide gene expression noise in Escherichia coli is condition-dependent and determined by propagation of noise through the regulatory network |
1544-9173 ; 1545-7885 |
PLoS Biology |
Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) |
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Cooperations () |
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ID |
Kreditinhaber |
Kooperationspartner |
Institution |
Laufzeit - von |
Laufzeit - bis |
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2310066 |
Zavolan, Mihaela; van Nimwegen, Erik |
Naef, Felix |
EPFL |
01.03.2013 |
31.12.2017 |
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2310071 |
Zavolan, Mihaela; van Nimwegen, Erik |
Lutolf, Matthias |
EPFL |
01.03.2013 |
31.12.2017 |
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2310073 |
Zavolan, Mihaela; van Nimwegen, Erik |
Gatfield, David |
Université de Lausanne |
01.03.2013 |
31.12.2017 |
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2331193 |
van Nimwegen, Erik |
Zavolan, Mihaela |
Biozentrum, University of Basel |
01.01.2000 |
31.12.2099 |
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2337900 |
van Nimwegen, Erik |
Pfohl, Thomas |
Dep. Chemistry, University of Basel |
01.03.2013 |
31.12.2020 |
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2337906 |
van Nimwegen, Erik |
Myers, Eugene |
Max Planck Institute of Molecular Cell Biology and Genetics |
01.03.2013 |
31.12.2025 |
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