DREAMY - Distributed Algorithms for Microbiological Systems

ANR-funded research project

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A key advantage of biological computing devices is their ability to sense, compute, and especially to respond to their biological environment, e.g., bacteria can be programmed to act as autonomous robots within the human body. Local presence of certain molecules in the environment allows sensing of neighboring cell types and acting accordingly, e.g., by activating an immune response. Current designs of synthetic circuits in bacteria, however, face severe resource limitations: each genetic part added to the cell imposes an additional burden, becoming progressively toxic for the cell.

The most common design techniques for biological logic gates rely on gene regulation via DNA-binding proteins, nucleic acid (DNA/RNA) interactions, or more recently the CRISPR machinery. Each comes with its own constraints: like limited availability of orthogonal signals for use within the cell (DNA-binding), small dynamic range (RNA-based), or reduced growth rates (the CRISPR machinery). This has led to recent efforts to distribute circuits among several cells to reduce the resource load per cell, taking the formative steps towards distributed bacterial circuits.

The DREAMY research project seeks to develop innovative solutions to the problem of building distributed circuits in bacteria from an algorithmic, theoretical perspective that contributes to real-world implementable solutions.


Joining the project team:

We are hiring interns, postdocs, and PhD students in the DREAMY project. For more information on currently open positions, please contact the coordinators: Matthias Függer, Thomas Nowak, and Manish Kushwaha.


We organize the following related workshops and seminar series:

Project members

Matthias's photo
Matthias Függer

Principal Investigator
chip design, distributed algorithms

Thomas's photo
Thomas Nowak

Principal Investigator
distributed algorithms, stochastic processes

Manish's photo
Manish Kushwaha

Local Coordinator @ Micalis
genetic circuits, phage communication

Rémi's photo
Rémi Baron


Joffroy's photo
Joffroy Beauquier

Project Member
population protocols

Benedikt's photo
Benedikt Bollig

Project Member
AI, model discovery

Catherine's photo
Catherine Bonnet

Project Member
control theory

Janna's photo
Janna Burman

Project Member
population protocols

Arnaud's photo
Arnaud Casteigts

Project Member
dynamic networks

Azammat's photo
Azammat Charaf Zadah

RL, distributed systems

Thomas's photo
Thomas Chatain

Project Member
timed concurrency, process mining

Fabricio's photo
Fabricio Cravo

PhD Student
data analysis

Jean-Loup's photo
Jean-Loup Faulon

Project Member
bio-retrosynthesis, biosensors

Luana's photo
Luana Martins Ferraz

genetic circuits

Laurent's photo
Laurent Fribourg

Project Member
hybrid systems

Stefan's photo
Stefan Haar

Project Member
concurrency, partial orders, systems biology, ecology

Gabriel's photo
Gabriel Le Bouder

stochastic cell processes, distributed computing

Mélanie's photo
Mélanie Pietri

PhD Student
bioproduction, predictive models, optimization

Cristina's photo
Cristina Stoica

Project Member
control theory, cooperative control of multi-agent systems

Abhinav's photo
Abhinav Vinayak Pujar

PhD Student
genetic circuits

Zhuofan's photo
Zhuofan Xu

PhD Student
AI, data science

Former members

Kevin's photo
Kevin E Awoufack

Intern (2023)
single-cell analysis, AI

Antonia's photo
Antonia Baies

Intern (2023)
model discovery, AI

Anisse's photo
Anisse Belhadj

Intern (2022)
bio simulation, C++ development

Thomas's photo
Thomas Chevet

Postdoc (2022/23)
dynamical systems, control theory

Raghda's photo
Raghda El Shehaby

PhD Student (2022/23)
asynchronous circuit design, robust circuits

Leticia's photo
Letícia Levin Diniz

Intern (2022)
bio simulation, full-stack web development

Artur's photo
Artur Piana

Intern (2022)
microfluidics, embedded systems

Elias' photo
Elias Pinter

Intern (2023)
single-cell analysis

Gayathri's photo
Gayathri Prakash

Intern (2022/23)
genetic circuits

Josephine's photo
Josephine L Ramirez

Intern (2023)
genetic circuits

Thomas' photo
Thomas Sadigh Rezvani

Intern (2023)
single-cell analysis

Shaunticlair's photo
Shaunticlair Ruiz

Intern (2023)
stochastic models, cell models

Margarita's photo
Margarita Shimanskaya

Intern (2023)
stochastic simulation

Berndt's photo
Berndt Uhlig

Intern (2023)
AI, neural networks

Jessica's photo
Jessica Vipin

Intern (2023)
AI, verification



We are grateful for the funding provided by ANR (grant ANR-21-CE48-0003), CNRS, Digicosme, INRAe, Institut Farman, RFSI, and Université Paris-Saclay.