Eugenio Cinquemani

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Announcements:

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Curriculum vitae

I received the Laurea degree in 2001 and the Ph.D. degree in 2005 from the Department of Information Engineering of the University of Padova, Italy. My formation included a 1-year visit at the University of California – Berkeley on a student exchange program. In 2005 I won a 1-year research grant (“assegno di ricerca”) at the same department. From 2006 to 2009 I have been working as a Post-Doc at the Automatic Control Laboratory of the ETH Zurich, Switzerland. In November 2009 I was appointed Research Scientist (“Chargé de Recherche”, CR) at INRIA Grenoble – Rhône-Alpes, France, where I started working in project-team IBIS (computational biology), and where I am currently working in the follow-up project-team MICROCOSME (modelling and control for life sciences). I successfully applied for a Research Director position (“directeur de recherche”, DR) in 2023.

I obtained the Italian qualification for Engineering (“Esame di Stato”) in 2002, the Italian scientific qualification (“Abilitazione”) for associate professorship in Automatic Control (in 2014, renewed in 2021) and in Bioengineering (in 2021), and the French accreditation to supervise research in Informatics and Applied Mathematics (HDR) in 2019.

Download CV here (last updated 07-Aug-2025)

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Research interests

• Modelling, identification, estimation and control of microbial dynamics
• Identification, estimation and control methods for stochastic and hybrid systems

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Projects

• IMOCEP: Innovations for modeling of growth – from a cellular level to pediatric development, PEPR Maths-Vives (2024–ongoing)
• ARBOREAL: Branching resource allocation processes for the analysis and inference of phenotypic growth variability, ANR JCJC (Aline Marguet, 2023–ongoing)
• Ctrl-AB – Optimization and control of the productivity of an algal-bacterial consortium, ANR Mathématiques et sciences du numérique pour la biologie et la santé (2021-ongoing). Coordinator
• AnaComBa: Analysis of bacterial communities: stochastic modelling. Équipe-Action PERSYVAL-lab (2021–2024)
• Plug-N-Bio – A plug-and-play platform for reproducible microbial culture control experiments, Action de Développement Technologique, Inria (2022–2024). Project leader
• OptiCo – OPTImal COntrol software for microbial communities in a system of mini-bioreactors. Action de Développement Technologique, Inria (2019–2021). Project leader
• CoSoft – Control software for a system of mini-bioreactors. Action de Développement
  Technologique, Inria Grenoble – Rhône-Alpes (2017 – 2019). Project leader
• RECOM – Competition of RNAs for RNase E, a mechanism regulating their degradation and the energy and carbon metabolism in the cell, ANR Biochimie et chimie du vivant (2023 – ongoing)
• RIB-ECO (RIBonucleotide ECOnomy) – Engineering RNA life cycle to optimize economy of microbial energy: Application to the bioconversion of biomass-derived carbon sources, ANR Bioéconomie : technologies spécifiques et approches systèmes (2018-2022)
• Maximic – Optimal control of microbial cells by natural and synthetic strategies, ANR (2017-2023)
• CoSy – Real-time control of synthetic microbial communities, Inria Project-Lab (2017-2021). Coordinator
• MEMIP – Mixed‐Effects Models of Intracellular Processes : Methods, Tools and Applications, ANR Société de l’information et de la communication (2017-2021). Partner leader
• RESET – Arrest and restart of the gene expression machinery in bacteria: from mathematical models to biotechnological applications (2012-2017), Investissements d’Avenir, Bioinformatique
• GemCO – Model reduction, experimental validation, and control for the gene expression machinery in E. coli (2010-2013), ANR Blanc
• ColAge – Natural and engineering solutions to the control of bacterial growth and aging. Large-Scale Initiative Action INRIA-INSERM (2009-2013)
• MetaGenoReg – Towards an understanding of the interrelations between metabolic and gene regulation: E. coli carbon metabolism as a test case, ANR Biologie systémique (BIOSYS, 2006-2010)

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Teaching

• Module on “Identification of biochemical reaction networks”, Phelma, Grenoble-INP

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Other activities

• Co-organizer of the Modelling Heterogeneous Populations with applications in Biology workshop, online, May 17-18, 2021
• Co-organizer of the 19th International Conference on Computational Methods in Systems Biology (CMSB 2021), Bordeaux (France), September 22-24, 2021
• Co-organizer of HSB 2016

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Publications

Highlights:

• A. Pavlou , E. Cinquemani , C. Pinel , N. Giordano , M. van Melle-Gateau, I. Mihalcescu, J. Geiselmann, H. de Jong, “Single-cell data reveal heterogeneity of investment in ribosomes across a bacterial population”, Nature Communications, 16:285, 2025 (Full text)
• M. Mauri, J.-L. Gouzé, H. de Jong, E. Cinquemani, “Enhanced production of heterologous proteins by a synthetic microbial community: Conditions and trade-offs”. PLoS Computational Biology, 16(4):e1007795, 2020 (Full text, bioRxiv preprint)
• A.Marguet, M.Lavielle, E.Cinquemani, “Inheritance and variability of kinetic gene expression parameters in microbial cells: Modelling and inference from lineage tree data”. Bioinformatics (Proceedings of ISMB/ECCB 2019), 35(14):i586–i595, 2019 (Full text)
• E.Cinquemani, “Stochastic reaction networks with input processes: Analysis and application to gene expression inference”, Automatica, 101:150-156, 2019 ( Full text, arXiv extended preliminary version)
• E.Cinquemani, “Identifiability and Reconstruction of Biochemical Reaction Networks from Population Snapshot Data”, Processes (Special Issue on Computational Synthetic Biology, J.R. Banga and F.Menolascina, Eds.), 6(9):136, 2018 (Full text)
• S.Berthoumieux, M.Brilli, H.de Jong, D.Kahn, E.Cinquemani, “Identification of metabolic network models from incomplete high-throughput datasets”. Bioinformatics, Vol.27, No.13 (ISMB 2011), pp.i186-i195.
  Selected as Outstanding Student Paper (Ian Lawson Van Toch Memorial Award) at ISMB/ECCB 2011.
  (Full text)
• E.Cinquemani,M.Agarwal, D.Chatterjee, J.Lygeros, “Convexity and convex approximations of discrete-time stochastic control problems with constraints”. Automatica, Vol.47, Issue 9, pp.2082-2087, September 2011.
  (Full text)

Editing:

• E.Cinquemani, L.Paulevé (Eds.). Special Issue of the 19th International Conference on Computational Methods in Systems Biology. BMC Bioinformatics Supplements, 24(1), 2023
• E.Cinquemani, L.Paulevé (Eds.). Computational Methods in Systems Biology. Proceedings of the 19th International Conference on Computational Methods in Systems Biology (CMSB). Lecture Notes in Bioinformatics (LNBI) 12881, Springer, 2021
• E.Cinquemani, A.Donzé (Eds.), “Hybrid Systems Biology” (Proceedings of the 5th international workshop, HSB 2016), Lecture Notes in Bioinformatics (LNBI) 9957, 2016 (Full book)

All:

• On Google Scholar
• On Hal
• Or see my CV

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(Last page update: 08-Aug-2025)