Eugenio Cinquemani

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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 at INRIA Grenoble – Rhône-Alpes, France, where I am currently working in the computational biology and bioinformatics project-team IBIS.

I obtained the Italian qualification for Engineering (“Esame di Stato”) in 2002 and the French accreditation to supervise research in Informatics and Applied Mathematics (HDR) in 2019.

Download CV here (last updated 25-Sept-2020)

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Research interests

• Modelling, identification and estimation of biochemical interaction network dynamics from experimental data
  Watch my presentation at IBM Research Lab Zurich ! (January 28, 2016)
  
• Identification, estimation and control methods for stochastic and hybrid systems

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Projects

• 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 (to be started)
• 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-ongoing).
• Maximic – Optimal control of microbial cells by natural and synthetic strategies, ANR (2017-ongoing)
• CoSy – Real-time control of synthetic microbial communities, Inria Project-Lab (2017-ongoing).
• MEMIP – Mixed‐Effects Models of Intracellular Processes : Methods, Tools and Applications, ANR Société de l’information et de la communication (2017-ongoing)
• 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 (2009-2013), Large-Scale Initiative Action INRIA-INSERM
• MetaGenoReg – Towards an understanding of the interrelations between metabolic and gene regulation: E. coli carbon metabolism as a test case (2006-2010), ANR Biologie systémique (BIOSYS)

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Teaching

• Course of Statistics, CRI Paris (My presentation, Course presentation, Moodle)
• Module on “Identification of biochemical reaction networks”, Phelma Grenoble
• Module on “Identification of biochemical reaction networks”, INSA Lyon

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Other activities

• Co-organizer of HSB 2016

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Publications

Publications in Systems Biology

• 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)
• E.Cinquemani, “Inference of the statistics of a modulated promoter process from population snapshot gene expression data”. Proceedings of the 21th IFAC World Congress, Berlin, Germany, July 12-17, 2020, accepted.
• 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, F.Mairet, I.Yegorov, H.de Jong, J.-L. Gouzé, “Optimal control of bacterial growth for metabolite production: The role of timing and costs of control”. Proceedings of the 17th European Control Conference (ECC 2019).
• 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), 6(9):136, 2018 (Full text)
• H.de Jong, S.Casagranda, N.Giordano, E.Cinquemani, D.Ropers, J.Geiselmann, J.-L.Gouzé, “Mathematical modelling of microbes: Metabolism, gene expression and growth”. Journal of the Royal Society Interface, 14:20170502, 2017 (Full text)
• M.Morin, D.Ropers, E.Cinquemani, J.C.Portais, B.Enjalbert, M.Cocaign-Bousquet, “The Csr system regulates Escherichia coli fitness by controlling glycogen accumulation and energy levels”. mBio, 8(5):e01628-17, 2017 (Full text)
• E.Cinquemani, V.Laroute, M.Cocaign-Bousquet, H.de Jong, D. Ropers, “Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data”. Bioinformatics (ISMB 2017), 33(14):i301–i310 (Full text)
• E.Cinquemani, “Structural identification of biochemical reaction networks from population snapshot data”. Proceedings of the 20th IFAC World Congress, Toulouse, France, July 9 – 14, 2017, Vol. 50, Issue 1, pp.12629-12634 (Preprint, Full text)
• 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)
• E.Cinquemani, “On observability and reconstruction of promoter activity statistics from reporter protein mean and variance profiles”. Proceedings of the 5th International Workshop on Hybrid Systems Biology, Grenoble, France, October 20-21, 2016
  (Full text)
• A.M. Gonzalez-Vargas, E.Cinquemani, G. Ferrari-Trecate, “Validation methods for population models
  of gene expression dynamics”. Proceedings of the 6th IFAC Conference on Foundations of Systems Biology in Engineering (FOSBE), Magdeburg, Germany, October 9-12, 2016
  (Technical report version)
• A. Llamosi, A.M. Gonzalez-Vargas, C. Versari, E. Cinquemani, G. Ferrari-Trecate, P. Hersen, G. Batt, “What population reveals about individual cell identity: Single-cell parameter estimation of models of gene expression in yeast”. PLoS Computational Biology, 12(2):e1004706, 2016
  (Full text)
• E.Cinquemani, “Reconstruction of promoter activity statistics from reporter protein population snapshot data”. Proceedings of the 54th IEEE Conference on Decision and Control, Osaka, Japan, December 15-18, 2015
  (Full text)
• E.Cinquemani, “Reconstructing statistics of promoter switching
  from reporter protein population snapshot data”. Proceedings of the 4th International Workshop on Hybrid Systems Biology, Madrid, Spain, September 4-5, 2015
  (Full text)
• D.Stefan, C.Pinel, S.Pinhal, E.Cinquemani, J.Geiselmann, H.de Jong, “Inference of quantitative models of bacterial promoters from time-series reporter gene data”. PLoS Computational Biology, 11(1):e1004028, 2015
  (Full text)
• M.A.Rapsomaniki, E.Cinquemani, N.N.Giakoumakis, P.Kotsantis, J.Lygeros, Z.Lygerou, “Inference of protein kinetics by stochastic modeling and simulation of Fluorescence Recovery After Photobleaching experiments”.
  Bioinformatics, 31(3):355-362, 2015
  (Advance online access)
• L.R.M. Maruthi, I.Tkachev, A.Carta, E.Cinquemani, P.Hersen, G.Batt, A.Abate, “Towards real-time control of gene expression at the single cell level: A stochastic control approach”, 12th International Conference on Computational Methods in Systems Biology, 2014
  (Full text)
• A.Gonzalez, J.Uhlendorf, J.Schaul, E.Cinquemani, G.Batt, G.Ferrari-Trecate, “Identification of biological models from single-cell data: A comparison between mixed-effects and moment-based inference”. Proceedings of the 12th European Control Conference, 2013
  (Tecnical report version)
• A.Carta, E.Cinquemani, “State estimation for gene networks with intrinsic and extrinsic noise: a case study on E.coli arabinose uptake dynamics”. Proceedings of the 12th European Control Conference, 2013
  (Full text)
• S.Berthoumieux, M.Brilli, D.Kahn, H.de Jong, E.Cinquemani, “On the identifiability of metabolic network models”. Journal of Mathematical Biology, Vol.67, Issue 6-7, pp. 1795-1832, December 2013
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• R.Porreca, E.Cinquemani, J.Lygeros, G.Ferrari-Trecate, “Invalidation of the structure of genetic network dynamics: A geometric approach”. International Journal of Robust and Nonlinear Control, Special Issue on System Identification for Biological Systems, Vol.22, Issue 10, pp.1140-1156, July 2012.
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• S.Berthoumieux, D.Kahn, H.de Jong, E.Cinquemani, “Structural and practical identifiability of approximate metabolic network models”. Proceedings of the 16th IFAC symposium on System Identification, Brussels, July 11-13, 2012.
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• 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)
• R.Porreca, E.Cinquemani, J.Lygeros, G.Ferrari-Trecate, “Learning the structure of genetic network dynamics : A geometric approach”. Proceedings of the 18th IFAC World Congress, Milano, Italy, August 28 – September 2, 2011, pp.11654-11659.
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• R. Porreca, E. Cinquemani, J. Lygeros, G. Ferrari-Trecate, “Identification of genetic network dynamics with unate structure”. Bioinformatics, vol.26, n.9, pp.1239-1245, May 2010.
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• R.Porreca, E.Cinquemani, J.Lygeros,G.Ferrari-Trecate, “Structural identification of unate-like genetic network models from time-lapse protein concentration measurements”, Proceedings of the 49th IEEE Conference on Decision and Control, Atlanta, GA, USA, December 15-17 2010, pp. 2529-2534.
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• E.Cinquemani, R.Porreca, J.Lygeros, G.Ferrari-Trecate, “Canalizing structure of genetic network dynamics: modelling and identification by mixed-integer programming”. Proceedings of the 48th IEEE Conference on Decision and Control, Shanghai, Popular Republic of China, December 16-18, 2009, pp.5618-5623.
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• E.Cinquemani, A.Milias-Argeitis, S.Summers, J.Lygeros, “Local identification of piecewise deterministic models of genetic networks”. In Proceedings of the 12th Hybrid Systems: Computation and Control conference, R.Mujumdar and P.Tabuada Eds., n.5469 of the LNCS series, pp.105-119, Springer, 2009.
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• E.Cinquemani, A.Milias-Argeitis, S.Summers, J.Lygeros, “Stochastic dynamics of genetic networks: modelling and parameter identification”. Bioinformatics, vol.24, n.23, pp.2748-2754, December 2008.
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• E.Cinquemani, V.Roukos, Z.Lygerou, J.Lygeros, “Numerical analysis of FRAP experiments for DNA replication and repair”. In {Proceedings of the 47th IEEE Conference on Decision and Control}, Cancun, Mexico, December 2008.
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• K. Koutroumpas, E. Cinquemani, P. Kouretas, J. Lygeros, “Parameter Identification for Stochastic Hybrid Systems Using Randomized Optimization: A Case Study on Subtilin Production by Bacillus Subtilis”. Nonlinear Analysis: Hybrid Systems, vol. 2, n.3, pp.786-802, Aug 2008.
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• E. Cinquemani, R. Porreca, G. Ferrari-Trecate, J. Lygeros, “Subtilin Production by Bacillus Subtilis: Stochastic Hybrid Models and Parameter Identification”, IEEE Transactions on Automatic Control & Transactions on Circuits and Systems-I, Joint Special Issue on Systems Biology, Jan 2008.
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• E.Cinquemani, A.Milias-Argeitis, J.Lygeros, “Identification of Genetic Regulatory Networks : A Stochastic Hybrid Approach”. Proceedings of the 17th IFAC World Congress, Seoul, Korea, July 2008.
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• E.Cinquemani, R.Porreca, G.Ferrari-Trecate, J.Lygeros, “Parameter identification for stochastic hybrid models of biological interaction networks”. Proceedings of the 46th IEEE Conference on Decision and Control, New Orleans, USA, December 2007.
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• K.Koutroumpas, E.Cinquemani, J.Lygeros, “Randomized optimization methods in parameter identification for biochemical network models”. Proceedings of the 2nd Foundations of Systems Biology in Engineering conference, September 2007.

Other journal publications

• P.Hokayem, E.Cinquemani, D.Chatterjee, F.Ramponi, J.Lygeros, “Stochastic receding horizon control with output feedback and bounded controls”, Automatica, Vol.48, Issue 1, pp.77-88, January 2012.
  (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)
• D.Chatterjee, E.Cinquemani, J.Lygeros, “Maximizing the probability of attaining a target prior to extinction”. Nonlinear Analysis: Hybrid Systems, No.5 pp.367-381, 2011.
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• E. Cinquemani, G.Pillonetto, “Wavelet estimation by Bayesian thresholding and model selection”, Automatica, vol.44, n.9, pp.2288-2297, Sep 2008.
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• E. Cinquemani, M.Micheli, “State estimation in stochastic hybrid systems with sparse observations”, IEEE Transactions on Automatic Control, vol.51, n.8, pp.1337-1342, Aug 2006.
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• E. Cinquemani, “A superposition principle for the Kalman filter”,Systems and Control Letters, vol.55, n.1, pp.38-44, Jan 2006.
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Other conference publications

• P.Hokayem, E.Cinquemani, D.Chatterjee, F.Ramponi, J.Lygeros, “Stochastic receding horizon control with output feedback and bounded control inputs”, Proceedings of the 49th IEEE Conference on Decision and Control, Atlanta, GA, USA, December 15-17, 2010, pp. 6095-6100.
  (Full text)
• P.Hokayem, E.Cinquemani, D.Chatterjee, J.Lygeros, “Stochastic MPC with imperfect state information and bounded controls”, Proceedings of the UKACC International Conference on Control, Coventry, UK, September 2010.
• D.Chatterjee, E.Cinquemani, G.Chaloulos, J.Lygeros, “On stochastic control up to a hitting time”. Proceedings of the 48th Conference on Decision and Control, Shanghai, Popular Republic of China, December 16-18, 2009, pp.531-536.
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• D.Chatterjee, E.Cinquemani, J.Lygeros, “Probabilistic regulation in stochastic hybrid systems subject to safety constraints”. Proceedings of the 3rd IFAC Conference on Analysis and Design of Hybrid Systems (ADHS) 2009, Zaragoza, Spain, Vol.3, Part 1.
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• M.Agarwal, E.Cinquemani, D.Chatterjee and J.Lygeros, “On convexity of stochastic optimization problems with constraints”. Proceedings of the 10th European Control Conference, Budapest, Hungary, August 2009, pp.2827-2832.
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• E.Cinquemani, R.Porreca, G.Ferrari-Trecate, J.Lygeros, “A general framework for the identification of jump Markov linear systems”. Proceedings of the 46th IEEE Conference on Decision and Control, New Orleans, USA, December 2007.
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• E.Cinquemani, G.Picci, “Identification of wood rings from sparse tomographic data”. Proceedings of the 45th IEEE Conference on Decision and Control, San Diego, USA, December 2006.
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• E.Cinquemani, M.Micheli, G.Picci, “Fault detection in a class of stochastic hybrid systems”. Proceedings of the 43rd IEEE Conference on Decision and Control, Paradise Island, Bahamas, pp.3197-3203, December 2004.
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• E.Cinquemani, M.Micheli, G.Picci, “State estimation and prediction in a class of stochastic hybrid systems”. Proceedings of the 16th International Symposium on Mathematical Theory of Networks and Systems, No.254, July 2004.

Theses

• E.Cinquemani, Identification, estimation and control of gene expression and metabolic network dynamics, HDR, École Doctorale MSTII, Université Grenoble-Alpes, 2019 (Manuscript).
• E.Cinquemani, Estimation problems in jump Markov systems. Ph.D. Thesis, Department of Information Engineering, University of Padova, Italy, February 2005.
• E.Cinquemani, Approccio Bayesiano alla deconvoluzione mediante wavelets (in Italian). Laurea Thesis, University of Padova, Italy, July 2001.

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(Last page update: September 25, 2020)