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### Short bio

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.

My research interests include identification, estimation and control methods for stochastic and hybrid systems, with focus on systems biology applications, notably the reconstruction of biological network models (structure and parameter estimation, model reduction) from experimental data.

Download my CV (last update 22-Dec-2015)

Publications in Systems Biology

Other journal publications

Other conference publications

Theses

### Publications in Systems Biology

### 2015

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.

(to appear)

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.

(to appear)

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.

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)

### 2014

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 link to be made available)

### 2013

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".
*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".
*12th European Control Conference*, 2013.

(Full text available soon)

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.

(Full text)

### 2012

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.

(Full text)

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.

(Full text)

### 2011

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.

(Full text)

### 2010

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.

(Full text)

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.

(Full text)

### 2009

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.

(Full text)

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.

(Preprint )

### 2008

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.

(Full text)

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.

(Full text)

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.

(Full text)

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.

(Full text)

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.

(Full text)

### 2007

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.

(Full text)

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.

(Preprint )

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### 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.

(Full text)

E. Cinquemani, G.Pillonetto, "Wavelet estimation by Bayesian thresholding and model selection", *Automatica*, vol.44, n.9, pp.2288-2297, Sep 2008.

(Full text)

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.

(Full text)

E. Cinquemani, "A superposition principle for the Kalman filter",*Systems and Control Letters*, vol.55, n.1, pp.38-44, Jan 2006.

(Full text)

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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.

(Preprint )

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.

(Full text)

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.

(Full text )

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.

(Preprint )

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.

(Full text)

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).

(Full text)

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, Pages
3197-3203, December 2004.

(Full text)

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.

(Preprint )

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### Theses

E.Cinquemani, Estimation problems in jump Markov systems. Ph.D. Thesis, Department of Information Engineering, University of Padova, Italy, February 2005.

(Dissertation )

E.Cinquemani, Approccio Bayesiano alla deconvoluzione mediante wavelets (in Italian). Laurea Thesis, University of Padova, Italy, July 2001.

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