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List of Publications

AUTHOR TITLE JOURNAL/CONFERENCE YEAR
(01)Article
F. Parise, M.E. Valcher, J. Lygeros On the use of hyperplane methods to compute the reachable set of controlled stochastic biochemical reaction networks IEEE Conference on Decision and Control Dec 2015
J. Ruess, F. Parise, A. Milias, M. Khammash, J. Lygeros Iterative experiment design guides the characterization of a light-inducible gene expression circuit Proceedings of the National Academy of Sciences Jun 2015
F. Parise, J. Lygeros, J. Ruess Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study Frontiers in Environmental Science Jun 2015
J. Ruess, J. Lygeros Moment-based methods for parameter inference and experiment design for biochemical reaction networks ACM Transactions on Modeling and Computer Simulation Dec 2014
F. Parise, M.E. Valcher, J. Lygeros On the Reachable Set of the Controlled Gene Expression System IEEE Conference on Decision and Control, Los Angeles, California, USA Dec 2014
F. Parise, J. Ruess, J. Lygeros Grey-box techniques for the identification of a controlled gene expression model European Control Conference (ECC), Strasbourg, France Jun 2014
A. Hjartarson, J. Ruess, J. Lygeros Approximating the solution of the chemical master equation by combining finite state projection and stochastic simulation IEEE Conference on Decision and Control, Florence, Italy, pp. 751-756 Dec 2013
J. Ruess, J. Lygeros Identifying stochastic biochemical networks from single-cell population experiments: a comparison of approaches based on the Fisher information IEEE Conference on Decision and Control, Florence, Italy Dec 2013
J. Ruess, A. Milias, J. Lygeros Designing experiments to understand the variability in biochemical reaction networks Journal of the Royal Society Interface, vol. 10, no. 88, pp. 20130588 Aug 2013
C. Zechner, J. Ruess, P. Krenn, S. Pelet, M. Peter, J. Lygeros, H. Koeppl Moment-Based Inference Predicts Bimodality in Transient Gene Expression PNAS, vol. 109, no. 21, pp. 8340-8345, C. Zechner and J. Ruess contributed equally to this work. May 2012
A. Milias, J. Lygeros Efficient stochastic simulation of metastable Markov chains IEEE Conference on Decision and Control Dec 2011
A. Milias, S. Summers, J. Stewart-Ornstein, I. Zuleta, D. Pincus, H. El-Samad, M. Khammash, J. Lygeros In silico feedback for in vivo regulation of a gene expression circuit Nature Biotechnology, vol. 29, no. 12, pp. 1114–1116, Andreas Milias-Argeitis, Sean Summers, and Jacob Stewart-Ornstein contributed equally to this work. Dec 2011
J. Ruess, A. Milias, S. Summers, J. Lygeros Moment estimation for chemically reacting systems by extended Kalman filtering The Journal of Chemical Physics, vol. 135, no. 16, pp. 165102 Oct 2011
R. Porreca, E. Cinquemani, J. Lygeros, G. Ferrari-Trecate Learning the structure of genetic network dynamics: A geometric approach IFAC World Congress, Milano, pp. 11654-11659 Aug 2011
R. Porreca, E. Cinquemani, J. Lygeros, G. Ferrari-Trecate Structural Identification of Unate-Like Genetic Network Models from Time-Lapse Protein Concentration Measurements IEEE Conference on Decision and Control, Atlanta, Georgia, USA Dec 2010
A. Milias, R. Porreca, S. Summers, J. Lygeros Bayesian model selection for the yeast GATA-factor network: a comparison of computational approaches IEEE Conference on Decision and Control, Atlanta, Georgia, USA Dec 2010
K. Koutroumpas, J. Lygeros Modeling and verification of Stochastic Hybrid Systems using HIOA: A case study on DNA replication Proceedings of the HSCC, 13th ACM International Conference on Hybrid Systems: Computation and Control (HSCC) accepted Apr 2010
R. Porreca, E. Cinquemani, J. Lygeros, G. Ferrari-Trecate Identification of genetic network dynamics with unate structure Bioinformatics, vol. 26, no. 9, pp. 1239-1245 Mar 2010
E. Cinquemani, R. Porreca, J. Lygeros, G. Ferrari-Trecate Canalizing structure of genetic network dynamics: Modelling and identification via mixed-integer programming IEEE Conference on Decision and Control, Shangai, China Dec 2009
E. Cinquemani, V. Roukos, Z. Lygerou, J. Lygeros Numerical analysis of FRAP experiments for DNA replication and repair IEEE Conference on Decision and Control Dec 2008
E. Cinquemani, A. Milias, S. Summers, J. Lygeros Stochastic dynamics of genetic networks: modelling and parameter identification Bioinformatics, vol. 24, no. 23, pp. 2748-2754 Dec 2008
K. Koutroumpas, Z. Lygerou, J. Lygeros Parameter Identification for a DNA Replication Model IEEE International Conference on BioInformatics and BioEngineering, Athens Oct 2008
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, no. 3, pp. 786-802 Aug 2008
J. Lygeros, K. Koutroumpas, S. Dimopoulos, I. Legouras, Panagiotis Kouretas, Christian Heichinger, Paul Nurse, Z. Lygerou Stochastic hybrid modeling of DNA replication across a complete genome PNAS, vol. 105, no. 34, pp. 12295-12300 Aug 2008
E. Cinquemani, A. Milias, J. Lygeros Identification of Genetic Regulatory Networks: A Stochastic Hybrid Approach IFAC World Congress, Seoul, Korea Jul 2008
E. Cinquemani, R. Porreca, G. Ferrari-Trecate, J. Lygeros Subtilin Production by Bacillus Subtilis: Stochastic Hybrid Models and Parameter Identification IEEE Trans. on Circuits and Systems-I, Special Issue on Systems Biology Jan 2008
E. Cinquemani, R. Porreca, G. Ferrari-Trecate, J. Lygeros Parameter identification for stochastic hybrid models of biological interaction networks IEEE Conference on Decision and Control Dec 2007
K. Koutroumpas, E. Cinquemani, J. Lygeros Randomized optimization methods in parameter identification for biochemical network models FOSBE 2007 Sep 2007
S. Dimopoulos, I. Legouras, Z. Lygerou, G. Xouri, J. Lygeros DNA replication in the fission yeast: robustness in the face of uncertainty Yeast, vol. 23, pp. 951-962 2006
P. Kouretas, K. Koutroumpas, J. Lygeros, Z. Lygerou Stochastic hybrid modelling of biochemical processes vol. 24, no. 9083, in C.G.Cassandras and J.Lygeros, editors, Stochastic Hybrid Systems, Automation and Control Engineering Series. Nov 2006
P. Kouretas, K. Koutroumpas, J. Lygeros Parameter identification for piecewise deterministic markov processes: a case study on a biochemical network IFAC Conference on Analysis and Design of Hybrid Systems (ADHS), ADHS06 Alghero , Italy Jun 2006
Book Chapter
J. Ruess, J. Lygeros On the use of the moment equations for parameter inference, control and experimental design in stochastic biochemical reaction networks Computational Methods in Systems Biology, vol. 8130 of Lecture Notes in Computer Science LNCS, pp. 1-4 Sep 2013
E. Cinquemani, A. Milias, S. Summers, J. Lygeros Local identification of piecewise deterministic models of genetic networks Lecture Notes in Computer Science LNCS, vol. 5469, pp. 105-119 2009
(04)Technical Report
R. Porreca, E. Cinquemani, J. Lygeros, G. Ferrari-Trecate Invalidation of the structure of genetic network dynamics: A geometric approach vol. AUT11-11 2011
A. Milias, R. Porreca, S. Summers, J. Lygeros Bayesian model selection for the yeast GATA-factor network: a comparison of computational approaches vol. AUT10-06 Aug 2010
R. Porreca, E. Cinquemani, J. Lygeros, G. Ferrari-Trecate Canalizing structure of genetic network dynamics: modelling and identification via mixed-integer programming vol. AUT09-10 Dec 2009
E. Cinquemani, R. Porreca, G. Ferrari-Trecate, J. Lygeros Subtilin Production by Bacillus Subtilis: Stochastic Hybrid Models and Parameter Identification vol. AUT06-13 Dec 2006
K. Koutroumpas, E. Cinquemani, P. Kouretas, J. Lygeros Parameter Identification for Stochastic Hybrid Systems: An application to Subtilin Production by Bacillus Subtilis vol. AUT06-12 Nov 2006
(06)Talk
A. Milias Bounds for HDMR approximations via concentration-of-measure inequalities IfA Internal Seminar Series, ETH Zürich Feb 2011
K. Koutroumpas DNA replication modeling and analysis IfA Internal Seminar Series Dec 2008
E. Cinquemani, V. Roukos, Z. Lygerou, J. Lygeros Numerical analysis of FRAP experiments for DNA replication and repair Conference on Decision and Control (CDC), Cancun, Mexico Dec 2008
E. Cinquemani Stochastic dynamics of genetic regulatory networks: modelling and parameter identification INRIA Rhone-Alpes Nov 2008
E. Cinquemani Stochastic dynamics of genetic regulatory networks: Modelling and identification Systems Biology workshop, Padova Nov 2008
K. Koutroumpas, Z. Lygerou, J. Lygeros Parameter Identification for a DNA Replication Model IEEE International Conference on BioInformatics and BioEngineering, Athens Oct 2008
E. Cinquemani Identification of stochastic hybrid models of genetic networks IfA Internal Seminar Series Oct 2008
A. Milias Iterated Function Systems: a brief overview and stability properties IfA Internal Seminar Series, ETH Zürich Jun 2008
E. Cinquemani, R. Porreca, G. Ferrari-Trecate, J. Lygeros A general framework for the identification of jump Markov linear systems IEEE Conference on Decision and Control Dec 2007
A general framework for the identification of jump Markov linear systems IEEE Conference on Decision and Control Dec 2007
E. Cinquemani Stochastic hybrid modeling and parameter identification of genetic networks Groningen Nov 2007
E. Cinquemani Stochastic modeling and parametric identification of genetic networks ERNSI Workshop 2007, Venice (Italy) Oct 2007
E. Cinquemani, A. Milias, J. Lygeros Identification of genetic regulatory networks: A stochastic hybrid approach ETH Zurich Aug 2007
Z. Lygerou, J. Lygeros Stochastic hybrid models for DNA replication IEEE Conference on Decision and Control Dec 2006
J. Lygeros An overview of the use of hybrid models in biochemical networks IEEE Conference on Decision and Control Dec 2006
E. Cinquemani, K. Koutroumpas, J. Lygeros Parameter identification for B.Subtilis HYGEIA meeting, Institut fur Automatik, ETH Zurich Oct 2006