PUBLICATIONS

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2007

G. Batt, B. Yordanov, R. Weiss, and C. Belta, Robustness Analysis and Tuning of Synthetic Gene Networks, Bioinformatics, vol.23, no.18, pp. 2415-2422, 2007 (pdf)

@article{10.1093/bioinformatics/btm362,
author = {Batt, Grégory and Yordanov, Boyan and Weiss, Ron and Belta, Calin},
title = “{Robustness analysis and tuning of synthetic gene networks}”,
journal = {Bioinformatics},
volume = {23},
number = {18},
pages = {2415-2422},
year = {2007},
month = {07},
abstract = “{Motivation: The goal of synthetic biology is to design and construct biological systems that present a desired behavior. The construction of synthetic gene networks implementing simple functions has demonstrated the feasibility of this approach. However, the design of these networks is difficult, notably because existing techniques and tools are not adapted to deal with uncertainties on molecular concentrations and parameter values.Results: We propose an approach for the analysis of a class of uncertain piecewise-multiaffine differential equation models. This modeling framework is well adapted to the experimental data currently available. Moreover, these models present interesting mathematical properties that allow the development of efficient algorithms for solving robustness analyses and tuning problems. These algorithms are implemented in the tool RoVerGeNe, and their practical applicability and biological relevance are demonstrated on the analysis of the tuning of a synthetic transcriptional cascade built in Escherichia coli.Availability: RoVerGeNe and the transcriptional cascade model are available at http://iasi.bu.edu/\\%7Ebatt/rovergene/rovergene.htmContact:  gregory.batt@imag.fr}”,
issn = {1367-4803},
doi = {10.1093/bioinformatics/btm362},
url = {https://doi.org/10.1093/bioinformatics/btm362},
eprint = {https://academic.oup.com/bioinformatics/article-pdf/23/18/2415/49818329/bioinformatics\_23\_18\_2415.pdf},
}

C. Belta, A. Bicchi, M. Egerstedt, E. Frazzoli, E. Klavins, and G. J. Pappas, Symbolic Planning and Control of Robot Motion, IEEE Robotics and Automation Magazine – special issue on Grand Challenges of Robotics, vol. 14, no. 1, pp. 61-71, 2007 (pdf)

@ARTICLE{4141034,
author={Belta, Calin and Bicchi, Antonio and Egerstedt, Magnus and Frazzoli, Emilio and Klavins, Eric and Pappas, George J.},
journal={IEEE Robotics & Automation Magazine},
title={Symbolic planning and control of robot motion [Grand Challenges of Robotics]},
year={2007},
volume={14},
number={1},
pages={61-70},
doi={10.1109/MRA.2007.339624}}

A. Halasz, V. Kumar, M. Imielinski, C. Belta, O. Sokolsky, S. Pathak, and H. Rubin, Analysis of Lactose Metabolism in E.coli using Reachability Analysis of Hybrid Systems, IET Systems Biology, vol.1, no.2, pp. 130-148, 2007 (pdf)

@article{Halsz2007AnalysisOL, title={Analysis of lactose metabolism in E. Coli using reachability analysis of hybrid systems.}, author={{\’A}d{\’a}m M. Hal{\’a}sz and Vijay R. Kumar and Marcin Imieliński and Calin A. Belta and Oleg Sokolsky and Saurav Pathak and Harvey Rubin}, journal={IET systems biology}, year={2007}, volume={1 2}, pages={ 130-48 }, url={https://api.semanticscholar.org/CorpusID:18028916} }

M. Kloetzer and C. Belta, Temporal Logic Planning and Control of Robotic Swarms by Hierarchical Abstractions, IEEE Transactions on Robotics, vol. 23, no. 2, pp. 320-331, 2007 (pdf)

@ARTICLE{4154829,
author={Kloetzer, Marius and Belta, Calin},
journal={IEEE Transactions on Robotics},
title={Temporal Logic Planning and Control of Robotic Swarms by Hierarchical Abstractions},
year={2007},
volume={23},
number={2},
pages={320-330},
doi={10.1109/TRO.2006.889492}}

G. Batt, C. Belta, and R. Weiss, Model checking liveness properties of genetic regulatory networks, 13th Int. Conf.on Tools and Algorithms for the Construction and Analysis of Systems (TACAS), Braga, Portugal, Lecture Notes in Computer Science, vol. 4424, pp. 323-338, 2007 (pdf)

@inproceedings{10.1007/978-3-540-71209-1_25,
abstract = {Recent studies have demonstrated the possibility to build genetic regulatory networks that confer a desired behavior to a living organism. However, the design of these networks is difficult, notably because of uncertainties on parameter values. In previous work, we proposed an approach to analyze genetic regulatory networks with parameter uncertainties. In this approach, the models are based on piecewise-multiaffine (PMA) differential equations, the specifications are expressed in temporal logic, and uncertain parameters are given by intervals. Abstractions are used to obtain finite discrete representations of the dynamics of the system, amenable to model checking. However, the abstraction process creates spurious behaviors along which time does not progress, called time-converging behaviors. Consequently, the verification of liveness properties, expressing that something will eventually happen, and implicitly assuming progress of time, often fails. In this work, we extend our previous approach to enforce progress of time. More precisely, we define transient regions as subsets of the state space left in finite time by every solution trajectory, show how they can be used to rule out time-converging behaviors, and provide sufficient conditions for their identification in PMA systems. This approach is implemented in RoVerGeNe and applied to the analysis of a network built in the bacterium E. coli.},
address = {Berlin, Heidelberg},
author = {Batt, Gr{\’e}gory and Belta, Calin and Weiss, Ron},
booktitle = {Tools and Algorithms for the Construction and Analysis of Systems},
editor = {Grumberg, Orna and Huth, Michael},
isbn = {978-3-540-71209-1},
pages = {323–338},
publisher = {Springer Berlin Heidelberg},
title = {Model Checking Liveness Properties of Genetic Regulatory Networks},
year = {2007}}

G. Batt, C. Belta and R. Weiss, Model checking genetic regulatory networks with parameter uncertainty, 10th International Workshop on Hybrid Systems: Computation and Control (HSCC), Pisa, Italy, Lecture Notes in Computer Science, vol. 4416, pp. 61-75, 2007 (pdf)

@inproceedings{10.1007/978-3-540-71493-4_8,
abstract = {The lack of precise numerical information for the values of biological parameters severely limits the development and analysis of models of genetic regulatory networks. To deal with this problem, we propose a method for the analysis of genetic regulatory networks with parameter uncertainty. We consider models based on piecewise-multiaffine differential equations, dynamical properties expressed in temporal logic, and intervals for the values of uncertain parameters. The problem is then either to guarantee that the system satisfies the expected properties for every possible parameter value – the corresponding parameter set is then called valid – or to find valid subsets of a given parameter set. The proposed method uses discrete abstractions and model checking, and allows for efficient search of the parameter space. This approach has been implemented in a tool for robust verification of gene networks (RoVerGeNe) and applied to the tuning of a synthetic network build in E. coli.},
address = {Berlin, Heidelberg},
author = {Batt, Gr{\’e}gory and Belta, Calin and Weiss, Ron},
booktitle = {Hybrid Systems: Computation and Control},
editor = {Bemporad, Alberto and Bicchi, Antonio and Buttazzo, Giorgio},
isbn = {978-3-540-71493-4},
pages = {61–75},
publisher = {Springer Berlin Heidelberg},
title = {Model Checking Genetic Regulatory Networks with Parameter Uncertainty},
year = {2007}}

M. Imielinski and C. Belta, Uncovering complex essential reaction sets in E.coli metabolism through pathway fragment analysis, 8th International Conference on Systems Biology (ICSB), Long Beach, California, Oct. 2007

content coming soon…

G. Batt, B. Yordanov, R. Weiss, and C. Belta, Robustness analysis and tuning of synthetic gene networks, Synthetic Biology 3.0, Zurich, Switzerland, 2007

content coming soon…

G. Batt, B. Yordanov, R. Weiss, and C. Belta, Robustness analysis and tuning of synthetic gene networks, Journales Ouvertes Biologie, Informatique et Mathematiques (JOBIM), Marseille, France, 2007

content coming soon…

M. Imielinski and C. Belta, Uncovering complex essential reaction sets in E.coli metabolism through pathway fragment analysis, 8th International Conference on Systems Biology (ICSB), Long Beach, California, Oct. 2007

content coming soon…

B. Yordanov, G. Batt, and C. Belta, Model checking discrete-time piecewise affine systems: application to gene networks, European Control Conference (ECC), 2007 (pdf)

@INPROCEEDINGS{7068809,
author={Yordanov, Boyan and Batt, Gregory and Belta, Calin},
booktitle={2007 European Control Conference (ECC)},
title={Model checking discrete-time Piecewise Affine systems: Application to gene networks},
year={2007},
volume={},
number={},
pages={2619-2626},
doi={10.23919/ECC.2007.7068809}}

M. Kloetzer and C. Belta, Managing non-determinism in symbolic robot motion planning and control, IEEE International Conference on Robotics and Automation (ICRA), Rome, Italy, 2007 (pdf)

@INPROCEEDINGS{4209563,
author={Kloetzer, Marius and Belta, Calin},
booktitle={Proceedings 2007 IEEE International Conference on Robotics and Automation},
title={Managing non-determinism in symbolic robot motion planning and control},
year={2007},
volume={},
number={},
pages={3110-3115},
doi={10.1109/ROBOT.2007.363945}}
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