Access the full text.
Sign up today, get DeepDyve free for 14 days.
Miles Miller, M. Hafner, Eduardo Sontag, Noah Davidsohn, Sairam Subramanian, Priscilla Purnick, D. Lauffenburger, Ron Weiss (2012)
Modular Design of Artificial Tissue Homeostasis: Robust Control through Synthetic Cellular HeterogeneityPLoS Computational Biology, 8
C. Zechner, J. Ruess, Peter Krenn, Serge Pelet, M. Peter, J. Lygeros, H. Koeppl (2012)
Moment-based inference predicts bimodality in transient gene expressionProceedings of the National Academy of Sciences, 109
L Bleris (2011)
519Mol Syst Biol, 7
L. Bleris, Zhen Xie, David Glass, Asa Adadey, Eduardo Sontag, Y. Benenson
Molecular Systems Biology Peer Review Process File Synthetic Incoherent Feed-forward Circuits Show Adaptation to the Amount of Their Genetic Template. Transaction Report
Andreas Hilfinger, J. Paulsson (2011)
Separating intrinsic from extrinsic fluctuations in dynamic biological systemsProceedings of the National Academy of Sciences, 108
P. Hansen (1996)
Rank-Deficient and Discrete Ill-Posed Problems
Nagarajan Nandagopal, M. Elowitz (2011)
Synthetic Biology: Integrated Gene CircuitsScience, 333
H. Engl, C. Flamm, P. Kügler, James Lu, S. Müller, P. Schuster (2009)
Inverse problems in systems biologyInverse Problems, 25
V. Hatzimanikatis, V. Hatzimanikatis, James Bailey, James Bailey (1996)
MCA has more to say.Journal of theoretical biology, 182 3
C. Baier, J. Katoen (2008)
Principles of model checking
Sara Hooshangi, S. Thiberge, Ron Weiss (2005)
Ultrasensitivity and noise propagation in a synthetic transcriptional cascade.Proceedings of the National Academy of Sciences of the United States of America, 102 10
James Lu, E. August, H. Koeppl (2013)
Inverse problems from biomedicineJournal of Mathematical Biology, 67
B. Ingalls, H. Sauro (2003)
Sensitivity analysis of stoichiometric networks: an extension of metabolic control analysis to non-steady state trajectories.Journal of theoretical biology, 222 1
E. August, K. Parker, Mauricio Barahona (2006)
A Dynamical Model of Lipoprotein MetabolismBulletin of Mathematical Biology, 69
Eĺıas Sillero, M. Hafner, Ariane Ibig, J. Stelling, A. Wagner (2011)
Supplementary Information for “ Efficient Characterization of High-Dimensional Parameter Spaces for Systems Biology ”
Aurélien Rizk, Grégory Batt, F. Fages, S. Soliman (2011)
Continuous valuations of temporal logic specifications with applications to parameter optimization and robustness measuresTheor. Comput. Sci., 412
M. Hafner, H. Koeppl, M. Hasler, A. Wagner (2009)
‘Glocal’ Robustness Analysis and Model Discrimination for Circadian OscillatorsPLoS Computational Biology, 5
T. Lu, Ahmad Khalil, J. Collins (2009)
Next-Generation Synthetic Gene NetworksNature biotechnology, 27
Clive Bowsher, P. Swain (2012)
Identifying sources of variation and the flow of information in biochemical networksProceedings of the National Academy of Sciences, 109
S. Vempala (2007)
Geometric Random Walks: a Survey
James Lu, H. Engl, P. Schuster (2006)
Inverse bifurcation analysis: application to simple gene systemsAlgorithms for Molecular Biology, 1
[With the improvement of protocols for the assembly of transcriptional parts, synthetic biological devices can now be reliably assembled based on a design. The standardization of the parts open up the way for in silico design tools that improve the construct and optimize devices with respect to given formal specifications. The simplest such optimization is the selection of kinetic parameters and protein abundances such that the specified constraints are robustly satisfied. In this chapter we address the problem of determining parameter values that fulfill specifications expressed in terms of a functional on the trajectories of a dynamical model. We solve this inverse problem by linearizing the forward operator that maps parameter sets to specifications, and then inverting it locally. This approach has two advantages over brute-force random sampling. First, the linearization approach allows us to map back intervals instead of points and second, every obtained value in the parameter region is satisfying the specifications by construction.]
Published: Jul 3, 2014
Keywords: Linearization; Parameters; Temporal logic; Linear temporal logic (LTL); Specification functionals; Stoichiometric matrix; State space; Equilibrium point; Bifurcation point; Inverse bifurcation analysis; Inverse bifurcation synthesis
Read and print from thousands of top scholarly journals.
Already have an account? Log in
Bookmark this article. You can see your Bookmarks on your DeepDyve Library.
To save an article, log in first, or sign up for a DeepDyve account if you don’t already have one.
Copy and paste the desired citation format or use the link below to download a file formatted for EndNote
Access the full text.
Sign up today, get DeepDyve free for 14 days.
All DeepDyve websites use cookies to improve your online experience. They were placed on your computer when you launched this website. You can change your cookie settings through your browser.