Coarse-grained optimization-driven design and piecewise linear modeling of synthetic genetic circuits
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DOI: 10.1016/j.ejor.2014.01.054
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- Weber, Gerhard-Wilhelm & Defterli, Ozlem & Alparslan Gök, SIrma Zeynep & Kropat, Erik, 2011. "Modeling, inference and optimization of regulatory networks based on time series data," European Journal of Operational Research, Elsevier, vol. 211(1), pages 1-14, May.
- Anselm Levskaya & Aaron A. Chevalier & Jeffrey J. Tabor & Zachary Booth Simpson & Laura A. Lavery & Matthew Levy & Eric A. Davidson & Alexander Scouras & Andrew D. Ellington & Edward M. Marcotte & Chr, 2005. "Engineering Escherichia coli to see light," Nature, Nature, vol. 438(7067), pages 441-442, November.
- Mario A Marchisio & Jörg Stelling, 2011. "Automatic Design of Digital Synthetic Gene Circuits," PLOS Computational Biology, Public Library of Science, vol. 7(2), pages 1-13, February.
- Alexandre Mazier & Jean-Charles Billaut & Jean-François Tournamille, 2010. "Scheduling preparation of doses for a chemotherapy service," Annals of Operations Research, Springer, vol. 178(1), pages 145-154, July.
- Nicole Radde, 2008. "The Effect Of Time Scale Differences And Time Delays On The Structural Stability Of Oscillations In A Two-Gene Network," Advances in Complex Systems (ACS), World Scientific Publishing Co. Pte. Ltd., vol. 11(03), pages 471-483.
- Gerhard-Wilhelm Weber & Erik Kropat & Basak Akteke-Öztürk & Zafer-Korcan Görgülü, 2009. "A survey on OR and mathematical methods applied on gene-environment networks," Central European Journal of Operations Research, Springer;Slovak Society for Operations Research;Hungarian Operational Research Society;Czech Society for Operations Research;Österr. Gesellschaft für Operations Research (ÖGOR);Slovenian Society Informatika - Section for Operational Research;Croatian Operational Research Society, vol. 17(3), pages 315-341, September.
- Michael B. Elowitz & Stanislas Leibler, 2000. "A synthetic oscillatory network of transcriptional regulators," Nature, Nature, vol. 403(6767), pages 335-338, January.
- Linh Huynh & John Kececioglu & Matthias Köppe & Ilias Tagkopoulos, 2012. "Automatic Design of Synthetic Gene Circuits through Mixed Integer Non-linear Programming," PLOS ONE, Public Library of Science, vol. 7(4), pages 1-9, April.
- Subhayu Basu & Yoram Gerchman & Cynthia H. Collins & Frances H. Arnold & Ron Weiss, 2005. "A synthetic multicellular system for programmed pattern formation," Nature, Nature, vol. 434(7037), pages 1130-1134, April.
- Tae Seok Moon & Chunbo Lou & Alvin Tamsir & Brynne C. Stanton & Christopher A. Voigt, 2012. "Genetic programs constructed from layered logic gates in single cells," Nature, Nature, vol. 491(7423), pages 249-253, November.
- Timothy S. Gardner & Charles R. Cantor & James J. Collins, 2000. "Construction of a genetic toggle switch in Escherichia coli," Nature, Nature, vol. 403(6767), pages 339-342, January.
- Gebert, J. & Radde, N. & Weber, G.-W., 2007. "Modeling gene regulatory networks with piecewise linear differential equations," European Journal of Operational Research, Elsevier, vol. 181(3), pages 1148-1165, September.
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Keywords
(B) Bioinformatics; Synthetic genetic circuits; Piecewise linear differential equations; Integer linear program;All these keywords.
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