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Dynamic Nucleic Acid Systems lab

## Journal publications |
## In preparation/submitted |
## Conference publications |
## Book chapters |

Journal publications

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- “Dynamic control of aptamer binding using strand displacement reactions”. J Lloyd, CH Tran, C Cuba Samaniego HKK Subramanian and E Franco, ACS Synthetic Biology (to appear), 2017.
- “Self-assembly of multi stranded RNA motifs into lattices and tubular structures”. JM Stewart, HKK Subramanian and E Franco, Nucleic Acids Research, 2017.
- “Aggregates of Monotonic Step Response systems: a structural classification”. F Blanchini, C Cuba Samaniego, E Franco, G Giordano, IEEE Transactions on Control of Network Systems, 2017.
- “Stability analysis of an artificial biomolecular oscillator with non-cooperative regulatory interactions”. C Cuba Samaniego, G Giordano, F Blanchini and E Franco, Journal of Biological Dynamics, 2016.
- “pH-controlled assembly of DNA tiles”. A Amodio, AF Adedeji, M Castronovo, E Franco and F Ricci, JACS, 2016.
- “Programmable RNA microstructures for coordinated delivery of siRNAs”. JM Stewart, M Viard, HKK Subramanian, BK Roark, KA Afonin and E Franco, Nanoscale, 2016.
- "The smallest eigenvalue of the generalized Laplacian matrix, with application to network-decentralized estimation for homogeneous systems" G Giordano, F Blanchini, E Franco, V Mardanlou and PL Montessoro. IEEE Transactions on Network Science and Engineering, to appear, 2016.
- "Self-assembly of large RNA structures: learning from DNA nanotechnology." JM Stewart and E Franco. DNA and RNA Nanotechnology, 2 (1), 2016.
- "Molecular titration promotes oscillations and bistability in minimal network models with monomeric regulators" C Cuba Samaniego, G Giordano, J Kim, F Blanchini, E Franco. ACS Synthetic Biology, 5 (4), pp 321–333, 2016.
- “Compartmental flow control: Decentralization, robustness and optimality” F Blanchini, E Franco, G Giordano, V Mardanlou, PL Montessoro. Automatica 64, 18-28, 2016.
- “Designing a self-regulating biomolecular comparator” DK Agrawal, E Franco, R Schulman. Journal of the Royal Society Interface, 12 (111), 20150586, 2015.
- “An analytical approach to bistable biological circuit discrimination using real algebraic geometry” D Siegal-Gaskins, E Franco, T Zhou, RM Murray. Journal of the Royal Society Interface, 12, 20150288, 2015.
- “Network-Decentralized Control Strategies for Stabilization” F Blanchini, E Franco, G Giordano. Automatic Control, IEEE Transactions on. 60 (2), 491-496, 2015.
- “Computing the structural influence matrix for biological systems” G Giordano, C Cuba Samaniego, E Franco, F Blanchini. Journal of mathematical biology, 1-32, 2015.
- “A structural classification of candidate oscillators and multistationary biochemical systems” F Blanchini, E Franco, G Giordano. Bulletin of mathematical biology, 76 (10), 2542-2569, 2014.
- “Negative autoregulation matches production and demand in synthetic transcriptional networks” E Franco, G Giordano, PO Forsberg, and RM Murray. ACS synthetic biology 3 (8), 589-599, 2014.
- "Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator" M Weitz, J Kim, K Kapsner, E Winfree, E Franco, FC Simmel. Nature chemistry 6 (4), 295-302, 2014.
- "Dynamically reshaping signaling networks to program cell fate via genetic controllers" KE Galloway, E Franco, CD Smolke. Science 341 (6152), 1235005, 2013.
- "Structural properties of the MAPK pathway topologies in PC12 cells" E Franco, F Blanchini. Journal of mathematical biology 67 (6-7), 1633-1668, 2013.
- "Timing molecular motion and production with a synthetic transcriptional clock" E Franco, E Friedrichs, J Kim, R Jungmann, RM Murray, E Winfree, FC Simmel. Proceedings of the National Academy of Sciences, 108(40), E784-E793, 2011.
- "Structurally robust biological networks" F Blanchini, E Franco. BMC systems biology 5 (1), 74, 2011.
- “Geometry of unsteady fluid transport during fluid-structure interactions” E Franco, D N Pekarek, J Peng and JO Dabiri, Journal of Fluid Mechanics, vol. 589, pages 125-145, 2007.
- “Belief Consensus and Distributed Hypothesis Testing in Sensor Networks” R Olfati-Saber, E Franco, E Frazzoli and JS Shamma. Lecture Notes in Control and Information Sciences, Volume 331, pages 169 - 182, 2006.
- “Cooperative Control of Discrete Time Agents with Delayed Information Exchange: a Receding--Horizon Approach” E Franco, T Parisini and MM Polycarpou. International Journal of Robust and Nonlinear Control, vol. 17, pages 982-1001, 2007.

#### 2017

#### 2016

#### 2015

#### 2014

#### 2013

#### 2011

#### 2010 and earlier

In preparation/submitted

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- “Autonomous dynamic control of DNA nanostructure self-assembly”. LN Green, HKK Subramanian, V Mardanlou, J Kim, RF Hariadi and E Franco, under review.
- “pH-driven reversible self-assembly of micron-scale DNA scaffolds”. LN Green, A. Amodio, HKK Subramanian, F. Ricci and E Franco, under review.
- "A coarse-grained model captures the temporal evolution of DNA nanotube length distributions". V Mardanlou, KC Yaghoubi, LN Green, HKK Subramanian, RF Hariadi, J Kim and E Franco, under review.
- “A biomolecular network motif for period doubling devices”. C Cuba Samaniego and E Franco, under review.
- “Engineering DNA nanotubes for resilience in the cytoplasmic environment”. MA Klocke, J Garamella, V Noireaux and E Franco, in preparation.
- “T7 RNA polymerase can transcribe and induce disassembly of DNA nanostructures”. SW Schaffter, LN Green, J Schneider, HKK Subramanian, R Schulman and E Franco, in preparation.

Refereed conference publications

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- “Design of a bistable network using the CRISPR/Cas system”. C Cuba Samaniego, HKK Subramanian and E Franco. Invited paper. Proceedings of the IEEE Conference on Control Technology and Applications, 2017.
- “An ultrasensitive biomolecular network for robust feedback control”. C Cuba Samaniego and E Franco. Invited paper. Proceedings of the 2017 IFAC conference, 2017.
- "Negative feedback enables structurally signed steady-state influences in artificial biomolecular networks". G Giordano and E Franco. Proceedings of the IEEE Conference on Decision and Control, 2016.
- "A coarse-grained model of DNA nanotube population growth". V Mardanlou, LN Green, HKK Subramanian, RF Hariadi, J Kim and E Franco. DNA Computing and Molecular Programming Conference, 2016.
- "An algebraic approach to parameter optimization in biomolecular bistable systems". V Mardanlou and E Franco. Proceedings of the American Control Conference, 2016.
- “A minimal biomolecular frequency divider”. C Cuba Samaniego and E Franco. Proceedings of the IEEE Conference on Decision and Control 2015.
- “A bistable biomolecular network based on monomeric inhibition reactions”. Invited paper. V Mardanlou, C Cuba Samaniego and E Franco. Proceedings of the IEEE Conference on Decision and Control 2015.
- “Structural conditions for oscillations and multistationarity in aggregate monotone systems”. Invited paper. F Blanchini, E Franco and G Giordano. Proceedings of the IEEE Conference on Decision and Control, 2015.
- “Design and analysis of a synthetic aptamer-based oscillator”. C Cuba Samaniego, S Kitada, E Franco. Proceedings of the American Control Conference, 2015.
- “Design of a molecular bistable system with RNA-mediated regulation” V Mardanlou, CH Tran, and E Franco. IEEE Conference on Decision and Control, 2014.
- “Design of a molecular clock with RNA-mediated regulation”, F Blanchini, C Cuba Samaniego, E Franco, and G Giordano. Proceedings of the IEEE Conference on Decision and Control, 2014.
- “Distributed Camera Control via Moving Horizon Bayesian Optimization”, AA Morye, E Franco, AK Roy-Chowdhury, JA Farrell. Proceedings of the American Control Conference, 2014.
- “Structured–LMI Sufficient Conditions for Stabilizing Network–Decentralized Controllers”, F Blanchini, E Franco and G Giordano. Proceedings of the IEEE Conference on Decision and Control, 2013.
- “Receding Horizon Control of a Two-Agent System with Competitive Objectives”, A Carron and E Franco. Proceedings of the American Control Conference, 2013.
- “Feedback architectures to regulate flux of components in artificial gene networks”, G Giordano, E Franco and RM Murray. Proceedings of the American Control Conference, 2013.
- “Determining the structural properties of a class of biological models”, F Blanchini, E Franco and G Giordano. Proceedings of the IEEE Conference on Decision and Control, 2012.
- “Analysis of a negative feedback biochemical oscillator”, E Franco and F Blanchini. Proceedings of the American Control Conference, 2012.
- "Multistability and robustness of the MAPK pathway", F Blanchini and E Franco. Invited paper. Proceedings of the IEEE Conference on Decision and Control, 2011.
- "Structural robustness in biological networks", F Blanchini and E Franco. American Control Conference, 2011. (Presentation only, not included in the proceedings.)
- "Tuning a synthetic in vitro oscillator using control-theoretic tools", C Sturk, E Franco and RM Murray. Invited paper. Proceedings of the IEEE Conference on Decision and Control, 2010.
- "Design of insulating devices for in vitro synthetic circuits", E Franco, D Del Vecchio and RM Murray. Invited paper. Proceedings of the IEEE Conference on Decision and Control, 2009.
- "Design and performance of in vitro transcription rate regulatory circuits", E Franco and RM Murray. Proceedings of the IEEE Conference on Decision and Control, 2008.
- "Design, modeling and synthesis of an in vitro transcription rate regulatory circuit", E Franco, PO Forsberg and RM Murray. Invited paper. Proceedings of the American Control Conference, 2008.
- "A Multi-Model Approach to Identification of Biosynthetic Pathways ", MJ Dunlop, E Franco and RM Murray. Invited paper. Proceedings of the American Control Conference, 2007.
- "Distributed Fault Diagnosis using Sensor Networks and Consensus-based Filters", E Franco, R Olfati-Saber, T Parisini and MM Polycarpou. Invited paper. Proceedings of the IEEE Conference on Decision and Control, 2006.
- “Cooperative Control of Distributed Agents with Nonlinear Dynamics and Delayed Information Exchange: a Stabilizing Receding-Horizon Approach”, E Franco, T Parisini and MM Polycarpou. Proceedings of the IEEE Conference on Decision and Control 2005.
- “Stable Receding-Horizon Cooperative Control of a Class of Distributed Agents“, E Franco, T Parisini and MM Polycarpou. Proceedings of the American Control Conference, 2005.
- “Cooperative Control of Discrete Time Agents with Delayed Information Exchange: a Receding--Horizon Approach“ E Franco, T Parisini and MM Polycarpou. Proceedings of the IEEE Conference on Decision and Control, 2004.
- “Determination of the Value of Information in Large Vehicle Arrays", JL Speyer, N Zika and E Franco. Proceedings of the American Control Conference, 2006.
- "A Hybrid Control Scheme for Freeway Systems", S Sacone, E Franco and T Parisini. Proceedings of the IFAC World Congress, 2005.
- "Practically Stable Nonlinear Receding Horizon Control of Multi Model Systems", E Franco, T Parisini and S Sacone. Proceedings of the Conference on Decision and Control, 2004.
- "Multi-model hybrid receding-horizon control of nonlinear system: stability analysis", E Franco, T Parisini and S Sacone. Proceedings of the American Control Conference, 2004.

Book chapters

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- M Schwarz-Schilling, J Kim, C Cuba Samaniego, M Weitz, E Franco, FC Simmel. "Building a Synthetic Transcriptional Oscillator". Cell Cycle Oscillators: Methods and Protocols, 185-199, 2016 .
- E. Franco, K.E. Galloway “Feedback Loops in Biological Networks”. Computational Methods in Synthetic Biology, 193-214, 2015.
- "Synthetic Biochemical Devices for Programmable Dynamic Behavior." J Kim, E Franco. A Systems Theoretic Approach to Systems and Synthetic Biology II: Analysis and Design of Cellular Systems. Springer Netherlands, 2014. 273-295.
- "Structural Analysis of Biological Networks" F Blanchini, E Franco. A Systems Theoretic Approach to Systems and Synthetic Biology II: Models and System Characterizations. Springer Netherlands, 2014. 47-71.
- “Nonlinear Dynamics: Genelets and Synthetic Biochemical Circuits ”, E Franco, J Kim and FC Simmel. Multiscale Analysis and Nonlinear Dynamics. From Genes to the Brain (Annual Reviews of Nonlinear Dynamics and Complexity). Wiley VCH, 2013.