.

Dynamic Nucleic Acid Systems lab

Journal publications

In preparation/submitted

Conference publications

Archive papers

Book chapters

Journal publications

    2024

  1. “Dynamic control of DNA condensation”. Preprint S Agarwal, D Osmanovic, M Klocke, and E Franco. Nature communications (accepted)
  2. “Optimization of RNA Pepper sensors for the detection of arbitrary RNA targets”. A Tang, A Afasizheva, C Cano, K Plath, D Black, and E Franco. ACS synthetic biology (accepted)

    3. 2023

  3. “Light-controlled growth of DNA organelles in synthetic cells”. S Agarwal, M Dizani, D Osmanovic, and E Franco. Interface Focus 13.5 (2023), p. 20230017
  4. “Robust microphase separation through chemical reaction networks”. F Blanchini, G Giordano, E Franco, and D Osmanovic. IEEE Control Systems Letters (2023).
  5. “Shaken, not heated: DNA self-assembly at room temperature”. E Franco (News & Views) Nature Nanotechnology (2023), pp. 1–2
  6. “Computational characterization of recombinase circuits for periodic behaviors”. J Landau, C Cuba Samaniego, and E Franco. Iscience 26.1 (2023)
  7. “A portable regulatory RNA array design enables tunable and complex regulation across diverse bacteria”. B Liu, C Cuba Samaniego, MR Bennett, E Franco, and J Chappell. Nature Communications 14.1 (2023), p. 5268
  8. “Chemical reaction motifs driving non-equilibrium behaviours in phase separating materials”. D Osmanovic and E Franco. Journal of the Royal Society Interface 20.208 (2023), p. 20230117.
  9. “Building Subtraction Operators and Controllers Via Molecular Sequestration”. C Cuba Samaniego, Y Qian, K Carleton, and E Franco. IEEE Control Systems Letters (2023).

    10. 2022

  10. “The growth rate of DNA condensate droplets increases with the size of participating subunits”. S Agarwal, D Osmanovic, M Klocke, and E Franco ACS nano, 2022
  11. “The living interface between synthetic biology and biomaterial design”. AP Liu, EA Appel, PD Ashby, MB Baker, E Franco, L Gu, K Haynes, NS Joshi, AM Kloxin, PH Kouwer, et al. Nature materials, 2022
  12. “Fueling DNA Self-Assembly via Gel-Released Regulators”. JV Le, D Osmanovic, MA Klocke, and E Franco. ACS nano, 2022
  13. “Dissipative DNA nanotechnology”. E Del Grosso, E Franco, LJ Prins, F Ricci . Nature chemistry, 2022
  14. “RNA Compensation: A Positive Feedback Insulation Strategy for RNA-Based Transcription Networks”. B Liu, C Cuba Samaniego, M Bennett, J Chappell, E Franco. ACS Synthetic Biology,2022

    15. 2021

  15. “Spontaneous Reorganization of DNA-Based Polymers in Higher Ordered Structures Fueled by RNA”. S Gentile, E Del Grosso, PE Pungchai, E Franco, LJ Prins, F Ricci Journal of the American Chemical Society 143 (48), 20296-20301, 2021
  16. “Dynamic self-assembly of compartmentalized DNA nanotubes”. S Agarwal, MA Klocke, PE Pungchai, E Franco. Nature communications 12 (1), 1-13, 2021.
  17. “Ultrasensitive molecular controllers for quasi-integral feedback”. CC Samaniego, E Franco. Cell Systems 12 272-288, 2021

    18. 2020

  18. “The challenges of modeling and forecasting the spread of COVID-19”. AL Bertozzi, E Franco, G Mohler, MB Short, D Sledge. Proceedings of the National Academy of Sciences 117 (29), 16732-16738, 2020
  19. “Characterizing the length-dependence of DNA nanotube end-to-end joining rates”. MS Pacella, V Mardanlou, S Agarwal, A Patel, E Jelezniakov, AM Mohammed, E Franco and R Schulman. Current Opinion in Biotechnology 63, 135-141, 2020
  20. “RNA nanotechnology in synthetic biology”. J Kim and E Franco, and J Kim, Current Opinion in Biotechnology 63, 135-141, 2020

    21. 2019

  21. “Periodic switching in a recombinase-based molecular circuit”. C Cuba Samaniego, G Giordano, E Franco IEEE Control Systems Letters 4 (1), 241-246, 2019
  22. “Cell-Free Synthetic Biology Platform for Engineering Synthetic Biological Circuits and Systems”. D Jeong, M Klocke, S Agarwal, J Kim, S Choi, E Franco, and J Kim, Methods and Protocols (Special Issue Cell-Free Synthetic Biology), 2019
  23. “Enzyme-Driven Assembly and Disassembly of Hybrid DNA–RNA Nanotubes”. S. Agarwal and E Franco, JACS, 2019.
  24. “Design and characterization of RNA nanotubes”. JM Stewart, C Geary and E Franco, ACS nano, 2019.
  25. “Autonomous dynamic control of DNA nanostructure self-assembly”. LN Green, HKK Subramanian, V Mardanlou, J Kim, RF Hariadi and E Franco, Nature chemistry, 2019.
  26. “A universal method for sensitive and cell-free detection of CRISPR-associated nucleases”. KJ Cox, HKK Subramanian, C Cuba Samaniego, E Franco, and A Choudhary, Chemical Science, 2019.

    27. 2018

  27. “Homogeneous time constants promote oscillations in negative feedback loops”. F Blanchini, C Cuba Samaniego, E Franco and G Giordano, ACS Synthetic Biology, 2018.
  28. “Mathematical modeling of RNA-based architectures for closed loop control of gene expression”. DK Agrawal, X Tang, A Westbrook, R Marshall, C Maxwell, JB Lucks, V Noireaux, C Beisel, MJ Dunlop, and E Franco, ACS Synthetic Biology, 2018.
  29. “T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures”. S Schaffter, LN Green, J Schneider, HKK Subramanian, R Schulman and E Franco, Nucleic Acids Research, 2018.
  30. “Engineering DNA nanotubes for resilience in the cytoplasmic environment” . MA Klocke, J Garamella, HKK Subramanian, V Noireaux and E Franco, Synthetic Biology, 2018.

    31. 2017

  31. “A robust molecular network motif for period doubling devices”. C Cuba Samaniego and E Franco, ACS Synthetic Biology, 2017.
  32. “pH-driven reversible self-assembly of micron-scale DNA scaffolds”. LN Green, A. Amodio, HKK Subramanian, F Ricci and E Franco, Nano Letters, 2017.
  33. "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, Natural Computing, 2017.
  34. “Dynamic control of aptamer–ligand activity using strand displacement reactions”. J Lloyd, CH Tran, K. Wadhwani, C Cuba Samaniego HKK Subramanian and E Franco, ACS Synthetic Biology, 2017.
  35. “Self-assembly of multi stranded RNA motifs into lattices and tubular structures”. JM Stewart, HKK Subramanian and E Franco, Nucleic Acids Research, 2017.
  36. “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.

    37. 2016

  37. “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.
  38. “pH-controlled assembly of DNA tiles”. A Amodio, AF Adedeji, M Castronovo, E Franco and F Ricci, JACS, 2016.
  39. “Programmable RNA microstructures for coordinated delivery of siRNAs”. JM Stewart, M Viard, HKK Subramanian, BK Roark, KA Afonin and E Franco, Nanoscale, 2016.
  40. "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.
  41. "Self-assembly of large RNA structures: learning from DNA nanotechnology." JM Stewart and E Franco. DNA and RNA Nanotechnology, 2 (1), 2016.
  42. "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.
  43. “Compartmental flow control: Decentralization, robustness and optimality” F Blanchini, E Franco, G Giordano, V Mardanlou, PL Montessoro. Automatica 64, 18-28, 2016.

    44. 2015

  44. “Designing a self-regulating biomolecular comparator” DK Agrawal, E Franco, R Schulman. Journal of the Royal Society Interface, 12 (111), 20150586, 2015.
  45. “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.
  46. “Network-Decentralized Control Strategies for Stabilization” F Blanchini, E Franco, G Giordano. Automatic Control, IEEE Transactions on. 60 (2), 491-496, 2015.
  47. “Computing the structural influence matrix for biological systems” G Giordano, C Cuba Samaniego, E Franco, F Blanchini. Journal of mathematical biology, 1-32, 2015.

    48. 2014

  48. “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.
  49. “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.
  50. "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.

    51. 2013

  51. "Dynamically reshaping signaling networks to program cell fate via genetic controllers" KE Galloway, E Franco, CD Smolke. Science 341 (6152), 1235005, 2013.
  52. "Structural properties of the MAPK pathway topologies in PC12 cells" E Franco, F Blanchini. Journal of mathematical biology 67 (6-7), 1633-1668, 2013.

    53. 2011

  53. "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.
  54. "Structurally robust biological networks" F Blanchini, E Franco. BMC systems biology 5 (1), 74, 2011.

    55. 2010 and earlier

  55. “Cooperative constrained control of distributed agents with nonlinear dynamics and delayed information exchange: A stabilizing receding-horizon approach” E Franco, L Magni, T Parisini, MM Polycarpou, DM Raimondo, IEEE Transactions on Automatic Control 53 (1), 324-338, 2008.
  56. “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.
  57. “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.
  58. “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.

In preparation/submitted

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  • "Co-transcriptional allosteric regulation of synthetic nucleic acid receptors”. D Sorrentino, S Ranallo, E Nakamura, E Franco, and F Ricci Submitted.
  • "Modular RNA motifs for orthogonal phase separated compartments”. JM Stewart, S Li, A Tang, MA Klocke, MV Gobry, G Fabrini, L Di Michele, PW Rothemund, E Franco. In revision.
  • "Co-transcriptional production of programmable RNA condensates and synthetic organelles”. G Fabrini, SP Nuccio, JM Stewart, S Li, A Tang, PW Rothemund, E Franco, M Di Antonio, and L Di Michele. In revision.

    • Refereed conference publications

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    1. “Hierarchical dynamic control allocation for over-actuated aircraft: Methodology and flight tests on a scaled-down model” R Baggi, A Serrani, and E Franco 2022 IEEE Conference on Control Technology and Applications (CCTA), 2022
    2. “Hierarchical dynamic control allocation for over-actuated aircraft: Methodology and flight tests on a scaled-down model” Y Zhang, C Cuba Samaniego, K Carleton, Y Qian, G Giordano, and E Franco. 2022 IEEE 61st Conference on Decision and Control (CDC). IEEE, 2022
    3. Bistable State Switch Enables Ultrasensitive Feedback Control in Heterogeneous Microbial Populations X Ren, C Cuba Samaniego, RM Murray, E Franco Proceedings of the American Control Conference, 2021
    4. Signaling-based neural networks for cellular computation C Cuba Samaniego, A Moorman, G Giordano, E Franco Proceedings of the American Control Conference, 2021
    5. Sequestration and delays enable the synthesis of a molecular derivative operator C Cuba Samaniego, J Kim, E Franco Proceedings of the IEEE Conference on Decision and Control, 2020
    6. Biomolecular stabilisation near the unstable equilibrium of a biological system C Cuba Samaniego, NA Delateur, G Giordano, E Franco Proceedings of the IEEE Conference on Decision and Control, 2019.
    7. “Dynamic Control Allocation for a Class of Over-actuated Aircraft”. R Baggi, E Franco, A Serrani AIAA Scitech 2020 Forum, 0841
    8. “A molecular device for frequency doubling enabled by molecular sequestration”. C Cuba Samaniego and E Franco. Proceedings of the European Control Conference, 2019.
    9. “Practical differentiation using ultrasensitive molecular circuits”. C Cuba Samaniego, G Giordano, and E Franco. Proceedings of the European Control Conference, 2019.
    10. “Design and analysis of a biomolecular positive-feedback oscillator”. C Cuba Samaniego, G Giordano, and E Franco. Proceedings of the IEEE Conference on Decision and Control, 2018.
    11. “An ultrasensitive motif for robust closed loop control of biomolecular systems”. C Cuba Samaniego and E Franco. Proceedings of the IEEE Conference on Decision and Control, 2017.
    12. “Aggregates of Positive Impulse Response systems: a decomposition approach for complex networks”. F Blanchini, C Cuba Samaniego, E Franco, and G Giordano. Proceedings of the IEEE Conference on Decision and Control, 2017.
    13. “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.
    14. “An ultrasensitive biomolecular network for robust feedback control”. C Cuba Samaniego and E Franco. Invited paper. Proceedings of the 2017 IFAC conference, 2017.
    15. "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.
    16. "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.
    17. "An algebraic approach to parameter optimization in biomolecular bistable systems". V Mardanlou and E Franco. Proceedings of the American Control Conference, 2016.
    18. “A minimal biomolecular frequency divider”. C Cuba Samaniego and E Franco. Proceedings of the IEEE Conference on Decision and Control 2015.
    19. “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.
    20. “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.
    21. “Design and analysis of a synthetic aptamer-based oscillator”. C Cuba Samaniego, S Kitada, E Franco. Proceedings of the American Control Conference, 2015.
    22. “Design of a molecular bistable system with RNA-mediated regulation” V Mardanlou, CH Tran, and E Franco. IEEE Conference on Decision and Control, 2014.
    23. “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.
    24. “Distributed Camera Control via Moving Horizon Bayesian Optimization”, AA Morye, E Franco, AK Roy-Chowdhury, JA Farrell. Proceedings of the American Control Conference, 2014.
    25. “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.
    26. “Receding Horizon Control of a Two-Agent System with Competitive Objectives”, A Carron and E Franco. Proceedings of the American Control Conference, 2013.
    27. “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.
    28. “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.
    29. “Analysis of a negative feedback biochemical oscillator”, E Franco and F Blanchini. Proceedings of the American Control Conference, 2012.
    30. "Multistability and robustness of the MAPK pathway", F Blanchini and E Franco. Invited paper. Proceedings of the IEEE Conference on Decision and Control, 2011.
    31. "Structural robustness in biological networks", F Blanchini and E Franco. American Control Conference, 2011. (Presentation only, not included in the proceedings.)
    32. "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.
    33. "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.
    34. "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.
    35. "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.
    36. "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.
    37. "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.
    38. “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.
    39. “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.
    40. “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.
    41. “Determination of the Value of Information in Large Vehicle Arrays", JL Speyer, N Zika and E Franco. Proceedings of the American Control Conference, 2006.
    42. "A Hybrid Control Scheme for Freeway Systems", S Sacone, E Franco and T Parisini. Proceedings of the IFAC World Congress, 2005.
    43. "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.
    44. "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.

    Archive papers

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    • "A feedback SIR (fSIR) model highlights advantages and limitations of infection-based social distancing" Elisa Franco ArXiv - https://arxiv.org/abs/2004.13216

    Book chapters

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    • “Assembly of RNA nanostructures from double crossover tiles” JM Stewart, H K K Subramanian, and E Franco. In: Cell-Free Gene Expression (Methods in Molecular Biology), 2021.
    • 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.