.

Dynamic Nucleic Acid Systems lab

Journal publications

In preparation/submitted

Conference publications

Archive papers

Book chapters

Journal publications

    2024

  1. “Developmental assembly of multi-component polymer systems through interconnected synthetic gene networks in vitro” D. Sorrentino, S. Ranallo, F. Ricci, and E. Franco. Nature Communications 15.1 (2024), p. 8561.
  2. “Modular RNA motifs for orthogonal phase separated compartments” J. M. Stewart, S. Li, A. A. Tang, M. A. Klocke, M. V. Gobry, G. Fabrini, L. Di Michele, P. W. Rothemund, and E. Franco. Nature Communications (2024), pp. 1–9.
  3. “Co-transcriptional production of programmable RNA condensates and synthetic organelles” G. Fabrini, N. Farag, S. P. Nuccio, S. Li, J. M. Stewart, A. A. Tang, R. McCoy, R. M. Owens, P. W. Rothemund, E. Franco, M. Di Antonio, and L. Di Michele Nature Nanotechnology (2024), pp. 1–9.
  4. “Synthetic Genes For Dynamic Regulation Of DNA-Based Receptors” D. Sorrentino, S. Ranallo, E. Nakamura, E. Franco, and F. Ricci. Angewandte Chemie (2024), e202319382.
  5. “Protein recruitment to dynamic DNA-RNA host condensates” M Dizani, D Sorrentino, S Agarwal, J M Stewart, and E Franco. Journal of the American Chemical Society (2024)
  6. “Cracking the Code: Enhancing Molecular Tools for Progress in Nanobiotechnology” Y. I. Avila, L. P. Rebolledo, E. Skelly, R. de Freitas Saito, H. Wei, D. Lilley, R. E. Stanley, Y.-M. Hou, H. Yang, J. Sztuba-Solinska, et al. ACS Applied Bio Materials (2024)
  7. “Dynamic control of DNA condensation” S Agarwal, D Osmanovic, M Klocke, and E Franco. Nature communications (2024)
  8. “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 (2024)

    9. 2023

  9. “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
  10. “Robust microphase separation through chemical reaction networks”. F Blanchini, G Giordano, E Franco, and D Osmanovic. IEEE Control Systems Letters (2023).
  11. “Shaken, not heated: DNA self-assembly at room temperature”. E Franco (News & Views) Nature Nanotechnology (2023), pp. 1–2
  12. “Computational characterization of recombinase circuits for periodic behaviors”. J Landau, C Cuba Samaniego, and E Franco. Iscience 26.1 (2023)
  13. “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
  14. “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.
  15. “Building Subtraction Operators and Controllers Via Molecular Sequestration”. C Cuba Samaniego, Y Qian, K Carleton, and E Franco. IEEE Control Systems Letters (2023).

    16. 2022

  16. “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
  17. “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
  18. “Fueling DNA Self-Assembly via Gel-Released Regulators”. JV Le, D Osmanovic, MA Klocke, and E Franco. ACS nano, 2022
  19. “Dissipative DNA nanotechnology”. E Del Grosso, E Franco, LJ Prins, F Ricci . Nature chemistry, 2022
  20. “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

    21. 2021

  21. “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
  22. “Dynamic self-assembly of compartmentalized DNA nanotubes”. S Agarwal, MA Klocke, PE Pungchai, E Franco. Nature communications 12 (1), 1-13, 2021.
  23. “Ultrasensitive molecular controllers for quasi-integral feedback”. CC Samaniego, E Franco. Cell Systems 12 272-288, 2021

    24. 2020

  24. “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
  25. “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
  26. “RNA nanotechnology in synthetic biology”. J Kim and E Franco, and J Kim, Current Opinion in Biotechnology 63, 135-141, 2020

    27. 2019

  27. “Periodic switching in a recombinase-based molecular circuit”. C Cuba Samaniego, G Giordano, E Franco IEEE Control Systems Letters 4 (1), 241-246, 2019
  28. “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
  29. “Enzyme-Driven Assembly and Disassembly of Hybrid DNA–RNA Nanotubes”. S. Agarwal and E Franco, JACS, 2019.
  30. “Design and characterization of RNA nanotubes”. JM Stewart, C Geary and E Franco, ACS nano, 2019.
  31. “Autonomous dynamic control of DNA nanostructure self-assembly”. LN Green, HKK Subramanian, V Mardanlou, J Kim, RF Hariadi and E Franco, Nature chemistry, 2019.
  32. “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.

    33. 2018

  33. “Homogeneous time constants promote oscillations in negative feedback loops”. F Blanchini, C Cuba Samaniego, E Franco and G Giordano, ACS Synthetic Biology, 2018.
  34. “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.
  35. “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.
  36. “Engineering DNA nanotubes for resilience in the cytoplasmic environment” . MA Klocke, J Garamella, HKK Subramanian, V Noireaux and E Franco, Synthetic Biology, 2018.

    37. 2017

  37. “A robust molecular network motif for period doubling devices”. C Cuba Samaniego and E Franco, ACS Synthetic Biology, 2017.
  38. “pH-driven reversible self-assembly of micron-scale DNA scaffolds”. LN Green, A. Amodio, HKK Subramanian, F Ricci and E Franco, Nano Letters, 2017.
  39. "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.
  40. “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.
  41. “Self-assembly of multi stranded RNA motifs into lattices and tubular structures”. JM Stewart, HKK Subramanian and E Franco, Nucleic Acids Research, 2017.
  42. “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.

    43. 2016

  43. “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.
  44. “pH-controlled assembly of DNA tiles”. A Amodio, AF Adedeji, M Castronovo, E Franco and F Ricci, JACS, 2016.
  45. “Programmable RNA microstructures for coordinated delivery of siRNAs”. JM Stewart, M Viard, HKK Subramanian, BK Roark, KA Afonin and E Franco, Nanoscale, 2016.
  46. "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.
  47. "Self-assembly of large RNA structures: learning from DNA nanotechnology." JM Stewart and E Franco. DNA and RNA Nanotechnology, 2 (1), 2016.
  48. "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.
  49. “Compartmental flow control: Decentralization, robustness and optimality” F Blanchini, E Franco, G Giordano, V Mardanlou, PL Montessoro. Automatica 64, 18-28, 2016.

    50. 2015

  50. “Designing a self-regulating biomolecular comparator” DK Agrawal, E Franco, R Schulman. Journal of the Royal Society Interface, 12 (111), 20150586, 2015.
  51. “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.
  52. “Network-Decentralized Control Strategies for Stabilization” F Blanchini, E Franco, G Giordano. Automatic Control, IEEE Transactions on. 60 (2), 491-496, 2015.
  53. “Computing the structural influence matrix for biological systems” G Giordano, C Cuba Samaniego, E Franco, F Blanchini. Journal of mathematical biology, 1-32, 2015.

    54. 2014

  54. “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.
  55. “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.
  56. "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.

    57. 2013

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

    59. 2011

  59. "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.
  60. "Structurally robust biological networks" F Blanchini, E Franco. BMC systems biology 5 (1), 74, 2011.

    61. 2010 and earlier

  61. “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.
  62. “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.
  63. “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.
  64. “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.