Publications

Journal articles

• “Programmable artificial RNA condensates in mammalian cells”. S. Li, Y. Kim, K. Wang, E. J. Payson, A. A. Tang, M. Villalba Nieto, D. Osmanovic, M. Yang, D. Dilao, A. Bermudez, et al.. Nature Nanotechnology (2026), pp. 1–10.
• “Molecular recruitment and release using DNA host condensates”. H. R. Mercieca, D. McGrory, B. Perlstein, B. Castañeda-Camacho, W. L. Yu, T. Anand, J. L. Blatti, E. Franco, and M. Dizani. Nanoscale Horizons (2026).

• “Investigating substrates Amplifu Red and ABTS in the colorimetric detection of DNAzyme activity localized to DNA condensates”. T. Anand, R. Salman, B. Castaneda Camacho, V. Gonzales, E. Safar, E. Franco, and J. L. Blatti. Journal of Advanced Technological Education (J-ATE) (2025).
• “Nanotubes Growth by Self-Assembly of DNA Strands at Room Temperature”. L. Bourdon, S. P. Afrose, S. Agarwal, D. Das, R. Singh, A. Di Cicco, D. Lévy, A. Yamada, D. Baigl, and E. Franco. ACS Nano (2025).
• “Light-modulated self-assembly of synthetic nanotubes”. M. Dizani, S. Agarwal, D. Osmanovic, and E. Franco. Nano Letters 25.8 (2025), pp. 3122–3129.
• “Design of an intracellular aptamer-based fluorescent biosensor to track burden in E. coli”. A. Grob, T. Copeman, S. L. Chen, J. Ganrielli, Y. Elani, E. Franco, and F. Ceroni. Trends in Biotechnology 43.10 (2025), pp. 2566–2585.
• “Hashing the message with cells”. J. Kim and E. Franco. Nature Chemical Biology (2025), pp. 1–2.
• “Generating forces in confinement via polymerization”. D. Osmanovic and E. Franco. Soft Matter (2025).
• “Complex dynamics in reaction-phase separation systems”. D. Osmanovic and E. Franco. Physical Review E 111.2 (2025), p. 025404.
• “Internal phase separation in synthetic DNA condensates”. D. A. Tanase, D. Osmanovic, R. Rubio-Sánchez, L. Malouf, E. Franco, and L. Di Michele. Advanced Science 12.41 (2025), e06275.
• “Switchable RNA motifs for dynamic transcriptional control of RNA condensates”. A. Tang, V. M. Gobry, S. Li, E. S. Andersen, and E. Franco. Nucleic Acids Research 53.12 (2025).

• “Dynamic control of DNA condensation”. S. Agarwal, D. Osmanovic, M. Dizani, M. A. Klocke, and E. Franco. Nature Communications 15.1 (2024), p. 1915.
• “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).
• “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 146.43 (2024), pp. 29344–29354.
• “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, et al.. Nature Nanotechnology (2024), pp. 1–9.
• “Ten Years of the Synthetic Biology Summer Course at Cold Spring Harbor Laboratory”. K. A. Haynes, L. B. Andrews, C. L. Beisel, J. Chappell, C. E. Cuba Samaniego, J. E. Dueber, M. J. Dunlop, E. Franco, J. B. Lucks, V. Noireaux, et al.. ACS Synthetic Biology 13.9 (2024), pp. 2635–2642.
• “Synthetic Genes For Dynamic Regulation Of DNA-Based Receptors”. D. Sorrentino, S. Ranallo, E. Nakamura, E. Franco, and F. Ricci. Angewandte Chemie (2024), e202319382.
• “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.
• “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 15.1 (2024), p. 6244.
• “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), pp. 2023–06.

• “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.
• “Robust microphase separation through chemical reaction networks”. F. Blanchini, E. Franco, G. Giordano, and D. Osmanovic. IEEE Control Systems Letters (2023).
• “Shaken, not heated: DNA self-assembly at room temperature”. E. Franco. Nature Nanotechnology (2023), pp. 1–2.
• “Computational characterization of recombinase circuits for periodic behaviors”. J. Landau, C. C. Samaniego, G. Giordano, and E. Franco. iScience 26.1 (2023).
• “A portable regulatory RNA array design enables tunable and complex regulation across diverse bacteria”. B. Liu, C. C. Samaniego, M. R. Bennett, E. Franco, and J. Chappell. Nature Communications 14.1 (2023), p. 5268.
• “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.
• “Building Subtraction Operators and Controllers Via Molecular Sequestration”. C. C. Samaniego, Y. Qian, K. Carleton, and E. Franco. IEEE Control Systems Letters (2023).

• “The growth rate of DNA condensate droplets increases with the size of participating subunits”. S. Agarwal, D. Osmanovic, M. A. Klocke, and E. Franco. ACS Nano 16.8 (2022), pp. 11842–11851.
• “Dissipative DNA nanotechnology”. E. Del Grosso, E. Franco, L. J. Prins, and F. Ricci. Nature Chemistry 14.6 (2022), pp. 600–613.
• “Fueling DNA Self-Assembly via Gel-Released Regulators”. J. Le, D. Osmanovic, M. A. Klocke, and E. Franco. ACS Nano 16.10 (2022), pp. 16372–16384.
• “The living interface between synthetic biology and biomaterial design”. A. P. Liu, E. A. Appel, P. D. Ashby, B. M. Baker, E. Franco, L. Gu, K. Haynes, N. S. Joshi, A. M. Kloxin, P. H. Kouwer, et al.. Nature Materials 21.4 (2022), pp. 390–397.
• “RNA Compensation: A Positive Feedback Insulation Strategy for RNA-Based Transcription Networks”. B. Liu, C. Cuba Samaniego, M. Bennett, J. Chappell, and E. Franco. ACS Synthetic Biology 11.3 (2022), pp. 1240–1250.

• “Dynamic self-assembly of compartmentalized DNA nanotubes”. S. Agarwal, M. A. Klocke, P. E. Pungchai, and E. Franco. Nature Communications 12.1 (2021), pp. 1–13.
• “Spontaneous Reorganization of DNA-Based Polymers in Higher Ordered Structures Fueled by RNA”. S. Gentile, E. Del Grosso, P. E. Pungchai, E. Franco, L. J. Prins, and F. Ricci. Journal of the American Chemical Society 143.48 (2021), pp. 20296–20301.
• “Ultrasensitive molecular controllers for quasi-integral feedback”. C. C. Samaniego and E. Franco. Cell Systems 12.3 (2021), pp. 272–288.

• “The challenges of modeling and forecasting the spread of COVID-19”. A. L. Bertozzi, E. Franco, G. Mohler, M. B. Short, and D. Sledge. Proceedings of the National Academy of Sciences 117.29 (2020), pp. 16732–16738.
• “RNA nanotechnology in synthetic biology”. J. Kim and E. Franco. Current Opinion in Biotechnology 63 (2020), pp. 135–141.
• “Characterizing the length-dependence of DNA nanotube end-to-end joining rates”. M. S. Pacella, V. Mardanlou, S. Agarwal, A. Patel, E. Jelezniakov, A. M. Mohammed, E. Franco, and R. Schulman. Molecular Systems Design & Engineering 5.2 (2020), pp. 544–558.

• “Enzyme-driven assembly and disassembly of hybrid DNA–RNA nanotubes”. S. Agarwal and E. Franco. Journal of the American Chemical Society 141.19 (2019), pp. 7831–7841.
• “A universal method for sensitive and cell-free detection of CRISPR-associated nucleases”. K. J. Cox, H. K. Subramanian, C. C. Samaniego, E. Franco, and A. Choudhary. Chemical Science 10.9 (2019), pp. 2653–2662.
• “Autonomous dynamic control of DNA nanostructure self-assembly”. L. N. Green, H. K. Subramanian, V. Mardanlou, J. Kim, R. F. Hariadi, and E. Franco. Nature Chemistry 11.6 (2019), pp. 510–520.
• “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 2.2 (2019), p. 39.
• “Periodic switching in a recombinase-based molecular circuit”. C. C. Samaniego, G. Giordano, and E. Franco. IEEE Control Systems Letters 4.1 (2019), pp. 241–246.
• “Design and characterization of RNA nanotubes”. J. M. Stewart, C. Geary, and E. Franco. ACS Nano 13.5 (2019), pp. 5214–5221.
• “Distinct timescales of RNA regulators enable the construction of a genetic pulse generator”. A. Westbrook, X. Tang, R. Marshall, C. S. Maxwell, J. Chappell, D. K. Agrawal, M. J. Dunlop, V. Noireaux, C. L. Beisel, J. Lucks, et al.. Biotechnology and Bioengineering 116.5 (2019), pp. 1139–1151.

• “Mathematical modeling of RNA-based architectures for closed loop control of gene expression”. D. K. Agrawal, X. Tang, A. Westbrook, R. Marshall, C. S. Maxwell, J. Lucks, V. Noireaux, C. L. Beisel, M. J. Dunlop, and E. Franco. ACS Synthetic Biology 7.5 (2018), pp. 1219–1228.
• “Homogeneous time constants promote oscillations in negative feedback loops”. F. Blanchini, C. Cuba Samaniego, E. Franco, and G. Giordano. ACS Synthetic Biology 7.6 (2018), pp. 1481–1487.
• “A robust molecular network motif for period-doubling devices”. C. Cuba Samaniego and E. Franco. ACS Synthetic Biology 7.1 (2018), pp. 75–85.
• “Engineering DNA nanotubes for resilience in an E. coli TXTL system”. M. A. Klocke, J. Garamella, H. K. Subramanian, V. Noireaux, and E. Franco. Synthetic Biology 3.1 (2018), ysy001.
• “A coarse-grained model captures the temporal evolution of DNA nanotube length distributions”. V. Mardanlou, K. C. Yaghoubi, L. N. Green, H. K. Subramanian, R. F. Hariadi, J. Kim, and E. Franco. Natural Computing 17.1 (2018), pp. 183–199.
• “RNA fibers as optimized nanoscaffolds for siRNA coordination and reduced immunological recognition”. L. Rackley, J. M. Stewart, J. Salotti, A. Krokhotin, A. Shah, J. R. Halman, R. Juneja, J. Smollett, L. Lee, K. Roark, et al.. Advanced Functional Materials 28.48 (2018), p. 1805959.
• “T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures”. S. W. Schaffter, L. N. Green, J. Schneider, H. K. Subramanian, R. Schulman, and E. Franco. Nucleic Acids Research 46.10 (2018), pp. 5332–5343.

• “Aggregates of Monotonic Step Response systems: a structural classification”. F. Blanchini, C. C. Samaniego, E. Franco, and 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 11.1 (2017), pp. 102–120.
• “pH-driven reversible self-assembly of micron-scale DNA scaffolds”. L. N. Green, A. Amodio, H. K. Subramanian, F. Ricci, and E. Franco. Nano Letters 17.12 (2017), pp. 7283–7288.
• “Dynamic control of aptamer-ligand activity using strand displacement reactions”. J. Lloyd, C. H. Tran, K. Wadhwani, C. Cuba Samaniego, H. K. Subramanian, and E. Franco. ACS Synthetic Biology (2017).
• “Self-assembly of multi-stranded RNA motifs into lattices and tubular structures”. J. M. Stewart, H. K. Subramanian, and E. Franco. Nucleic Acids Research 45.9 (2017), pp. 5449–5457.

• “pH-controlled assembly of DNA tiles”. A. Amodio, A. F. Adedeji, M. Castronovo, E. Franco, and F. Ricci. Journal of the American Chemical Society 138.39 (2016), p. 12735.
• “Compartmental flow control: Decentralization, robustness and optimality”. F. Blanchini, E. Franco, G. Giordano, V. Mardanlou, and P. L. Montessoro. Automatica 64 (2016), pp. 18–28.
• “Molecular titration promotes oscillations and bistability in minimal network models with monomeric regulators”. C. Cuba Samaniego, G. Giordano, J. Kim, F. Blanchini, and E. Franco. ACS Synthetic Biology 5.4 (2016), pp. 321–333.
• “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 P. L. Montessoro. IEEE Transactions on Network Science and Engineering 3.4 (2016), pp. 312–324.
• “Computing the structural influence matrix for biological systems”. G. Giordano, C. C. Samaniego, E. Franco, and F. Blanchini. Journal of Mathematical Biology 72.7 (2016), pp. 1927–1958.
• “Programmable RNA microstructures for coordinated delivery of siRNAs”. J. M. Stewart, M. Viard, H. K. Subramanian, B. K. Roark, K. A. Afonin, and E. Franco. Nanoscale 8.40 (2016), pp. 17542–17550.

• “A self-regulating biomolecular comparator for processing oscillatory signals”. D. K. Agrawal, E. Franco, and R. Schulman. Journal of the Royal Society Interface 12.111 (2015), p. 20150586.
• “Network-decentralized control strategies for stabilization”. F. Blanchini, E. Franco, and G. Giordano. IEEE Transactions on Automatic Control 60.2 (2015), pp. 491–496.
• “An analytical approach to bistable biological circuit discrimination using real algebraic geometry”. D. Siegal-Gaskins, E. Franco, T. Zhou, and R. M. Murray. Journal of the Royal Society Interface 12.108 (2015), p. 20150288.
• “Self-assembly of large RNA structures: learning from DNA nanotechnology”. J. M. Stewart and E. Franco. DNA and RNA Nanotechnology 2.1 (2015), pp. 23–35.

• “A structural classification of candidate oscillatory and multistationary biochemical systems”. F. Blanchini, E. Franco, and G. Giordano. Bulletin of Mathematical Biology 76.10 (2014), pp. 2542–2569.
• “Negative autoregulation matches production and demand in synthetic transcriptional networks”. E. Franco, G. Giordano, P.-O. Forsberg, and R. M. Murray. ACS Synthetic Biology 3.8 (2014), pp. 589–599.
• “Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator”. M. Weitz, J. Kim, K. Kapsner, E. Winfree, E. Franco, and F. C. Simmel. Nature Chemistry 6.4 (2014), pp. 295–302.

• “Structural properties of the MAPK pathway topologies in PC12 cells”. E. Franco and F. Blanchini. Journal of Mathematical Biology 67.6-7 (2013), pp. 1633–1668.
• “Dynamically reshaping signaling networks to program cell fate via genetic controllers”. K. E. Galloway, E. Franco, and C. D. Smolke. Science 341.6152 (2013), p. 1235005.

• “Structurally robust biological networks”. F. Blanchini and E. Franco. BMC Systems Biology 5.1 (2011), p. 74.
• “Timing molecular motion and production with a synthetic transcriptional clock”. E. Franco, E. Friedrichs, J. Kim, R. Jungmann, R. Murray, E. Winfree, and F. C. Simmel. Proceedings of the National Academy of Sciences 108.40 (2011), E784–E793.

• “Cooperative constrained control of distributed agents with nonlinear dynamics and delayed information exchange: A stabilizing receding-horizon approach”. E. Franco, L. Magni, T. Parisini, M. M. Polycarpou, and D. M. Raimondo. IEEE Transactions on Automatic Control 53.1 (2008), pp. 324–338.

• “Design and stability analysis of cooperative receding-horizon control of linear discrete-time agents”. E. Franco, T. Parisini, and M. M. Polycarpou. International Journal of Robust and Nonlinear Control 17.10-11 (2007), pp. 982–1001.
• “Geometry of unsteady fluid transport during fluid–structure interactions”. E. Franco, D. N. Pekarek, J. Peng, and J. O. Dabiri. Journal of Fluid Mechanics 589 (2007), pp. 125–145.

Peer-reviewed conference proceedings

• “ Asymptotic propagation of pulsatile dynamics in biological cascades ”. B. Whitley, D. Breda, F. Blanchini, E. Nakamura, and E. Franco. 2026 IEEE 65th Conference on Decision and Control (to appear). 2026.

• “Temporal Dose-Response Inversion in a Biological Circuit” . E. Nakamura, E. Franco, and F. Blanchini. 2025 IEEE 64th Conference on Decision and Control. 2025.

• “Design of a sequestration-based network with tunable pulsing dynamics”. E. Nakamura, C. C. Samaniego, F. Blanchini, G. Giordano, and E. Franco. 2024 IEEE 63rd Conference on Decision and Control (CDC). IEEE. 2024, pp. 6286–6291.
• “Neural networks built from enzymatic reactions can operate as linear and nonlinear classifiers”. C. C. Samaniego, E. Wallace, F. Blanchini, E. Franco, and G. Giordano. 2024 IEEE 63rd Conference on Decision and Control (CDC). 2024, pp. 6292–6297.

• “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). IEEE. 2022, pp. 273–278.
• “Building molecular band-pass filters via molecular sequestration”. Y. Zhang, C. C. Samaniego, K. Carleton, Y. Qian, G. Giordano, and E. Franco. 2022 IEEE 61st Conference on Decision and Control (CDC). IEEE. 2022, pp. 3890–3895.

• “Bistable State Switch Enables Ultrasensitive Feedback Control in Heterogeneous Microbial Populations”. X. Ren, C. C. Samaniego, R. M. Murray, and E. Franco. 2021 American Control Conference (ACC). IEEE. 2021, pp. 652–659.
• “Signaling-based neural networks for cellular computation”. C. C. Samaniego, A. Moorman, G. Giordano, and E. Franco. 2021 American Control Conference (ACC). IEEE. 2021, pp. 1883–1890.

• “Dynamic Control Allocation for a Class of Over-actuated Aircraft”. R. Baggi, E. Franco, and A. Serrani. AIAA Scitech 2020 Forum. 2020, p. 0841.
• “Sequestration and delays enable the synthesis of a molecular derivative operator”. C. C. Samaniego, J. Kim, and E. Franco. 2020 59th IEEE Conference on Decision and Control (CDC). IEEE. 2020, pp. 5106–5112.

• “Biomolecular stabilisation near the unstable equilibrium of a biological system”. C. C. Samaniego, N. A. Delateur, G. Giordano, and E. Franco. 2019 IEEE 58th Conference on Decision and Control (CDC). IEEE. 2019, pp. 958–964.
• “A molecular device for frequency doubling enabled by molecular sequestration”. C. C. Samaniego and E. Franco. 2019 18th European Control Conference (ECC). IEEE. 2019, pp. 2146–2151.
• “Practical differentiation using ultrasensitive molecular circuits”. C. C. Samaniego, G. Giordano, and E. Franco. 2019 18th European Control Conference (ECC). IEEE. 2019, pp. 692–697.

• “Design and analysis of a biomolecular positive-feedback oscillator”. C. C. Samaniego, E. Franco, and G. Giordano. 2018 IEEE Conference on Decision and Control (CDC). IEEE. 2018, pp. 1083–1088.

• “Aggregates of Positive Impulse Response systems: a decomposition approach for complex networks”. F. Blanchini, C. C. Samaniego, E. Franco, and G. Giordano. 56th IEEE Conference on Decision and Control (CDC). 2017.
• “An ultrasensitive biomolecular network for robust feedback control”. C. C. Samaniego and E. Franco. IFAC-PapersOnLine. Vol. 50.1. Elsevier, 2017, pp. 10950–10956.
• “An ultrasensitive motif for robust closed loop control of biomolecular systems”. C. C. Samaniego and E. Franco. 2017 IEEE 56th Annual Conference on Decision and Control (CDC). IEEE. 2017, pp. 5334–5340.
• “Design of a bistable network using the CRISPR/Cas system”. C. C. Samaniego, H. K. Subramanian, and E. Franco. 2017 IEEE Conference on Control Technology and Applications (CCTA). IEEE. 2017, pp. 973–978.

• “Negative feedback enables structurally signed steady-state influences in artificial biomolecular networks”. G. Giordano and E. Franco. 2016 IEEE 55th Conference on Decision and Control (CDC). IEEE. 2016, pp. 3369–3374.
• “An algebraic approach to parameter optimization in biomolecular bistable systems”. V. Mardanlou and E. Franco. 2016 American Control Conference (ACC). IEEE. 2016, pp. 6670–6675.
• “A coarse-grained model of DNA nanotube population growth”. V. Mardanlou, L. N. Green, H. K. Subramanian, R. F. Hariadi, J. Kim, and E. Franco. International Conference on DNA-Based Computers. Springer. 2016, pp. 135–147.

• “Designing a self-regulating biomolecular comparator”. D. K. Agrawal, E. Franco, and R. Schulman. 2015 American Control Conference (ACC). IEEE. 2015, pp. 2661–2666.
• “Structural conditions for oscillations and multistationarity in aggregate monotone systems”. F. Blanchini, E. Franco, and G. Giordano. 2015 IEEE 54th Conference on Decision and Control (CDC). IEEE. 2015, pp. 609–614.
• “A bistable biomolecular network based on monomeric inhibition reactions”. V. Mardanlou, C. C. Samaniego, and E. Franco. 2015 IEEE 54th Conference on Decision and Control (CDC). IEEE. 2015, pp. 3858–3863.
• “A minimal biomolecular frequency divider”. C. C. Samaniego and E. Franco. 2015 IEEE 54th Conference on Decision and Control (CDC). IEEE. 2015, pp. 1277–1282.
• “Design and analysis of a synthetic aptamer-based oscillator”. C. C. Samaniego, S. Kitada, and E. Franco. 2015 American Control Conference (ACC). IEEE. 2015, pp. 2655–2660.

• “Design of a molecular clock with RNA-mediated regulation”. F. Blanchini, C. C. Samaniego, E. Franco, and G. Giordano. 2014 IEEE 53rd Conference on Decision and Control (CDC). IEEE. 2014, pp. 4611–4616.
• “Design of a molecular bistable system with RNA-mediated regulation”. V. Mardanlou, C. H. Tran, and E. Franco. 2014 IEEE 53rd Conference on Decision and Control (CDC). IEEE. 2014, pp. 4605–4610.
• “Distributed camera control via moving horizon bayesian optimization”. A. A. Morye, E. Franco, A. K. Roy-Chowdhury, and J. A. Farrell. 2014 American Control Conference (ACC). IEEE. 2014, pp. 2083–2089.

• “Structured-LMI conditions for stabilizing network-decentralized control”. F. Blanchini, E. Franco, and G. Giordano. 2013 IEEE 52nd Conference on Decision and Control (CDC). IEEE. 2013, pp. 6880–6885.
• “Receding horizon control of a two-agent system with competitive objectives”. A. Carron and E. Franco. 2013 American Control Conference (ACC). IEEE. 2013, pp. 2533–2538.
• “Feedback architectures to regulate flux of components in artificial gene networks”. G. Giordano, E. Franco, and R. M. Murray. 2013 American Control Conference (ACC). IEEE. 2013, pp. 4747–4752.

• “Determining the structural properties of a class of biological models”. F. Blanchini, E. Franco, and G. Giordano. 2012 IEEE 51st Conference on Decision and Control (CDC). IEEE. 2012, pp. 5505–5510.
• “Analysis of a negative feedback biochemical oscillator”. E. Franco and F. Blanchini. 2012 American Control Conference (ACC). IEEE. 2012, pp. 3445–3450.

• “Multistability and robustness of the MAPK pathway”. F. Blanchini and E. Franco. 2011 IEEE Conference on Decision and Control and European Control Conference (CDC-ECC). 2011.

• “Tuning a synthetic in vitro oscillator using control-theoretic tools”. C. Sturk, E. Franco, and R. M. Murray. 2010 49th IEEE Conference on Decision and Control (CDC). IEEE. 2010, pp. 2554–2559.

• “Design of insulating devices for in vitro synthetic circuits”. E. Franco, D. Del Vecchio, and R. M. Murray. 48th IEEE Conference on Decision and Control (CDC/CCC). IEEE. 2009, pp. 4584–4589.

• “Design, modeling and synthesis of an in vitro transcription rate regulatory circuit”. E. Franco, P.-O. Forsberg, and R. M. Murray. 2008 American Control Conference. IEEE. 2008, pp. 2786–2791.
• “Design and performance of in vitro transcription rate regulatory circuits”. E. Franco and R. M. Murray. 2008 47th IEEE Conference on Decision and Control (CDC). IEEE. 2008, pp. 161–166.

• “A multi-model approach to identification of biosynthetic pathways”. M. J. Dunlop, E. Franco, and R. M. Murray. 2007 American Control Conference (ACC). IEEE. 2007, pp. 1600–1605.

• “Distributed fault diagnosis using sensor networks and consensus-based filters”. E. Franco, R. Olfati-Saber, T. Parisini, and M. M. Polycarpou. 2006 45th IEEE Conference on Decision and Control. IEEE. 2006, pp. 386–391.
• “Determination of the value of information in large vehicle arrays”. J. L. Speyer, N. Zika, and E. Franco. 2006 American Control Conference. IEEE. 2006, 7 pp.

• “Cooperative control of distributed agents with nonlinear dynamics and delayed information exchange: a stabilizing receding-horizon approach”. E. Franco, T. Parisini, and M. M. Polycarpou. 2005 44th IEEE Conference on Decision and Control (CDC-ECC). IEEE. 2005, pp. 2206–2211.
• “Stable receding-horizon cooperative control of a class of distributed agents”. E. Franco, T. Parisini, and M. M. Polycarpou. 2005 American Control Conference. IEEE. 2005, pp. 4673–4678.
• “A hybrid control scheme for freeway systems”. S. Sacone, E. Franco, and T. Parisini. IFAC Proceedings Volumes. Vol. 38.1. Elsevier, 2005, pp. 108–113.

• “Cooperative control of discrete-time agents with delayed information exchange: A receding-horizon approach”. E. Franco, T. Parisini, and M. M. Polycarpou. 2004 43rd IEEE Conference on Decision and Control (CDC). Vol. 4. IEEE. 2004, pp. 4274–4279.
• “Practically stable nonlinear receding-horizon control of multi-model systems”. E. Franco, S. Sacone, and T. Parisini. 2004 43rd IEEE Conference on Decision and Control (CDC). Vol. 3. IEEE. 2004, pp. 3241–3246.
• “Stable multi-model switching control of a class of nonlinear systems”. E. Franco, S. Sacone, and T. Parisini. 2004 American Control Conference. Vol. 2. IEEE. 2004, pp. 1873–1878.

Book chapters

• “Assembly of RNA Nanostructures from Double-Crossover Tiles”. J. M. Stewart, H. K. Subramanian, and E. Franco. Cell-Free Gene Expression. Springer, 2022, pp. 293–302.
• “Structural Properties of Biological and Ecological Systems”. F. Blanchini, E. Franco, and G. Giordano. Encyclopedia of Systems and Control. Ed. by J. Baillieul and T. Samad. Springer-Verlag London, 2021.
• “Building a Synthetic Transcriptional Oscillator”. M. Schwarz-Schilling, J. Kim, C. Cuba, M. Weitz, E. Franco, and F. C. Simmel. Springer New York, 2016, pp. 185–199.
• “Feedback Loops in Biological Networks”. E. Franco and K. E. Galloway. Springer New York, 2015, pp. 193–214.
• “Structural analysis of biological networks”. F. Blanchini and E. Franco. A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations. Springer Netherlands, 2014, pp. 47–71.
• “Synthetic Biochemical Devices for Programmable Dynamic Behavior”. J. Kim and E. Franco. A Systems Theoretic Approach to Systems and Synthetic Biology II: Analysis and Design of Cellular Systems. Springer Netherlands, 2014, pp. 273–295.
• “Transcriptional oscillators”. E. Franco, J. Kim, and F. C. Simmel. Wiley-VCH Verlag GmbH & Co. KGaA, 2013, pp. 83–112.
• “Belief consensus and distributed hypothesis testing in sensor networks”. R. Olfati-Saber, E. Franco, E. Frazzoli, and J. S. Shamma. Networked Embedded Sensing and Control. Springer Berlin Heidelberg, 2006, pp. 169–182.

Patents

• “Methods for building artificial RNA organelles in living cells”. E. Franco, S. Li, and A. Tang. U.S. Provisional Patent Application No. 63/679,560. 2024.
• “Single stranded RNA motifs for in vitro cotranscriptional production of orthogonal phase separated condensates”. E. Franco, S. Li, A. Tang, G. Fabrini, and L. Di Michele. U.S. Provisional Patent Application No. 63/660,018. 2024.
• “CRISPR protein inhibitors”. A. Choudhary, K. Cox, B. Maji, P. Wu, H. Subramanian, and E. Franco. US Patent 11,760,984. Sept. 2023.
• “Compositions and methods for regulating proteins and nucleic acids activities”. A. Choudhary, K. Cox, H. Subramanian, and E. Franco. US Patent App. 16/776,503. July 2020.
• “Inhibitors of RNA guided nucleases and uses thereof”. A. Choudhary, P. Wu, B. Maji, E. Franco, and H. K. Subramanian. US Patent App. 16/346,392. Aug. 2019.

Archival & pre-prints

• “Programming the Internal Architecture of Synthetic Compartments by Coassembling Filamentous and Liquid DNA Phases ”. M. Dizani, B. Perlstein, D. McGrory, S. P. Afrose, S. Agarwal, and E. Franco. bioRxiv (2026).
• “Temporal dose inversion properties of adaptive biomolecular circuits (in revision with Cell Systems)”. E. Nakamura, F. Blanchini, G. Giordano, A. Hoffmann, and E. Franco. bioRxiv (2025).
• “A feedback SIR (fSIR) model highlights advantages and limitations of infection-dependent mitigation strategies”. E. Franco. arXiv:2004.13216 [q-bio.PE] (2020).