Wang, L., Xu, W., Zhang, S., Gundberg, G.C., Zheng, C.R., Wan, Z., Mustafina, K., Caliendo, F., Sandt, H., Kamm, R., & Weiss, R., (2024). Sensing and guiding cell-state transitions by using genetically encoded endoribonuclease-mediated microRNA sensors. Nature Biomedical Engineering. doi: 10.1038/s41551-024-01095-1.

Beaver, L.E., Sokolich, M., Alsalehi, S., Weiss, R., Das, S., & Belta, C., (February 2024). Learning a Tracking Controller for Rolling μ bots. IEEE Robotics and Automation Letters. doi: 10.1109/LRA.2024.3350968.

Xue, Y., Zhang, Y., Zhong, Y., Du, S., Hou, X., Li, W., Li, H., Wang, S., Wang, C., Yan, J., Kang, D.D., Deng, B., McComb, D.W., Irvine, D.J., Weiss, R., & Dong, Y., (January 2024). LNP-RNA-engineered adipose stem cells for accelerated diabetic wound healing. Nature Communications. doi: 10.1038/s41467-024-45094-5.


Wauford, N., Patel, A., Tordoff, J., Enghuus, C., Jin, A., Toppen, J., Kemp, M., Weiss, R., (September 2023). Synthetic symmetry breaking and programmable multicellular structure formation. Cell Systems. doi: 10.1016/j.cels.2023.08.001.

Wauford, N., Jones, R., Van De Mark, C., Weiss, R., (February 2023). Rapid development of cell state identification circuits with poly-transfection. Jove. doi: 10.3791/64793-v.


Cabera, A., Edelstein, H., Glykofrydis, F., Love, K., Palacios, S., Tycko, J., Zhang, M., Lensch, S., Shields, C., Livingston, M., Weiss, R., Zhao, H., Haynes, K., Morsut, L., Chen, Y., Khalil, A., Wong, W., Collins, J., Rosser, S., Polizzi, K., Elowitz, M., Fussenegger, M., Hilton, I., Leonard, J., Bintu, L., Galloway, K., Deans, T, (December 2022). The sound of silence: Transgene silencing in mammalian cell engineering. Cell Systems. doi: 10.1016/j.cels.2022.11.005.

Alsalehi, S., Aasi, E., Weiss, R., Belta, C., (October 2022). Learning Spatio-Temporal Specifications for Dynamical Systems. Proceedings of The 4th Annual Learning for Dynamics and Control Conference, PMLR 168:968-980, 2022.

Chen, W., Gaidukov, L., Lai, Y., Wu, M., Cao, J., Gutbrod, M., Choi, G., Utomo, R., Chen, Y., Wroblewska, L., Kellis, M., Zhang, L., Weiss, R., Lu., T., (October 2022). A synthetic transcription platform for programmable gene expression in mammalian cells. Nat Commun 13, 6167. DIO:10.1038/s41467-022-33287-9

Rizik, L., Danial, L., Habib, M., Weiss, R., Daniel, R., (September 2022). Synthetic neuromorphic computing in living cells. Nature Communications, DIO:10.1038/s41467-022-33288-8.

DiAndreth, B., Wauford, N., Hu, E., Palacios, S., Weiss, R., (May 2022). PERSIST platform provides programmable RNA regulation using CRISPR endoRNases. Nature Communications, DIO:10.1038/s41467-022-30172-3.

Kudithipudi, D., Aguilar-Simon, M., Babb, J., Bazhenov, M., Blackiston, D., Bongard, J., Brna, A., Chakravarthi Raja, S., Cheney, N., Clune, J., Daram, A., Fusi, S., Helfer, P., Kay, L., Ketz, N., Kira, Z., Kolouri, S., Krichmar,J., Kriegman, S., Levin, M., Madireddy, S., Manicka, S., Marjaninejad, A., McNaughton, B., Miikkulainen, R., Navratilova, Z., Pandit, T., Parker, A., Pilly, P., Risi, S., Sejnowski, T., Soltoggio, A., Soures, N., Tolias, A., Urbina-Meléndez, D., Valero-Cuevas, F., van de Ven, G., Vogelstein, J., Wang, F., Weiss, R., Yanguas-Gil, A., Zou, X., Siegelmann, H., (March 2022). Biological underpinnings for lifelong learning machines. Nat Mach Intell 4, 196–210 (2022). DOI:10.1038/s42256-022-00452-0

Jones, R., Qian, Y., Ilia, K., Wang, B., Laub, M., Del Vecchio, D., Weiss, R., (March 2022). Robust and tunable signal processing in mammalian cells via engineered covalent modification cycles. Nature Communications, DIO:10.1038/s41467-022-29338-w.

Aydin, O., Passaro, A., Raman, R., Spellicy, S., Weinberg, R., Kamm, R., Sample, M., Truskey, G., Zartman, J., Dar, R., Palacios, S., Wang, J., Tordoff, J., Montserrat, N., Bashir, R., Saif, M., Weiss, R., (March 2022). Principles for the design of multicellular engineered living systems. APL Bioengineering, DIO:DIO:10.1063/5.0076635. [AIP Science Highlight Article]

Beal, J., Teague, B., Sexton, J., Castillo-Hair, S., DeLateur, N., Samineni, M., Tabor, J., Weiss, R., Calibrated Flow Cytometry Study Consortium, (February 2022). Meeting Measurement Precision Requirements for Effective Engineering of Genetic Regulatory Networks. ACS Synthetic Biology, DIO: 0.1021/acssynbio.1c00488.


Kiwimagi, K., Letendre, J., Weingerg, B., Wang, J., Chen, M., Watanabe, L., Myers, C., Beal, J., Wong, W., Weiss, R., (July 2021). Quantitative characterization of recombinase-based digitizer circuits enables predictable amplification of biological signals. Communications Biology, DIO: 10.1038/s42003-021-02325-5.

Mishra, D., Bepler, T., Teague, B., Berger, B., Broach, J., Weiss, R., (July 2021). An engineered protein-phosphorylation toggle network with implications for endogenous network discovery. Science, DIO: 10.1126/science.aav0780. [MIT News Article]

Shakiba, N., Jones, R., Weiss, R., Del Vecchio, D., (June 2021). Context-aware synthetic biology by controller design: Engineering the mammalian cell. Cell Systems, DIO: 10.1016/j.cels.2021.05.011.

Mc Cafferty, S., De Temmerman J., Kitada, T., Becraft, J., Weiss, R., Irvine, D., Devreese, M., De Baere, S., Combes, F., Sanders, N., (March 2021). In Vivo Validation of a Reversible Small Molecule-Based Switch for Synthetic Self-Amplifying mRNA Regulation. Molecular Therapy, DIO: 10.1016/j.ymthe.2020.11.010.

Tordoff, J., Krajnc,M., Walczak, N., Lima, M., Beal, J., Shvartsman, S., Weiss, R., (January 2021). Incomplete Cell Sorting Creates Engineerable Structures with Long-Term Stability. Cell Reports Physical Science, DIO: 10.1016/j.xcrp.2020.100305.


Cafferty, S, De Temmerman, J., Kitada, T., Becraft, J., Weiss, R., Irvine, D., Devreese, M., De Baere, S., Combes, F., Sanders, N., (November 2020). In Vivo Validation of a Reversible Small Molecule-Based Switch for Synthetic Self-Amplifying mRNA Regulation. Molecular Therapy, DIO: 10.1016/j.ymthe.2020.11.010

Garreta, E., Kamm, R., Chuva de Sousa Lopes, S., Lancaster, M., Weiss, R., Trepat, X., Hyun, I., Monserat, N., (November 2020). Rethinking organoid technology through bioengineering. Nature Materials, DIO: 10.1038/s41563-020-00804-4

Jones, R., Qian, Y., Siciliano, V., DiAndreth, B., Huh, J., Weiss, R., Del Vecchio, D., (November 2020). An endoribonuclease-based feedforward controller for decoupling resource-limited genetic modules in mammalian cells. Nature Communications, DIO: 10.1101/2019.12.15.867150

Li, Y., Su, Z., Zhao, W., Zhang, X., Momin, N., Zhang, C., Wittrup, K., Dong, Y., Irvine, D., Weiss, R., (August 2020). Multifunctional oncolytic nanoparticles deliver self-replicating IL-12 RNA to eliminate established tumors and prime systemic immunityNature Cancer, DIO: 10.1038/s43018-020-0095-6

Morley, C., Tordoff, J., O'Bryan, C., Weiss, R., Angelini, T., (June 2020). 3D aggregation of cells in packed microgel mediaSoft MatterDIO: 10.1039/D0SM00517G

Duhkinova, M., Crina, C., Weiss, R., Siciliano, V., (April 2020). Engineering Intracellular Protein Sensors in Mammalian CellsJournal of Visualized ExperimentsDIO: 10.3791/60878


Moorman, A., Cuba Samaniego, C., Maley, C., Weiss, R., (December 2019). A Dynamical Biomolecular Neural Network2019 IEEE Conference on Decision and Control, DIO: 10.1109/CDC40024.2019.9030122

Melo, M., Porter, E., Zhang, Y., Silva, M., Li, N., Dobosh, B., Liguori, A., Skog, P., Landais, E., Menis, S., Sok, D., Nemazee, D., Schief, W., Weiss, R., Irvine, D., (August 2019). Immunogenicity of RNA Replicons Encoding HIV Env Immunogens Designed for Self-Assembly into NanoparticlesMolecular Therapy, DIO: 10.1016/j.ymthe.2019.08.007

Gam, J., DiAndreth, B., Jones, R., Huh, J., Weiss, R., (August 2019). A 'poly-transfection' method for rapid, one-pot characterization and optimization of genetic systemsNucleic Acids Research, DIO: 10.1093/nar/gkz623

Wu, M., Nissim, L., Stupp, D., Pery, E., Binder-Nissim, A., Weisinger, K., Enghuus, C., Palacios, S., Humphrey, M., Zhang, Z., Novoa, E., Kellis, M., Weiss, R., Rabkin, S., Tabach, Y., Lu, T., (July 2019). A high-throughput screening and computation platform for identifying synthetic promoters with enhanced cell-state specificity (SPECS)Nature Communications, DIO: 10.1007/s12213-019-00119-x

Das, S., Hunter, E., DeLateur, N., Steager, E., Weiss, R., Kumar, V., (June 2019). Cellular expression through morphogen delivery by light activated magnetic microrobotsJournal of Micro-Bio Robotics, DIO: 10.1007/s12213-019-00119-x

Mapar, F., Weiss, R., (May 2019). Switching Delay Analysis for Two Neuronal Toggle Switch Designs: Direct and Staged Mutual Inhibition9th International IEEE/EMBS Conference on Neural Engineering (NER)DIO: 10.1109/NER.2019.8717123

Chang, M., Gaidukov, L., Jung, G., Tseng, W., Scarcelli, J., Cornell, R., Marshall, J., Lyles, J., Sakorafas, P., Chu, A., Cote, K., Tzvetkova, B., Dolatshahi, S., Sumit, M., Mulukutla, B., Lauffenburger, B., Figueroa, B., Summers, N., Lu, T., Weiss, R., (May 2019). Small-molecule control of antibody N-glycosylation in engineered mammalian cellsNature Chemical Biology, DIO: 10.1038/s41589-019-0288-4

Anderson, D., Jones, R., Arkin, A., Weiss, R., (May 2019). Principles of Synthetic Biology: A MOOC for an Emerging FieldSynthetic Biology, DIO: 10.1093/synbio/ysz010

Jusiak, B., Jagtap, K., Gaidukov, L., Duportet, X., Bandara, K., Chu, J., Zhang, L., Weiss, R., Lu, T., (May 2019). Comparison of Integrases Identifies Bxb1-GA Mutant as the Most Efficient Site-Specific Integrase System in Mammalian CellsACS Synthetic Biology, DIO: 10.1021/acssynbio.8b00089

Li, Y., Teague, B., Zhang, Y., Su, Z., Porter, E., Dobosh, B., Wagner, T., Irvine, D., Weiss, R., (May 2019). In vitro evolution of enhanced RNA replicons for immunotherapyNature Scientific Reports, DIO:

Teo, J., Weiss, R., Sarpeshkar, R., (March 2019). An Artificial Tissue Homeostasis Circuit Designed via Analog Circuit TechniquesIEEE Transactions on Biomedical Circuits and Systems, DIO: 10.1109/TBCAS.2019.2907074

Sumit, M., Dolatshahi, S., Chu, A., Cote, K., Scarcelli, J., Marshall, J., Cornell, R., Weiss, R., Lauffenburger, D., Mulukutla, B., Figueroa, B., (January 2019). Dissecting N-Glycosylation Dynamics in Chinese Hamster Ovary Cells Fed-batch Cultures using Time Course Omics AnalysesiScience, DIO: 10.1016/j.isci.2019.01.006


Madsen, C., Vaidyanathan, P., Sadraddini, S., Vasile, C., DeLateur, N., Weiss, R., Densmore, D., Belta, C., (December 2018). Metrics for Signal Temporal Logic Formulae. Proceedings of the 2018 IEEE COnference on Decision and Control (CDC). DOI: 10.1109/CDC.2018.8619541. Published Conference Proceeding.

Mapar, F., Weiss, R., (October 2018). Design and Analysis of Staged Mutual Inhibition to Implement Bi-Stable Neuronal Toggle Switch. Proceedings of the 2018 IEEE Biomedical Circuits and Systems Conference (BioCAS). DOI: 10.1109/BIOCAS.2018.8584816. Published Conference Proceeding.

Cella, F., Wroblewska, L., Weiss, R., Siciliano, V., (October 2018). Engineering protein-protein devices for multilayered regulation of mRNA translation using orthogonal proteases in mammalian cellsNature Communications, DIO: 10.1038/s41467-018-06825-7.

Wagner, T., Becraft, J., Bodner, K., Teague, B., Zhang, X., Woo, A., Porter, E., Alburquerque, B., Dobosh, B., Andries, O., Sanders, N., Beal J., Densmore, D., Kitada, T., Weiss, R., (October 2018). Small-molecule-based regulation of RNA-delivered circuits in mammalian cellsNature Chemical Biology, DIO: 10.1038/s41589-018-0146-9. [MIT News Article] [GEN News] [Fiercebiotech News]

Kamm, R., Bashir, R., Arora, N., Dar, R., Gillette, M., Griffith, L., Kemp, M., Kinlaw, K., Levin, L., Martin, A., McDevitt, T., Nerem, R., Powers, M., Saif, T., Sharpe, J., Takayama, S., Takeuchi, S., Weiss, R., Ye, K., Yevick, H., Zaman, M., (October 2018). Perspective: The promise of multi-cellular engineered living systemsAPL Bioengineering, DIO: 10.1063/1.5038337

Tordoff, Weiss, R., (July 2018). Living shapes engineered. Nature News and ViewsDOI:10.1038/d41586-018-05564-5

Tordoff, J., Beal, J., Weiss, R., Bartley, B., Gumuskaya, G., Kiwimagi, K., Krajnc, M., Lebo, K., Shvartsman, S., Tseng, A., Walczak, N., (July 2018). Toward programming 3D shape formation in mammalian cellsProceedings of the 10th International Workshop on Bio-Design Automation (IWBDA), pp. 69-70

Das, S., Hunter, E., DeLateur, N., Steager, E., Weiss, R., Kumar, V., (July 2018). Controlled Delivery of Signaling Molecules Using Magnetic Microrobots. 2018 International Conference on Manipulation, Automation and Robotics at Small Scales (MARSS), DOI: 10.1109/MARSS.2018.8481163

Gam, J., Babb, J., Weiss, R., (July 2018). A mixed antagonistic/synergistic miRNA repression model enables accurate predictions of multi-input miRNA sensor activity. Nature CommunicationsDOI:10.1038/s41467-018-04575-0

Karig, D., Martini, M., Lu, T., DeLateur, N., Goldenfeld, N., Weiss, R., (June 2018). Stochastic Turing patterns in a synthetic bacterial population. PNASDOI:10.1073/pnas.1720770115

Siciliano, V., DiAndreth, B., Monel, B., Beal, J., Huh, J., Clayton, K., Wroblewska, L., McKeon, A., Walker, B., Weiss, R., (May 2018). Engineering modular intracellular protein sensor-actuator devices. Nature CommunicationsDOI:10.1038/s41467-018-03984-5

Dar, R., Weiss, R., (April 2018). Perspective: Engineering noise in biological systems towards predictive stochastic design. APL Bioengineering, DOI:10.1063/1.5025033

Gaidukov, L., Wroblewska, L., Teague, B., Nelson, T., Zhang, X., Liu, Y., Jagtap, S., Mamo, S., Tseng, W.A., Lowe Jishnu Das, A., Bandara, K., Baijuraj, S., Summers, N., Lu, T., Zhang, L., Weiss, R., (March 2018). A multi-landing pad DNA integration platform for mammalian cell engineering. Nucleic Acids Research, DOI:10.1093/nar/gky216

Kitada, T., DiAndreth, B., Teague, B., Weiss, R., (February 2018). Programming gene and engineered-cell therapies with synthetic biology. Science, DOI: 10.1126/science.aad1067


Vaidyanathan, P., Ivison, R., Bombara, G., DeLateur, N., Weiss, R., Belta, C., Densmore, D., (December 2017). Grid-Based Temporal Logic Inference. Proceedings of the 56th IEEE Conference on Decision and Control.

Beal, J., Delateur, N., Teague, B., Weiss, R., Sexton, J., Castillo-Hair, S., Tabor, J., (August 2017). Toward Quantitative Comparison of Fluorescent Protein Expression Levels via Fluorescent Beads.Proceedings of the 9th International Workshop on Bio-Design Automation (IWBDA), pp. 48-49.

Li, Y., Weiss, R., (August 2017). A Modular Approach to Building Complex Synthetic Circuits.Mammalian Synthetic Promoterspp. 231–248, DOI:10.1007/978-1-4939-7223-4_17.

Kong, D., Thorsen, T., Babb, J., Wick, S., Gam, J., Weiss, R., and Carr, P., (June 2017). Open-source, community-driven microfluidics with Metafluidics. Nature Biotechnology, DOI:10.1038/nbt.3873

Inniss, M., Bandara, K., Jusiak, B., Lu, T., Weiss, R., Wroblewska, L., Zhang, L., (March 2017). A Novel Bxb1 Integrase RMCE System for High Fidelity Site-Specific Integration of mAb Expression Cassette in CHO cells. Biotechnology and Bioengineering, DOI:10.1002/bit.26268.


Beal, J., Weiss, R., (August 2016). Design for Improved Repression in RNA Replicons. Proceedings of the 8th International Workshop on Bio-Design Automation (IWBDA), pp. 21-22.

Teague, B., Guye, P., Weiss, R., (June 2016). Synthetic Morphogenesis. Cold Spring Harbor Perspectives in Biology, DOI:10.1101/cshperspect.a023929.

Guye, P., Ebrahimkhani, M.R., Kipniss, N., Velazquez, JJ., Schoenfeld, E., Kiani, S., Griffith, L.G., Weiss, R., (January 2016). Genetically engineering self-organization of human pluripotent stem cells into a liver bud-like tissue using Gata6. Nature Communications, DOI:10.1038/ncomms10243. [MIT News Article]


Kiani, S., Chavez, A., Tuttle, M., Hall, R. N., Chari, R., Ter-Ovanesyan, D., Qian, J., Pruitt, B. W., Beal, J., Vora, S., Buchthal, J., Kowal, E. J. K., Ebrahimkhani, M. R., Collins, J. J., Weiss, R., and Church, G., (September 2015). Cas9 gRNA engineering for genome editing, activation and repression. Nature Methods, DOI:10.1038/nmeth.3580. [Wyss Press Release]

Teague, B. P., and Weiss, R., (August 2015). Synthetic communities, the sum of parts. Science, DOI:10.1126/science.aad0876

Wroblewska, L., Kitada, T., Endo, K., Siciliano, V., Stillo, B., Saito, H., and Weiss, R., (August 2015). Mammalian synthetic circuits with RNA binding proteins for RNA-only delivery. Nature Biotechnology, DOI:10.1038/nbt.3301

Bhatt, S., Gupta, M. K., Khamaisi, M., Martinez, R., Gritsenko, M. A., Wagner, B. K., Guye, P., Busskamp, V., Shirakawa, J., Wu, G., Liew, C. W., Clauss, T. R., Valdez, I., El Ouaamari, A., Dirice, E., Takatani, T., Keenan, H. A., Smith, R. D., Church, G., Weiss, R., Wagers, A. J., Qian, W.-J., King, G. L., and Kulkarni, R. N., (August 2015). Preserved DNA Damage Checkpoint Pathway Protects against Complications in Long-Standing Type 1 DiabetesCell Metabolism, DOI:10.1016/j.cmet.2015.07.015

Gyorgy, A., Jiménez, J. I., Yazbek, J., Huang, H.-H., Chung, H., Weiss, R., and Del Vecchio, D., (June 2015). Isocost Lines Describe the Cellular Economy of Genetic CircuitsBiophysical Journal, DOI:10.1016/j.bpj.2015.06.034

Chavez, A., Scheiman, J., Vora, S., Pruitt, B. W., Tuttle, M., Iyer, E. P. R., Lin, S., Kiani, S., Guzman, C. D., Wiegand, D. J., Ter-Ovanesyan, D., Braff, J. L., Davidsohn, N., Housden, B. E., Perrimon, N., Weiss, R., Aach, J., Collins, J. J., and Church, G. M., (March 2015). Highly efficient Cas9-mediated transcriptional programmingNature Methods, DOI:10.1038/nmeth.3312

Li, Y., Jiang, Y., Chen, H., Liao, W., Li, Z., Weiss, R., and Xie, Z., (February 2015). Modular construction of mammalian gene circuits using TALE transcriptional repressorsNature Chemical Biology, DOI:10.1038/nchembio.1736

Andries, O., Kitada, T., Bodner, K., Sanders, N. N., and Weiss, R., (January 2015). Synthetic biology devices and circuits for RNA-based “smart vaccines”: a propositional review. Expert Review of Vaccines, DOI:10.1586/14760584.2015.997714


Mishra, D., Rivera, P. M., Lin, A., Del Vecchio, D., and Weiss, R., (November 2014). A load driver device for engineering modularity in biological networksNature Biotechnology, DOI:10.1038/nbt.3044. [Nature Biotech News and Views] [MIT News Article]

Busskamp, V., Lewis, N. E., Guye, P., Ng, A. H., Shipman, S. L., Byrne, S. M., Sanjana, N. E., Murn, J., Li, Y., Li, S., Stadler, M., Weiss, R., and Church, G. M., (November 2014). Rapid neurogenesis through transcriptional activation in human stem cellsMolecular Systems Biology, DOI:10.15252/msb.20145508

Davidsohn, N., Beal, J., Kiani, S., Adler, A., Yaman, F., Li, Y., Xie, Z., and Weiss, R., (November 2014). Accurate Predictions of Genetic Circuit Behavior from Part Characterization and Modular CompositionACS Synthetic Biology, DOI:10.1021/sb500263b

Duportet, X., Wroblewska, L., Guye, P., Li, Y., Eyquem, J., Rieders, J., Rimchala, T., Batt, G., and Weiss, R., (October 2014). A platform for rapid prototyping of synthetic gene networks in mammalian cellsNucleic Acids Research, DOI:10.1093/nar/gku1082

Stanton, B. C., Siciliano, V., Ghodasara, A., Wroblewska, L., Clancy, K., Trefzer, A. C., Chesnut, J. D., Weiss, R., and Voigt, C. A., (October 2014). Systematic Transfer of Prokaryotic Sensors and Circuits to Mammalian CellsACS Synthetic Biology, DOI:10.1021/sb5002856

Steager, E. B., Wong, D., Mishra, D., Weiss, R., and Kumar, V., (June 2014). Sensors for micro bio robots via synthetic biology. 2014 IEEE International Conference on Robotics and Automation (ICRA) (pp. 3783–3788), DOI:10.1109/ICRA.2014.6907407

Weiss, R., (May 2014). Synthetic Biology, How Best to Build A Cell: Automate Efficient Design. Comment, Nature, DOI:10.1038/509155a.

Beal, J., Wagner, T. E., Kitada, T., Azizgolshani, O., Parker, J. M., Densmore, D., and Weiss, R., (May 2014). Model-Driven Engineering of Gene Expression from RNA RepliconsACS Synthetic Biology, DOI:10.1021/sb500173f

Kiani, S., Beal, J., Ebrahimkhani, M. R., Huh, J., Hall, R. N., Xie, Z., Li, Y., and Weiss, R., (May 2014). CRISPR transcriptional repression devices and layered circuits in mammalian cells. Nature Methods, DOI:10.1038/nmeth.2969

Church, G. M., Elowitz, M. B., Smolke, C. D., Voigt, C. A., and Weiss, R., (March 2014). Realizing the potential of synthetic biologyNature Reviews Molecular Cell Biology, DOI:10.1038/nrm3767


Li, W., Lee, S., Ma, M., Kim, S. M., Guye, P., Pancoast, J. R., Anderson, D. G., Weiss, R., Lee, R. T., and Hammond, P. T., (October 2013). Microbead-based biomimetic synthetic neighbors enhance survival and function of rat pancreatic β-cells. Scientific Reports, DOI:10.1038/srep02863

Guye, P., Li, Y., Wroblewska, L., Duportet, X., and Weiss, R., (June 2013). Rapid, modular and reliable construction of complex mammalian gene circuits. Nucleic Acids Research, DOI:10.1093/nar/gkt605

Gupta, S., Bram, E. E., and Weiss, R., (June 2013). Genetically Programmable Pathogen Sense and DestroyACS Synthetic Biology, DOI:10.1021/sb4000417


Sakar, M. S., Neal, D., Boudou, T., Borochin, M. A., Li, Y., Weiss, R., Kamm, R. D., Chen, C. S., and Asada, H. H., (August 2012). Formation and optogenetic control of engineered 3D skeletal muscle bioactuatorsLab on a Chip, DOI:10.1039/C2LC40338B. [MIT News Article]

Beal, J., Weiss, R., Densmore, D., Adler, A., Appleton, E., Babb, J., Bhatia, S., Davidsohn, N., Haddock, T., Loyall, J., Schantz, R., Vasilev, V., and Yaman, F., (July 2012). An End-to-End Workflow for Engineering of Biological Networks from High-Level Specifications. ACS Synthetic Biology, DOI:10.1021/sb300030d

Miller, M., Hafner, M., Sontag, E., Davidsohn, N., Subramanian, S., Purnick, P. E. M., Lauffenburger, D., and Weiss, R., (July 2012). Modular Design of Artificial Tissue Homeostasis: Robust Control through Synthetic Cellular Heterogeneity. PLoS Comput Biol, DOI:10.1371/journal.pcbi.1002579

Slusarczyk, A. L., Lin, A., and Weiss, R., (June 2012). Foundations for the design and implementation of synthetic genetic circuitsNature Reviews Genetics, DOI:10.1038/nrg3227

Beal, J., Weiss, R., Densmore, D., Adler, A., Appleton, E., Babb, J., Bhatia, S., Davidsohn, N., Haddock, T., Loyall, J., Schantz, R., Vasilev, V., and Yaman, F.,(June 2012). Results from TASBEProceedings of the Fourth International Workshop on Bio-Design Automation (IWBDA).Published Conference Proceeding.

Slusarczyk, A. L., and Weiss, R., (April 2012). Understanding Signaling Dynamics Through SynthesisSci. Signal., DOI:10.1126/scisignal.2003092

Beal, J., Weiss, R., Yaman, F., Davidsohn, N., and Adler, A.,(April 2012). A Method for Fast, High-Precision Characterization of Synthetic Biology DevicesMIT CSAIL Tech Report, 2012-008.

Silver, P. A., Haynes, K., and Weiss, R., (March 2012). Synthetic meets cell biologyMolecular Biology of the Cell, DOI:10.1091/mbc.E11-12-0978


Xie, Z., Wroblewska, L., Prochazka, L., Weiss, R., and Benenson, Y., (September 2011). Multi-Input RNAi-Based Logic Circuit for Identification of Specific Cancer Cells. Science, DOI:10.1126/science.1205527. [MIT News Article]

Beal, J., Lu, T., and Weiss, R., (August 2011). Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks. PLoS ONE, DOI:10.1371/journal.pone.0022490

Beal, J., Weiss, R., Densmore, D., Adler, A., Babb, J., Bhatia, S., Davidsohn, N., Haddock, T., Yaman, F., Schantz, R., and Loyall, J.,(June 2011). TASBE: A Tool-Chain to Accelerate Synthetic Biological EngineeringProceedings of the Third International Workshop on Bio-Design Automation(IWBDA). Published Conference Proceeding.

Yaman, F., Bhatia, S., Adler, A., Densmore, D., Beal, J., Weiss, R., and Davidsohn, N., (June 2011). Toward Automated Selection of Parts for Genetic Regulatory Networks. Proceedings of the Third International Workshop on Bio-Design Automation (IWBDA).Published Conference Proceeding.

Vasilev, V., Liu, C., Haddock, T., Bhatia, S., Adler, A., Yaman, F., Beal, J., Babb, J., Weiss, R., and Densmore, D., (June 2011). A Software Stack for Specification and Robotic Execution of Protocols for Synthetic Biological EngineeringProceedings of the Third International Workshop on Bio-Design Automation (IWBDA).Published Conference Proceeding.

Randall, A., Guye, P., Gupta, S., Duportet, X., and Weiss, R., (May 2011). Design and Connection of Robust Genetic Circuits. In C. Voigt (Ed.), Methods in Enzymology, Synthetic Biology, Part A (Vol. 497, pp. 159–186). Academic Press, Retrieved from

Teuscher, C., Grecu, C., Lu, T., and Weiss, R., (May 2011). Challenges and Promises of Nano and Bio Communication Networks. Proceedings of the Fifth ACM/IEEE International Symposium on Networks-on-Chip, DOI:10.1145/1999946.1999986


Riedel, M., Hassoun, S., Weiss, R., Silver, P., Anderson, J. C., and Murray, R., (June 2010). Joint DAC/IWBDA Special Session Engineering Biology: Fundamentals and Applications. Proceedings of the 47th Design Automation Conference, DOI:10.1145/1837274.1837330

Weiss, R., (May 2010). Synthetic Biology: From Modules to Systems. Proceedings of the 20th Symposium on Great Lakes Symposium on VLSI, DOI:10.1145/1785481.1785524


Weiss, R., and Panke, S., (October 2009). Synthetic biology—paths to moving forwardCurrent Opinion in Biotechnology, Protein technologies / Systems and synthetic biology, DOI:10.1016/j.copbio.2009.09.007

Purnick, P. E. M., and Weiss, R., (June 2009). The second wave of synthetic biology: from modules to systems. Nature Reviews Molecular Cell Biology, DOI:10.1038/nrm2698


Lu, T., Ferry, M., Weiss, R., and Hasty, J., (August 2008). A molecular noise generator. Physical Biology, DOI:10.1088/1478-3975/5/3/036006

Guye, P., and Weiss, R., (May 2008). Customized signaling with reconfigurable protein scaffoldsNature Biotechnology, DOI:10.1038/nbt0508-526

Batt, G., Belta, C., and Weiss, R., (Jan 2008). Temporal Logic Analysis of Gene Networks Under Parameter UncertaintyIEEE Transactions on Automatic Control, DOI:10.1109/TAC.2007.911330


Brenner, K., Karig, D. K., Weiss, R., and Arnold, F. H., (September 2007). Engineered bidirectional communication mediates a consensus in a microbial biofilm consortiumProceedings of the National Academy of Sciences, DOI:10.1073/pnas.0704256104

Kattamis, N. T., Purnick, P. E., Weiss, R., and Arnold, C. B., (October 2007). Thick film laser induced forward transfer for deposition of thermally and mechanically sensitive materialsApplied Physics Letters, DOI:10.1063/1.2799877

Batt, G., Yordanov, B., Weiss, R., and Belta, C., (July 2007). Robustness analysis and tuning of synthetic gene networks. Bioinformatics, DOI:10.1093/bioinformatics/btm362

Rinaudo, K., Bleris, L., Maddamsetti, R., Subramanian, S., Weiss, R., and Benenson, Y., (May 2007). A universal RNAi-based logic evaluator that operates in mammalian cells. Nature Biotechnology, DOI:10.1038/nbt1307

Weiss, R., (June 2007). Synthetic Biology: From Bacteria to Stem CellsProceedings of the 44th Annual Design Automation Conference, DAC ’07 (pp. 634–635), DOI:10.1145/1278480.1278640

Batt, G., Belta, C., and Weiss, R., (April 2007). Model Checking Genetic Regulatory Networks with Parameter UncertaintyProceedings of the 10th International Conference on Hybrid Systems: Computation and ControlPublished Conference Proceeding.

Batt, G., Belta, C., and Weiss, R., (March 2007). Model Checking Liveness Properties of Genetic Regulatory NetworksProceedings of the 13th International Conference on Tools and Algorithms for the Construction and Analysis of SystemsPublished Conference Proceeding.


Dhar, P. K., and Weiss, R., (October 2006). Enabling the new biology of the 21(st) century. Systems and synthetic biology.

Bio FAB Group, Baker, D., Church, G., Collins, J., Endy, D., Jacobson, J., Keasling, J., Modrich, P., Smolke, C., and Weiss, R., (June 2006). Engineering life: building a fab for biologyScientific American.

Hooshangi, S., and Weiss, R., (June 2006). The effect of negative feedback on noise propagation in transcriptional gene networksChaos: An Interdisciplinary Journal of Nonlinear Science, DOI:10.1063/1.2208927

Andrianantoandro, E., Basu, S., Karig, D. K., and Weiss, R., (May 2006). Synthetic biology: new engineering rules for an emerging discipline. Molecular Systems Biology, DOI:10.1038/msb4100073


Chen, M.-T., and Weiss, R., (November 2005). Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana. Nature Biotechnology, DOI:10.1038/nbt1162

McDaniel, R., and Weiss, R., (July 2005). Advances in synthetic biology: on the path from prototypes to applications. Current Opinion in Biotechnology, Protein technologies and commercial enzymes, DOI:10.1016/j.copbio.2005.07.002

Basu, S., Gerchman, Y., Collins, C. H., Arnold, F. H., and Weiss, R., (April 2005). A synthetic multicellular system for programmed pattern formation. Nature, DOI:10.1038/nature03461

Hooshangi, S., Thiberge, S., and Weiss, R., (February 2005). Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. Proceedings of the National Academy of Sciences of the United States of America, DOI:10.1073/pnas.0408507102

Karig, D., and Weiss, R., (January 2005). Signal-amplifying genetic circuit enables in vivo observation of weak promoter activation in the Rhl quorum sensing system. Biotechnology and Bioengineering, DOI:10.1002/bit.20371

Karig, D., Ku, J., and Weiss, R., (August 2005). Engineering Multi-signal Systems for Complex Pattern Formation. Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference – Workshops, DOI:10.1109/CSBW.2005.63

Braun, D., Basu, S., and Weiss, R., (March 2005). Parameter estimation for two synthetic gene networks: a case study. IEEE International Conference on Acoustics, Speech, and Signal Processing, DOI:10.1109/ICASSP.2005.1416417


Feng, X., Hooshangi, S., Chen, D., Li, G., Weiss, R., and Rabitz, H., (October 2004). Optimizing Genetic Circuits by Global Sensitivity Analysis. Biophysical Journal, DOI:10.1529/biophysj.104.044131

Basu, S., Mehreja, R., Thiberge, S., Chen, M.-T., and Weiss, R., (April 2004). Spatiotemporal control of gene expression with pulse-generating networks. Proceedings of the National Academy of Sciences of the United States of America, DOI:10.1073/pnas.0307571101

You, L., Cox, R. S., Weiss, R., and Arnold, F. H., (April 2004). Programmed population control by cell–cell communication and regulated killing. Nature, DOI:10.1038/nature02491

Gerchman, Y., and Weiss, R., (February 2004). Teaching bacteria a new language. Proceedings of the National Academy of Sciences of the United States of America, DOI:10.1073/pnas.0400473101


Basu, S., Karig, D., and Weiss, R., (June 2003). Engineering Signal Processing in Cells: Towards Molecular Concentration Band Detection. Revised Papers from the 8th International Workshop on DNA Based Computers: DNA ComputingPublished Conference Proceeding.

Weiss, R., Basu, S., Hooshangi, S., Kalmbach, A., Karig, D., Mehreja, R., and Netravali, I., (April 2003).Genetic Circuit Building Blocks for Cellular Computation, Communications, and Signal ProcessingNatural Computing, DOI:10.1023/A:1023307812034


Yokobayashi, Y., Weiss, R., and Arnold, F. H., (December 2002). Directed evolution of a genetic circuitProceedings of the National Academy of Sciences, DOI:10.1073/pnas.252535999

Weiss, R., Homsy, G. E., and Jr, T. F. K., (2002). Toward in vivo Digital Circuits. In P. D. L. F. Landweber and P. D. E. Winfree (Eds.), Evolution as Computation, Natural Computing Series (pp. 275–295). Springer Berlin Heidelberg, Retrieved from


Weiss, R., (2001). Cellular computation and communications using engineered genetic regulatory networks. Ph.D .Thesis, Massachusetts Institute of Technology.

Weiss, R., and Knight, T. F., Jr., (June 2001). Engineered Communications for Microbial RoboticsRevised Papers from the 6th International Workshop on DNA-Based Computers: DNA Computing, DNA ’00 (pp. 1–16). Published Conference Proceeding. [link]

Lahiri, T., Ganesh, A., Weiss, R., and Joshi, A., (May 2001). Fast-Start: Quick Fault Recovery in OracleProceedings of the 2001 ACM SIGMOD International Conference on Management of Data, DOI:10.1145/375663.375751.


Abelson, H., Allen, D., Coore, D., Hanson, C., Homsy, G., Knight, T. F., Jr., Nagpal, R., Rauch, E., Sussman, G. J., and Weiss, R., (May 2000). Amorphous Computing. Commun. ACM, DOI:10.1145/332833.332842


Vélez, B., Weiss, R., Sheldon, M. A., and Gifford, D. K., (July 1997). Fast and Effective Query Refinement.Proceedings of the 20th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval, SIGIR ’97 (pp. 6–15). New York, NY, USA: ACM, DOI:10.1145/258525.258528

Weiss, R., Vélez, B., and Sheldon, M. A., (March 1996). HyPursuit: A Hierarchical Network Search Engine That Exploits Content-link Hypertext Clustering. Proceedings of the the Seventh ACM Conference on Hypertext, HYPERTEXT ’96 (pp. 180–193). New York, NY, USA: ACM, DOI:10.1145/234828.234846

Sheldon, M. A., Duda, A., Weiss, R., and Gifford, D. K., (February 1995). Discover: a resource discovery system based on content routingComputer Networks and ISDN Systems, Proceedings of the Third International World-Wide Web Conference, DOI:10.1016/0169-7552(95)00044-8

Sheldon, M. A., Duda, A., Weiss, R., O’Toole, J. W., Jr., and Gifford, D. K., (May 1994). Content Routing for Distributed Information Servers. Proceedings of the 4th International Conference on Extending Database Technology: Advances in Database Technology, EDBT ’94 (pp. 109–122). Published Conference Proceeding.

Duda, A., and Weiss, R., (September 1993). Structured Video: A Data Type with Content-Based Access.Massachusetts Institute of Technology. Published Conference Proceeding.

Sheldon, M., Duda, A., Weiss, R., O”Toole, J., and J. Gifford, D., (1993). A CONTENT ROUTING SYSTEM FOR DISTRIBUTED INFORMATION SYSTEMS. Massachusetts Institute of Technology. Published Conference Proceeding.