2024
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.
2023
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.
2022
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.
2021
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.
2020
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 immunity. Nature 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 media. Soft Matter, DIO: 10.1039/D0SM00517G
Duhkinova, M., Crina, C., Weiss, R., Siciliano, V., (April 2020). Engineering Intracellular Protein Sensors in Mammalian Cells. Journal of Visualized Experiments, DIO: 10.3791/60878
2019
Moorman, A., Cuba Samaniego, C., Maley, C., Weiss, R., (December 2019). A Dynamical Biomolecular Neural Network. 2019 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 Nanoparticles. Molecular 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 systems. Nucleic 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 microrobots. Journal 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 Inhibition. 9th 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 cells. Nature 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 Field. Synthetic 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 Cells. ACS 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 immunotherapy. Nature Scientific Reports, DIO: oi.org/10.1038/s41598-019-43422
Teo, J., Weiss, R., Sarpeshkar, R., (March 2019). An Artificial Tissue Homeostasis Circuit Designed via Analog Circuit Techniques. IEEE 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 Analyses. iScience, DIO: 10.1016/j.isci.2019.01.006
2018
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 cells. Nature 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 cells. Nature 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 systems. APL Bioengineering, DIO: 10.1063/1.5038337
Tordoff, Weiss, R., (July 2018). Living shapes engineered. Nature News and Views, DOI: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 cells. Proceedings 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 Communications, DOI: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. PNAS, DOI: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 Communications, DOI: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
2017
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 Promoters, pp. 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.
2016
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]
2015
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 Diabetes. Cell 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 Circuits. Biophysical 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 programming. Nature 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 repressors. Nature 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
2014
Mishra, D., Rivera, P. M., Lin, A., Del Vecchio, D., and Weiss, R., (November 2014). A load driver device for engineering modularity in biological networks. Nature 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 cells. Molecular 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 Composition. ACS 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 cells. Nucleic 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 Cells. ACS 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 Replicons. ACS 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 biology. Nature Reviews Molecular Cell Biology, DOI:10.1038/nrm3767
2013
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 Destroy. ACS Synthetic Biology, DOI:10.1021/sb4000417
2012
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 bioactuators. Lab 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 circuits. Nature 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 TASBE. Proceedings 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 Synthesis. Sci. 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 Devices. MIT CSAIL Tech Report, 2012-008.
Silver, P. A., Haynes, K., and Weiss, R., (March 2012). Synthetic meets cell biology. Molecular Biology of the Cell, DOI:10.1091/mbc.E11-12-0978
2011
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 Engineering. Proceedings 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 Engineering. Proceedings 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 http://www.sciencedirect.com/science/article/pii/B978012385075100007X
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
2010
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
2009
Weiss, R., and Panke, S., (October 2009). Synthetic biology—paths to moving forward. Current 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
2008
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 scaffolds. Nature Biotechnology, DOI:10.1038/nbt0508-526
Batt, G., Belta, C., and Weiss, R., (Jan 2008). Temporal Logic Analysis of Gene Networks Under Parameter Uncertainty. IEEE Transactions on Automatic Control, DOI:10.1109/TAC.2007.911330
2007
Brenner, K., Karig, D. K., Weiss, R., and Arnold, F. H., (September 2007). Engineered bidirectional communication mediates a consensus in a microbial biofilm consortium. Proceedings 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 materials. Applied 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 Cells. Proceedings 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 Uncertainty. Proceedings of the 10th International Conference on Hybrid Systems: Computation and Control. Published Conference Proceeding.
Batt, G., Belta, C., and Weiss, R., (March 2007). Model Checking Liveness Properties of Genetic Regulatory Networks. Proceedings of the 13th International Conference on Tools and Algorithms for the Construction and Analysis of Systems. Published Conference Proceeding.
2006
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 biology. Scientific American.
Hooshangi, S., and Weiss, R., (June 2006). The effect of negative feedback on noise propagation in transcriptional gene networks. Chaos: 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
2005
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
2004
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
2003
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 Computing. Published 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 Processing. Natural Computing, DOI:10.1023/A:1023307812034
2002
Yokobayashi, Y., Weiss, R., and Arnold, F. H., (December 2002). Directed evolution of a genetic circuit. Proceedings 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 http://link.springer.com/chapter/10.1007/978-3-642-55606-7_14
2001
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 Robotics. Revised 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 Oracle. Proceedings of the 2001 ACM SIGMOD International Conference on Management of Data, DOI:10.1145/375663.375751.
2000
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
1990s
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 routing. Computer 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.