2017

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.

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