Publications

2025

STL-based Optimization of Biomolecular Neural Networks for Regression and Control — E. Palanques-Tost, H. Krasowski, M. Arcak, R. Weiss, C. Belta , Preprint (2025)
ETV2 mediated differentiation of human pluripotent stem cells results in functional endothelial cells for engineering advanced vascularized microphysiological models — S. Zhang, Z. Wan, L. Wang, C. Wu, J. Zhang, S. Spitz, X. Wang, M.A. Floryan, M.F. Coughlin, F.M. Pramotton, L. Xu, R. Weiss, R.D. Kamm , Preprint (2025)
Analog epigenetic memory revealed by targeted chromatin editing — S. Palacios, S. Bruno, R. Weiss, E. Salibi, I. Goodchild-Michelman, A. Kane, K. Ilia, D. Del Vecchio , Cell Genomics (2025)
Genetic Toggle Switch in Plants — T.K. Kassaw, W. Xu, C.S. Zalewski, K. Kiwimagi, R. Weiss, M.S. Antunes, A. Prasad, J.I. Medford , ACS Synthetic Biology (2025)
Autonomous Vision-Based Magnetic Microrobotic Pushing of Micro-Objects and Cells — M. Sokolich, C. Kirmizitas, S. Das, R. Weiss , Preprint (2025)
Customizable gene sensing and response without altering endogenous coding sequences — F. Caliendo, E. Vitu, J. Wang, S. Kuo, H. Sandt, C.N. Enghuus, J. Tordoff, N. Estrada, J.J. Collins, R. Weiss , Nature Chemical Biology (2025)
Magnetized Cellbots to Spatiotemporally Control Differentiation of Human-Induced Pluripotent Stem Cells — R.P. Mohanty, S. Mallick, P. Crowley, M. Sokolich, K. Kiwimagi, S. Razavi, C. Belta, S. Das, R. Weiss , Preprint (2025)
LNP-RNA-mediated antigen presentation leverages SARS-CoV-2-specific immunity for cancer treatment — Y. Xue, X. Hou, Y. Zhong, Y. Zhang, S. Du, D.D. Kang, L. Wang, C. Wang, H. Li, S. Wang, Z. Liu, M. Tian, K. Guo, D. Cao, B. Deng, D.W. McComb, E. Purisic, J. Dai, P. Hamon, B.D. Brown, N.M. Tsankova, M. Merad, D.J. Irvine, R. Weiss, Y. Dong , Nature Communications (2025)
Development of a Lentiviral Vector for High-Yield Production of Synthetic and Recombinant GCase for Gaucher Disease Therapy — A.C. Coelho, C.E.V. Wiezel, A.C. de Campos, L.L.S. Figueiredo, G.A.M. Suardi, J. de Paula Bernardes, D.P. da Cunha Tirapelli, V.M. Faça, K.J. Abraham, C.G. Carlotti-Júnior, V. Siciliano, R. Weiss, S. Gerson, A.M. Fontes , International Journal of Molecular Sciences (2025)

2024

Sensing and guiding cell-state transitions by using genetically encoded endoribonuclease-mediated microRNA sensors — L. Wang, W. Xu, S. Zhang, G.C. Gundberg, C.R. Zheng, Z. Wan, K. Mustafina, F. Caliendo, H. Sandt, R. Kamm, R. Weiss , Nature Biomedical Engineering (2024)
A Tunable Long Duration Pulse Generation Circuit in Mammalian Cells — N. Wauford, G. Wachter, K. Kiwimagi, R. Weiss , ACS Synthetic Biology (2024)
The restricted N-glycome of neurons is programmed during differentiation — K. Kiwimagi, M. Noel, M. Cetinbas, R.I. Sadreyev, L. Wang, J.W. Smoller, R.D. Cummings, R. Weiss, R.G. Mealer , Preprint (2024)
Engineering synthetic and recombinant human lysosomal β-glucocerebrosidase for enzyme replacement therapy for Gaucher disease — L.L.S. Figueiredo, W.L. Junior, V.W. da Silva Goncalves, E.S. Ramos, V. D’Almeida, L.E.B. de Souza, M.D. Orellana, K.J. Abraham, F. Lichtenstein, L. Bleicher, V. Azevedo, R.G. Chaves, G. Bonfá, V. Siciliano, R. Weiss, S. Gerson, A.M. Fontes , Discover Applied Sciences (2024)
EFRI BEGIN OI Teaching non-brain organoids how to think: PRogrammable OrGanoid intElligence using neuronal Networks implemented by gene Circuits (PROGENIC) — R. Weiss, C.A. Belta, L. Zoloth, S. Das , NSF Award (2024)
Janus Mazebots and Cellbots Navigating Obstacles in Dense Mammalian Environment — M. Sokolich, S. Mallick, C. Belta, R. Weiss, S. Das , Preprint (2024)
Model Predictive Control for Magnetically-Actuated Cellbots — M. Kermanshah, L.E. Beaver, M. Sokolich, F. Ceren Kirmizitas, S. Das, R. Tron, R. Weiss, C. Belta (2024)
Learning a Tracking Controller for Rolling μbots — L.E. Beaver, M. Sokolich, S. Alsalehi, R. Weiss, S. Das, C. Belta , IEEE Robotics and Automation Letters (2024)
LNP-RNA-engineered adipose stem cells for accelerated diabetic wound healing — Y. Xue, Y. Zhang, Y. Zhong, S. Du, X. Hou, W. Li, H. Li, S. Wang, C. Wang, J. Yan, D.D. Kang, B. Deng, D.W. McComb, D.J. Irvine, R. Weiss, Y. Dong , Nature Communications (2024)
Extracellular carriers control lipid-dependent secretion, delivery, and activity of WNT morphogens — T.D.A. Magalhaes, J. Liu, C. Chan, K.S. Borges, J. Zhang, A.J. Kane, B.M. Wierbowski, Y. Ge, Z. Liu, P. Mannam, D. Zeve, R. Weiss, D.T. Breault, P. Huang, A. Salic , Developmental Cell (2024)

2023

Synthetic genetic circuits to uncover the OCT4 trajectories of successful reprogramming of human fibroblasts — K. Ilia, N. Shakiba, T. Bingham, R.D. Jones, M.M. Kaminski, E. Aravera, S. Bruno, S. Palacios, R. Weiss, J.J. Collins, D. Del Vecchio, T.M. Schlaeger , Science Advances (2023)
A NOVEL SYNTHETIC AND RECOMBINANT GLUCOCEREBROSIDASE FOR GAUCHER DISEASE: <i>IN SILICO</i> MOLECULAR EVOLUTION AND GENE THERAPY APPROACHES TO ENHANCE ENZYME ACTIVITY — L. Figueiredo, L. Souza, M. Orellana, D. Covas, F. Lichtenstein, V. Siciliano, K. Abraham, R. Weiss, S. Gerson, A. Fontes , Hematology, Transfusion and Cell Therapy (2023)
Synthetic symmetry breaking and programmable multicellular structure formation — N. Wauford, A. Patel, J. Tordoff, C. Enghuus, A. Jin, J. Toppen, M.L. Kemp, R. Weiss , Cell Systems (2023)
Author Correction: Robust and tunable signal processing in mammalian cells via engineered covalent modification cycles — R.D. Jones, Y. Qian, K. Ilia, B. Wang, M.T. Laub, D. Del Vecchio, R. Weiss , Nature Communications (2023)
Rapid Development of Cell State Identification Circuits with Poly-Transfection — N. Wauford, R. Jones, C.V.D. Mark, R. Weiss, N. Wauford , Journal of Visualized Experiments (JoVE) (2023)
Synthetic genetic circuits to uncover and enforce the OCT4 trajectories of successful reprogramming of human fibroblasts — K. Ilia, N. Shakiba, T. Bingham, R.D. Jones, M.M. Kaminski, E. Aravera, S. Bruno, S. Palacios, R. Weiss, J.J. Collins, D.D. Vecchio, T.M. Schlaeger , Preprint (2023)

2022

The sound of silence: Transgene silencing in mammalian cell engineering — A. Cabrera, H.I. Edelstein, F. Glykofrydis, K.S. Love, S. Palacios, J. Tycko, M. Zhang, S. Lensch, C.E. Shields, M. Livingston, R. Weiss, H. Zhao, K.A. Haynes, L. Morsut, Y.Y. Chen, A.S. Khalil, W.W. Wong, J.J. Collins, S.J. Rosser, K. Polizzi, M.B. Elowitz, M. Fussenegger, I.B. Hilton, J.N. Leonard, L. Bintu, K.E. Galloway, T.L. Deans , Cell Systems (2022)
A synthetic transcription platform for programmable gene expression in mammalian cells — W.C.W. Chen, L. Gaidukov, Y. Lai, M. Wu, J. Cao, M.J. Gutbrod, G.C.G. Choi, R.P. Utomo, Y. Chen, L. Wroblewska, M. Kellis, L. Zhang, R. Weiss, T.K. Lu , Nature Communications (2022)
Synthetic neuromorphic computing in living cells — L. Rizik, L. Danial, M. Habib, R. Weiss, R. Daniel , Nature Communications (2022)
PERSIST platform provides programmable RNA regulation using CRISPR endoRNases — B. DiAndreth, N. Wauford, E. Hu, S. Palacios, R. Weiss , Nature Communications (2022)
Biological underpinnings for lifelong learning machines — D. Kudithipudi, M. Aguilar-Simon, J. Babb, M. Bazhenov, D. Blackiston, J. Bongard, A.P. Brna, S. Chakravarthi Raja, N. Cheney, J. Clune, A. Daram, S. Fusi, P. Helfer, L. Kay, N. Ketz, Z. Kira, S. Kolouri, J.L. Krichmar, S. Kriegman, M. Levin, S. Madireddy, S. Manicka, A. Marjaninejad, B. McNaughton, R. Miikkulainen, Z. Navratilova, T. Pandit, A. Parker, P.K. Pilly, S. Risi, T.J. Sejnowski, A. Soltoggio, N. Soures, A.S. Tolias, D. Urbina-Meléndez, F.J. Valero-Cuevas, G.M. van de Ven, J.T. Vogelstein, F. Wang, R. Weiss, A. Yanguas-Gil, X. Zou, H. Siegelmann , Nature Machine Intelligence (2022)
Robust and tunable signal processing in mammalian cells via engineered covalent modification cycles — R.D. Jones, Y. Qian, K. Ilia, B. Wang, M.T. Laub, D. Del Vecchio, R. Weiss , Nature Communications (2022)
Guiding principles for the creation of multicellular engineered living systems — M. Kim , Scilight (2022)
Principles for the design of multicellular engineered living systems — O. Aydin, A.P. Passaro, R. Raman, S.E. Spellicy, R.P. Weinberg, R.D. Kamm, M. Sample, G.A. Truskey, J. Zartman, R.D. Dar, S. Palacios, J. Wang, J. Tordoff, N. Montserrat, R. Bashir, M.T.A. Saif, R. Weiss , APL Bioengineering (2022)
Editorial overview: Control engineering in synthetic biology: Foundations and applications — R. Weiss, V. Siciliano , Current Opinion in Systems Biology (2022)

2021

Addition of histone deacetylase inhibitor in transgenic human cell culture inhibits the secretion of lysosomal enzyme — L.L.S. Figueiredo, A.C. Coelho, C.E.V. Wiezel, D.P.D.C. Tirapelli, V. D'almeida, K.J. Abraham, V. Siciliano, R. Weiss, S. Gerson, A.M. Fontes , Resumos (2021)
Learning Spatio-Temporal Specifications for Dynamical Systems — S. Alsalehi, E. Aasi, R. Weiss, C. Belta , Preprint (2021)
Quantitative characterization of recombinase-based digitizer circuits enables predictable amplification of biological signals — K.A. Kiwimagi, J.H. Letendre, B.H. Weinberg, J. Wang, M. Chen, L. Watanabe, C.J. Myers, J. Beal, W.W. Wong, R. Weiss , Communications Biology (2021)
An engineered protein-phosphorylation toggle network with implications for endogenous network discovery — D. Mishra, T. Bepler, B. Teague, B. Berger, J. Broach, R. Weiss , Science (2021)
Context-aware synthetic biology by controller design: Engineering the mammalian cell — N. Shakiba, R.D. Jones, R. Weiss, D.D. Vecchio , Cell Systems (2021)
NSF/MCB-BSF: Sentinels: Viral First Responder Cells (VFRCs) for COVID-19 and Future Rapidly Emerging Infectious Diseases — R. Weiss , NSF Award (2021)
In Vivo Validation of a Reversible Small Molecule-Based Switch for Synthetic Self-Amplifying mRNA Regulation — S.M. Cafferty, J.D. Temmerman, T. Kitada, J.R. Becraft, R. Weiss, D.J. Irvine, M. Devreese, S.D. Baere, F. Combes, N.N. Sanders , Molecular Therapy (2021)
Rethinking organoid technology through bioengineering — E. Garreta, R.D. Kamm, S.M. Chuva de Sousa Lopes, M.A. Lancaster, R. Weiss, X. Trepat, I. Hyun, N. Montserrat , Nature Materials (2021)
Incomplete Cell Sorting Creates Engineerable Structures with Long-Term Stability — J. Tordoff, M. Krajnc, N. Walczak, M. Lima, J. Beal, S. Shvartsman, R. Weiss , Cell Reports Physical Science (2021)

2020

Tumor-Selective Gene Circuits Enable Highly Specific Localized Cancer Immunotherapy — M. Wu*, L. Nissim*, E. Pery, Y. Tabach, P.A. Sharp, D. Stupp, A. Binder-Nissim, K. Weisinger, C. Enghuus, S.R. Palacios, M. Humphrey, Z. Zhang, E.M. Novoa, M. Kellis, R. Weiss, S.D. Rabkin, R.S. Wong, R.M. Gordley, T.K. Lu , Molecular Therapy (2020)
An endoribonuclease-based feedforward controller for decoupling resource-limited genetic modules in mammalian cells — R.D. Jones, Y. Qian, V. Siciliano, B. DiAndreth, J. Huh, R. Weiss, D. Del Vecchio , Nature Communications (2020)
Multifunctional oncolytic nanoparticles deliver self-replicating IL-12 RNA to eliminate established tumors and prime systemic immunity — Y. Li, Z. Su, W. Zhao, X. Zhang, N. Momin, C. Zhang, K.D. Wittrup, Y. Dong, D.J. Irvine, R. Weiss , Nature Cancer (2020)
3D aggregation of cells in packed microgel media — C.D. Morley, J. Tordoff, C.S. O’Bryan, R. Weiss, T.E. Angelini , Soft Matter (2020)
Engineering Intracellular Protein Sensors in Mammalian Cells — M. Duhkinova, C. Crina, R. Weiss, V. Siciliano , Journal of Visualized Experiments (JoVE) (2020)

2019

Cellular expression through morphogen delivery by light activated magnetic microrobots — S. Das, E.E. Hunter, N.A. DeLateur, E.B. Steager, R. Weiss, V. Kumar , Journal of Micro-Bio Robotics (2019)
Immunogenicity of RNA Replicons Encoding HIV Env Immunogens Designed for Self-Assembly into Nanoparticles — M. Melo, E. Porter, Y. Zhang, M. Silva, N. Li, B. Dobosh, A. Liguori, P. Skog, E. Landais, S. Menis, D. Sok, D. Nemazee, W.R. Schief, R. Weiss, D.J. Irvine , Molecular Therapy (2019)
An Artificial Tissue Homeostasis Circuit Designed via Analog Circuit Techniques — J.J.Y. Teo, R. Weiss, R. Sarpeshkar , IEEE Transactions on Biomedical Circuits and Systems (2019)
PERSIST: A programmable RNA regulation platform using CRISPR endoRNases — B. DiAndreth, N. Wauford, E. Hu, S. Palacios, R. Weiss , Preprint (2019)
A ‘poly-transfection’ method for rapid, one-pot characterization and optimization of genetic systems — J.J. Gam, B. DiAndreth, R.D. Jones, J. Huh, R. Weiss , Nucleic Acids Research (2019)
Fabrication of Autonomously Constructed Engineered Three-dimensional Shapes (FACETS) — R. Weiss (2019)
Small-molecule control of antibody N-glycosylation in engineered mammalian cells — M.M. Chang, L. Gaidukov, G. Jung, W.A. Tseng, J.J. Scarcelli, R. Cornell, J.K. Marshall, J.L. Lyles, P. Sakorafas, A.A. Chu, K. Cote, B. Tzvetkova, S. Dolatshahi, M. Sumit, B.C. Mulukutla, D.A. Lauffenburger, B. Figueroa, N.M. Summers, T.K. Lu, R. Weiss , Nature Chemical Biology (2019)
A high-throughput screening and computation platform for identifying synthetic promoters with enhanced cell-state specificity (SPECS) — M. Wu, L. Nissim, D. Stupp, E. Pery, A. Binder-Nissim, K. Weisinger, C. Enghuus, S.R. Palacios, M. Humphrey, Z. Zhang, E. Maria Novoa, M. Kellis, R. Weiss, S.D. Rabkin, Y. Tabach, T.K. Lu , Nature Communications (2019)
One-pot Optimization of Genetic Circuits using Poly-transfections — J. Gam, B. DiAndreth, J. Huh, R. Jones, R. Weiss (2019)
In vitro evolution of enhanced RNA replicons for immunotherapy — Y. Li, B. Teague, Y. Zhang, Z. Su, E. Porter, B. Dobosh, T. Wagner, D.J. Irvine, R. Weiss , Scientific Reports (2019)
Dissecting N-Glycosylation Dynamics in Chinese Hamster Ovary Cells Fed-batch Cultures using Time Course Omics Analyses — M. Sumit, S. Dolatshahi, A.A. Chu, K. Cote, J.J. Scarcelli, J.K. Marshall, R.J. Cornell, R. Weiss, D.A. Lauffenburger, B.C. Mulukutla, B. Figueroa , iScience (2019)
Comparison of Integrases Identifies Bxb1-GA Mutant as the Most Efficient Site-Specific Integrase System in Mammalian Cells — B. Jusiak, K. Jagtap, L. Gaidukov, X. Duportet, K. Bandara, J. Chu, L. Zhang, R. Weiss, T.K. Lu , ACS Synthetic Biology (2019)
Principles of synthetic biology: a MOOC for an emerging field — D.A. Anderson, R.D. Jones, A.P. Arkin, R. Weiss , Synthetic Biology (2019)

2018

Small-molecule-based regulation of RNA-delivered circuits in mammalian cells — T.E. Wagner, J.R. Becraft, K. Bodner, B. Teague, X. Zhang, A. Woo, E. Porter, B. Alburquerque, B. Dobosh, O. Andries, N.N. Sanders, J. Beal, D. Densmore, T. Kitada, R. Weiss , Nature Chemical Biology (2018)
Generation of a human cell line with stable production of lysosomal recombinant ?-glucosylceramidase enzyme by lentiviral system — J.L. Cardoso, A.C. Coelho, W. Lau Junior, C.E.V. Wiezel, A.L. Simões, Z.L.P. Simões, D.P.D.C. Tirapelli, C.G. Carlotti Júnior, K.J. Abraham, V. D'Almeida, V. Siciliano, R. Weiss, S.L. Gerson, A.M. Fontes , Abstracts (2018)
Dissecting the Dynamics of N-Linked Glycosylation in Fed-Batch Cultures of Chinese Hamster Ovary Cells Through Time Course Omics Analyses — M. Sumit, S. Dolatshahi, A.A. Chu, K. Cote, J.J. Scarcelli, J.K. Marshall, R.J. Cornell, R. Weiss, D.A. Lauffenburger, B. Figueroa, B.C. Mulukutla (2018)
Perspective: The promise of multi-cellular engineered living systems — R.D. Kamm, R. Bashir, N. Arora, R.D. Dar, M.U. Gillette, L.G. Griffith, M.L. Kemp, K. Kinlaw, M. Levin, A.C. Martin, T.C. McDevitt, R.M. Nerem, M.J. Powers, T.A. Saif, J. Sharpe, S. Takayama, S. Takeuchi, R. Weiss, K. Ye, H.G. Yevick, M.H. Zaman , APL Bioengineering (2018)
Author Correction: A mixed antagonistic/synergistic miRNA repression model enables accurate predictions of multi-input miRNA sensor activity — J.J. Gam, J. Babb, R. Weiss , Nature Communications (2018)
Engineering protein-protein devices for multilayered regulation of mRNA translation using orthogonal proteases in mammalian cells — F. Cella, L. Wroblewska, R. Weiss, V. Siciliano , Nature Communications (2018)
Caspases maintain tissue integrity by an apoptosis-independent inhibition of cell migration and invasion — A. Gorelick-Ashkenazi, R. Weiss, L. Sapozhnikov, A. Florentin, L. Tarayrah-Ibraheim, D. Dweik, K. Yacobi-Sharon, E. Arama , Nature Communications (2018)
Self-organizing multicellular structures designed using synthetic biology — J. Tordoff, R. Weiss , Nature (2018)
Stochastic Turing patterns in a synthetic bacterial population — D. Karig, K.M. Martini, T. Lu, N.A. DeLateur, N. Goldenfeld, R. Weiss , Proceedings of the National Academy of Sciences (2018)
A mixed antagonistic/synergistic miRNA repression model enables accurate predictions of multi-input miRNA sensor activity — J.J. Gam, J. Babb, R. Weiss , Nature Communications (2018)
Perspective: Engineering noise in biological systems towards predictive stochastic design — R. Weiss , American Institute of Physics (AIP) (2018)
Engineering modular intracellular protein sensor-actuator devices — V. Siciliano, B. DiAndreth, B. Monel, J. Beal, J. Huh, K.L. Clayton, L. Wroblewska, A. McKeon, B.D. Walker, R. Weiss , Nature Communications (2018)
A multi-landing pad DNA integration platform for mammalian cell engineering — L. Gaidukov, L. Wroblewska, B. Teague, T. Nelson, X. Zhang, Y. Liu, K. Jagtap, S. Mamo, W.A. Tseng, A. Lowe, J. Das, K. Bandara, S. Baijuraj, N.M. Summers, T.K. Lu, L. Zhang, R. Weiss , Nucleic Acids Research (2018)
Programming gene and engineered-cell therapies with synthetic biology — T. Kitada, B. DiAndreth, B. Teague, R. Weiss , Science (2018)

2017

A novel Bxb1 integrase RMCE system for high fidelity site‐specific integration of mAb expression cassette in CHO Cells — M.C. Inniss, K. Bandara, B. Jusiak, T.K. Lu, R. Weiss, L. Wroblewska, L. Zhang , Biotechnology and Bioengineering (2017)
Production of recombinant therapeutic enzyme for metabolic disease using the lentiviral system — A.C. Coelho, J.L.S. Cardoso, C.E.V. Wiezel, A.L. Simões, J. Pinto, V. D'Almeida, V. Siciliano, R. Weiss, A.M. Fontes , Abstracts (2017)
Open-source, community-driven microfluidics with Metafluidics — D.S. Kong, T.A. Thorsen, J. Babb, S.T. Wick, J.J. Gam, R. Weiss, P.A. Carr , Nature Biotechnology (2017)

2016

Synthetic Morphogenesis — B.P. Teague, P. Guye, R. Weiss , Cold Spring Harbor Perspectives in Biology (2016)
Genetically engineering self-organization of human pluripotent stem cells into a liver bud-like tissue using Gata6 — P. Guye, M.R. Ebrahimkhani, N. Kipniss, J.J. Velazquez, E. Schoenfeld, S. Kiani, L.G. Griffith, R. Weiss , Nature Communications (2016)

2015

Synthetic biology devices and circuits for RNA-based ‘smart vaccines’: a propositional review — O. Andries, T. Kitada, K. Bodner, N.N. Sanders, R. Weiss , Expert Review of Vaccines (2015)
Preserved DNA Damage Checkpoint Pathway Protects against Complications in Long-Standing Type 1 Diabetes — S. Bhatt, M. Gupta, M. Khamaisi, R. Martinez, M. Gritsenko, B. Wagner, P. Guye, V. Busskamp, J. Shirakawa, G. Wu, C. Liew, T. Clauss, I. Valdez, A. El Ouaamari, E. Dirice, T. Takatani, H. Keenan, R. Smith, G. Church, R. Weiss, A. Wagers, W. Qian, G. King, R. Kulkarni , Cell Metabolism (2015)
Cas9 gRNA engineering for genome editing, activation and repression — S. Kiani, A. Chavez, M. Tuttle, R.N. Hall, R. Chari, D. Ter-Ovanesyan, J. Qian, B.W. Pruitt, J. Beal, S. Vora, J. Buchthal, E.J.K. Kowal, M.R. Ebrahimkhani, J.J. Collins, R. Weiss, G. Church , Nature Methods (2015)
Collaborative Research: Evolable Living Computing: Understanding and Qunatifying Synthetic Biological Systems' Applicability, Performance and Limits — R. Weiss, D. Del Vecchio, T. Lu , NSF Award (2015)
N1-methylpseudouridine-incorporated mRNA outperforms pseudouridine-incorporated mRNA by providing enhanced protein expression and reduced immunogenicity in mammalian cell lines and mice — O. Andries, S. Mc Cafferty, S.C. De Smedt, R. Weiss, N.N. Sanders, T. Kitada , Journal of Controlled Release (2015)
Mammalian synthetic circuits with RNA binding proteins for RNA-only delivery — L. Wroblewska, T. Kitada, K. Endo, V. Siciliano, B. Stillo, H. Saito, R. Weiss , Nature Biotechnology (2015)
Synthetic communities, the sum of parts — B.P. Teague, R. Weiss , Science (2015)
Isocost Lines Describe the Cellular Economy of Genetic Circuits — A. Gyorgy, J.I. Jiménez, J. Yazbek, H. Huang, H. Chung, R. Weiss, D. Del Vecchio , Biophysical Journal (2015)
Accurate Predictions of Genetic Circuit Behavior from Part Characterization and Modular Composition — N. Davidsohn, J. Beal, S. Kiani, A. Adler, F. Yaman, Y. Li, Z. Xie, R. Weiss , ACS Synthetic Biology (2015)
Highly efficient Cas9-mediated transcriptional programming — A. Chavez, J. Scheiman, S. Vora, B.W. Pruitt, M. Tuttle, E. P R Iyer, S. Lin, S. Kiani, C.D. Guzman, D.J. Wiegand, D. Ter-Ovanesyan, J.L. Braff, N. Davidsohn, B.E. Housden, N. Perrimon, R. Weiss, J. Aach, J.J. Collins, G.M. Church , Nature Methods (2015)
Modular construction of mammalian gene circuits using TALE transcriptional repressors — Y. Li, Y. Jiang, H. Chen, W. Liao, Z. Li, R. Weiss, Z. Xie , Nature Chemical Biology (2015)
Model-Driven Engineering of Gene Expression from RNA Replicons — J. Beal, T.E. Wagner, T. Kitada, O. Azizgolshani, J.M. Parker, D. Densmore, R. Weiss , ACS Synthetic Biology (2015)

2014

CRISPR transcriptional repression devices and layered circuits in mammalian cells — S. Kiani, J. Beal, M.R. Ebrahimkhani, J. Huh, R.N. Hall, Z. Xie, Y. Li, R. Weiss , Nature Methods (2014)
Rapid neurogenesis through transcriptional activation in human stem cells — V. Busskamp, N.E. Lewis, P. Guye, A.H. Ng, S.L. Shipman, S.M. Byrne, N.E. Sanjana, J. Murn, Y. Li, S. Li, M. Stadler, R. Weiss, G.M. Church , Molecular Systems Biology (2014)
Realizing the potential of synthetic biology — G.M. Church, M.B. Elowitz, C.D. Smolke, C.A. Voigt, R. Weiss , Nature Reviews Molecular Cell Biology (2014)
A load driver device for engineering modularity in biological networks — D. Mishra, P.M. Rivera, A. Lin, D. Del Vecchio, R. Weiss , Nature Biotechnology (2014)
Engineering in vitro human hepatic organoids: 103 — M.R. Ebrahimkhani, P. Guye, N. Kipniss, J. Velazquez, R. Weiss, L. Griffith , Hepatology (2014)
Systematic Transfer of Prokaryotic Sensors and Circuits to Mammalian Cells — B.C. Stanton, V. Siciliano, A. Ghodasara, L. Wroblewska, K. Clancy, A.C. Trefzer, J.D. Chesnut, R. Weiss, C.A. Voigt , ACS Synthetic Biology (2014)
A platform for rapid prototyping of synthetic gene networks in mammalian cells — X. Duportet, L. Wroblewska, P. Guye, Y. Li, J. Eyquem, J. Rieders, T. Rimchala, G. Batt, R. Weiss , Nucleic Acids Research (2014)
Synthetic biology: How best to build a cell , Nature (2014)

2013

Genetically Programmable Pathogen Sense and Destroy — S. Gupta, E.E. Bram, R. Weiss , ACS Synthetic Biology (2013)
Competition for Shared Resources in the Cellular Chassis: Impact on Synthetic Circuits — D. Del Vecchio, R. Weiss (2013)
Microbead-based biomimetic synthetic neighbors enhance survival and function of rat pancreatic β-cells — W. Li, S. Lee, M. Ma, S.M. Kim, P. Guye, J.R. Pancoast, D.G. Anderson, R. Weiss, R.T. Lee, P.T. Hammond , Scientific Reports (2013)
Rapid, modular and reliable construction of complex mammalian gene circuits — P. Guye, Y. Li, L. Wroblewska, X. Duportet, R. Weiss , Nucleic Acids Research (2013)
An RNAi-Enhanced Logic Circuit for Cancer Specific Detection and Destruction — R. Weiss, L. Wroblewska, Z. Xie (2013)
Synthetic Biology: From Parts to Modules to Therapeutic Systems — R. Weiss , Biophysical Journal (2013)

2012

Foundations for the design and implementation of synthetic genetic circuits — A.L. Slusarczyk, A. Lin, R. Weiss , Nature Reviews Genetics (2012)
Formation and optogenetic control of engineered 3D skeletal muscle bioactuators — M.S. Sakar, D. Neal, T. Boudou, M.A. Borochin, Y. Li, R. Weiss, R.D. Kamm, C.S. Chen, H.H. Asada , Lab on a Chip (2012)
An End-to-End Workflow for Engineering of Biological Networks from High-Level Specifications — J. Beal, R. Weiss, D. Densmore, A. Adler, E. Appleton, J. Babb, S. Bhatia, N. Davidsohn, T. Haddock, J. Loyall, R. Schantz, V. Vasilev, F. Yaman , ACS Synthetic Biology (2012)
Modular Design of Artificial Tissue Homeostasis: Robust Control through Synthetic Cellular Heterogeneity — M. Miller, M. Hafner, E. Sontag, N. Davidsohn, S. Subramanian, P.E.M. Purnick, D. Lauffenburger, R. Weiss , PLoS Computational Biology (2012)
Understanding Signaling Dynamics Through Synthesis — A.L. Slusarczyk, R. Weiss , Science Signaling (2012)
A Method for Fast, High-Precision Characterization of Synthetic Biology Devices — J. Beal, R. Weiss, F. Yaman, N. Davidsohn, A. Adler (2012)
Synthetic meets cell biology — P.A. Silver, K. Haynes, R. Weiss , Molecular Biology of the Cell (2012)

2011

Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks — J. Beal, T. Lu, R. Weiss , PLOS ONE (2011)
Highly Extensible Programmed Biosensing Circuits with Fast Memory — J. Broach, A. Morozov, R. Weiss (2011)
Multi-Input RNAi-Based Logic Circuit for Identification of Specific Cancer Cells — Z. Xie, L. Wroblewska, L. Prochazka, R. Weiss, Y. Benenson , Science (2011)

2010

Mammalian synthetic biology--from tools to therapies — D. Aubel, M. Fussenegger , BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology (2010)

2009

Synthetic biology—paths to moving forward — R. Weiss, S. Panke , Current Opinion in Biotechnology (2009)
What's in a name? — A. Arkin, D. Berry, G. Church, F. Arnold, J. Boldt, O. Müller, A.D. Ellington, D. Endy, M. Fussenegger, E.R. Gold, J. Greenwood, S.Y. Lee, W. Lim, J. Minshull, T.H. Murray, G. Poste, K.L. Prather, H. El-Samad, C. Smolke, R. Weiss , Nature biotechnology (2009)
Engineered quorum sensing and programmed multi-step differentiation of mammalian stem cells into pancreatic beta cells — R. Weiss , NSF Award (2009)
CAREER: Artificial Pattern Formation with Synthetic Gene Networks — R. Weiss , NSF Award (2009)
The second wave of synthetic biology: from modules to systems — P.E.M. Purnick, R. Weiss , Nature Reviews Molecular Cell Biology (2009)
Programmed Pathogen Sense and Destroy Circuits — R. Weiss (2009)

2008

Customized signaling with reconfigurable protein scaffolds — P. Guye, R. Weiss , Nature Biotechnology (2008)
A molecular noise generator — T. Lu, M. Ferry, R. Weiss, J. Hasty , Physical Biology (2008)
Temporal Logic Analysis of Gene Networks Under Parameter Uncertainty — G. Batt, C. Belta, R. Weiss , IEEE Transactions on Automatic Control (2008)

2007

Engineered bidirectional communication mediates a consensus in a microbial biofilm consortium — K. Brenner, D.K. Karig, R. Weiss, F.H. Arnold , Proceedings of the National Academy of Sciences (2007)
Thick film laser induced forward transfer for deposition of thermally and mechanically sensitive materials — N.T. Kattamis, P.E. Purnick, R. Weiss, C.B. Arnold , Applied Physics Letters (2007)
Robustness analysis and tuning of synthetic gene networks — G. Batt, B. Yordanov, R. Weiss, C. Belta , Bioinformatics (2007)
A universal RNAi-based logic evaluator that operates in mammalian cells — K. Rinaudo, L. Bleris, R. Maddamsetti, S. Subramanian, R. Weiss, Y. Benenson , Nature Biotechnology (2007)

2006

Synthetic biology: new engineering rules for an emerging discipline — E. Andrianantoandro, S. Basu, D.K. Karig, R. Weiss , Molecular Systems Biology (2006)
Engineering life: Building a FAB for Biology. (Cover story) — D. Baker, G. Church, J. Collins, D. Endy, J. Jacobson, J. Keasling, P. Modrich, C. Smolke, R. Weiss , Scientific American (2006)
The effect of negative feedback on noise propagation in transcriptional gene networks — S. Hooshangi, R. Weiss , Chaos: An Interdisciplinary Journal of Nonlinear Science (2006)
Automated Design and Programming of a Microfluidic DNA Computer — M.S. Livstone, R. Weiss, L.F. Landweber , Natural Computing (2006)

2005

A synthetic multicellular system for programmed pattern formation — S. Basu, Y. Gerchman, C.H. Collins, F.H. Arnold, R. Weiss , Nature (2005)
Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana — M. Chen, R. Weiss , Nature Biotechnology (2005)
Signal-amplifying genetic circuit enables in vivo observation of weak promoter activation in the Rhl quorum sensing system — D. Karig, R. Weiss , Biotechnology and Bioengineering (2005)
BIC: Collaborative Research: Evolutionary Optimization of Biological Circuits: Towards Cellular Programming — R. Weiss , NSF Award (2005)
Advances in synthetic biology: on the path from prototypes to applications — R. McDaniel, R. Weiss , Current Opinion in Biotechnology (2005)
CAREER: Artificial Pattern Formation with Synthetic Gene Networks — R. Weiss , NSF Award (2005)
Ultrasensitivity and noise propagation in a synthetic transcriptional cascade — S. Hooshangi, S. Thiberge, R. Weiss , Proceedings of the National Academy of Sciences (2005)

2004

Optimizing Genetic Circuits by Global Sensitivity Analysis — X. Feng, S. Hooshangi, D. Chen, G. Li, R. Weiss, H. Rabitz , Biophysical Journal (2004)
BIC: Collaborative Research: Rational Design of Synthetic Gene Networks using Formal Analysis of Hybrid Systems — R. Weiss , NSF Award (2004)
Programmed population control by cell–cell communication and regulated killing — L. You, R.S. Cox, R. Weiss, F.H. Arnold , Nature (2004)
Spatiotemporal control of gene expression with pulse-generating networks — S. Basu, R. Mehreja, S. Thiberge, M. Chen, R. Weiss , Proceedings of the National Academy of Sciences (2004)
Teaching bacteria a new language — Y. Gerchman, R. Weiss , Proceedings of the National Academy of Sciences (2004)

2003

Engineering signal processing in cells: Towards molecular concentration band detection — S. Basu, D. Karig, R. Weiss , Natural Computing (2003)
Evolutionary design of genetic circuits and cell-cell communications — Y. Yokobayashi, C.H. Collins, J.R. Leadbetter, F.H. Arnold, R. Weiss , Advances in Complex Systems (2003)
Genetic circuit building blocks for cellular computation, communications, and signal processing — R. Weiss, S. Basu, S. Hooshangi, A. Kalmbach, D. Karig, R. Mehreja, I. Netravali , Natural Computing (2003)

2002

Directed evolution of a genetic circuit — Y. Yokobayashi, R. Weiss, F.H. Arnold , Proceedings of the National Academy of Sciences (2002)

2000

Amorphous computing — H. Abelson, D. Allen, D. Coore, C. Hanson, G. Homsy, T.F. Knight, R. Nagpal, E. Rauch, G.J. Sussman, R. Weiss , Communications of the ACM (2000)

1997

Paradigms for Structure in an Amorphous Computer — D. Coore, R. Nagpal, R. Weiss (1997)

1995

Composition and search with a video algebra — R. Weiss, A. Duda, D. Gifford , IEEE MultiMedia (1995)
Discover: a resource discovery system based on content routing — M.A. Sheldon, A. Duda, R. Weiss, D.K. Gifford , Computer Networks and ISDN Systems (1995)

1993

Structured Video: A Data Type with Content-based Access — A. Duda, R. Weiss (1993)
A Content Routing System for Distributed Information Systems — M.A. Sheldon, A. Duda, R. Weiss, J. O'Toole, D.K. Gifford (1993)

No year

Toward Quantitative Comparison of Fluorescent Protein Expression Levels via Fluorescent Beads — J. Beal, N. DeLateur, R. Weiss, J. Sexton, J.J. Tabor
TASBE: A Tool-Chain to Accelerate Synthetic Biological Engineering — J. Beal, R. Weiss, D. Densmore, A. Adler, J. Babb, S. Bhatia, N. Davidsohn, T. Haddock, F. Yaman, R. Schantz, J. Loyall
Synthetic Gene Regulatory Systems — M. Kærn, R. Weiss
A Content Routing System for Distributed Information Servers — M.A. Sheldon, A. Duday, R. Weiss, J.W. O'Toole
Toward Programming 3D Shape Formation in Mammalian Cells — J. Tordoff, J. Beal, R. Weiss
Automatic Compilation from High-Level Languages to Genetic Regulatory Networks — J. Beal, T. Lu, R. Weiss
Erratum: Open-source, community-driven microfluidics with Metafluidics — D.S. Kong, T.A. Thorsen, J. Babb, S.T. Wick, J.J. Gam, R. Weiss, P.A. Carr, H. König, S. Mukherjee, R. Seshadri, N.J. Varghese, E.A. Eloe-Fadrosh, J.P. Meier-Kolthoff, M. Göker, R.C. Coates, M. Hadjithomas, G.A. Pavlopoulos, D. Paez-Espino, Y. Yoshikuni, A. Visel, W.B. Whitman, G.M. Garrity, J.A. Eisen, P. Hugenholtz, A. Pati, N.N. Ivanova, T. Woyke, H. Klenk, N.C. Kyrpides, R.K. Varshney, C. Shi, M. Thudi, C. Mariac, J. Wallace, P. Qi, H. Zhang, Y. Zhao, X. Wang, A. Rathore, R.K. Srivastava, A. Chitikineni, G. Fan, P. Bajaj, S. Punnuri, S.K. Gupta, H. Wang, Y. Jiang, M. Couderc, V. Garg, N. Desai, D. Doddamani, N.A. Kane, J.A. Conner, A. Ghatak, P. Chaturvedi, S. Subramaniam, O.P. Yadav, C. Berthouly-Salazar, F. Hamidou, J. Wang, X. Liang, J. Clotault, H.D. Upadhyaya, P. Cubry, B. Rhoné, M.C. Gueye, R. Sunkar, C. Dupuy, F. Sparvoli, S. Cheng, R.S. Mahala, B. Singh, R.S. Yadav, E. Lyons, S.K. Datta, C.T. Hash, K.M. Devos, E. Buckler, J.L. Bennetzen, A.H. Paterson, P. Ozias-Akins, S. Grando, J. Wang, T. Mohapatra, W. Weckwerth, J.C. Reif, X. Liu, Y. Vigouroux, X. Xu, H. Xu, R.S.T. Gilliam, S.D. Peddada, G.M. Buchold, T.R.L. Collins
A Software Stack for Speciﬁcation and Robotic Execution of Protocols for Synthetic Biological Engineering — V. Vasilev, C. Liu, T. Haddock, S. Bhatia, A. Adler, F. Yaman, J. Beal, J. Babb, R. Weiss, D. Densmore
The Device Physics of Cellular Logic Gates — R. Weiss, S. Basu
Toward Automated Selection of Parts for Genetic Regulatory Networks — F. Yaman, S. Bhatia, A. Adler, D. Densmore, J. Beal, R. Weiss, N. Davidsohn

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