Publications
Research Papers
60. Prochazka, L., Michaels, M., Lau, C., Siu, M., Yin, T., Wu, D., Jang, E., Jones, R.D., Vazquez-Cantu, M., Gilbert, P. M., Kaul, H., Benenson, Y. and Zandstra, P. Discrete-to-analog signal conversion in human pluripotent stem cells. bioRxiv, https://doi.org/10.1101/2021.11.05.467377 (2021). external page To the manuscript
59. Doshi, J., Willis, K., Madurga, A., Stelzer, C., Benenson, Y. Multiple alternative promoters and alternative splicing enable universal transcription-based logic computation in mammalian cells. Cell Reports 33: 108437 (2020). external page To the manuscript
58. Stelzer, C., Benenson, Y. Precise determination of input-output mapping for multimodal gene circuits using data from transient transfection. PLoS Computational Biology 16: e1008389 (2020). external page To the manuscript
57. Höllerer, S., Papaxanthos, L., Gumpinger, A.C., Fischer, K., Beisel, C., Borgwardt, K.*, Benenson, Y.*, Jeschek, M*. Large-scale DNA-based phenotypic recording and deep learning enable highly accurate sequence-function mapping. Nature Communications 11, Art. 3551 (2020). external page To the manuscript
56. Tarvirdipour, S., Schoenenberger, C.-A., Benenson, Y* & Palivan, C and Palivan, C. A self-assembling amphiphilic peptide nanoparticle for the efficient entrapment of DNA cargoes up to 100 nucleotides in length. Soft Matter DOI: 10.1039/C9SM01990A (2020). external page To the manuscript
55. Mazé, A. & Benenson, Y. Artificial signaling in mammalian cells enabled by prokaryotic two-component system. Nature Chemical Biology 16, 179–187 (2020). external page To the manuscript
54. Lilacci, G., Benenson, Y.* & Khammash, M.*. Synthetic control systems for high performance gene expression in mammalian cells. Nucleic Acids Research 46, 9855–9863 (2018). Texternal page o the manuscript
53. Dastor, M., Schreiber, J., Prochazka, L., Angelici, B., Kleinert, J., Klebba, I., Doshi, J., Shen, L*. & Benenson, Y.*. A workflow for in vivo evaluation of candidate inputs and outputs for cell classifier gene circuits. ACS Synth. Biol 7, 474-489 (2018). external page To the manuscript
52. Lapique, N & Benenson, Y. Genetic programs can be compressed and autonomously decompressed in live cells. Nature Nanotechnology 13, pages309–315(2018). external page To the manuscript
51. Mohammadi, P., Beerenwinkel, N*. & Benenson, Y*. Automated design of synthetic cell classifier circuits using a two-step optimization strategy. Cell Systems 4, 1-12 (2017). external page To the manuscript
50. Schreiber, J., Arter, M., Lapique, N., Haefliger, B. & Benenson, Y. Model-guided combinatorial optimization of complex synthetic gene networks. Molecular Systems Biology 12, 899 (2016). external page To the manuscript
49. Angelici, B., Mailan, E., Haefliger, B. & Benenson, Y. Synthetic biology platform for sensing and integrating endogenous transcriptional inputs in mammalian cells. Cell Reports 16, 2525-2537 (2016). external page To the manuscript
48. Haefliger, B., Prochazka, L., Angelici, B & Benenson, Y. Precision multidimensional assay for high-throughput microRNA drug discovery. Nature Communications 7:10709 (2016). external page To the manuscript
47. Hansen, J., Mailand, E., Swaminathan, K. K., Schreiber, J., Angelici, B., Benenson, Y. Transplantation of prokaryotic two-component signaling pathways into mammalian cells. Proc. Natl. Acad. Sci. USA 111, 15705–15710 (2014). external page To the manuscript
46. Lapique, N & Benenson, Y. Digital switching in a biosensor circuit via programmable timing of gene availability. Nature Chemical Biology 10, 1020–1027 (2014). external page To the manuscript
45. Prochazka, L., Angelici, A., Haefliger, B and Benenson, Y. Highly modular bow-tie gene circuits with programmable dynamic behavior. Nature Communications 5:4729 (2014). external page To the manuscript
44. Schmid-Burkg, J.L., Xie, Z., Benenson, Y. Hierarchical ligation-independent assembly of PCR fragments. Methods in Molecular Biology 1116, 49-58 (2014). external page To the manuscript
43. Kang, T., White, J. T., Xie, Z., Benenson, Y., Sontag, E., Bleris, L. Reverse engineering validation using a benchmark synthetic gene circuit in human cells. ACS Synth. Biol. DOI: 10.1021/sb300093y (2013). external page To the manuscript
42. Schmid-Burgk, J. L., Xie, Z., Frank, S., Virreira Winter, S., Mitschka, S., Kolanus, W., Murray, A., Benenson, Y. Rapid hierarchical assembly of medium-size DNA cassettes. Nucleic Acids Research doi: 10.1093/nar/gks236 (2012). external page To the manuscript
41. Leisner, M., Bleris, L., Lohmueller, J., Xie, Z., Benenson, Y. MicroRNA circuits for transcriptional logic. Methods in Molecular Biology 813, Part 2, 169-186 (2012). external page To the manuscript
40. Xie, Z., Wroblewska, L., Prochazka, L., Weiss, R., Benenson, Y. Multi-input RNAi-based logic circuit for identification of specific cancer cells. Science 333, 1307-1311 (2011). external page To the manuscript
39. Bleris, L., Xie, Z., Glass, D., Adadey, A., Sontag, E., Benenson, Y. Synthetic incoherent feedforward circuits show adaptation to the amount of their genetic template. Molecular Systems Biology 7:519 (2011). News&Views in the same issue. external page To the manuscript
38. Benenson, Y. Engineering RNAi circuits. Methods in Enzymology 497, 187-205 (2011). external page To the manuscript
37. Leisner, M., Bleris, L., Lohmueller, J., Xie, Z. & Benenson, Y. Rationally designed logic integration of regulatory signals in mammalian cells. Nature Nanotechnology 5, 666-670 (2010). News&Views in the same issue. external page To the manuscript
36. Xie, Z., Liu, S. J., Bleris, L. & Benenson, Y. Logic integration of mRNA signals by an RNAi-based molecular computer. Nucleic Acids Res. 38, 2692-2701 (2010). external page To the manuscript
35. Rinaudo, K., Bleris, L., Maddamsetti, R., Subramanian, S., Weiss, R. & Benenson, Y. A universal RNAi-based logic evaluator that operates in mammalian cells. Nature Biotechnology 25, 795-801 (2007). external page To the manuscript
34. Adar, R., Benenson, Y., Linshiz, G., Rosner, A., Tishbi, N. & Shapiro, E. Stochastic computing with biomolecular automata, Proc. Natl. Acad. Sci. USA 101, 9960-9965 (2004). external page To the manuscript
33. Benenson, Y., Gil, B., Ben-Dor, U., Adar, R. & Shapiro, E. An autonomous molecular computer for logical control of gene expression. Nature 429, 423-429 (2004). News&Views on p. 351 of the same issue. external page To the manuscript
32. Benenson, Y., Adar, R.; Paz-Elizur, T., Livneh, Z. & Shapiro, E. DNA molecule provides a computing machine with both data and fuel. Proc. Natl. Acad. Sci. USA, 100, 2191-2196 (2003). external page To the manuscript
31. Benenson, Y., Paz-Elizur, T., Adar, R., Keinan, E., Livneh, Z. & Shapiro, E. Programmable and autonomous computing machine made of biomolecules. Nature 414, 430-434 (2001). external page To the manuscript
30. Liang, P.H., Lewis, J., Anderson, K.S., Kohen, A., D'Souza, W., Benenson, Y. & Baasov, T. Catalytic mechanism of Kdo8P synthase: transient kinetic studies and evaluation of a putative reaction intermediate. Biochemistry 37, 16390-16399 (1998). external page To the manuscript
29. D’Souza, W., Benenson, Y. & Baasov, T. Catalytic mechanism of Kdo8P synthase: Synthesis and evaluation of a putative reaction intermediate. Bioorg. Med. Chem. Lett. 7, 2457-2462 (1997). external page To the manuscript
28. Benenson, Y., Belakhov, V. & Baasov, T. 1-(dihydroxyphosphynyl)vinyl phosphate: The phosphonate analogue of phosphoenolpyruvate is a pH-dependent substrate of Kdo8P synthase. Bioorg. Med. Chem. Lett. 6, 2901-2906 (1996). external page To the manuscript
Reviews, News & Views
27. Jaekel, J.J., Schweingruber, D., Cheras, V., Doshi, J. and Benenson, Y. Multi-input biocomputer gene circuits for therapeutic applications. Curr. Opin. Syst. Biol. 28:100371 (2021). external page To the manuscript
26. Prochazka, L., Benenson, Y.* and Zanstra, P.* Synthetic gene circuits and cellular decision-making in human pluripotent stem cells. Current Opinion in Systems Biology 5, 93-103 (2017). external page To the manuscript
25. Benenson, Y and Lutholf, M. Editorial overview: Tissue, cell and pathway engineering: The advent of complexity. Current Opinion in Biotechnology 47, iv-v1 (2017). external page To the manuscript
24. Benenson, Y. Complexity from simple building blocks: Engineering large-scale information-processing networks from molecules. CHIMIA 70, 392-392 (2016). external page To the manuscript
23. Hansen, J. & Benenson, Y. Synthetic biology of cell signaling. Natural Computing 15, 5-13 (2016). external page To the manuscript
22. Lapique, N. & Benenson, Y. Vue de l’intérieur. Des circuits génétiques pour l’analyse de profils moléculaires intracellulaires. Médicine/Sciences (Paris), 31, 487-491 (2015). external page To the manuscript
21. Benenson, Y. Recombinatorial Logic (Perspective). Science 340, 554-555 (2013). external page To the manuscript
20. Benenson, Y. Synthetic Biology with RNA: progress report (Review). Curr. Opin. in Chem. Biol. 16, 278-284 (2012). external page To the manuscript
19. Benenson, Y. Biomolecular computing systems: principles, progress and potential (Review). Nature Reviews Genetics 13, 445-468 (2012). external page To the manuscript
18. Benenson, Y. Biocomputing: DNA computes a square root (News&Views). Nature Nanotechnology 6, 465-467 (2011). external page To the manuscript
17. Benenson, Y. RNA interference-based computing in mammalian cells (Review). Israel Journal of Chemistry 51, 87-98 (2011). external page To the manuscript
16. Benenson, Y. RNA-based computation in live cells (Review). Curr. Opin. in Biotechnology 20, 471-478 (2009). external page To the manuscript
15. Benenson, Y. Biocomputers: from test tubes to live cells (Review). Molecular Biosystems 5, 675-685 (2009). external page To the manuscript
14. Benenson, Y. Small hairpin RNA as a small molecule sensor (News&Views). Molecular Systems Biology 4:227 (2008). external page To the manuscript
13. Shapiro, E. & Benenson, Y. Bringing DNA computers to life. Scientific American 294, 44-51 (2006). external page To the manuscript
Book Chapters
12. Benenson, Y. In vivo information processing using RNA interference. In Biomolecular Infomration Processing: from Logic Systems to Smart Sensors and Actuators. E. Katz, Ed. Wiley-VCH, Weinheim Germany, 2012; pp 181-198. external page To the chapter
11. Benenson, Y. & Shapiro, E. Molecular computing machines. In Dekker Encyclopedia of Nanoscience and Nanotechnology, James A. Schwarz, Cristian I. Contescu, and Karol Putyera, Eds.; Marcel Dekker, Inc.: New York, 2004; pp 2043-2056. external page To the chapter
Patents
10. Doshi, J & Benenson, Y. DNA constructs comprising alternative promoters. Priority filing
9. Angelici, B. & Benenson, Y. Cell classifier circuits and methods of use thereof. PCT filing
8. Angelici, B. & Benenson, Y. A method to treat disease using a nucleic acid vector encoding a highly compact multi-input logic gate. National Phase
7. Maze, A. & Benenson, Y. European Patent Application Novel method for transducing protein-protein interactions. National Phase
6. Altamura, R., Doshi, J. & Benenson, Y. Multiple copy gene constructs and methods for the rapid generation of recombinant protein production cell lines. PCT filing.
5. Lapique, N., Benenson, Y. Near-perfect digital switching in a synthetic biosensor circuit achieved through temporal control of circuit's genetic makeup. Granted US, EU
4. Haefliger, B., Benenson, Y. Screening assay for identifying miRNA-specific drug compounds. Granted US, pending EU
3. Hansen, J., Swaminathan, K.K. and Benenson, Y. Prokaryotic 2-component signaling pathways for use as logic gates in mammalian cells. Granted US, EU
2. Benenson, Y., Weiss, R., Xie, Z., Wroblewska, L. Multiple Input Biological Classifier Circuits for Cells. Granted US, EU, Canada, NZ
1. Shapiro, E., Benenson, Y., Adar, R., Paz-Elizur, T. Programmable and autonomous computing machine made of biomolecules. US Patent 7,970,547