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 pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

55. Mazé, A. & Benenson, Y. Artificial signaling in mammalian cells enabled by prokaryotic two-component system. Nature Chemical Biology 16, 179–187 (2020). external pageTo the manuscriptcall_made

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 pageo the manuscriptcall_made

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 pageTo the manuscriptcall_made

52. Lapique, N & Benenson, Y. Genetic programs can be compressed and autonomously decompressed in live cells. Nature Nanotechnology 13, pages309–315(2018). external pageTo the manuscriptcall_made  

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 pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

48. Haefliger, B., Prochazka, L., Angelici, B & Benenson, Y.  Precision multidimensional assay for high-throughput microRNA drug discovery. Nature Communications 7:10709 (2016). external pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

38. Benenson, Y. Engineering RNAi circuits. Methods in Enzymology 497, 187-205 (2011). external pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made  

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 pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made 

24. Benenson, Y. Complexity from simple building blocks: Engineering large-scale information-processing networks from molecules. CHIMIA 70, 392-392 (2016). external pageTo the manuscriptcall_made

23. Hansen, J. & Benenson, Y. Synthetic biology of cell signaling. Natural Computing 15, 5-13 (2016). external pageTo the manuscriptcall_made

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 pageTo the manuscriptcall_made

21. Benenson, Y. Recombinatorial Logic (Perspective). Science 340, 554-555 (2013). external pageTo the manuscriptcall_made

20. Benenson, Y. Synthetic Biology with RNA: progress report (Review). Curr. Opin. in Chem. Biol. 16, 278-284 (2012). external pageTo the manuscriptcall_made

19. Benenson, Y. Biomolecular computing systems: principles, progress and potential (Review). Nature Reviews Genetics 13, 445-468 (2012). external pageTo the manuscriptcall_made

18. Benenson, Y. Biocomputing: DNA computes a square root (News&Views). Nature Nanotechnology 6, 465-467 (2011). external pageTo the manuscriptcall_made

17. Benenson, Y. RNA interference-based computing in mammalian cells (Review). Israel Journal of Chemistry 51, 87-98 (2011). external pageTo the manuscriptcall_made

16. Benenson, Y. RNA-based computation in live cells (Review). Curr. Opin. in Biotechnology 20, 471-478 (2009). external pageTo the manuscriptcall_made

15. Benenson, Y. Biocomputers: from test tubes to live cells (Review). Molecular Biosystems 5, 675-685 (2009). external pageTo the manuscriptcall_made

14. Benenson, Y. Small hairpin RNA as a small molecule sensor (News&Views). Molecular Systems Biology 4:227 (2008). external pageTo the manuscriptcall_made

13. Shapiro, E. & Benenson, Y. Bringing DNA computers to life. Scientific American 294, 44-51 (2006). external pageTo the manuscriptcall_made

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 pageTo the chaptercall_made

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 pageTo the chaptercall_made

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