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Yaakov Benenson, Ph.D. - Publications

Affiliations: 
2005 Weizmann Institute of Science, Rehovot, Israel 
Area:
Bioinformatics Biology
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39 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 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. PMID 33264624 DOI: 10.1016/j.celrep.2020.108437  0.306
2020 Höllerer S, Papaxanthos L, Gumpinger AC, 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: 3551. PMID 32669542 DOI: 10.1038/S41467-020-17222-4  0.318
2019 Mazé A, Benenson Y. Artificial signaling in mammalian cells enabled by prokaryotic two-component system. Nature Chemical Biology. PMID 31844302 DOI: 10.1038/S41589-019-0429-9  0.306
2018 Lillacci G, Benenson Y, Khammash M. Synthetic control systems for high performance gene expression in mammalian cells. Nucleic Acids Research. PMID 30203050 DOI: 10.1093/Nar/Gky795  0.379
2017 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 Synthetic Biology. PMID 29257672 DOI: 10.1021/Acssynbio.7B00303  0.356
2017 Lapique N, Benenson Y. Genetic programs can be compressed and autonomously decompressed in live cells. Nature Nanotechnology. PMID 29133926 DOI: 10.1038/S41565-017-0004-Z  0.383
2017 Mohammadi P, Beerenwinkel N, Benenson Y. Automated Design of Synthetic Cell Classifier Circuits Using a Two-Step Optimization Strategy. Cell Systems. PMID 28189580 DOI: 10.1016/J.Cels.2017.01.003  0.363
2017 Prochazka L, Benenson Y, Zandstra PW. Synthetic gene circuits and cellular decision-making in human pluripotent stem cells Current Opinion in Systems Biology. 5: 93-103. DOI: 10.1016/J.Coisb.2017.09.003  0.36
2016 Schreiber J, Arter M, Lapique N, Haefliger B, Benenson Y. Model-guided combinatorial optimization of complex synthetic gene networks. Molecular Systems Biology. 12: 899. PMID 28031353 DOI: 10.15252/Msb.20167265  0.336
2016 Angelici B, Mailand E, Haefliger B, Benenson Y. Synthetic Biology Platform for Sensing and Integrating Endogenous Transcriptional Inputs in Mammalian Cells. Cell Reports. PMID 27545896 DOI: 10.1016/J.Celrep.2016.07.061  0.386
2016 Benenson Y. Complexity from Simple Building Blocks: Engineering Large-scale Information-processing Networks from Molecules. Chimia. 70: 392-4. PMID 27363365 DOI: 10.2533/Chimia.2016.392  0.382
2016 Hansen J, Benenson Y. Synthetic biology of cell signaling Natural Computing. 15: 5-13. DOI: 10.1007/S11047-015-9526-1  0.368
2015 Lapique N, Benenson Y. [View of the inside: genetic circuits for the analysis of intracellular molecular profiles]. MéDecine Sciences : M/S. 31: 487-91. PMID 26059298 DOI: 10.1051/Medsci/20153105009  0.307
2014 Hansen J, Mailand E, Swaminathan KK, Schreiber J, Angelici B, Benenson Y. Transplantation of prokaryotic two-component signaling pathways into mammalian cells. Proceedings of the National Academy of Sciences of the United States of America. 111: 15705-10. PMID 25331891 DOI: 10.1073/Pnas.1406482111  0.363
2014 Prochazka L, Angelici B, Haefliger B, Benenson Y. Highly modular bow-tie gene circuits with programmable dynamic behaviour. Nature Communications. 5: 4729. PMID 25311543 DOI: 10.1038/Ncomms5729  0.381
2014 Lapique N, Benenson Y. Digital switching in a biosensor circuit via programmable timing of gene availability. Nature Chemical Biology. 10: 1020-7. PMID 25306443 DOI: 10.1038/Nchembio.1680  0.35
2014 Schmid-Burgk JL, Xie Z, Benenson Y. Hierarchical ligation-independent assembly of PCR fragments. Methods in Molecular Biology (Clifton, N.J.). 1116: 49-58. PMID 24395356 DOI: 10.1007/978-1-62703-764-8_4  0.349
2013 Kang T, White JT, Xie Z, Benenson Y, Sontag E, Bleris L. Reverse engineering validation using a benchmark synthetic gene circuit in human cells. Acs Synthetic Biology. 2: 255-62. PMID 23654266 DOI: 10.1021/Sb300093Y  0.358
2012 Benenson Y. Biomolecular computing systems: principles, progress and potential. Nature Reviews. Genetics. 13: 455-68. PMID 22688678 DOI: 10.1038/Nrg3197  0.378
2012 Benenson Y. Synthetic biology with RNA: progress report. Current Opinion in Chemical Biology. 16: 278-84. PMID 22676891 DOI: 10.1016/J.Cbpa.2012.05.192  0.374
2012 Schmid-Burgk JL, Xie Z, Frank S, Winter SV, Mitschka S, Kolanus W, Murray A, Benenson Y. Rapid hierarchical assembly of medium-size DNA cassettes Nucleic Acids Research. 40: e92. PMID 22422837 DOI: 10.1093/Nar/Gks236  0.352
2012 Leisner M, Bleris L, Lohmueller J, Xie Z, Benenson Y. MicroRNA circuits for transcriptional logic. Methods in Molecular Biology (Clifton, N.J.). 813: 169-86. PMID 22083742 DOI: 10.1007/978-1-61779-412-4_10  0.399
2011 Xie Z, Wroblewska L, Prochazka L, Weiss R, Benenson Y. Multi-input RNAi-based logic circuit for identification of specific cancer cells. Science (New York, N.Y.). 333: 1307-11. PMID 21885784 DOI: 10.1126/Science.1205527  0.397
2011 Benenson Y. Biocomputing: DNA computes a square root. Nature Nanotechnology. 6: 465-7. PMID 21814231 DOI: 10.1038/Nnano.2011.128  0.395
2011 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. PMID 21811230 DOI: 10.1038/Msb.2011.49  0.358
2011 Benenson Y. Engineering RNAi circuits. Methods in Enzymology. 497: 187-205. PMID 21601087 DOI: 10.1016/B978-0-12-385075-1.00008-1  0.457
2011 Benenson Y. RNA interference-based computing in mammalian cells Israel Journal of Chemistry. 51: 87-98. DOI: 10.1002/Ijch.201000070  0.468
2010 Leisner M, Bleris L, Lohmueller J, Xie Z, Benenson Y. Rationally designed logic integration of regulatory signals in mammalian cells. Nature Nanotechnology. 5: 666-70. PMID 20622866 DOI: 10.1038/Nnano.2010.135  0.397
2010 Xie Z, Liu SJ, Bleris L, Benenson Y. Logic integration of mRNA signals by an RNAi-based molecular computer. Nucleic Acids Research. 38: 2692-701. PMID 20194121 DOI: 10.1093/Nar/Gkq117  0.467
2009 Benenson Y. RNA-based computation in live cells. Current Opinion in Biotechnology. 20: 471-8. PMID 19720518 DOI: 10.1016/J.Copbio.2009.08.002  0.412
2009 Benenson Y. Biocomputers: from test tubes to live cells. Molecular Biosystems. 5: 675-85. PMID 19562106 DOI: 10.1039/B902484K  0.352
2008 Benenson Y. Small hairpin RNA as a small molecule sensor. Molecular Systems Biology. 4: 227. PMID 18956014 DOI: 10.1038/Msb.2008.67  0.399
2007 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. PMID 17515909 DOI: 10.1038/Nbt1307  0.427
2006 Shapiro E, Benenson Y. Tapping the computing power of biological molecules gives rise to tiny machines that can speak directly to living cells. Scientific American. 294: 44-51. PMID 16708487  0.516
2006 Shapiro E, Benenson Y. Bringing DNA computers to life Scientific American. 294: 44-51. DOI: 10.1038/Scientificamerican0907-40Sp  0.565
2004 Adar R, Benenson Y, Linshiz G, Rosner A, Tishby N, Shapiro E. Stochastic computing with biomolecular automata. Proceedings of the National Academy of Sciences of the United States of America. 101: 9960-5. PMID 15215499 DOI: 10.1073/Pnas.0400731101  0.575
2004 Benenson Y, Gil B, Ben-Dor U, Adar R, Shapiro E. An autonomous molecular computer for logical control of gene expression. Nature. 429: 423-9. PMID 15116117 DOI: 10.1038/Nature02551  0.622
2003 Benenson Y, Adar R, Paz-Elizur T, Livneh Z, Shapiro E. DNA molecule provides a computing machine with both data and fuel. Proceedings of the National Academy of Sciences of the United States of America. 100: 2191-6. PMID 12601148 DOI: 10.1073/Pnas.0535624100  0.589
2001 Benenson Y, Paz-Elizur T, Adar R, Keinan E, Llvneh Z, Shapiro E. Programmable and autonomous computing machine made of biomolecules Nature. 414: 430-434. PMID 11719800 DOI: 10.1038/35106533  0.354
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