TY - JOUR AU - Liberman, E. A. PY - 1979 DA - 1979// TI - Analog-digital molecular cell computer JO - BioSystems VL - 11 UR - https://doi.org/10.1016/0303-2647(79)90005-4 DO - 10.1016/0303-2647(79)90005-4 ID - Liberman1979 ER - TY - JOUR AU - Adleman, L. M. PY - 1994 DA - 1994// TI - Molecular computation of solutions to combinatorial problems JO - Science VL - 266 UR - https://doi.org/10.1126/science.7973651 DO - 10.1126/science.7973651 ID - Adleman1994 ER - TY - JOUR AU - Isaacs, F. J. AU - Dwyer, D. J. AU - Collins, J. J. PY - 2006 DA - 2006// TI - RNA synthetic biology JO - Nat Biotechnol VL - 24 UR - https://doi.org/10.1038/nbt1208 DO - 10.1038/nbt1208 ID - Isaacs2006 ER - TY - JOUR AU - Rinaudo, K. AU - Bleris, L. AU - Maddamsetti, R. AU - Subramanian, S. AU - Weiss, R. AU - Benenson, Y. PY - 2007 DA - 2007// TI - A universal RNAi-based logic evaluator that operates in mammalian cells JO - Nat Biotechnol VL - 25 UR - https://doi.org/10.1038/nbt1307 DO - 10.1038/nbt1307 ID - Rinaudo2007 ER - TY - JOUR AU - Beisel, C. L. AU - Bayer, T. S. AU - Hoff, K. G. AU - Smolke, D. PY - 2008 DA - 2008// TI - Model-guided design of ligand-regulated RNAi for Programmable control of gene expression JO - Mol Syst Biol VL - 4 ID - Beisel2008 ER - TY - JOUR AU - Win, M. N. AU - Smolke, C. D. PY - 2008 DA - 2008// TI - Higher-order cellular information processing with synthetic RNA devices JO - Science VL - 322 UR - https://doi.org/10.1126/science.1160311 DO - 10.1126/science.1160311 ID - Win2008 ER - TY - JOUR AU - Xie, Z. AU - Wroblewska, L. AU - Prochazka, L. AU - Weiss, R. AU - Benenson, Y. PY - 2002 DA - 2002// TI - Multi-input RNAi-based logic circuit for identification of specific cancer cells JO - Science VL - 333 UR - https://doi.org/10.1126/science.1205527 DO - 10.1126/science.1205527 ID - Xie2002 ER - TY - JOUR AU - Couzin, J. PY - 2002 DA - 2002// TI - Small RNAs make big splash JO - Science VL - 298 UR - https://doi.org/10.1126/science.298.5602.2296 DO - 10.1126/science.298.5602.2296 ID - Couzin2002 ER - TY - JOUR AU - Hannon, G. J. PY - 2002 DA - 2002// TI - RNA interference JO - Nature VL - 418 UR - https://doi.org/10.1038/418244a DO - 10.1038/418244a ID - Hannon2002 ER - TY - CHAP AU - Petersen, C. P. AU - Doench, J. G. AU - Grishok, A. AU - Sharp, P. A. ED - Gesteland, R. F. ED - Cech, T. R. ED - Atkins, J. F. PY - 2006 DA - 2006// TI - The biology of short RNAs BT - RNA world PB - Cold Spring Harbor Laboratory Press CY - New York ID - Petersen2006 ER - TY - JOUR AU - Zamore, P. D. AU - Haley, B. PY - 2005 DA - 2005// TI - Ribo-gnome: The big world of small RNAs JO - Science VL - 309 UR - https://doi.org/10.1126/science.1111444 DO - 10.1126/science.1111444 ID - Zamore2005 ER - TY - JOUR AU - Mandal, M. AU - Breaker, R. R. PY - 2004 DA - 2004// TI - Gene regulation by riboswitches JO - Mol Cell Biol VL - 5 ID - Mandal2004 ER - TY - JOUR AU - Nudler, E. AU - Mironov, A. S. PY - 2004 DA - 2004// TI - The riboswitch control of bacterial metabolism JO - Trends Biochem Sci VL - 29 UR - https://doi.org/10.1016/j.tibs.2003.11.004 DO - 10.1016/j.tibs.2003.11.004 ID - Nudler2004 ER - TY - JOUR AU - Stojanovic, M. N. AU - Stefanovic, D. PY - 2003 DA - 2003// TI - A Deoxyribozyme-based molecular automaton JO - Nature Biotechnol VL - 21 UR - https://doi.org/10.1038/nbt862 DO - 10.1038/nbt862 ID - Stojanovic2003 ER - TY - JOUR AU - Penchovsky, R. AU - Breaker, R. R. PY - 2005 DA - 2005// TI - Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes JO - Nat Biotechnol VL - 23 UR - https://doi.org/10.1038/nbt1155 DO - 10.1038/nbt1155 ID - Penchovsky2005 ER - TY - JOUR AU - Porta, H. AU - Lizardi, P. M. PY - 1995 DA - 1995// TI - An allosteric hammherhead ribozyme JO - Bio/Technology VL - 13 UR - https://doi.org/10.1038/nbt0295-161 DO - 10.1038/nbt0295-161 ID - Porta1995 ER - TY - JOUR AU - Hertel, K. J. AU - Herschlag, D. AU - Uhlenbeck, O. C. PY - 1994 DA - 1994// TI - A kinetic and thermodynamic framework for the hammerhead ribozyme reaction JO - Biochemistry VL - 33 UR - https://doi.org/10.1021/bi00177a031 DO - 10.1021/bi00177a031 ID - Hertel1994 ER - TY - JOUR AU - Symons, R. H. PY - 1997 DA - 1997// TI - Plant pathogenic RNAs and RNA catalysis JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.14.2683 DO - 10.1093/nar/25.14.2683 ID - Symons1997 ER - TY - JOUR AU - Birikh, K. R. AU - Heaton, P. A. AU - Eckstein, F. PY - 1997 DA - 1997// TI - The Structure, function and application of the hammerhead ribozyme JO - Eur J Biochem VL - 245 UR - https://doi.org/10.1111/j.1432-1033.1997.t01-3-00001.x DO - 10.1111/j.1432-1033.1997.t01-3-00001.x ID - Birikh1997 ER - TY - JOUR AU - Soukup, G. A. AU - Breaker, R. R. PY - 1999 DA - 1999// TI - Nucleic acid molecular switches JO - Trends Biotechnol VL - 17 UR - https://doi.org/10.1016/S0167-7799(99)01383-9 DO - 10.1016/S0167-7799(99)01383-9 ID - Soukup1999 ER - TY - JOUR AU - Silverman, S. K. PY - 2003 DA - 2003// TI - Rube goldberg goes (Ribo)Nuclear? Molecular switches and sensors made from RNA JO - RNA VL - 9 UR - https://doi.org/10.1261/rna.2200903 DO - 10.1261/rna.2200903 ID - Silverman2003 ER - TY - JOUR AU - Kuwabara, T. AU - Warashina, M. AU - Taira, K. PY - 2000 DA - 2000// TI - Allosterically controllable ribozymes with biosensor functions JO - Curr Opin Chem Biol VL - 4 UR - https://doi.org/10.1016/S1367-5931(00)00150-2 DO - 10.1016/S1367-5931(00)00150-2 ID - Kuwabara2000 ER - TY - JOUR AU - Stojanovic, M. N. AU - Nikic, D. B. AU - Stefanovic, D. PY - 2003 DA - 2003// TI - Implicit-OR Tiling of Deoxyribozymes: construction of molecular scale OR, NAND and four-input logic gates JO - J Serb Chem Soc VL - 68 UR - https://doi.org/10.2298/JSC0305321S DO - 10.2298/JSC0305321S ID - Stojanovic2003 ER - TY - JOUR AU - Stojanovic, M. N. AU - Stefanovic, D. PY - 2003 DA - 2003// TI - Deoxyribozyme-based half-adder JO - J Am Chem Soc VL - 125 UR - https://doi.org/10.1021/ja0296632 DO - 10.1021/ja0296632 ID - Stojanovic2003 ER - TY - JOUR AU - Lederman, H. AU - Macdonald, J. AU - Stefanovic, D. AU - Stojanovic, M. PY - 2006 DA - 2006// TI - Deoxyribozyme-based three input logic gates and construction of a molecular full adder JO - Biochemistry VL - 45 UR - https://doi.org/10.1021/bi051871u DO - 10.1021/bi051871u ID - Lederman2006 ER - TY - JOUR AU - Pei, R. AU - Taylor, S. K. AU - Stefanovic, D. AU - Rudchenko, S. AU - Mitchell, T. E. AU - Stojanovic, M. N. PY - 2006 DA - 2006// TI - Behaviour of polycatalytic assemblies in a substrate-displaying matrix JO - J Am Chem Soc VL - 128 UR - https://doi.org/10.1021/ja058394n DO - 10.1021/ja058394n ID - Pei2006 ER - TY - JOUR AU - Macdonald, J. AU - Li, Y. AU - Sutovic, M. AU - Lederman, H. AU - Pendri, K. AU - Lu, W. AU - Andrews, B. L. AU - Stefanovic, D. AU - Stojanovic, M. N. PY - 2006 DA - 2006// TI - Medium scale integration of molecular logic gates in an automaton JO - Nano Lett VL - 6 UR - https://doi.org/10.1021/nl0620684 DO - 10.1021/nl0620684 ID - Macdonald2006 ER - TY - JOUR AU - Hofacker, I. L. AU - Fontana, W. AU - Stadler, P. F. AU - Bonhoeffer, L. S. AU - Tacker, M. AU - Schuster, P. PY - 1994 DA - 1994// TI - Fast folding and comparison of RNA secondary structures JO - Chem Mon VL - 125 UR - https://doi.org/10.1007/BF00818163 DO - 10.1007/BF00818163 ID - Hofacker1994 ER - TY - JOUR AU - Zauner, K. P. PY - 2005 DA - 2005// TI - Molecular information technology JO - Crit Rev Solid State Mater Sci VL - 30 UR - https://doi.org/10.1080/10408430590918387 DO - 10.1080/10408430590918387 ID - Zauner2005 ER - TY - JOUR AU - Ramlan, E. I. AU - Zauner, K. P. PY - 2009 DA - 2009// TI - Nucleic acid enzymes: the fusion of self-assembly and conformational computing JO - Int J Unconventional Comput VL - 5 ID - Ramlan2009 ER - TY - JOUR AU - Andronescu, M. PY - 2003 DA - 2003// TI - Anguirre-Hernández R, Condon A, Hoos HH: RNAsoft: A suite of RNA secondary structure prediction and design software tools JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg612 DO - 10.1093/nar/gkg612 ID - Andronescu2003 ER - TY - STD TI - Zuker M, Mathews DH, Turner DH: RNA Biochemistry and Biotechnology. Dordrecht: Kluwer Academic Publishers. NATO ASI 1999 chap. Algorithm and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide :11–43 ID - ref32 ER - TY - JOUR AU - Penchovsky, R. AU - Ackermann, J. PY - 2003 DA - 2003// TI - DNA Library design for molecular computation JO - J Comput Biol VL - 10 UR - https://doi.org/10.1089/106652703321825973 DO - 10.1089/106652703321825973 ID - Penchovsky2003 ER - TY - JOUR AU - Flamm, C. AU - Fontana, W. AU - Hofacker, I. L. AU - Schuster, P. PY - 2000 DA - 2000// TI - RNA folding at elementary step resolution JO - RNA VL - 6 UR - https://doi.org/10.1017/S1355838200992161 DO - 10.1017/S1355838200992161 ID - Flamm2000 ER - TY - JOUR AU - Shapiro, E. AU - Gil, B. PY - 2008 DA - 2008// TI - RNA computing in a living cell JO - Science VL - 322 UR - https://doi.org/10.1126/science.1165665 DO - 10.1126/science.1165665 ID - Shapiro2008 ER - TY - JOUR AU - Nudler, E. PY - 2006 DA - 2006// TI - Flipping riboswitches JO - Cell VL - 126 UR - https://doi.org/10.1016/j.cell.2006.06.024 DO - 10.1016/j.cell.2006.06.024 ID - Nudler2006 ER - TY - JOUR AU - Suess, B. AU - Weigand, J. E. PY - 2008 DA - 2008// TI - Engineered riboswitches: overview, problems and trends JO - RNA Biol VL - 5 UR - https://doi.org/10.4161/rna.5.1.5955 DO - 10.4161/rna.5.1.5955 ID - Suess2008 ER - TY - JOUR AU - Ramlan, E. I. AU - Zauner, K. P. PY - 2011 DA - 2011// TI - Design of interacting multi-stable nucleic acids for molecular information processing JO - Biosystems VL - 105 UR - https://doi.org/10.1016/j.biosystems.2011.02.006 DO - 10.1016/j.biosystems.2011.02.006 ID - Ramlan2011 ER - TY - JOUR AU - Tang, J. AU - Breaker, R. R. PY - 1997 DA - 1997// TI - Rational design of allosteric ribozymes JO - Chem Biol VL - 4 UR - https://doi.org/10.1016/S1074-5521(97)90197-6 DO - 10.1016/S1074-5521(97)90197-6 ID - Tang1997 ER - TY - STD TI - Tang J, Breaker RR: Structural diversity of self-cleaving ribozymes. Proc Natl Acad Sci USA. 97: 5784-5789. ID - ref40 ER - TY - JOUR AU - Mückstein, U. AU - Tafer, H. AU - Hackermüller, J. AU - Bernhard, S. AU - Stadler, P. F. AU - Hofacker, I. L. PY - 2006 DA - 2006// TI - Thermodynamics of RNA-RNA binding JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl024 DO - 10.1093/bioinformatics/btl024 ID - Mückstein2006 ER - TY - JOUR AU - Benenson, Y. AU - Gil, B. AU - Ben-Dor, U. AU - Adar, R. AU - Shapiro, E. PY - 2004 DA - 2004// TI - An autonomous molecular computer for logical control of gene expression JO - Nature VL - 429 UR - https://doi.org/10.1038/nature02551 DO - 10.1038/nature02551 ID - Benenson2004 ER - TY - JOUR AU - Simpson, M. L. PY - 2004 DA - 2004// TI - Rewiring the cell: synthetic biology moves towards higher functional complexity JO - Trends Biotechnol VL - 22 UR - https://doi.org/10.1016/j.tibtech.2004.09.003 DO - 10.1016/j.tibtech.2004.09.003 ID - Simpson2004 ER -