Browse data: Reference Materials
From Thermodynamics of Computation
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- Bernard Yurke, Andrew J. Turberfield, Allen P. Mills, Friedrich C. Simmel, Jennifer L. Neumann A DNA-fuelled molecular machine made of DNA Nature 406, 605-608 (2000)
- A general purpose RNA-cleaving DNA enzyme ,
- Dana Angluin, James Aspnes, David Eisenstat A simple population protocol for fast robust approximate majority Distributed Computing 21, 87-102 (2008)
- Algorithmic Self-Assembly of DNA Sierpinski Triangles ,
- Hal Abelson, Jacob Beal, Gerald Jay Sussman Amorphous computing Computational Complexity: Theory, Techniques, and Applications 9781461418009, 147-160 (2012)
- Tianqi Song, Sudhanshu Garg, Reem Mokhtar, Hieu Bui, John Reif Analog Computation by DNA Strand Displacement Circuits ACS Synthetic Biology 5, 898-912 (2016)
- Breaking DES Using a Molecular Computer ,
- Arkadiusz Chworos, Isil Severcan, Alexey Y. Koyfman, Patrick Weinkam, Emin Oroudjev, Helen G. Hansma, Luc Jaeger Building programmable jigsaw puzzles with RNA Science 306, 2068-2072 (2004)
- CURRENT OPINION IN STRUCTURAL BIOLOGY ,
- David Soloveichik, Matthew Cook, Erik Winfree, Jehoshua Bruck Computation with finite stochastic chemical reaction networks Natural Computing 7, 615-633 (2008)
- Robert Penchovsky, Ronald R. Breaker Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes Nature Biotechnology 23, 1424-1433 (2005)
- Bradley Hall, Jay R. Hesselberth, Andrew D. Ellington Computational selection of nucleic acid biosensors via a slip structure model Biosensors and Bioelectronics 22, 1939-1947 (2007)
- Jongmin Kim, Kristin S. White, Erik Winfree Construction of an in vitro bistable circuit from synthetic transcriptional switches Molecular Systems Biology 2, (2006)
- David Yu Zhang, Erik Winfree Control of DNA strand displacement kinetics using toehold exchange Journal of the American Chemical Society 131, 17303-17314 (2009)
- Cooperative binding of effectors by an allosteric ribozyme. ,
- Johann Elbaz, Michal Moshe, Bella Shlyahovsky, Itamar Willner Cooperative multicomponent self-assembly of nucleic acid structures for the activation of DNAzyme cascades: A paradigm for DNA sensors and aptasensors Chemistry - A European Journal 15, 3411-3418 (2009)
- DNA COMPUTING ,
- David Soloveichik, Georg Seelig, Erik Winfree DNA as a universal substrate for chemical kinetics (Extended Abstract) Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 5347 LNCS, 57-69 (2009)
- Jeffrey J. Tabor, Matthew Levy, Andrew D. Ellington Deoxyribozymes that recode sequence information Nucleic Acids Research 34, 2166-2172 (2006)
- Ho Lin Chen, David Doty, David Soloveichik Deterministic function computation with chemical reaction networks Natural Computing 13, 517-534 (2014)
- David Yu Zhang, Georg Seelig Dynamic DNA nanotechnology using strand-displacement reactions Nature Chemistry 3, 103-113 (2011)
- Lulu Qian, David Soloveichik, Erik Winfree Efficient turing-universal computation with DNA polymers Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 6518 LNCS, 123-140 (2011)
- Vandana Sharma, Yoko Nomura, Yohei Yokobayashi Engineering complex riboswitch regulation by dual genetic selection Journal of the American Chemical Society 130, 16310-16315 (2008)
- Engineering precision RNA molecular switches ,
- Niranjan Srinivas, James Parkin, Georg Seelig, Erik Winfree, David Soloveichik Enzyme-free nucleic acid dynamical systems Science 358, (2017)
- Exponential growth by cross-catalytic cleavage of deoxyribozymogens. ,
- Alexander Dobrinevski, Erwin Frey Extinction in neutrally stable stochastic Lotka-Volterra models Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 85, (2012)
- Juewen Liu, Zehui Cao, Yi Lu Functional nucleic acid sensors Chemical Reviews 109, 1948-1998 (2009)
- Xiaohong Cheng, Xiangjun Liu, Tao Bing, Zehui Cao, Dihua Shangguan General peroxidase activity of G-quadruplex-hemin complexes and its application in ligand screening Biochemistry 48, 7817-7823 (2009)
- Shawn K. Desai, Justin P. Gallivan Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation Journal of the American Chemical Society 126, 13247-13254 (2004)
- Information Theory, Inference and Learning Algorithms ,
- David Doty, Monir Hajiaghayi Leaderless deterministic chemical reaction networks Natural Computing 14, 213-223 (2015)
- Bella Shlyahovsky, Yang Li, Oleg Lioubashevski, Johann Elbaz, Itamar Willner Logic gates and antisense DNA devices operating on a translator nucleic acid scaffold ACS Nano 3, 1831-1843 (2009)
- Modelling amorphous computations with transcription networks ,
- Matthew R. Lakin, Darko Stefanovic, Andrew Phillips Modular verification of chemical reaction network encodings via serializability analysis Theoretical Computer Science 632, 21-42 (2016)
- Molecular computation of solutions to combinatorial problems ,
- Luca Cardelli Morphisms of reaction networks that couple structure to function BMC Systems Biology 8, (2014)
- Yaakov Benenson, Tamar Paz-Elizur, Rivka Adar, Ehud Keinan, Zvi Llvneh, Ehud Shapiro Programmable and autonomous computing machine made of biomolecules Nature 414, 430-434 (2001)
- Yuan Jyue Chen, Neil Dalchau, Niranjan Srinivas, Andrew Phillips, Luca Cardelli, David Soloveichik, Georg Seelig Programmable chemical controllers made from DNA Nature Nanotechnology 8, 755-762 (2013)
- Programmable chemical reaction networks: emulating regulatory functions in living cells using a bottom-up approach ,
- Travis S. Bayer, Christina D. Smolke Programmable ligand-controlled riboregulators of eukaryotic gene expression Nature Biotechnology 23, 337-343 (2005)
- Ravinderjit S. Braich, Nickolas Chelyapov, Cliff Johnson, Paul W.K. Rothemund, Leonard Adleman Solution of a 20-variable 3-SAT problem on a DNA computer Science 296, 499-502 (2002)
- Stably computable predicates are semilinear ,
- M. Antoniotti, C. Piazza, A. Policriti, M. Simeoni, B. Mishra Taming the complexity of biochemical models through bisimulation and collapsing: Theory and practice Theoretical Computer Science 325, 45-67 (2004)
- Luca Cardelli, Attila Csikász-Nagy The cell cycle switch computes approximate majority Scientific Reports 2, (2012)
- Michael Lachmann, Guy Sella The computationally complete ant colony: Global coordination in a system with no hierarchy Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 929, 784-800 (1995)
- Priscilla E.M. Purnick, Ron Weiss The second wave of synthetic biology: From modules to systems Nature Reviews Molecular Cell Biology 10, 410-422 (2009)
- Triggered amplification by hybridization chain reaction ,
- Two-Domain DNA Strand Displacement ,
- Pier Luigi Gentili Untangling Complex Systems: A Grand Challenge for Science , (2018)
- Seung Woo Shin, Chris Thachuk, Erik Winfree Verifying chemical reaction network implementations: A pathway decomposition approach Theoretical Computer Science 765, 67-96 (2019)
- Matthew R. Lakin, Simon Youssef, Filippo Polo, Stephen Emmott, Andrew Phillips Visual DSD: A design and analysis tool for DNA strand displacement systems Bioinformatics 27, 3211-3213 (2011)
