MPP Publications
From MPPWiki
Here you will find publications by MPP members since August, 2008, when the project formally began. This is an inclusive list for theory, basic research, and applications in the spirit of the MPP -- being on the list does not imply that the research was funded by the MPP.
In reverse-chronological order...
Contents |
2011
- "Neural Network Computation with DNA Strand Displacement Cascades"
- Lulu Qian, Erik Winfree, and Jehoshua Bruck
- Nature 475:368-372, July 21, 2011
- "Structurally robust biological networks"
- Franco Blanchini and Elisa Franco
- BMC Systems Biology 2011, 5:74.
- "Timing molecular motion and production with a synthetic transcriptional clock"
- Elisa Franco, Eike Friedrichs, Jongmin Kim, Ralf Jungmann, Richard M. Murray, Erik Winfree and Friedrich C. Simmel
- PNAS 108:E784-E793, 2011.
- "Analysis and design of a synthetic transcriptional network for exact adaptation"
- Jongmin Kim and Richard M. Murray
- IEEE BioCAS 2011 p.345-348 abstract
- "Bistability of a synthetic autoregulatory switch"
- Pakpoom Subsoontorn, Jongmin Kim and Erik Winfree
- Arxiv preprint (to be submitted).
- "Programmable molecular recognition based on the geometry of DNA nanostructures"
- Sungwook Woo and Paul Rothemund
- Nature Chemistry 3: 620-627, 2011 abstract
- "A biomolecular implementation of linear I/O systems"
- Kevin Oishi and Eric Klavins
- IET Systems Biology 5: 252-260, 2011 abstract
- "Nucleic acid sequence design via efficient ensemble defect optimization"
- Joseph N. Zadeh, Brian R. Wolfe, and Niles A. Pierce
- J Comput Chem 32: 439-452, 2011 abstract
- "NUPACK: Analysis and design of nucleic acid systems"
- Joseph N. Zadeh, Conrad D. Steenberg, Justin S. Bois, Brian R. Wolfe, Marshall B. Pierce, Asif R. Khan, Robert M. Dirks, Niles A. Pierce
- J Comput Chem 32: 170-173, 2011 abstract
- "Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades"
- Lulu Qian and Erik Winfree
- Science 332: 1196-1201, June 3, 2011
- "A simple DNA gate motif for synthesizing large-scale circuits"
- Lulu Qian and Erik Winfree
- Journal of the Royal Society Interface 8: 1281-1297, 2011
- "Synthetic in vitro transcriptional oscillators"
- Jongmin Kim and Erik Winfree
- Molecular Systems Biology 7: 465, February 1, 2011
- "Remote Toehold: A Mechanism for Flexible Control of DNA Hybridization Kinetics"
- Anthony J. Genot, David Yu Zhang, Jonathan Bath, and Andrew J. Turberfield
- J. Am. Chem. Soc. 133: 2177–2182, 2011
- "Dynamic DNA Nanotechnology using Strand Displacement Reactions"
- David Yu Zhang and Georg Seelig
- Nature Chemistry 3: 103-113, 2011
- "Cooperative Hybridization of Oligonucleotides"
- David Yu Zhang
- J. Am. Chem. Soc. 133: 1077-1086, 2011
- "Efficient Turing-universal computation with DNA polymers"
- Lulu Qian, David Soloveichik, Erik Winfree
- DNA Computing and Molecular Programming 16, LNCS 6518: 123-140, 2011
- "Simple Evolution of Complex Crystal Species"
- Rebecca Schulman and Erik Winfree
- DNA Computing and Molecular Programming 16, LNCS 6518: 147-161, 2011
- "Towards Domain-based Sequence Design for DNA Strand Displacement Reactions"
- "DNA-based Fixed Gain Amplifiers and Linear Classifier Circuits"
- David Yu Zhang and Georg Seelig
- DNA Computing and Molecular Programming 16, LNCS 6518: 176-186, 2011
2010
- "Elongational-flow-induced scission of DNA nanotubes in laminar flow"
- Rizal F. Hariadi and Bernard Yurke
- Physical Review E 82: 046307, 2010
- "Programmable in situ amplification for multiplexed imaging of mRNA expression"
- Harry M.T. Choi, Joann Y. Chang, Le A. Trinh, Jennifer E. Padilla, Scott E. Fraser, and N.A. Pierce
- Nature Biotechnology 28:1208–1212 online 31 Oct 2010 (abstract) (supp movie 1) (supp movie 2) (supp info)
- "Selective cell death mediated by small conditional RNAs"
- Suvir Venkataraman, Robert M. Dirks, Christine T. Ueda, and Niles A. Pierce
- PNAS 107(39):16777-16782, 2010 (open access)
- "Tuning a synthetic in vitro oscillator using control-theoretic tools"
- Christopher Sturk, Elisa Franco and Richard M Murray
- 2010 Conference on Decision and Control (CDC)
- "Proportional-Integral Control of Stochastic Gene Regulatory Networks"
- Eric Klavins
- 2010 Conference on Decision and Control (CDC)
- "Approximating Stochastic Biochemical Processes With Wasserstein Pseudometrics"
- David Thorsley and Eric Klavins
- IET Systems Biology 4: 193-211, 2010
- "Model Discrimination of Chemical Reaction Networks by Linearization"
- Daniel Georgiev, Maryam Fazel, Eric Klavins
- To appear at ACC, 2010
- "Diagnosability of Stochastic Chemical Kinetic Systems: A Discrete Event Systems Approach"
- David Thorsley
- To appear at ACC, 2010
- "Molecular robots guided by prescriptive landscapes"
- Kyle Lund, Anthony T. Manzo, Nadine Dabby, Nicole Micholotti, Alexander Johnson-Buck, Jeanette Nangreave, Steven Taylor, Renjun Pei, Milan N. Stojanovic, Nils G. Walter, Erik Winfree, and Hao Yan
- Nature 465: 206-210, May 13, 2010
- "DNA as a Universal Substrate for Chemical Kinetics"
- David Soloveichik, Georg Seelig, and Erik Winfree
- PNAS 107: 5393-5398, online March 4, 2010
- "Robustness and modularity properties of a non-covalent DNA catalytic reaction"
- David Yu Zhang and Erik Winfree
- NAR 38: 4182-4197,online March 1, 2010
- "On the Synthesis of Stochastic Flow Networks"
- Hongchao Zhou, Ho-Lin Chen, Jehoshua Bruck
- Technical Report ETR101, February, 2010
2009
- "Programmable Control of Nucleation for Algorithmic Self-Assembly"
- Rebecca Schulman and Erik Winfree
- SIAM Journal on Computing 39 (4) pages 1581-1616, December 4, 2009
- "Design of insulating devices for in vitro synthetic circuits"
- Elisa Franco, Domitilla Del Vecchio, Richard M. Murray
- Conference on Decision and Control (CDC), pages 4584-4589 December 16-18, 2009
- "Time-Complexity of Multilayered DNA Strand Displacement Circuits"
- Georg Seelig and David Soloveichik
- In LNCS 5877, Springer Berlin / Heidelberg, pages 144-153, November 16, 2009
- "Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates"
- Hareem T. Maune, Si-Ping Han, Robert D. Barish, Marc Bockrath, William A. Goddard III, Paul W. K. Rothemund, Erik Winfree
- Nature Nanotechnology, online, November 8, 2009
- "Control of DNA Strand Displacement Kinetics Using Toehold Exchange"
- David Yu Zhang and Erik Winfree
- JACS, online, November 6, 2009
- "A Theory of Approximation for Stochastic Biochemical Processes"
- David Thorsley and Eric Klavins
- In Control Theory and Systems Biology, Eds. P. A. Iglesias and B. P. Ingalls, MIT Press, pages 243-264, November, 2009
- "DNA as a Universal Substrate for Chemical Kinetics"
- David Soloveichik, Georg Seelig, and Erik Winfree
- In LNCS 5347, Springer Berlin / Heidelberg, pages 57-69, October 6, 2009
- "A simple DNA gate motif for synthesizing large-scale circuits"
- Lulu Qian and Erik Winfree
- In LNCS 5347, Springer Berlin / Heidelberg, pages 70-89, October 6, 2009
- "Placement and orientation of individual DNA shapes on lithographically patterned surfaces"
- RJ Kershner, LD Bozano, CM Micheel, AH Hung, AR Fornof, JN Cha, CT Rettner, M Bersani, J Frommer, PWK Rothemund, GM Wallraff
- Nature Nanotechnology 4: 557-561, August 16, 2009
- "Programmability of Chemical Reaction Networks"
- Matthew Cook, David Soloveichik, Erik Winfree, and Jehoshua Bruck
- In Algorithmic Bioprocesses, Springer Berlin / Heidelberg, Eds. A. Condon, D. Harel, J. N. Kok, A. Salomaa, E. Winfree, pages 543-584, August 14, 2009
- "An Information-Bearing Seed for Nucleating Algorithmic Self-Assembly"
- Robert D. Barish, Rebecca Schulman, Paul W. K. Rothemund, and Erik Winfree
- PNAS 106: 6054-6059, March 24, 2009
- "Robust Stochastic Chemical Reaction Networks and Bounded Tau-Leaping"
- David Soloveichik
- Journal of Computational Biology 16(3): 501-522, March 5, 2009
- "On the Expressability of Stochastic Switching Circuits"
- Hongchao Zhou and Jehoshua Bruck
- Technical Report ETR093, February, 2009
- IEEE Symposium on Information Theory, pages 2061-2065, 2009
- "The Robustness of Stochastic Switching Networks"
- Po-Ling Loh, Hongchao Zhou and Jehoshua Bruck
- Technical Report ETR092, January, 2009 (revised May 1, 2009)
- IEEE Symposium on Information Theory, pages 2066-2070, 2009
2008
- "Design and performance of in vitro transcription rate regulatory circuit"
- Elisa Franco, Richard M. Murray
- Conference on Decision and Control (CDC), December 12-14, 2008
- "Dynamic Allosteric Control of Noncovalent DNA Catalysis Reactions"
- David Yu Zhang and Erik Winfree
- JACS 130:13921–13926, September 20, 2008
- "Stochastic Switching Circuit Synthesis"
- Daniel Wilhelm and Jehoshua Bruck
- Technical Report ETR089, September, 2008 (revised May 19, 2009)
- "Programming DNA Tube Circumferences"
- Peng Yin, Rizal F. Hariadi, Sudheer Sahu, Harry M. T. Choi, Sung Ha Park, Thomas H. LaBean, John H. Reif
- Science 321: 824-826, August 8, 2008
