Biomod/2011/Caltech/DeoxyriboNucleicAwesome/References

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Monday, December 29, 2014

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References

Contents

Referenced Papers

Alphabetical by First Author

A

  • Ahmed El-Shehawy (1992). On absorption probabilities for a random walk between two different barriers. Annals De La Faculte Des Sciences De Toulouse, 1(1), 95-103.
  • Alessandro Blasi (1976). On a Random Walk Between a Reflecting and an Absorbing Barrier. The Annals of Probability, 4(4), 695-696.

B

  • Baker, B. A., & Milam, V. T. . (2011). Hybridization kinetics between immobilized double-stranded DNA probes and targets containing empedded recognition segments. Nucleic Acids Research, 1-13.
  • Bath, J., Green, S. J, Allen, K. E., & Tuberfield, A. J. (2009). Mechanism for a directional, processive, and reversible DNA motor. Small, 5(13), 1513-1516.
  • Bonnet, G., Krichevsky, O., & Libchaber, A. (1998). Kinetics of conformational fluctuations in DNA haripin-loops. PNAS, 95, 8602-8606.

D

  • Dirks, R. M. , Lin, M., Winfree, E., & Pierce, N. A. (2004). Sensitive fluorescence-based thermodynamic and kinetic measurements of DNA hybridization in solutions. Nucleic Acids Research, 32(4), 1392-1403.

F

  • Feller, W. (1971). An introduction to probability theory and its applications.
  • Fujibayashi, K., Hariadi, R., Park, S. H., Winfree, E., & Murata, S. (2007). Toward relaible algorithmic self-assembly of DNA tiles: a fixed-width cellular automaton pattern. Nano Letters, 8(7), 1791-1797.

G

  • Gu, H. , Chao, J., Xiao, S., & Seeman, N. C. (2010). A proximity-based programmable DNA nanoscale assembly line. Nature, 465, 202-205.

H

  • Hardin, J. C., & Sweet, A. L. (1969). A Note on Absorption Probabilities for a Random Walk between a Reflecting and an Absorbing Barrier. Journal of Applied Probability, 6(1), 224-226.

L

  • Lund, K., Manzo, A. J., Dabby, N., Michelotti, N., Johnson-Buck, A., & Nangreave, J., et al. (2010). Molecular robots guided by prescriptive landscapes. Nature, 465(7295), 206-210.

M

  • Morrison, L. E. , & Stols, L. M. . (1993). Sensitive fluorescence-based thermodynamic and kinetic measurements of DNA hybridization in solutions. Biochemestry, 32, 3095-3104.
  • Muscat, R. A. , Bath, J., & Tuberfield, A. J. (2011). A programmable molecular robot. Nano Letters, 11, 982-987.

N

  • Netus, M. (1963). Absorption probabilities for a random walk between a reflecting and an absorbing barrier. Bull. Soc. Math. Belgique, 15, 253-258.

P

  • Penchovsky, R., & Breaker, R. R. (2005). Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes. Nature Biotechnology, 23(11), 1424-1433.

Q

  • Qian, L., & Winfree, E. (2011). Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades. Science, 332(6034), 1196.

R

  • Rothemund, P. W. K. (2006). Folding DNA to create nanoscale shapes and patterns. Nature, 440(7082), 297-302.

S

  • SantaLucia, J. (1998). A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. PNAS, 95, 1460-1465.
  • Seelig, G., Soloveichik, D., Zhang, D. Y., & Winfree, E. (2006). Enzyme-free nucleic acid logic circuits. Science, 314(5805), 1585-1588.
  • Seeman, N. C., & Kallenbach, N. R. (1983). Design of immobile nucleic acid junctions. Biophysical Journal, 44(2), 201-209.

V

  • Venkataraman, S., Dirks, R. M, Rothemund, P. W. K., Winfree, E., & Pierce, N. A. (2007). An autonomous polymerization motor powered by DNA hybridization. Nature Nanotechnology, 1-5.

W

  • Wang, Z., Elbaz, J., Remacle, F., Levine, R. D., & Willner, I. (2010). All-DNA finite-state automata with finite memory. PNAS, 107(51), 21996-22001.
  • Weesakul, B. (1961). The random walk between a reflecting and an absorbing barrier. The Annals of Mathematical Statistics, 32(3), 765-765.
  • Wetmur, J. G. (1991). DNA probes: applications of the principles of nucleic acid hybridization. Critical Reviews in Biochemistry and Molecular Biology, 26(3/4), 227-259.
  • Wickham, S. F. J., Endo, M., Katsuda, Y., Hidaka, K., Bath, J., Sugiyama, H., & Tuberfield, A. J. (2010). Direct observation of stepwise movement of a synthetic molecular transporter. Nature Nanotechnology, 6, 166–169.
  • Winfree, E., Liu, F., Wenzler, L. A., & Seeman, N. C. (1998). Design and self-assembly of two-dimensional DNA crystals. Nature, 394(6693), 539-544.

Z

  • Zadeh, J. N., Steenberg, C. D., Bois, J. S., Wolfe, B. R., Pierce, M. B., & Khan, A. R., et al. (2011). NUPACK Analysis and design of nucleic acid systems. Journal of Computational Chemistry, 32(1), 170-173.
  • Zhang, D. Y., & Winfree, E. (2009). Control of DNA strand displacement kinetics using toehold exchange. JACS, 131, 17303-17314.


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