Biomod/2011/Caltech/DeoxyriboNucleicAwesome/References - Revision history

Zibo Chen: /* References */

2011-10-02T11:43:04Z

References

←Older revision		Revision as of 11:43, 2 October 2011
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	==Referenced Papers==		==Referenced Papers==
	:''Alphabetical by First Author''		:''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===		===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.		*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.
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	*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.		*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===		===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.		*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===		===G===
	*Gu, H. , Chao, J., Xiao, S., & Seeman, N. C. (2010). A proximity-based programmable DNA nanoscale assembly line. ''Nature, 465,'' 202-205.		*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===		===M===
	*Morrison, L. E. , & Stols, L. M. . (1993). Sensitive fluorescence-based thermodynamic and kinetic measurements of DNA hybridization in solutions. ''Biochemestry, 32,'' 3095-3104.		*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.		*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===		===S===
	*SantaLucia, J. (1998). A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. ''PNAS, 95,'' 1460-1465.		*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===		===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.		*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===		===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.		*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.		*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.		*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===		===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.		*Zhang, D. Y., & Winfree, E. (2009). Control of DNA strand displacement kinetics using toehold exchange. ''JACS, 131,'' 17303-17314.
	<br>		<br>

Sarah Wittman: /* Useful Links */

2011-06-22T17:15:10Z

Useful Links

←Older revision		Revision as of 17:15, 22 June 2011
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	==Useful Links==		==Useful Links==
-	[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Format\|DeoxyriboNucleicAwesome Wiki Page Format Guide]]	+	*[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Format\|DeoxyriboNucleicAwesome Wiki Page Format Guide]]
	*[http://en.wikipedia.org/wiki/Wikipedia:Cheatsheet Wiki Editing Cheatsheet]		*[http://en.wikipedia.org/wiki/Wikipedia:Cheatsheet Wiki Editing Cheatsheet]
	*[http://en.wikipedia.org/wiki/Help:Contents Wiki Help Navigator]		*[http://en.wikipedia.org/wiki/Help:Contents Wiki Help Navigator]

Sarah Wittman: /* Useful Links */

2011-06-22T17:14:52Z

Useful Links

←Older revision		Revision as of 17:14, 22 June 2011
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	==Useful Links==		==Useful Links==
		+	[[Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Format\|DeoxyriboNucleicAwesome Wiki Page Format Guide]]
	*[http://en.wikipedia.org/wiki/Wikipedia:Cheatsheet Wiki Editing Cheatsheet]		*[http://en.wikipedia.org/wiki/Wikipedia:Cheatsheet Wiki Editing Cheatsheet]
	*[http://en.wikipedia.org/wiki/Help:Contents Wiki Help Navigator]		*[http://en.wikipedia.org/wiki/Help:Contents Wiki Help Navigator]

Sarah Wittman at 21:22, 21 June 2011

2011-06-21T21:22:09Z

←Older revision		Revision as of 21:22, 21 June 2011
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	==Referenced Papers==		==Referenced Papers==
	:''Alphabetical by First Author''		:''Alphabetical by First Author''
-	~~<br>~~
	===B===		===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.		*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.

Sarah Wittman: /* Referenced Papers */

2011-06-21T21:05:00Z

Referenced Papers

←Older revision		Revision as of 21:05, 21 June 2011
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	<br>		<br>
	===B===		===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.	+	*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.
-	*Bonnet, G., Krichevsky, O., & Libchaber, A. (1998). Kinetics of conformational fluctuations in ~~dna~~ haripin-loops. ''PNAS, 95,'' 8602-8606.	+	*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===		===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.	+	*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===
		+	*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===		===G===
-	*Gu, H. , Chao, J., Xiao, S., & Seeman, N. C. (2010). A proximity-based programmable ~~dna~~ nanoscale assembly line. ''Nature, 465,'' 202-205.	+	*Gu, H. , Chao, J., Xiao, S., & Seeman, N. C. (2010). A proximity-based programmable DNA nanoscale assembly line. ''Nature, 465,'' 202-205.
	===M===		===M===
-	*Morrison, L. E. , & Stols, L. M. . (1993). Sensitive fluorescence-based thermodynamic and kinetic measurements of ~~dna~~ hybridization in solutions. ''Biochemestry, 32,'' 3095-3104.	+	*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.		*Muscat, R. A. , Bath, J., & Tuberfield, A. J. (2011). A programmable molecular robot. ''Nano Letters, 11,'' 982-987.
	===S===		===S===
-	*SantaLucia, J. (1998). A unified view of polymer, dumbbell, and oligonucleotide ~~dna~~ nearest-neighbor thermodynamics. ''PNAS, 95,'' 1460-1465.	+	*SantaLucia, J. (1998). A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. ''PNAS, 95,'' 1460-1465.
		+	===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===		===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.	+	*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.
-	*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.	+	*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.		*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.
		+	===Z===
		+	*Zhang, D. Y., & Winfree, E. (2009). Control of DNA strand displacement kinetics using toehold exchange. ''JACS, 131,'' 17303-17314.
	<br>		<br>

Sarah Wittman at 20:46, 21 June 2011

2011-06-21T20:46:29Z

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Sarah Wittman at 20:46, 21 June 2011

2011-06-21T20:46:18Z

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	:''Alphabetical by First Author''		:''Alphabetical by First Author''

Sarah Wittman at 20:23, 21 June 2011

2011-06-21T20:23:49Z

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Sarah Wittman at 20:23, 21 June 2011

2011-06-21T20:23:35Z

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	==Referenced Papers==		==Referenced Papers==
	:''Alphabetical by First Author''		:''Alphabetical by First Author''

Sarah Wittman at 20:23, 21 June 2011

2011-06-21T20:23:01Z

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		+	=References=
	==Referenced Papers==		==Referenced Papers==
	:''Alphabetical by First Author''		:''Alphabetical by First Author''