-
1
-
-
33745454125
-
Synthetic biology: New engineering rules for an emerging discipline
-
20060028
-
Andrianantoandro, E., Basu, S., Karig, D. K., and Weiss, R. (2006) Synthetic biology: New engineering rules for an emerging discipline. Mol. Syst. Biol. 2, No. 2006.0028.
-
(2006)
Mol. Syst. Biol.
, vol.2
-
-
Andrianantoandro, E.1
Basu, S.2
Karig, D.K.3
Weiss, R.4
-
2
-
-
21344458620
-
Synthetic biology
-
DOI 10.1038/nrg1637
-
Benner, S. A., and Sismour, A. M. (2005) Synthetic biology. Nat. Rev. Genet. 6, 533-543. (Pubitemid 40910430)
-
(2005)
Nature Reviews Genetics
, vol.6
, Issue.7
, pp. 533-543
-
-
Benner, S.A.1
Sismour, A.M.2
-
3
-
-
77951107086
-
Synthetic biology: Applications come of age
-
Khalil, A. S., and Collins, J. J. (2010) Synthetic biology: Applications come of age. Nat. Rev. Genet. 11, 367-379.
-
(2010)
Nat. Rev. Genet.
, vol.11
, pp. 367-379
-
-
Khalil, A.S.1
Collins, J.J.2
-
4
-
-
28544451327
-
Foundations for engineering biology
-
DOI 10.1038/nature04342, PII N04342
-
Endy, D. (2005) Foundations for engineering biology. Nature 438, 449-453. (Pubitemid 41742010)
-
(2005)
Nature
, vol.438
, Issue.7067
, pp. 449-453
-
-
Endy, D.1
-
6
-
-
0033169046
-
Biotechnology as a route to nanotechnology
-
DOI 10.1016/S0167-7799(99)01335-9, PII S0167779999013359
-
Merkle, R. C. (1999) Biotechnology as a route to nanotechnology. Trends Biotechnol. 17, 271-274. (Pubitemid 29287248)
-
(1999)
Trends in Biotechnology
, vol.17
, Issue.7
, pp. 271-274
-
-
Merkle, R.C.1
-
7
-
-
77953310230
-
Structural DNA nanotechnology: Growing along with nano letters
-
Seeman, N. C. (2010) Structural DNA nanotechnology: Growing along with Nano Letters. Nano Lett. 10, 1971-1978.
-
(2010)
Nano Lett.
, vol.10
, pp. 1971-1978
-
-
Seeman, N.C.1
-
8
-
-
10044298236
-
Reductionism and complexity in molecular biology
-
Regenmortel, M. V. (2004) Reductionism and complexity in molecular biology. EMBO Rep. 5, 1016-1020.
-
(2004)
EMBO Rep.
, vol.5
, pp. 1016-1020
-
-
Regenmortel, M.V.1
-
9
-
-
77949479491
-
So what do we really mean when we say that systems biology is holistic?
-
Gatherer, D. (2010) So what do we really mean when we say that systems biology is holistic? BMC Syst. Biol. 4, 22.
-
(2010)
BMC Syst. Biol.
, vol.4
, pp. 22
-
-
Gatherer, D.1
-
10
-
-
78650334784
-
Build life to understand it
-
Elowitz, M., and Lim, W. A. (2010) Build life to understand it. Nature 468, 889-890.
-
(2010)
Nature
, vol.468
, pp. 889-890
-
-
Elowitz, M.1
Lim, W.A.2
-
11
-
-
33646582649
-
RNA synthetic biology
-
Isaacs, F. J., Dwyer, D. J., and Collins, J. J. (2006) RNA synthetic biology. Nat. Biotechnol. 24, 545-554.
-
(2006)
Nat. Biotechnol.
, vol.24
, pp. 545-554
-
-
Isaacs, F.J.1
Dwyer, D.J.2
Collins, J.J.3
-
12
-
-
77952903892
-
Rewiring cells: Synthetic biology as a tool to interrogate the organizational principles of living systems
-
Bashor, C. J., Horwitz, A. A., Peisajovich, S. G., and Lim, W. A. (2010) Rewiring cells: Synthetic biology as a tool to interrogate the organizational principles of living systems. Annu. Rev. Biophys. 39, 515-537.
-
(2010)
Annu. Rev. Biophys.
, vol.39
, pp. 515-537
-
-
Bashor, C.J.1
Horwitz, A.A.2
Peisajovich, S.G.3
Lim, W.A.4
-
13
-
-
75149167486
-
Five hard truths for synthetic biology
-
Kwok, R. (2010) Five hard truths for synthetic biology. Nature 463, 288-290.
-
(2010)
Nature
, vol.463
, pp. 288-290
-
-
Kwok, R.1
-
14
-
-
83255164998
-
Cell-free synthetic biology: Thinking outside the cell
-
Hodgman, C. E., and Jewett, M. C. (2012) Cell-free synthetic biology: Thinking outside the cell. Metab. Eng. 14, 261-269.
-
(2012)
Metab. Eng.
, vol.14
, pp. 261-269
-
-
Hodgman, C.E.1
Jewett, M.C.2
-
15
-
-
84899469245
-
Breaking down complexity
-
Rondelez, Y. (2011) Breaking down complexity. Physics 4, 8.
-
(2011)
Physics
, vol.4
, pp. 8
-
-
Rondelez, Y.1
-
16
-
-
0034904102
-
Cell-free translation reconstituted with purified components
-
DOI 10.1038/90802
-
Shimizu, Y., Inoue, A., Tomari, Y., Suzuki, T., Yokogawa, T., Nishikawa, K., and Ueda, T. (2001) Cell-free translation reconstituted with purified components. Nat. Biotechnol. 19, 751-755. (Pubitemid 32729537)
-
(2001)
Nature Biotechnology
, vol.19
, Issue.8
, pp. 751-755
-
-
Shimizu, Y.1
Inoue, A.2
Tomari, Y.3
Suzuki, T.4
Yokogawa, T.5
Nishikawa, K.6
Ueda, T.7
-
17
-
-
0242268453
-
Principles of cell-free genetic circuit assembly
-
DOI 10.1073/pnas.2135496100
-
Noireaux, V., Bar-Ziv, R., and Libchaber, A. (2003) Principles of cell-free genetic circuit assembly. Proc. Natl. Acad. Sci. U.S.A. 100, 12672-12677. (Pubitemid 37339957)
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.22
, pp. 12672-12677
-
-
Noireaux, V.1
Bar-Ziv, R.2
Libchaber, A.3
-
18
-
-
26944433403
-
Toward an artificial cell based on gene expression in vesicles
-
Noireaux, V., Bar-Ziv, R., Godefroy, J., Salman, H., and Libchaber, A. (2005) Toward an artificial cell based on gene expression in vesicles. Phys. Biol. 2 (3), 1-8.
-
(2005)
Phys. Biol.
, vol.2
, Issue.3
, pp. 1-8
-
-
Noireaux, V.1
Bar-Ziv, R.2
Godefroy, J.3
Salman, H.4
Libchaber, A.5
-
19
-
-
23044504786
-
Protein synthesis by pure translation systems
-
DOI 10.1016/j.ymeth.2005.04.006, PII S1046202305000897, Engineering Translation
-
Shimizu, Y., Kanamori, T., and Ueda, T. (2005) Protein synthesis by pure translation systems. Methods 36, 299-304. (Pubitemid 41074961)
-
(2005)
Methods
, vol.36
, Issue.3
, pp. 299-304
-
-
Shimizu, Y.1
Kanamori, T.2
Ueda, T.3
-
20
-
-
53949093950
-
An integrated cell-free metabolic platform for protein production and synthetic biology
-
Jewett, M. C., Calhoun, K. A., Voloshin, A., Wuu, J. J., and Swartz, J. R. (2008) An integrated cell-free metabolic platform for protein production and synthetic biology. Mol. Syst. Biol. 4, 220.
-
(2008)
Mol. Syst. Biol.
, vol.4
, pp. 220
-
-
Jewett, M.C.1
Calhoun, K.A.2
Voloshin, A.3
Wuu, J.J.4
Swartz, J.R.5
-
21
-
-
79952775158
-
Development of an artificial cell, from self-organization to computation and selfreproduction
-
Noireaux, V., Maeda, Y., and Libchaber, A. (2011) Development of an artificial cell, from self-organization to computation and selfreproduction. Proc. Natl. Acad. Sci. U.S.A. 108, 3473-3480.
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 3473-3480
-
-
Noireaux, V.1
Maeda, Y.2
Libchaber, A.3
-
22
-
-
79251480753
-
Coarse-grained dynamics of protein synthesis in a cell-free system
-
Karzbrun, E., Shin, J., Bar-Ziv, R., and Noireaux, V. (2011) Coarse-grained dynamics of protein synthesis in a cell-free system. Phys. Rev. Lett. 106, 048104.
-
(2011)
Phys. Rev. Lett.
, vol.106
, pp. 048104
-
-
Karzbrun, E.1
Shin, J.2
Bar-Ziv, R.3
Noireaux, V.4
-
23
-
-
84860375823
-
Expression optimization and synthetic gene networks in cell-free systems
-
Karig, D. K., Iyer, S., Simpson, M. L., and Doktycz, M. J. (2012) Expression optimization and synthetic gene networks in cell-free systems. Nucleic Acids Res. 40, 3763-3774.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 3763-3774
-
-
Karig, D.K.1
Iyer, S.2
Simpson, M.L.3
Doktycz, M.J.4
-
24
-
-
84863610029
-
An E. coli cell-free expression toolbox: Application to synthetic gene circuits and artificial cells
-
Shin, J., and Noireaux, V. (2012) An E. coli cell-free expression toolbox: Application to synthetic gene circuits and artificial cells. ACS Synth. Biol. 1, 29-41.
-
(2012)
ACS Synth. Biol.
, vol.1
, pp. 29-41
-
-
Shin, J.1
Noireaux, V.2
-
25
-
-
0030887814
-
A molecular predator and its prey: Coupled isothermal amplification of nucleic acids
-
Wlotzka, B., and McCaskill, J. S. (1997) A molecular predator and its prey: Coupled isothermal amplification of nucleic acids. Chem. Biol. 4, 25-33. (Pubitemid 27158643)
-
(1997)
Chemistry and Biology
, vol.4
, Issue.1
, pp. 25-33
-
-
Wlotzka, B.1
McCaskill, J.S.2
-
26
-
-
0035936116
-
Programmable and autonomous computing machine made of biomolecules
-
DOI 10.1038/35106533
-
Benenson, Y., Paz-Elizur, T., Adar, R., Keinan, E., Livneh, Z., and Shapiro, E. (2001) Programmable and autonomous computing machine made of biomolecules. Nature 414, 430-434. (Pubitemid 34173721)
-
(2001)
Nature
, vol.414
, Issue.6862
, pp. 430-434
-
-
Benenson, Y.1
Paz-Elizur, T.2
Adar, R.3
Keinan, E.4
Llvneh, Z.5
Shapiro, E.6
-
27
-
-
2642555548
-
An autonomous molecular computer for logical control of gene expression
-
DOI 10.1038/nature02551
-
Benenson, Y., Gil, B., Ben-Dor, U., Adar, R., and Shapiro, E. (2004) An autonomous molecular computer for logical control of gene expression. Nature 429, 423-429. (Pubitemid 38715134)
-
(2004)
Nature
, vol.429
, Issue.6990
, pp. 423-429
-
-
Benenson, Y.1
Gil, B.2
Ben-Dor, U.3
Adar, R.4
Shapiro, E.5
-
28
-
-
17244373578
-
Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro
-
DOI 10.1126/science.1108451
-
Nakajima, M., Imai, K., Ito, H., Nishiwaki, T., Murayama, Y., Iwasaki, H., Oyama, T., and Kondo, T. (2005) Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro. Science 308, 414-415. (Pubitemid 40530079)
-
(2005)
Science
, vol.308
, Issue.5720
, pp. 414-415
-
-
Nakajima, M.1
Imai, K.2
Ito, H.3
Nishiwaki, T.4
Murayama, Y.5
Iwasaki, H.6
Oyama, T.7
Kondo, T.8
-
29
-
-
67650666435
-
Modelling amorphous computations with transcription networks
-
Simpson, Z. B., Tsai, T. L., Nguyen, N., Chen, X., and Ellington, A. D. (2009) Modelling amorphous computations with transcription networks. J. R. Soc. Interface 6, S523-S533.
-
(2009)
J. R. Soc. Interface
, vol.6
-
-
Simpson, Z.B.1
Tsai, T.L.2
Nguyen, N.3
Chen, X.4
Ellington, A.D.5
-
30
-
-
84255209210
-
RTRACS: A modularized RNA-dependent RNA transcription system with high programmability
-
Ayukawa, S., Takinoue, M., and Kiga, D. (2011) RTRACS: A modularized RNA-dependent RNA transcription system with high programmability. Acc. Chem. Res. 44, 1369-1379.
-
(2011)
Acc. Chem. Res.
, vol.44
, pp. 1369-1379
-
-
Ayukawa, S.1
Takinoue, M.2
Kiga, D.3
-
31
-
-
79551586208
-
Programming an in vitro DNA oscillator using a molecular networking strategy
-
Montagne, K., Plasson, R., Sakai, Y., Fujii, T., and Rondelez, Y. (2011) Programming an in vitro DNA oscillator using a molecular networking strategy. Mol. Syst. Biol. 7, 466.
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 466
-
-
Montagne, K.1
Plasson, R.2
Sakai, Y.3
Fujii, T.4
Rondelez, Y.5
-
32
-
-
33845411737
-
Enzyme-free nucleic acid logic circuits
-
DOI 10.1126/science.1132493
-
Seelig, G., Soloveichik, D., Zhang, D. Y., and Winfree, E. (2006) Enzyme-free nucleic acid logic circuits. Science 314, 1585-1588. (Pubitemid 44907149)
-
(2006)
Science
, vol.314
, Issue.5805
, pp. 1585-1588
-
-
Seelig, G.1
Soloveichik, D.2
Zhang, D.Y.3
Winfree, E.4
-
33
-
-
36248972215
-
Engineering entropy-driven reactions and networks catalyzed by DNA
-
DOI 10.1126/science.1148532
-
Zhang, D. Y., Turberfield, A. J., Yurke, B., and Winfree, E. (2007) Engineering entropy-driven reactions and networks catalyzed by DNA. Science 318, 1121-1125. (Pubitemid 350134891)
-
(2007)
Science
, vol.318
, Issue.5853
, pp. 1121-1125
-
-
Zhang, D.Y.1
Turberfield, A.J.2
Yurke, B.3
Winfree, E.4
-
34
-
-
77950444491
-
DNA as a universal substrate for chemical kinetics
-
Soloveichik, D., Seelig, G., and Winfree, E. (2010) DNA as a universal substrate for chemical kinetics. Proc. Natl. Acad. Sci. U.S.A. 107, 5393-5398.
-
(2010)
Proc. Natl. Acad. Sci. U.S.A.
, vol.107
, pp. 5393-5398
-
-
Soloveichik, D.1
Seelig, G.2
Winfree, E.3
-
35
-
-
79960650829
-
Neural network computation with DNA strand displacement cascades
-
Qian, L., Winfree, E., and Bruck, J. (2011) Neural network computation with DNA strand displacement cascades. Nature 475, 368-372.
-
(2011)
Nature
, vol.475
, pp. 368-372
-
-
Qian, L.1
Winfree, E.2
Bruck, J.3
-
36
-
-
33846095183
-
Neural network computation by in vitro transcriptional circuits
-
MIT Press, Cambridge, MA
-
Kim, J., Hopfield, J. J., and Winfree, E. (2004) Neural network computation by in vitro transcriptional circuits. Advances in Neural Information Processing Systems (NIPS), Vol. 17, pp 681-688, MIT Press, Cambridge, MA.
-
(2004)
Advances in Neural Information Processing Systems (NIPS)
, vol.17
, pp. 681-688
-
-
Kim, J.1
Hopfield, J.J.2
Winfree, E.3
-
37
-
-
33846116559
-
Construction of an in vitro bistable circuit from synthetic transcriptional switches
-
Kim, J., White, K. S., and Winfree, E. (2006) Construction of an in vitro bistable circuit from synthetic transcriptional switches. Mol. Syst. Biol. 2, 68.
-
(2006)
Mol. Syst. Biol.
, vol.2
, pp. 68
-
-
Kim, J.1
White, K.S.2
Winfree, E.3
-
38
-
-
79551599731
-
Synthetic in vitro transcriptional oscillators
-
Kim, J., and Winfree, E. (2011) Synthetic in vitro transcriptional oscillators. Mol. Syst. Biol. 7, 465.
-
(2011)
Mol. Syst. Biol.
, vol.7
, pp. 465
-
-
Kim, J.1
Winfree, E.2
-
39
-
-
80053650824
-
Timing molecular motion and production with a synthetic transcriptional clock
-
Franco, E., Friedrichs, E., Kim, J., Jungmann, R., Murray, R., Winfree, E., and Simmel, F. C. (2011) Timing molecular motion and production with a synthetic transcriptional clock. Proc. Natl. Acad. Sci. U.S.A. 108, E784-E793.
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
-
-
Franco, E.1
Friedrichs, E.2
Kim, J.3
Jungmann, R.4
Murray, R.5
Winfree, E.6
Simmel, F.C.7
-
40
-
-
14844358192
-
Ultrasensitivity and noise propagation in a synthetic transcriptional cascade
-
DOI 10.1073/pnas.0408507102
-
Hooshangi, S., Thiberge, S., and Weiss, R. (2005) Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. Proc. Natl. Acad. Sci. U.S.A. 102, 3581-3586. (Pubitemid 40354655)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.10
, pp. 3581-3586
-
-
Hooshangi, S.1
Thiberge, S.2
Weiss, R.3
-
41
-
-
0034632783
-
A DNA-fuelled molecular machine made of DNA
-
DOI 10.1038/35020524
-
Yurke, B., Turberfield, A., Mills, A., Jr, Simmel, F., and Neumann, J. (2000) A DNA-fuelled molecular machine made of DNA. Nature 406, 605-608. (Pubitemid 30641042)
-
(2000)
Nature
, vol.406
, Issue.6796
, pp. 605-608
-
-
Yurke, B.1
Turberfield, A.J.2
Mills Jr., A.P.3
Simmel, F.C.4
Neumann, J.L.5
-
42
-
-
0023198428
-
Kinetic analysis of T7 RNA polymerase-promoter interactions with small synthetic promoters
-
DOI 10.1021/bi00384a006
-
Martin, C. T., and Coleman, J. E. (1987) Kinetic analysis of T7 RNA polymerase-promoter interactions with small synthetic promoters. Biochemistry 26, 2690-2696. (Pubitemid 17084639)
-
(1987)
Biochemistry
, vol.26
, Issue.10
, pp. 2690-2696
-
-
Martin, C.T.1
Coleman, J.E.2
-
43
-
-
3543133526
-
Using DNA to power nanostructures
-
DOI 10.1023/A:1023928811651
-
Yurke, B., and Mills, A. P., Jr. (2003) Using DNA to power nanostructures. Genetic Program. Evolvable Machines 4, 111-122. (Pubitemid 36768091)
-
(2003)
Genetic Programming and Evolvable Machines
, vol.4
, Issue.2
, pp. 111-122
-
-
Yurke, B.1
Mills Jr., A.P.2
-
44
-
-
72249110882
-
Control of DNA strand displacement kinetics using toehold exchange
-
Zhang, D. Y., and Winfree, E. (2009) Control of DNA strand displacement kinetics using toehold exchange. J. Am. Chem. Soc. 131, 17303-17314.
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 17303-17314
-
-
Zhang, D.Y.1
Winfree, E.2
-
45
-
-
0030735085
-
Cleavage of single strand RNA adjacent to RNA-DNA duplex regions by Escherichia coli RNase H1
-
DOI 10.1074/jbc.272.44.27513
-
Lima, W. F., and Crooke, S. T. (1997) Cleavage of single strand RNA adjacent to RNA-DNA duplex regions by Escherichia coli RNase H1. J. Biol. Chem. 272, 27513-27516. (Pubitemid 27473536)
-
(1997)
Journal of Biological Chemistry
, vol.272
, Issue.44
, pp. 27513-27516
-
-
Lima, W.F.1
Crooke, S.T.2
-
46
-
-
0037077311
-
Purification and characterization of the Escherichia coli exoribonuclease RNase R. Comparison with RNase II
-
DOI 10.1074/jbc.M202942200
-
Cheng, Z.-F., and Deutscher, M. P. (2002) Purification and characterization of the Escherichia coli exoribonuclease RNase R. J. Biol. Chem. 277, 21624-21629. (Pubitemid 34952311)
-
(2002)
Journal of Biological Chemistry
, vol.277
, Issue.24
, pp. 21624-21629
-
-
Cheng, Z.-F.1
Deutscher, M.P.2
-
47
-
-
34249772381
-
Fast folding and comparison of RNA secondary structures
-
Hofacker, I. L., Fontana, W., Stadler, P., Bonhoeffer, L., Tacker, M., and Schuster, P. (1994) Fast folding and comparison of RNA secondary structures. Monatsh. Chem. 125, 167-188.
-
(1994)
Monatsh. Chem.
, vol.125
, pp. 167-188
-
-
Hofacker, I.L.1
Fontana, W.2
Stadler, P.3
Bonhoeffer, L.4
Tacker, M.5
Schuster, P.6
-
48
-
-
0020373595
-
Nucleic-acid junctions and lattices
-
Seeman, N. C. (1982) Nucleic-acid junctions and lattices. J. Theor. Biol. 99, 237-247.
-
(1982)
J. Theor. Biol.
, vol.99
, pp. 237-247
-
-
Seeman, N.C.1
-
49
-
-
0025635653
-
De novo design of sequences for nucleic acid structural engineering
-
Seeman, N. C. (1990) De novo design of sequences for nucleic acid structural engineering. J. Biomol. Struct. Dyn. 8, 573-581.
-
(1990)
J. Biomol. Struct. Dyn.
, vol.8
, pp. 573-581
-
-
Seeman, N.C.1
-
50
-
-
0028924624
-
Self-coded 3′-extension of run-off transcripts produces abberant products during in vitro transcription with T7 RNA polymerase
-
Triana-Alonso, F. J., Dabrowski, M., Wadzack, J., and Nierhaus, K. H. (1995) Self-coded 3′-extension of run-off transcripts produces abberant products during in vitro transcription with T7 RNA polymerase. J. Biol. Chem. 270, 6298-6307.
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 6298-6307
-
-
Triana-Alonso, F.J.1
Dabrowski, M.2
Wadzack, J.3
Nierhaus, K.H.4
-
51
-
-
0037169502
-
Substitution of ribonucleotides in the T7 RNA polymerase promoter element
-
DOI 10.1074/jbc.M108820200
-
McGinness, K. E., and Joyce, G. F. (2002) Substitution of ribonucleotides in the T7 RNA polymerase promoter element. J. Biol. Chem. 277, 2987-2991. (Pubitemid 34953334)
-
(2002)
Journal of Biological Chemistry
, vol.277
, Issue.4
, pp. 2987-2991
-
-
McGinness, K.E.1
Joyce, G.F.2
-
52
-
-
0024819449
-
Synthesis of small RNAs using T7 RNA polymerase
-
DOI 10.1016/0076-6879(89)80091-6
-
Milligan, J. F., and Uhlenbeck, O. C. (1989) Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol. 180, 51-62. (Pubitemid 20039565)
-
(1989)
Methods in Enzymology
, vol.180
, pp. 51-62
-
-
Milligan, J.F.1
Uhlenbeck, O.C.2
-
53
-
-
0023924749
-
Processivity in early stages of transcription by T7 RNA polymerase
-
Martin, C. T., Muller, D. K., and Coleman, J. E. (1988) Processivity in early stages of transcription by T7 RNA polymerase. Biochemistry 27, 3966-3974.
-
(1988)
Biochemistry
, vol.27
, pp. 3966-3974
-
-
Martin, C.T.1
Muller, D.K.2
Coleman, J.E.3
-
54
-
-
0032539693
-
A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
-
SantaLucia, J., Jr. (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. U.S.A. 95, 1460-1465. (Pubitemid 128624151)
-
(1998)
Proceedings of the National Academy of Sciences of the United States of America
, vol.95
, Issue.4
, pp. 1460-1465
-
-
SantaLucia Jr., J.1
-
55
-
-
0029134549
-
Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes
-
Sugimoto, N., Nakano, S., Katoh, M., Matsumura, A., Nakamuta, H., Ohmichi, T., Yoneyama, M., and Sasaki, M. (1995) Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. Biochemistry 34, 11211-11216.
-
(1995)
Biochemistry
, vol.34
, pp. 11211-11216
-
-
Sugimoto, N.1
Nakano, S.2
Katoh, M.3
Matsumura, A.4
Nakamuta, H.5
Ohmichi, T.6
Yoneyama, M.7
Sasaki, M.8
-
56
-
-
33746207804
-
Secondary structure effects on DNA hybridization kinetics: A solution versus surface comparison
-
Gao, Y., Wolf, L. K., and Georgiadis, R. M. (2006) Secondary structure effects on DNA hybridization kinetics: A solution versus surface comparison. Nucleic Acids Res. 34, 3370-3377.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 3370-3377
-
-
Gao, Y.1
Wolf, L.K.2
Georgiadis, R.M.3
-
57
-
-
0003803285
-
-
University Science Books, Sausalito, CA
-
Bloomfield, V. A., Crothers, D. M., Tinoco, I., Hearst, J. E., Wemmer, D. E., Killman, P. A., Turner, D. H. (1999) Nucleic Acids: Structures, Properties, and Functions, University Science Books, Sausalito, CA.
-
(1999)
Nucleic Acids: Structures, Properties, and Functions
-
-
Bloomfield, V.A.1
Crothers, D.M.2
Tinoco, I.3
Hearst, J.E.4
Wemmer, D.E.5
Killman, P.A.6
Turner, D.H.7
-
58
-
-
0030999232
-
Kinetic mechanism of transcription initiation by bacteriophage T7 RNA polymerase
-
DOI 10.1021/bi9630467
-
Jia, Y., and Patel, S. S. (1997) Kinetic mechanism of transcription initiation by bacteriophage T7 RNA polymerase. Biochemistry 36, 4223-4232. (Pubitemid 27171595)
-
(1997)
Biochemistry
, vol.36
, Issue.14
, pp. 4223-4232
-
-
Jia, Y.1
Patel, S.S.2
-
59
-
-
0036835759
-
Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes
-
Marras, S. A. E., Kramer, F. R., and Tyagi, S. (2002) Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nucleic Acids Res. 30, e122.
-
(2002)
Nucleic Acids Res.
, vol.30
-
-
Marras, S.A.E.1
Kramer, F.R.2
Tyagi, S.3
-
60
-
-
42749109054
-
Statistical mechanical approaches to models with many poorly known parameters
-
Brown, K. S., and Sethna, J. P. (2003) Statistical mechanical approaches to models with many poorly known parameters. Phys. Rev. E 68, 021904.
-
(2003)
Phys. Rev. E
, vol.68
, pp. 021904
-
-
Brown, K.S.1
Sethna, J.P.2
-
61
-
-
35748977901
-
Universally sloppy parameter sensitivities in systems biology models
-
DOI 10.1371/journal.pcbi.0030189
-
Gutenkunst, R., Waterfall, J., Casey, F., Brown, K., Myers, C., and Sethna, J. (2007) Universally sloppy parameter sensitivities in systems biology models. PLoS Comput. Biol. 3, 1871-1878. (Pubitemid 350043403)
-
(2007)
PLoS Computational Biology
, vol.3
, Issue.10
, pp. 1871-1878
-
-
Gutenkunst, R.N.1
Waterfall, J.J.2
Casey, F.P.3
Brown, K.S.4
Myers, C.R.5
Sethna, J.P.6
-
62
-
-
58549083142
-
Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data
-
Chen, W. W., Schoeberl, B., Jasper, P. J., Niepel, M., Nielsen, U. B., Lauffenburger, D. A., and Sorger, P. K. (2009) Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data. Mol. Syst. Biol. 5, 239.
-
(2009)
Mol. Syst. Biol.
, vol.5
, pp. 239
-
-
Chen, W.W.1
Schoeberl, B.2
Jasper, P.J.3
Niepel, M.4
Nielsen, U.B.5
Lauffenburger, D.A.6
Sorger, P.K.7
-
63
-
-
84860899405
-
Bayesian design strategies for synthetic biology
-
Barnes, C. P., Silk, D., and Stumpf, M. P. H. (2011) Bayesian design strategies for synthetic biology. Interface Focus 1, 895-908.
-
(2011)
Interface Focus
, vol.1
, pp. 895-908
-
-
Barnes, C.P.1
Silk, D.2
Stumpf, M.P.H.3
-
64
-
-
80053056624
-
Bayesian design of synthetic biological systems
-
Barnes, C. P., Silk, D., Sheng, X., and Stumpf, M. P. H. (2011) Bayesian design of synthetic biological systems. Proc. Natl. Acad. Sci. U.S.A. 108, 15190-15195.
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 15190-15195
-
-
Barnes, C.P.1
Silk, D.2
Sheng, X.3
Stumpf, M.P.H.4
-
65
-
-
0036693201
-
Chimeric RNA-DNA molecular beacon assay for ribonuclease H activity
-
Rizzo, J., Gifford, L. K., Zhang, X., Gewirtz, A. M., and Lu, P. (2002) Chimeric RNA-DNA molecular beacon assay for ribonuclease H activity. Mol. Cell. Probes 16, 277-283.
-
(2002)
Mol. Cell. Probes
, vol.16
, pp. 277-283
-
-
Rizzo, J.1
Gifford, L.K.2
Zhang, X.3
Gewirtz, A.M.4
Lu, P.5
-
66
-
-
84868223564
-
Synthetic networks
-
John Wiley & Sons, Ltd., New York
-
Kim, J. (2009) Synthetic networks. Automation in Proteomics and Genomics, pp 251-271, John Wiley & Sons, Ltd., New York.
-
(2009)
Automation in Proteomics and Genomics
, pp. 251-271
-
-
Kim, J.1
-
67
-
-
84855481443
-
Competition for catalytic resources alters biological network dynamics
-
Rondelez, Y. (2012) Competition for catalytic resources alters biological network dynamics. Phys. Rev. Lett. 108, 018102.
-
(2012)
Phys. Rev. Lett.
, vol.108
, pp. 018102
-
-
Rondelez, Y.1
-
68
-
-
35748931160
-
Data-based identifiability analysis of non-linear dynamical models
-
DOI 10.1093/bioinformatics/btm382
-
Hengl, S., Kreutz, C., Timmer, J., and Maiwald, T. (2007) Databased identifiability analysis of non-linear dynamical models. Bioinformatics 23, 2612-2618. (Pubitemid 350048365)
-
(2007)
Bioinformatics
, vol.23
, Issue.19
, pp. 2612-2618
-
-
Hengl, S.1
Kreutz, C.2
Timmer, J.3
Maiwald, T.4
-
69
-
-
0035910269
-
Pre-steady-state kinetics of initiation of transcription by T7 RNA polymerase: A new kinetic model
-
DOI 10.1006/jmbi.2000.4316
-
Kuzmine, I., and Martin, C. T. (2001) Pre-steady-state kinetics of initiation of transcription by T7 RNA polymerase: A new kinetic model. J. Mol. Biol. 305, 559-566. (Pubitemid 33032861)
-
(2001)
Journal of Molecular Biology
, vol.305
, Issue.3
, pp. 559-566
-
-
Kuzmine, I.1
Martin, C.T.2
-
70
-
-
33745699611
-
Sensitivity analysis practices: Strategies for model-based inference
-
Saltelli, A., Ratto, M., Tarantola, S., and Campolongo, F. (2006) Sensitivity analysis practices: Strategies for model-based inference. Reliability Engineering and System Safety 91, 1109-1125.
-
(2006)
Reliability Engineering and System Safety
, vol.91
, pp. 1109-1125
-
-
Saltelli, A.1
Ratto, M.2
Tarantola, S.3
Campolongo, F.4
-
73
-
-
84860912186
-
Inference in complex systems
-
Balding, D. (2011) Inference in complex systems. Interface Focus 1, 805-806.
-
(2011)
Interface Focus
, vol.1
, pp. 805-806
-
-
Balding, D.1
-
74
-
-
0036500993
-
Systems biology: A brief overview
-
DOI 10.1126/science.1069492
-
Kitano, H. (2002) Systems biology: A brief overview. Science 295, 1662-1664. (Pubitemid 34202893)
-
(2002)
Science
, vol.295
, Issue.5560
, pp. 1662-1664
-
-
Kitano, H.1
-
75
-
-
34247587012
-
Getting closer to the whole picture
-
DOI 10.1126/science.1142502
-
Sauer, U., Heinemann, M., and Zamboni, N. (2007) Getting closer to the whole picture. Science 316, 550-551. (Pubitemid 46683128)
-
(2007)
Science
, vol.316
, Issue.5824
, pp. 550-551
-
-
Sauer, U.1
Heinemann, M.2
Zamboni, N.3
-
76
-
-
33846017352
-
The nature of systems biology
-
DOI 10.1016/j.tim.2006.11.003, PII S0966842X06002642
-
Bruggeman, F. J., and Westerhoff, H. V. (2007) The nature of systems biology. Trends Microbiol. 15, 45-50. (Pubitemid 46043550)
-
(2007)
Trends in Microbiology
, vol.15
, Issue.1
, pp. 45-50
-
-
Bruggeman, F.J.1
Westerhoff, H.V.2
-
77
-
-
0842288337
-
Inferring cellular networks using probabilistic graphical models
-
DOI 10.1126/science.1094068
-
Friedman, N. (2004) Inferring cellular networks using probabilistic graphical models. Science 303, 799-805. (Pubitemid 38174650)
-
(2004)
Science
, vol.303
, Issue.5659
, pp. 799-805
-
-
Friedman, N.1
-
78
-
-
7644238181
-
Biological robustness
-
DOI 10.1038/nrg1471
-
Kitano, H. (2004) Biological robustness. Nat. Rev. Genet. 5, 826-837. (Pubitemid 39457498)
-
(2004)
Nature Reviews Genetics
, vol.5
, Issue.11
, pp. 826-837
-
-
Kitano, H.1
-
79
-
-
49549094042
-
Sloppiness, robustness, and evolvability in systems biology
-
Daniels, B., Chen, Y.-J., Sethna, J., Gutenkunst, R., and Myers, C. (2008) Sloppiness, robustness, and evolvability in systems biology. Curr. Opin. Biotechnol. 19, 389-395.
-
(2008)
Curr. Opin. Biotechnol.
, vol.19
, pp. 389-395
-
-
Daniels, B.1
Chen, Y.-J.2
Sethna, J.3
Gutenkunst, R.4
Myers, C.5
|