-
2
-
-
78049402859
-
Molecular signals of epigenetic states
-
Bonasio, R., Tu, S., and Reinberg, D. (2010) Molecular signals of epigenetic states Science 330, 612 - 6
-
(2010)
Science
, vol.330
, pp. 612-616
-
-
Bonasio, R.1
Tu, S.2
Reinberg, D.3
-
3
-
-
78049414227
-
Epigenetic reprogramming in plant and animal development
-
Feng, S., Jacobsen, S. E., and Reik, W. (2010) Epigenetic reprogramming in plant and animal development Science 330, 622 - 7
-
(2010)
Science
, vol.330
, pp. 622-627
-
-
Feng, S.1
Jacobsen, S.E.2
Reik, W.3
-
4
-
-
84875229795
-
Basic concepts of epigenetics
-
Inbar-Feigenberg, M., Choufani, S., Butcher, D. T., Roifman, M., and Weksberg, R. (2013) Basic concepts of epigenetics Fertil. Steril. 99, 607 - 15
-
(2013)
Fertil. Steril.
, vol.99
, pp. 607-615
-
-
Inbar-Feigenberg, M.1
Choufani, S.2
Butcher, D.T.3
Roifman, M.4
Weksberg, R.5
-
5
-
-
0003620778
-
-
Pearson/Addison Wesley, Boston
-
Hopcroft, J. E., Motwani, R., and Ullman, J. D. (2007) Introduction to Automata Theory, Languages, and Computation, Pearson/Addison Wesley, Boston.
-
(2007)
Introduction to Automata Theory, Languages, and Computation
-
-
Hopcroft, J.E.1
Motwani, R.2
Ullman, J.D.3
-
7
-
-
0004449398
-
Three models for the description of language
-
Chomsky, N. (1956) Three models for the description of language IEEE Trans. Inf. Theory 2, 113 - 124
-
(1956)
IEEE Trans. Inf. Theory
, vol.2
, pp. 113-124
-
-
Chomsky, N.1
-
8
-
-
0002703887
-
Gedanken-experiments on sequential machines
-
Moore, E. F. (1956) Gedanken-experiments on sequential machines Automata Studies 34, 129 - 153
-
(1956)
Automata Studies
, vol.34
, pp. 129-153
-
-
Moore, E.F.1
-
9
-
-
0000973916
-
Finite Automata and their decision problems
-
Rabin, M. O. and Scott, D. (1959) Finite Automata and their decision problems IBM J. Res. Dev. 3, 114 - 125
-
(1959)
IBM J. Res. Dev.
, vol.3
, pp. 114-125
-
-
Rabin, M.O.1
Scott, D.2
-
10
-
-
84911240782
-
The logic of Automata - Part I
-
Burks, A. W. and Wang, H. (1957) The logic of Automata-Part I J. ACM 4, 193 - 218
-
(1957)
J. ACM
, vol.4
, pp. 193-218
-
-
Burks, A.W.1
Wang, H.2
-
11
-
-
0001699148
-
Recursive unsolvability of Post's problem of "tag" and other topics in theory of turing machines
-
Minsky, M. L. (1961) Recursive unsolvability of Post's problem of "tag" and other topics in theory of turing machines Ann. Math. 74, 437 - 455
-
(1961)
Ann. Math.
, vol.74
, pp. 437-455
-
-
Minsky, M.L.1
-
12
-
-
0025112578
-
A logical calculus of the ideas immanent in nervous activity
-
McCulloch, W. S. and Pitts, W. (1943) A logical calculus of the ideas immanent in nervous activity Bull.f Math. Biol. 52, 99 - 115
-
(1943)
Bull.f Math. Biol.
, vol.52
, pp. 99-115
-
-
McCulloch, W.S.1
Pitts, W.2
-
14
-
-
84862666539
-
Engineering molecular circuits using synthetic biology in mammalian cells
-
Wieland, M. and Fussenegger, M. (2012) Engineering molecular circuits using synthetic biology in mammalian cells Annu. Rev. Chem. Biomol. Eng. 3, 209 - 34
-
(2012)
Annu. Rev. Chem. Biomol. Eng.
, vol.3
, pp. 209-234
-
-
Wieland, M.1
Fussenegger, M.2
-
15
-
-
84874035997
-
Synthesizing biomolecule-based Boolean logic gates
-
Miyamoto, T., Razavi, S., DeRose, R., and Inoue, T. (2012) Synthesizing biomolecule-based Boolean logic gates ACS Synth. Biol. 2, 72 - 82
-
(2012)
ACS Synth. Biol.
, vol.2
, pp. 72-82
-
-
Miyamoto, T.1
Razavi, S.2
DeRose, R.3
Inoue, T.4
-
16
-
-
84862180741
-
A tunable zinc finger-based framework for Boolean logic computation in mammalian cells
-
Lohmueller, J. J., Armel, T. Z., and Silver, P. A. (2012) A tunable zinc finger-based framework for Boolean logic computation in mammalian cells Nucleic Acids Res. 40, 5180 - 5187
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 5180-5187
-
-
Lohmueller, J.J.1
Armel, T.Z.2
Silver, P.A.3
-
17
-
-
80055035853
-
Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology
-
Wang, B., Kitney, R. I., Joly, N., and Buck, M. (2011) Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology Nat. Commun. 2, 508
-
(2011)
Nat. Commun.
, vol.2
, pp. 508
-
-
Wang, B.1
Kitney, R.I.2
Joly, N.3
Buck, M.4
-
18
-
-
0034688174
-
Construction of a genetic toggle switch in Escherichia coli
-
Gardner, T. S., Cantor, C. R., and Collins, J. J. (2000) Construction of a genetic toggle switch in Escherichia coli Nature 403, 339 - 42
-
(2000)
Nature
, vol.403
, pp. 339-342
-
-
Gardner, T.S.1
Cantor, C.R.2
Collins, J.J.3
-
19
-
-
17144456808
-
Positive feedback in eukaryotic gene networks: Cell differentiation by graded to binary response conversion
-
Becskei, A., Séraphin, B., and Serrano, L. (2001) Positive feedback in eukaryotic gene networks: Cell differentiation by graded to binary response conversion EMBO J. 20, 2528 - 35
-
(2001)
EMBO J.
, vol.20
, pp. 2528-2535
-
-
Becskei, A.1
Séraphin, B.2
Serrano, L.3
-
20
-
-
0037079012
-
Engineered gene circuits
-
Hasty, J., McMillen, D., and Collins, J. J. (2002) Engineered gene circuits Nature 420, 224 - 230
-
(2002)
Nature
, vol.420
, pp. 224-230
-
-
Hasty, J.1
McMillen, D.2
Collins, J.J.3
-
21
-
-
84861865655
-
Rewritable digital data storage in live cells via engineered control of recombination directionality
-
Bonnet, J., Subsoontorn, P., and Endy, D. (2012) Rewritable digital data storage in live cells via engineered control of recombination directionality Proc. Natl. Acad. Sci. U.S.A. 109, 8884 - 9
-
(2012)
Proc. Natl. Acad. Sci. U.S.A.
, vol.109
, pp. 8884-8889
-
-
Bonnet, J.1
Subsoontorn, P.2
Endy, D.3
-
22
-
-
17844374314
-
A synthetic multicellular system for programmed pattern formation
-
Basu, S., Gerchman, Y., Collins, C. H., Arnold, F. H., and Weiss, R. (2005) A synthetic multicellular system for programmed pattern formation Nature 434, 1130 - 4
-
(2005)
Nature
, vol.434
, pp. 1130-1134
-
-
Basu, S.1
Gerchman, Y.2
Collins, C.H.3
Arnold, F.H.4
Weiss, R.5
-
23
-
-
66149172363
-
Diversity-based, model-guided construction of synthetic gene networks with predicted functions
-
Ellis, T., Wang, X., and Collins, J. J. (2009) Diversity-based, model-guided construction of synthetic gene networks with predicted functions Nat. Biotechnol. 27, 465 - 71
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 465-471
-
-
Ellis, T.1
Wang, X.2
Collins, J.J.3
-
24
-
-
84875230351
-
Synthetic circuits integrating logic and memory in living cells
-
Siuti, P., Yazbek, J., and Lu, T. K. (2013) Synthetic circuits integrating logic and memory in living cells Nat. Biotechnol. 31, 448 - 52
-
(2013)
Nat. Biotechnol.
, vol.31
, pp. 448-452
-
-
Siuti, P.1
Yazbek, J.2
Lu, T.K.3
-
25
-
-
75149191906
-
A synchronized quorum of genetic clocks
-
Danino, T., Mondragón-Palomino, O., Tsimring, L., and Hasty, J. (2010) A synchronized quorum of genetic clocks Nature 463, 326 - 30
-
(2010)
Nature
, vol.463
, pp. 326-330
-
-
Danino, T.1
Mondragón-Palomino, O.2
Tsimring, L.3
Hasty, J.4
-
26
-
-
1942467023
-
Programmed population control by cell-cell communication and regulated killing
-
You, L., Cox, R. S., Weiss, R., and Arnold, F. H. (2004) Programmed population control by cell-cell communication and regulated killing Nature 428, 868 - 71
-
(2004)
Nature
, vol.428
, pp. 868-871
-
-
You, L.1
Cox, R.S.2
Weiss, R.3
Arnold, F.H.4
-
27
-
-
67549145283
-
A synthetic genetic edge detection program
-
Tabor, J. J., Salis, H. M., Simpson, Z. B., Chevalier, A. A., Levskaya, A., Marcotte, E. M., Voigt, C. A., and Ellington, A. D. (2009) A synthetic genetic edge detection program Cell 137, 1272 - 81
-
(2009)
Cell
, vol.137
, pp. 1272-1281
-
-
Tabor, J.J.1
Salis, H.M.2
Simpson, Z.B.3
Chevalier, A.A.4
Levskaya, A.5
Marcotte, E.M.6
Voigt, C.A.7
Ellington, A.D.8
-
28
-
-
80054124775
-
Sequential establishment of stripe patterns in an expanding cell population
-
Liu, C., Fu, X., Liu, L., Ren, X., Chau, C. K. L., Li, S., Xiang, L., Zeng, H., Chen, G., Tang, L.-H. H., Lenz, P., Cui, X., Huang, W., Hwa, T., and Huang, J.-D. D. (2011) Sequential establishment of stripe patterns in an expanding cell population Science 334, 238 - 41
-
(2011)
Science
, vol.334
, pp. 238-241
-
-
Liu, C.1
Fu, X.2
Liu, L.3
Ren, X.4
Chau, C.K.L.5
Li, S.6
Xiang, L.7
Zeng, H.8
Chen, G.9
Tang, L.-H.H.10
Lenz, P.11
Cui, X.12
Huang, W.13
Hwa, T.14
Huang, J.-D.D.15
-
29
-
-
78651397316
-
Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'
-
Tamsir, A., Tabor, J. J., and Voigt, C. A. (2011) Robust multicellular computing using genetically encoded NOR gates and chemical 'wires' Nature 469, 212 - 5
-
(2011)
Nature
, vol.469
, pp. 212-215
-
-
Tamsir, A.1
Tabor, J.J.2
Voigt, C.A.3
-
30
-
-
78651406505
-
Distributed biological computation with multicellular engineered networks
-
Regot, S., Macia, J., Conde, N., Furukawa, K., Kjellén, J., Peeters, T., Hohmann, S., de Nadal, E., Posas, F., and Solé, R. (2011) Distributed biological computation with multicellular engineered networks Nature 469, 207 - 11
-
(2011)
Nature
, vol.469
, pp. 207-211
-
-
Regot, S.1
Macia, J.2
Conde, N.3
Furukawa, K.4
Kjellén, J.5
Peeters, T.6
Hohmann, S.7
De Nadal, E.8
Posas, F.9
Solé, R.10
-
31
-
-
71849110893
-
Next-generation synthetic gene networks
-
Lu, T. K., Khalil, A. S., and Collins, J. J. (2009) Next-generation synthetic gene networks Nat. Biotechnol. 27, 1139 - 50
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 1139-1150
-
-
Lu, T.K.1
Khalil, A.S.2
Collins, J.J.3
-
32
-
-
84874687019
-
Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression
-
Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P., and Lim, W. A. (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression Cell 152, 1173 - 83
-
(2013)
Cell
, vol.152
, pp. 1173-1183
-
-
Qi, L.S.1
Larson, M.H.2
Gilbert, L.A.3
Doudna, J.A.4
Weissman, J.S.5
Arkin, A.P.6
Lim, W.A.7
-
33
-
-
0036168937
-
Engineering polydactyl zinc-finger transcription factors
-
Beerli, R. R. and Barbas, C. F. (2002) Engineering polydactyl zinc-finger transcription factors Nat. Biotechnol. 20, 135 - 41
-
(2002)
Nat. Biotechnol.
, vol.20
, pp. 135-141
-
-
Beerli, R.R.1
Barbas, C.F.2
-
34
-
-
72149090954
-
A simple cipher governs DNA recognition by TAL effectors
-
Moscou, M. J. and Bogdanove, A. J. (2009) A simple cipher governs DNA recognition by TAL effectors Science 326, 1501
-
(2009)
Science
, vol.326
, pp. 1501
-
-
Moscou, M.J.1
Bogdanove, A.J.2
-
35
-
-
84870786425
-
Transcription activator-like effector hybrids for conditional control and rewiring of chromosomal transgene expression
-
Li, Y., Moore, R., Guinn, M., and Bleris, L. (2012) Transcription activator-like effector hybrids for conditional control and rewiring of chromosomal transgene expression Sci. Rep. 2, 897
-
(2012)
Sci. Rep.
, vol.2
, pp. 897
-
-
Li, Y.1
Moore, R.2
Guinn, M.3
Bleris, L.4
-
36
-
-
84864634066
-
A synthetic biology framework for programming eukaryotic transcription functions
-
Khalil, A. S., Lu, T. K., Bashor, C. J., Ramirez, C. L., Pyenson, N. C., Joung, J. K., and Collins, J. J. (2012) A synthetic biology framework for programming eukaryotic transcription functions Cell 150, 647 - 58
-
(2012)
Cell
, vol.150
, pp. 647-658
-
-
Khalil, A.S.1
Lu, T.K.2
Bashor, C.J.3
Ramirez, C.L.4
Pyenson, N.C.5
Joung, J.K.6
Collins, J.J.7
-
37
-
-
84868233914
-
Specification and simulation of synthetic multicelled behaviors
-
Jang, S. S., Oishi, K. T., Egbert, R. G., and Klavins, E. (2012) Specification and simulation of synthetic multicelled behaviors ACS Synth. Biol. 1, 365 - 374
-
(2012)
ACS Synth. Biol.
, vol.1
, pp. 365-374
-
-
Jang, S.S.1
Oishi, K.T.2
Egbert, R.G.3
Klavins, E.4
-
38
-
-
84867300642
-
Engineering synthetic TAL effectors with orthogonal target sites
-
Garg, A., Lohmueller, J. J., Silver, P. A., and Armel, T. Z. (2012) Engineering synthetic TAL effectors with orthogonal target sites Nucleic Acids Res. 40, 7584 - 7595
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 7584-7595
-
-
Garg, A.1
Lohmueller, J.J.2
Silver, P.A.3
Armel, T.Z.4
-
39
-
-
84865848723
-
A synthetic approach reveals extensive tunability of auxin signaling
-
Havens, K. A., Guseman, J. M., Jang, S. S., Pierre-Jerome, E., Bolten, N., Klavins, E., and Nemhauser, J. L. (2012) A synthetic approach reveals extensive tunability of auxin signaling Plant Physiol. 160, 135 - 42
-
(2012)
Plant Physiol.
, vol.160
, pp. 135-142
-
-
Havens, K.A.1
Guseman, J.M.2
Jang, S.S.3
Pierre-Jerome, E.4
Bolten, N.5
Klavins, E.6
Nemhauser, J.L.7
-
40
-
-
84880571335
-
CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes
-
Gilbert, L. A., Larson, M. H., Morsut, L., Liu, Z., Brar, G. A., Torres, S. E., Stern-Ginossar, N., Brandman, O., Whitehead, E. H., Doudna, J. A., Lim, W. A., Weissman, J. S., and Qi, L. S. (2013) CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes Cell 154, 442 - 51
-
(2013)
Cell
, vol.154
, pp. 442-451
-
-
Gilbert, L.A.1
Larson, M.H.2
Morsut, L.3
Liu, Z.4
Brar, G.A.5
Torres, S.E.6
Stern-Ginossar, N.7
Brandman, O.8
Whitehead, E.H.9
Doudna, J.A.10
Lim, W.A.11
Weissman, J.S.12
Qi, L.S.13
-
41
-
-
0014489272
-
Metabolic stability and epigenesis in randomly constructed genetic nets
-
Kauffman, S. A. (1969) Metabolic stability and epigenesis in randomly constructed genetic nets J. Theor. Biol. 22, 437 - 67
-
(1969)
J. Theor. Biol.
, vol.22
, pp. 437-467
-
-
Kauffman, S.A.1
-
42
-
-
0015823097
-
Boolean formalization of genetic control circuits
-
Thomas, R. (1973) Boolean formalization of genetic control circuits J. Theor. Biol. 42, 563 - 85
-
(1973)
J. Theor. Biol.
, vol.42
, pp. 563-585
-
-
Thomas, R.1
-
43
-
-
0035826155
-
Exploring complex networks
-
Strogatz, S. H. (2001) Exploring complex networks Nature 410, 268 - 276
-
(2001)
Nature
, vol.410
, pp. 268-276
-
-
Strogatz, S.H.1
-
44
-
-
0036207347
-
Modeling and simulation of genetic regulatory systems: A literature review
-
de Jong, H. (2002) Modeling and simulation of genetic regulatory systems: A literature review J. Comput. Biol. 9, 67 - 103
-
(2002)
J. Comput. Biol.
, vol.9
, pp. 67-103
-
-
De Jong, H.1
-
45
-
-
0036578795
-
Network motifs in the transcriptional regulation network of Escherichia coli
-
Shen-Orr, S. S., Milo, R., Mangan, S., and Alon, U. (2002) Network motifs in the transcriptional regulation network of Escherichia coli Nat. Genet. 31, 64 - 8
-
(2002)
Nat. Genet.
, vol.31
, pp. 64-68
-
-
Shen-Orr, S.S.1
Milo, R.2
Mangan, S.3
Alon, U.4
-
46
-
-
46249112705
-
Boolean network models of cellular regulation: Prospects and limitations
-
Bornholdt, S. (2008) Boolean network models of cellular regulation: Prospects and limitations J. R. Soc. Interface 5 (Suppl 1) S85 - 94
-
(2008)
J. R. Soc. Interface
, vol.5
, pp. S85-S94
-
-
Bornholdt, S.1
-
47
-
-
84875089912
-
Information-theoretic analysis of the dynamics of an executable biological model
-
Sadot, A., Sarbu, S., Kesseli, J., Amir-Kroll, H., Zhang, W., Nykter, M., and Shmulevich, I. (2013) Information-theoretic analysis of the dynamics of an executable biological model PLoS One 8, e59303
-
(2013)
PLoS One
, vol.8
, pp. e59303
-
-
Sadot, A.1
Sarbu, S.2
Kesseli, J.3
Amir-Kroll, H.4
Zhang, W.5
Nykter, M.6
Shmulevich, I.7
-
48
-
-
0030768931
-
The Hill equation revisited: Uses and misuses
-
Weiss, J. N. (1997) The Hill equation revisited: Uses and misuses FASEB J. 11, 835 - 41
-
(1997)
FASEB J.
, vol.11
, pp. 835-841
-
-
Weiss, J.N.1
-
49
-
-
78049442327
-
Method for synthesizing sequential circuits
-
Mealy, G. H. (1955) Method for synthesizing sequential circuits Bell Syst. Tech. J. 34, 1045 - 1079
-
(1955)
Bell Syst. Tech. J.
, vol.34
, pp. 1045-1079
-
-
Mealy, G.H.1
-
51
-
-
66349125024
-
Synthetic gene networks that count
-
Friedland, A. E., Lu, T. K., Wang, X., Shi, D., Church, G., and Collins, J. J. (2009) Synthetic gene networks that count Science 324, 1199 - 202
-
(2009)
Science
, vol.324
, pp. 1199-1202
-
-
Friedland, A.E.1
Lu, T.K.2
Wang, X.3
Shi, D.4
Church, G.5
Collins, J.J.6
-
52
-
-
84878381909
-
Synthetic analog computation in living cells
-
Daniel, R., Rubens, J. R., Sarpeshkar, R., and Lu, T. K. (2013) Synthetic analog computation in living cells Nature 497, 619 - 23
-
(2013)
Nature
, vol.497
, pp. 619-623
-
-
Daniel, R.1
Rubens, J.R.2
Sarpeshkar, R.3
Lu, T.K.4
-
53
-
-
39149113411
-
Modular cell biology: Retroactivity and insulation
-
Del Vecchio, D., Ninfa, A. J., and Sontag, E. D. (2008) Modular cell biology: Retroactivity and insulation Mol. Syst. Biol. 4, 161
-
(2008)
Mol. Syst. Biol.
, vol.4
, pp. 161
-
-
Del Vecchio, D.1
Ninfa, A.J.2
Sontag, E.D.3
-
54
-
-
79952619978
-
-
Wolfram Research, Inc. Champaign, IL
-
Wolfram Research, Inc. (2010) Mathematica, Version 8.0, Wolfram Research, Inc., Champaign, IL.
-
(2010)
Mathematica, Version 8.0
-
-
Wolfram Research, Inc.,1
|