-
2
-
-
0037109057
-
Single molecule analysis of RNA polymerase elongation reveals uniform kinetic behavior
-
Adelman, K., La Porta, A., Santangelo, T.J., Lis, J.T., Roberts, J.W., Wang, M.D., 2002. Single molecule analysis of RNA polymerase elongation reveals uniform kinetic behavior. Proc. Natl. Acad. Sci. U.S.A. 99, 13538-13543.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 13538-13543
-
-
Adelman, K.1
La Porta, A.2
Santangelo, T.J.3
Lis, J.T.4
Roberts, J.W.5
Wang, M.D.6
-
3
-
-
7444253928
-
Sequence-dependent kinetic model for transcription elongation by RNA polymerase
-
Bai, L., Shundrovsky, A., Wang, M.D., 2004. Sequence-dependent kinetic model for transcription elongation by RNA polymerase. J. Mol. Biol. 344, 335-349.
-
(2004)
J. Mol. Biol.
, vol.344
, pp. 335-349
-
-
Bai, L.1
Shundrovsky, A.2
Wang, M.D.3
-
4
-
-
0019974626
-
Role of feedback inhibition in stabilizing the classical operon
-
Bliss, R.D., Painter, P.R., Marr, A.G., 1982. Role of feedback inhibition in stabilizing the classical operon. J. Theor. Biol. 97, 177-193.
-
(1982)
J. Theor. Biol.
, vol.97
, pp. 177-193
-
-
Bliss, R.D.1
Painter, P.R.2
Marr, A.G.3
-
5
-
-
0023648905
-
Computer simulation of T3/T7 phage infection using lag times
-
Buchholtz, F., Schneider, F.W., 1987. Computer simulation of T3/T7 phage infection using lag times. Biophys. Chem. 26, 171-179.
-
(1987)
Biophys. Chem.
, vol.26
, pp. 171-179
-
-
Buchholtz, F.1
Schneider, F.W.2
-
6
-
-
17644404265
-
The effects of dimension and size for a compartmental model of repression
-
Busenberg, S.N., Mahaffy, J.M., 1988. The effects of dimension and size for a compartmental model of repression. SIAM. J. Appl. Math. 48, 882-903.
-
(1988)
SIAM. J. Appl. Math.
, vol.48
, pp. 882-903
-
-
Busenberg, S.N.1
Mahaffy, J.M.2
-
8
-
-
0000209631
-
Discrete delay, distributed delay and stability switches
-
Cooke, K.L., Grossman, Z., 1982. Discrete delay, distributed delay and stability switches. J. Math. Anal. Appl. 86, 592-627.
-
(1982)
J. Math. Anal. Appl.
, vol.86
, pp. 592-627
-
-
Cooke, K.L.1
Grossman, Z.2
-
9
-
-
0034737593
-
Single-molecule study of transcriptional pausing and arrest by E. coli RNA polymerase
-
Davenport, R.J., Wuite, G.J.L., Landick, R., Bustamante, C., 2000. Single-molecule study of transcriptional pausing and arrest by E. coli RNA polymerase. Science 287, 2497-2500.
-
(2000)
Science
, vol.287
, pp. 2497-2500
-
-
Davenport, R.J.1
Wuite, G.J.L.2
Landick, R.3
Bustamante, C.4
-
10
-
-
0001655501
-
Geometric approach to multiple-time-scale kinetics: A nonlinear master equation describing vibration-to-vibration relaxation
-
Davis, M.J., Skodje, R.T., 2001. Geometric approach to multiple-time-scale kinetics: A nonlinear master equation describing vibration-to-vibration relaxation. Z. Phys. Chem. 215, 233-252.
-
(2001)
Z. Phys. Chem.
, vol.215
, pp. 233-252
-
-
Davis, M.J.1
Skodje, R.T.2
-
12
-
-
0034968287
-
A mathematical model for prokaryotic protein synthesis
-
Drew, D.A., 2001. A mathematical model for prokaryotic protein synthesis. Bull. Math. Biol. 63, 329-351.
-
(2001)
Bull. Math. Biol.
, vol.63
, pp. 329-351
-
-
Drew, D.A.1
-
13
-
-
0029808466
-
Cell cycle checkpoints: Preventing an identity crisis
-
Elledge, S.J., 1996. Cell cycle checkpoints: Preventing an identity crisis. Science 274, 1664-1672.
-
(1996)
Science
, vol.274
, pp. 1664-1672
-
-
Elledge, S.J.1
-
14
-
-
0037119587
-
Stochastic gene expression in a single cell
-
Elowitz, M.B., Levine, A.J., Siggia, E.D., Swain, P.S., 2002. Stochastic gene expression in a single cell. Science 297, 1183-1186.
-
(2002)
Science
, vol.297
, pp. 1183-1186
-
-
Elowitz, M.B.1
Levine, A.J.2
Siggia, E.D.3
Swain, P.S.4
-
16
-
-
12244269952
-
Stochastic simulation of the mammalian circadian clock
-
Forger, D.B., Peskin, C.S., 2005. Stochastic simulation of the mammalian circadian clock. Proc. Natl. Acad. Sci. U.S.A. 102, 321-324.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 321-324
-
-
Forger, D.B.1
Peskin, C.S.2
-
17
-
-
0017030517
-
A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
-
Gillespie, D.T., 1976. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comp. Phys. 22, 403-434.
-
(1976)
J. Comp. Phys.
, vol.22
, pp. 403-434
-
-
Gillespie, D.T.1
-
18
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
Gillespie, D.T., 1977. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81, 2340-2361.
-
(1977)
J. Phys. Chem.
, vol.81
, pp. 2340-2361
-
-
Gillespie, D.T.1
-
19
-
-
44049109914
-
A rigorous derivation of the chemical master equation
-
Gillespie, D.T., 1992. A rigorous derivation of the chemical master equation. Physica A 188, 404-425.
-
(1992)
Physica A
, vol.188
, pp. 404-425
-
-
Gillespie, D.T.1
-
20
-
-
0036578786
-
Translating the noise
-
Hasty, J., Collins, J.J., 2002. Translating the noise. Nat. Gen. 31, 13-14.
-
(2002)
Nat. Gen.
, vol.31
, pp. 13-14
-
-
Hasty, J.1
Collins, J.J.2
-
21
-
-
0344100118
-
A mathematical model for elongation of a peptide chain
-
Heyd, A., Drew, D.A., 2003. A mathematical model for elongation of a peptide chain. Bull. Math. Biol. 65, 1095-1109.
-
(2003)
Bull. Math. Biol.
, vol.65
, pp. 1095-1109
-
-
Heyd, A.1
Drew, D.A.2
-
22
-
-
0142127778
-
Motion of RNA polymerase along DNA: A stochastic model
-
Jülicher, F., Bruinsma, R., 1998. Motion of RNA polymerase along DNA: A stochastic model. Biophys. J. 74, 1169-1185.
-
(1998)
Biophys. J.
, vol.74
, pp. 1169-1185
-
-
Jülicher, F.1
Bruinsma, R.2
-
23
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
Lee, T.I., Rinaldi, N.J., Robert, F., Odom, D.T., Z. Bar-Joseph, Gerber, G.K., Hannett, N.M., Harbison, C.T., Thompson, C.M., Simon, I., Zeitlinger, J., Jennings, E.G., Murray, H.L., Gordon, D.B., Ren, B., Wyrick, J.J., Tagne, J.B., Volkert, T.L., Fraenkel, E., Gifford, D.K., Young, R.A., 2002. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799-804.
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
Rinaldi, N.J.2
Robert, F.3
Odom, D.T.4
Bar-Joseph, Z.5
Gerber, G.K.6
Hannett, N.M.7
Harbison, C.T.8
Thompson, C.M.9
Simon, I.10
Zeitlinger, J.11
Jennings, E.G.12
Murray, H.L.13
Gordon, D.B.14
Ren, B.15
Wyrick, J.J.16
Tagne, J.B.17
Volkert, T.L.18
Fraenkel, E.19
Gifford, D.K.20
Young, R.A.21
more..
-
24
-
-
0041677612
-
Autoinhibition with transcriptional delay: A simple mechanism for the zebrafish somitogenesis oscillator
-
Lewis, J., 2003. Autoinhibition with transcriptional delay: A simple mechanism for the zebrafish somitogenesis oscillator. Curr. Biol. 13, 1398-1408.
-
(2003)
Curr. Biol.
, vol.13
, pp. 1398-1408
-
-
Lewis, J.1
-
26
-
-
0026487626
-
Oscillations in a model of repression with external control
-
Mahaffy, J.M., Jorgensen, D.A., Vanderheyden, R.L., 1992. Oscillations in a model of repression with external control. J. Math. Biol. 30, 669-691.
-
(1992)
J. Math. Biol.
, vol.30
, pp. 669-691
-
-
Mahaffy, J.M.1
Jorgensen, D.A.2
Vanderheyden, R.L.3
-
27
-
-
0033083733
-
It's a noisy business! Genetic regulation at the nanomolar scale
-
McAdams, H.H., Arkin, A., 1999. It's a noisy business! Genetic regulation at the nanomolar scale. Trends Genet. 15, 65-69.
-
(1999)
Trends Genet.
, vol.15
, pp. 65-69
-
-
McAdams, H.H.1
Arkin, A.2
-
28
-
-
1842383693
-
Rate-limiting steps in RNA chain initiation
-
McClure, W.R., 1980. Rate-limiting steps in RNA chain initiation. Proc. Natl. Acad. Sci. U.S.A. 77, 5634-5638.
-
(1980)
Proc. Natl. Acad. Sci. U.S.A.
, vol.77
, pp. 5634-5638
-
-
McClure, W.R.1
-
29
-
-
0014583992
-
Portrait of a gene
-
Miller, O.L., Beatty, B.R., 1969. Portrait of a gene. J. Cell. Physiol. 74 (Suppl. 1), 225-232.
-
(1969)
J. Cell. Physiol.
, vol.74
, Issue.1 SUPPL.
, pp. 225-232
-
-
Miller, O.L.1
Beatty, B.R.2
-
30
-
-
0343779625
-
Electron microscopic visualization of transcription
-
Miller, O.L., Beatty, B.R., Hamkalo, B.A., Thomas, C.A., 1970. Electron microscopic visualization of transcription. Cold Spring Harb. Symp. Quant. Biol. 35, 505-512.
-
(1970)
Cold Spring Harb. Symp. Quant. Biol.
, vol.35
, pp. 505-512
-
-
Miller, O.L.1
Beatty, B.R.2
Hamkalo, B.A.3
Thomas, C.A.4
-
31
-
-
0043180477
-
Oscillatory expression of Hes1, p53, and NF-κB driven by transcriptional time delays
-
Monk, N.A.M., 2003. Oscillatory expression of Hes1, p53, and NF-κB driven by transcriptional time delays. Curr. Biol. 13, 1409-1413.
-
(2003)
Curr. Biol.
, vol.13
, pp. 1409-1413
-
-
Monk, N.A.M.1
-
32
-
-
0036741847
-
The physics of traffic jams
-
Nagatani, T., 2002. The physics of traffic jams. Rep. Prog. Phys. 65, 1331-1386.
-
(2002)
Rep. Prog. Phys.
, vol.65
, pp. 1331-1386
-
-
Nagatani, T.1
-
33
-
-
0003808930
-
-
MIT Press, Cambridge, MA
-
Oppenheim, I., Shuler, K.E., Weiss, G.H., 1977. Stochastic Processes in Chemical Physics: The Master Equation. MIT Press, Cambridge, MA.
-
(1977)
Stochastic Processes in Chemical Physics: The Master Equation
-
-
Oppenheim, I.1
Shuler, K.E.2
Weiss, G.H.3
-
34
-
-
33748691544
-
Comprehensive analysis of delay in transcriptional regulation using expression profiles
-
Ota, K., Yamada, T., Yamanishi, Y., Goto, S., Kanehisa, M., 2003. Comprehensive analysis of delay in transcriptional regulation using expression profiles. Genome Inform. 14, 302-303.
-
(2003)
Genome Inform.
, vol.14
, pp. 302-303
-
-
Ota, K.1
Yamada, T.2
Yamanishi, Y.3
Goto, S.4
Kanehisa, M.5
-
35
-
-
3142738659
-
Delay-differential equations and the model equivalence problem in chemical kinetics
-
Roussel, C.J., Roussel, M.R., 2001. Delay-differential equations and the model equivalence problem in chemical kinetics. Phys. Can. 57, 114-120.
-
(2001)
Phys. Can.
, vol.57
, pp. 114-120
-
-
Roussel, C.J.1
Roussel, M.R.2
-
36
-
-
0030134446
-
The use of delay differential equations in chemical kinetics
-
Roussel, M.R., 1996. The use of delay differential equations in chemical kinetics. J. Phys. Chem. 100, 8323-8330.
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 8323-8330
-
-
Roussel, M.R.1
-
38
-
-
0031935932
-
Frequency selectivity, multistability, and oscillations emerge from models of genetic regulatory systems
-
Smolen, P., Baxter, D.A., Byrne, J.H., 1998. Frequency selectivity, multistability, and oscillations emerge from models of genetic regulatory systems. Am. J. Physiol. 274, C531-C542.
-
(1998)
Am. J. Physiol.
, vol.274
-
-
Smolen, P.1
Baxter, D.A.2
Byrne, J.H.3
-
39
-
-
0032698943
-
Effects of macromolecular transport and stochastic fluctuations on dynamics of genetic regulatory systems
-
Smolen, P., Baxter, D.A., Byrne, J.H., 1999. Effects of macromolecular transport and stochastic fluctuations on dynamics of genetic regulatory systems. Am. J. Physiol. 277, C777-C790.
-
(1999)
Am. J. Physiol.
, vol.277
-
-
Smolen, P.1
Baxter, D.A.2
Byrne, J.H.3
-
40
-
-
0033782304
-
Modeling transcriptional control in gene networks - Methods, recent results, and future directions
-
Smolen, P., Baxter, D.A., Byrne, J.H., 2000. Modeling transcriptional control in gene networks - Methods, recent results, and future directions. Bull. Math. Biol. 62, 247-292.
-
(2000)
Bull. Math. Biol.
, vol.62
, pp. 247-292
-
-
Smolen, P.1
Baxter, D.A.2
Byrne, J.H.3
-
41
-
-
0035449932
-
Modeling circadian oscillations with interlocking positive and negative feedback loops
-
Smolen, P., Baxter, D.A., Byrne, J.H., 2001. Modeling circadian oscillations with interlocking positive and negative feedback loops. J. Neurosci. 21, 6644-6656.
-
(2001)
J. Neurosci.
, vol.21
, pp. 6644-6656
-
-
Smolen, P.1
Baxter, D.A.2
Byrne, J.H.3
-
42
-
-
0031742022
-
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
-
Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D., Futcher, B., 1998. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9, 3273-3297.
-
(1998)
Mol. Biol. Cell
, vol.9
, pp. 3273-3297
-
-
Spellman, P.T.1
Sherlock, G.2
Zhang, M.Q.3
Iyer, V.R.4
Anders, K.5
Eisen, M.B.6
Brown, P.O.7
Botstein, D.8
Futcher, B.9
-
45
-
-
0028113846
-
Fluctuation analysis of motor protein movement and single enzyme kinetics
-
Svoboda, K., Mitra, P.P., Block, S.M., 1994. Fluctuation analysis of motor protein movement and single enzyme kinetics. Proc. Natl. Acad. Sci. U.S.A. 91, 11782-11786.
-
(1994)
Proc. Natl. Acad. Sci. U.S.A.
, vol.91
, pp. 11782-11786
-
-
Svoboda, K.1
Mitra, P.P.2
Block, S.M.3
-
46
-
-
0028837312
-
The human dystrophin gene requires 16 hours to be transcribed and is cotranscriptionally spliced
-
Tennyson, C.N., Klamut, H.J., Worton, R.G., 1995. The human dystrophin gene requires 16 hours to be transcribed and is cotranscriptionally spliced. Nat. Genet. 9, 184-190.
-
(1995)
Nat. Genet.
, vol.9
, pp. 184-190
-
-
Tennyson, C.N.1
Klamut, H.J.2
Worton, R.G.3
-
47
-
-
19244382579
-
Diversity in the rates of transcript elongation by single RNA polymerase molecules
-
Tolić-Nørrelykke, S.F., Engh, A.M., Landick, R., Gelles, J., 2004. Diversity in the rates of transcript elongation by single RNA polymerase molecules. J. Biol. Chem. 279, 3292-3299.
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 3292-3299
-
-
Tolić-Nørrelykke, S.F.1
Engh, A.M.2
Landick, R.3
Gelles, J.4
-
48
-
-
0031008221
-
Basic mechanisms of transcript elongation and its regulation
-
Uptain, S.M., Kane, C.M., Chamberlin, M.J., 1997. Basic mechanisms of transcript elongation and its regulation. Annu. Rev. Biochem. 66, 117-172.
-
(1997)
Annu. Rev. Biochem.
, vol.66
, pp. 117-172
-
-
Uptain, S.M.1
Kane, C.M.2
Chamberlin, M.J.3
-
49
-
-
0032584643
-
An integrated model of the transcription complex in elongation, termination, and editing
-
von Hippel, P.H., 1998. An integrated model of the transcription complex in elongation, termination, and editing. Science 281, 660-665.
-
(1998)
Science
, vol.281
, pp. 660-665
-
-
Von Hippel, P.H.1
-
50
-
-
0037058904
-
Reaction pathways in transcript elongation
-
von Hippel, P.H., Pasman, Z., 2002. Reaction pathways in transcript elongation. Biophys. Chem. 101-102, 401-423.
-
(2002)
Biophys. Chem.
, vol.101-102
, pp. 401-423
-
-
Von Hippel, P.H.1
Pasman, Z.2
-
51
-
-
0031934004
-
Force generation in RNA polymerase
-
Wang, H.-Y., Elston, T., Mogilner, A., Oster, G., 1998. Force generation in RNA polymerase. Biophys. J. 74, 1186-1202.
-
(1998)
Biophys. J.
, vol.74
, pp. 1186-1202
-
-
Wang, H.-Y.1
Elston, T.2
Mogilner, A.3
Oster, G.4
|