-
2
-
-
18744361871
-
Enhancement of cellular memory by reducing stochastic transitions
-
Acar, M., Becskei, A. & van Oudenaarden, A. (2005). Enhancement of cellular memory by reducing stochastic transitions. Nature435, 228–232.
-
(2005)
Nature
, vol.435
, pp. 228-232
-
-
Acar, M.1
Becskei, A.2
Van Oudenaarden, A.3
-
3
-
-
30744470375
-
Simulating rare events in equilibrium or nonequilibrium stochastic systems
-
Allen, R. J., Frenkel, D. & ten Wolde, P. R. (2006). Simulating rare events in equilibrium or nonequilibrium stochastic systems. J. Chem. Phys.124, 024102.
-
(2006)
J. Chem. Phys
, vol.124
, pp. 024102
-
-
Allen, R.J.1
Frenkel, D.2
Ten Wolde, P.R.3
-
4
-
-
18144425774
-
Sampling rare switching events in biochemical networks
-
Allen, R. J., Warren, P. B. & Wolde, P. R. T. (2005). Sampling rare switching events in biochemical networks. Phys. Rev. Lett.94, 018104.
-
(2005)
Phys. Rev. Lett
, vol.94
, pp. 018104
-
-
Allen, R.J.1
Warren, P.B.2
Wolde, P.R.T.3
-
5
-
-
1242274449
-
Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems
-
Angeli, D., Ferrell, J. E. & Sontag, E. D. (2004). Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems. Proc. Natl. Acad. Sci. USA101, 1822–1827.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 1822-1827
-
-
Angeli, D.1
Ferrell, J.E.2
Sontag, E.D.3
-
6
-
-
37649030145
-
Stability puzzles in phage lambda
-
Aurell, E., Brown, S., Johanson, J. & Sneppen, K. (2002). Stability puzzles in phage lambda. Phys. Rev. E65, 051914.
-
(2002)
Phys. Rev. E
, vol.65
, pp. 051914
-
-
Aurell, E.1
Brown, S.2
Johanson, J.3
Sneppen, K.4
-
7
-
-
33745287724
-
Noise in protein expression scales with natural protein abundance
-
Bar-Even, A., Paulsson, J., Maheshri, N., et al. (2006). Noise in protein expression scales with natural protein abundance. Nat. Genet.38, 636–643.
-
(2006)
Nat. Genet
, vol.38
, pp. 636-643
-
-
Bar-Even, A.1
Paulsson, J.2
Maheshri, N.3
-
8
-
-
34247583988
-
Affinity of antigen encounter and other early b-cell signals determine b-cell fate
-
Benson, M. J., Erickson, L. D., Gleeson, M.W. & Noelle, R. J. (2007). Affinity of antigen encounter and other early B-cell signals determine B-cell fate. Curr. Opin. Immunol.19, 275–280.
-
(2007)
Curr. Opin. Immunol
, vol.19
, pp. 275-280
-
-
Benson, M.J.1
Erickson, L.D.2
Gleeson, M.W.3
Noelle, R.J.4
-
9
-
-
0035875668
-
Cell signaling can direct either binary or graded transcriptional responses
-
Biggar, S. R. & Crabtree, G. R. (2001). Cell signaling can direct either binary or graded transcriptional responses. EMBO J. 20, 3167–3176.
-
(2001)
EMBO J
, vol.20
, pp. 3167-3176
-
-
Biggar, S.R.1
Crabtree, G.R.2
-
10
-
-
15744387380
-
Transcriptional regulation by the numbers: Applications
-
Bintu, L., Buchler, N. E., Garcia, H. G., et al. (2005). Transcriptional regulation by the numbers: applications. Curr. Opin. Gen. Dev.15, 125–135.
-
(2005)
Curr. Opin. Gen. Dev
, vol.15
, pp. 125-135
-
-
Bintu, L.1
Buchler, N.E.2
Garcia, H.G.3
-
11
-
-
0036424048
-
Transition path sampling: Throwing ropes over rough mountain passes, in the dark
-
Bolhuis, P. G., Chandler, D., Dellago, C. & Geissler, P. L. (2002). Transition path sampling: throwing ropes over rough mountain passes, in the dark. Annu. Rev. Phys. Chem.53, 291–318.
-
(2002)
Annu. Rev. Phys. Chem
, vol.53
, pp. 291-318
-
-
Bolhuis, P.G.1
Chandler, D.2
Dellago, C.3
Geissler, P.L.4
-
12
-
-
27144517984
-
Interlinked fast and slow positive feedback loops drive reliable cell decisions
-
Brandman, O., Ferrell, J. E., Li, R. & Meyer, T. (2005). Interlinked fast and slow positive feedback loops drive reliable cell decisions. Science310, 496–498.
-
(2005)
Science
, vol.310
, pp. 496-498
-
-
Brandman, O.1
Ferrell, J.E.2
Li, R.3
Meyer, T.4
-
13
-
-
33645027986
-
Stochastic protein expression in individual cells at the single molecule level
-
Cai, L., Friedman, N. & Xie, X. S. (2006). Stochastic protein expression in individual cells at the single molecule level. Nature440, 358–362.
-
(2006)
Nature
, vol.440
, pp. 358-362
-
-
Cai, L.1
Friedman, N.2
Xie, X.S.3
-
14
-
-
33947730608
-
Asymmetric t lymphocyte division in the initiation of adaptive immune responses
-
Chang, J. T., Palanivel, V. R., Kinjyo, I., et al. (2007). Asymmetric T lymphocyte division in the initiation of adaptive immune responses. Science315, 1687–1691.
-
(2007)
Science
, vol.315
, pp. 1687-1691
-
-
Chang, J.T.1
Palanivel, V.R.2
Kinjyo, I.3
-
15
-
-
34848853915
-
Conversion of mature b cells into t cells by dedifferentiation to uncommitted progenitors
-
Cobaleda, C., Jochum, W. & Busslinger, M. (2007). Conversion of mature B cells into T cells by dedifferentiation to uncommitted progenitors. Nature449, 473–477.
-
(2007)
Nature
, vol.449
, pp. 473-477
-
-
Cobaleda, C.1
Jochum, W.2
Busslinger, M.3
-
16
-
-
26944476331
-
Regulated cell-to-cell variation in a cell-fate decision system
-
Colman-Lerner, A., Gordon, A., Serra, E., et al. (2005). Regulated cell-to-cell variation in a cell-fate decision system. Nature437, 699–706.
-
(2005)
Nature
, vol.437
, pp. 699-706
-
-
Colman-Lerner, A.1
Gordon, A.2
Serra, E.3
-
17
-
-
34249108271
-
Regulation of aid expression in the immune response
-
Crouch, E. E., Li, Z., Takizawa, M., et al. (2007). Regulation of AID expression in the immune response. J. Exp. Med.204, 1145–1156.
-
(2007)
J. Exp. Med
, vol.204
, pp. 1145-1156
-
-
Crouch, E.E.1
Li, Z.2
Takizawa, M.3
-
18
-
-
34249714440
-
The transcriptional repressor gfi-1 antagonizes pu.1 activity through protein-protein interaction
-
Dahl, R., Iyer, S. R., Owens, K. S., et al. (2007). The transcriptional repressor GFI-1 antagonizes PU.1 activity through protein-protein interaction. J. Biol. Chem.282, 6473–6483.
-
(2007)
J. Biol. Chem
, vol.282
, pp. 6473-6483
-
-
Dahl, R.1
Iyer, S.R.2
Owens, K.S.3
-
19
-
-
0036500609
-
A genomic regulatory network for development
-
Davidson, E. H., Rast, J. P., Oliveri, P., et al. (2002). A genomic regulatory network for development. Science295, 1669–1678.
-
(2002)
Science
, vol.295
, pp. 1669-1678
-
-
Davidson, E.H.1
Rast, J.P.2
Oliveri, P.3
-
20
-
-
0000729781
-
Transition path sampling and calculation of rate constants
-
Dellago, C., Bolhuis, P. G., Csajka, F. & Chandler, D. (1998). Transition path sampling and calculation of rate constants. J. Chem. Phys.108, 1964–1977.
-
(1998)
J. Chem. Phys
, vol.108
, pp. 1964-1977
-
-
Dellago, C.1
Bolhuis, P.G.2
Csajka, F.3
Chandler, D.4
-
21
-
-
17144422917
-
Interleukin-7 is necessary to maintain the b cell potential in common lymphoid progenitors
-
Dias, S., Silva, H., Cumano, A. & Vieira, P. (2005). Interleukin-7 is necessary to maintain the B cell potential in common lymphoid progenitors. J. Exp. Med.201, 971–979.
-
(2005)
J. Exp. Med
, vol.201
, pp. 971-979
-
-
Dias, S.1
Silva, H.2
Cumano, A.3
Vieira, P.4
-
22
-
-
15744396343
-
Revisited gene regulation in bacteriophage lambda
-
Dodd, I. B., Shearwin, K. E. & Egan, J. B. (2005). Revisited gene regulation in bacteriophage lambda. Curr. Opin. Genet. Dev.15, 145–152.
-
(2005)
Curr. Opin. Genet. Dev
, vol.15
, pp. 145-152
-
-
Dodd, I.B.1
Shearwin, K.E.2
Egan, J.B.3
-
23
-
-
36449004539
-
Large fluctuations and optimal paths in chemical kinetics
-
Dykman, M. I., Mori, E., Ross, J. & Hunt, P. M. (1994). Large fluctuations and optimal paths in chemical kinetics. J. Chem. Phys.100, 5735–5750.
-
(1994)
J. Chem. Phys
, vol.100
, pp. 5735-5750
-
-
Dykman, M.I.1
Mori, E.2
Ross, J.3
Hunt, P.M.4
-
24
-
-
34249932435
-
Probing transcription factor dynamics at the single-molecule level in a living cell
-
Elf, J., Li, G.-W. & Xie, X. S. (2007). Probing transcription factor dynamics at the single-molecule level in a living cell. Science316, 1191–1194.
-
(2007)
Science
, vol.316
, pp. 1191-1194
-
-
Elf, J.1
Li, G.-W.2
Xie, X.S.3
-
25
-
-
0034688173
-
A synthetic oscillatory network of transcriptional regulators
-
Elowitz, M. B. & Leibler, S. (2000). A synthetic oscillatory network of transcriptional regulators. Nature403, 335–338.
-
(2000)
Nature
, vol.403
, pp. 335-338
-
-
Elowitz, M.B.1
Leibler, S.2
-
26
-
-
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. Science297, 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
-
27
-
-
33751572545
-
Gene regulatory networks: A coarse-grained, equation-free approach to multiscale computation
-
Erban, R., Kevrekidis, I. G., Adalsteinsson, D. & Elston, T. C. (2006). Gene regulatory networks: a coarse-grained, equation-free approach to multiscale computation. J. Chem. Phys.124, 084106.
-
(2006)
J. Chem. Phys
, vol.124
, pp. 084106
-
-
Erban, R.1
Kevrekidis, I.G.2
Adalsteinsson, D.3
Elston, T.C.4
-
29
-
-
21444438810
-
A stochastic analysis of first-order reaction networks
-
Gadgil, C., Lee, C. H. & Othmer, H. G. (2005). A stochastic analysis of first-order reaction networks. Bull. Math. Biol.67, 901–946.
-
(2005)
Bull. Math. Biol
, vol.67
, pp. 901-946
-
-
Gadgil, C.1
Lee, C.H.2
Othmer, H.G.3
-
30
-
-
0034688174
-
Construction of a genetic toggle switch in
-
Gardner, T. S., Cantor, C. R. & Collins, J. J. (2000). Construction of a genetic toggle switch in Escherichia coli. Nature403, 339–342.
-
(2000)
Nature
, vol.403
, pp. 339-342
-
-
Gardner, T.S.1
Cantor, C.R.2
Collins, J.J.3
-
31
-
-
33645525254
-
Direct evaluation of large-deviation functions
-
Giardina, C., Kurchan, J. & Peliti, L. (2006). Direct evaluation of large-deviation functions. Phys. Rev. Lett.96, 120603.
-
(2006)
Phys. Rev. Lett
, vol.96
, pp. 120603
-
-
Giardina, C.1
Kurchan, J.2
Peliti, L.3
-
32
-
-
0001144902
-
Efficient exact stochastic simulation of chemical systems with many species and many channels
-
Gibson, M. A. & Bruck, J. (2000). Efficient exact stochastic simulation of chemical systems with many species and many channels. J. Phys. Chem. A104, 1876–1889.
-
(2000)
J. Phys. Chem. A
, vol.104
, pp. 1876-1889
-
-
Gibson, M.A.1
Bruck, J.2
-
33
-
-
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
-
34
-
-
0035933994
-
Approximate accelerated stochastic simulation of chemically reacting systems
-
Gillespie, D. T. (2001). Approximate accelerated stochastic simulation of chemically reacting systems. J. Chem. Phys.115, 1716–1733.
-
(2001)
J. Chem. Phys
, vol.115
, pp. 1716-1733
-
-
Gillespie, D.T.1
-
35
-
-
34249950625
-
Stochastic simulation of chemical kinetics
-
Gillespie, D. T. (2007). Stochastic simulation of chemical kinetics. Annu. Rev. Phys. Chem.58, 35–55.
-
(2007)
Annu. Rev. Phys. Chem
, vol.58
, pp. 35-55
-
-
Gillespie, D.T.1
-
36
-
-
0015609281
-
The logical analysis of continuous, nonlinear biochemical control networks
-
Glass, L. & Kauffman, S. A. (1973). The logical analysis of continuous, nonlinear biochemical control networks. J. Theor. Biol.39, 103–129.
-
(1973)
J. Theor. Biol
, vol.39
, pp. 103-129
-
-
Glass, L.1
Kauffman, S.A.2
-
37
-
-
34447099234
-
Probing the limits to positional information
-
Gregor, T., Tank, D.W., Wieschaus, E. F. & Bialek, W. (2007a). Probing the limits to positional information. Cell130, 153–164.
-
(2007)
Cell
, vol.130
, pp. 153-164
-
-
Gregor, T.1
Tank, D.W.2
Wieschaus, E.F.3
Bialek, W.4
-
38
-
-
34447104600
-
Stability and nuclear dynamics of the bicoid morphogen gradient
-
Gregor, T., Wieschaus, E. F., McGregor, A. P., Bialek, W. & Tank, D.W. (2007b). Stability and nuclear dynamics of the bicoid morphogen gradient. Cell130, 141–152.
-
(2007)
Cell
, vol.130
, pp. 141-152
-
-
Gregor, T.1
Wieschaus, E.F.2
McGregor, A.P.3
Bialek, W.4
Tank, D.W.5
-
39
-
-
32844455250
-
A bottom-up approach to gene regulation
-
Guido, N. J., Wang, X., Adalsteinsson, D., et al. (2006). A bottom-up approach to gene regulation. Nature439, 856–860.
-
(2006)
Nature
, vol.439
, pp. 856-860
-
-
Guido, N.J.1
Wang, X.2
Adalsteinsson, D.3
-
40
-
-
33746047649
-
Grand canonical markov model: A stochastic theory for open nonequilibrium biochemical networks
-
Heuett, W. J. & Qian, H. (2006). Grand canonical markov model: a stochastic theory for open nonequilibrium biochemical networks. J. Chem. Phys.124, 044110.
-
(2006)
J. Chem. Phys
, vol.124
, pp. 044110
-
-
Heuett, W.J.1
Qian, H.2
-
41
-
-
33644843788
-
Zinc-finger transcription factor gfi-1: Versatile regulator of lymphocytes, neutrophils and hematopoietic stem cells
-
Hock, H. & Orkin, S. H. (2006). Zinc-finger transcription factor Gfi-1: versatile regulator of lymphocytes, neutrophils and hematopoietic stem cells. Curr. Opin. Hematol.13, 1–6.
-
(2006)
Curr. Opin. Hematol
, vol.13
, pp. 1-6
-
-
Hock, H.1
Orkin, S.H.2
-
42
-
-
0037047149
-
Gata-3 transcriptional imprinting in th2 lymphocytes: A mathematical model
-
Hofer, T., Nathansen, H., Lohning, M., Radbruch, A. & Heinrich, R. (2002). GATA-3 transcriptional imprinting in Th2 lymphocytes: a mathematical model. Proc. Natl. Acad. Sci. USA99, 9364–9368.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 9364-9368
-
-
Hofer, T.1
Nathansen, H.2
Lohning, M.3
Radbruch, A.4
Heinrich, R.5
-
43
-
-
28844496741
-
Self-regulating gene: An exact solution
-
Hornos, J. E. M., Schultz, D., Innocentini, G. C. P., et al. (2005). Self-regulating gene: an exact solution. Phys. Rev. E72, 051907.
-
(2005)
Phys. Rev. E
, vol.72
, pp. 051907
-
-
Hornos, J.E.M.1
Schultz, D.2
Innocentini, G.C.P.3
-
44
-
-
0037075022
-
Establishment of developmental precision and proportions in the early
-
Houchmandzadeh, B., Wieschaus, E. & Leibler, S. (2002). Establishment of developmental precision and proportions in the early Drosophila embryo. Nature415, 798–802.
-
(2002)
Nature
, vol.415
, pp. 798-802
-
-
Houchmandzadeh, B.1
Wieschaus, E.2
Leibler, S.3
-
45
-
-
28844448557
-
Finding the center reliably: Robust patterns of developmental gene expression
-
Howard, M. & ten Wolde, P. R. (2005). Finding the center reliably: robust patterns of developmental gene expression. Phys. Rev. Lett.95, 208103.
-
(2005)
Phys. Rev. Lett
, vol.95
, pp. 208103
-
-
Howard, M.1
Ten Wolde, P.R.2
-
46
-
-
0030954167
-
Multilineage gene expression precedes commitment in the hemopoietic system
-
Hu, M., Krause, D., Greaves, M., et al. (1997). Multilineage gene expression precedes commitment in the hemopoietic system. Genes Dev. 11, 774–785.
-
(1997)
Genes Dev
, vol.11
, pp. 774-785
-
-
Hu, M.1
Krause, D.2
Greaves, M.3
-
47
-
-
34248199004
-
Bifurcation dynamics in lineage-commitment in bipotent progenitor cells
-
Huang, S., Guo, Y.-P., May, G. & Enver, T. (2007). Bifurcation dynamics in lineage-commitment in bipotent progenitor cells. Dev. Biol.305, 695–713.
-
(2007)
Dev. Biol
, vol.305
, pp. 695-713
-
-
Huang, S.1
Guo, Y.-P.2
May, G.3
Enver, T.4
-
48
-
-
33845629747
-
Solving the chemical master equation for monomolecular reaction systems analytically
-
Jahnke, T. & Huisinga, W. (2007). Solving the chemical master equation for monomolecular reaction systems analytically. J. Math. Biol.54, 1–26.
-
(2007)
J. Math. Biol
, vol.54
, pp. 1-26
-
-
Jahnke, T.1
Huisinga, W.2
-
49
-
-
33749137281
-
Quantitative and predictive model of transcriptional control of the drosophila melanogaster even skipped gene
-
Janssens, H., Hou, S., Jaeger, J., et al. (2006). Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene. Nat. Genet.38, 1159–1165.
-
(2006)
Nat. Genet
, vol.38
, pp. 1159-1165
-
-
Janssens, H.1
Hou, S.2
Jaeger, J.3
-
50
-
-
7244231012
-
Plasma cell ontogeny defined by quantitative changes in blimp-1 expression
-
Kallies, A., Hasbold, J., Tarlinton, D. M., et al. (2004). Plasma cell ontogeny defined by quantitative changes in Blimp-1 expression. J. Exp. Med.200, 967–977.
-
(2004)
J. Exp. Med
, vol.200
, pp. 967-977
-
-
Kallies, A.1
Hasbold, J.2
Tarlinton, D.M.3
-
51
-
-
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, 437–467.
-
(1969)
J. Theor. Biol
, vol.22
, pp. 437-467
-
-
Kauffman, S.A.1
-
52
-
-
34548686549
-
Heritable stochastic switching revealed by single-cell genealogy
-
Kaufmann, B. B., Yang, Q., Mettetal, J. T. & van Oudenaarden, A. (2007). Heritable stochastic switching revealed by single-cell genealogy. PLoS Biol. 5, e239.
-
(2007)
Plos Biol
, vol.5
-
-
Kaufmann, B.B.1
Yang, Q.2
Mettetal, J.T.3
Van Oudenaarden, A.4
-
53
-
-
18244386710
-
Il-7 receptor signaling is necessary for stage transition in adult b cell development through up-regulation of ebf
-
Kikuchi, K., Lai, A. Y., Hsu, C.-L. & Kondo, M. (2005). IL-7 receptor signaling is necessary for stage transition in adult B cell development through up-regulation of EBF. J. Exp. Med.201, 1197–1203.
-
(2005)
J. Exp. Med
, vol.201
, pp. 1197-1203
-
-
Kikuchi, K.1
Lai, A.Y.2
Hsu, C.-L.3
Kondo, M.4
-
54
-
-
0023946242
-
Hemopoietic lineage switch: V-raf oncogene converts emu-myc transgenic b cells into macrophages
-
Klinken, S. P., Alexander, W. S. & Adams, J. M. (1988). Hemopoietic lineage switch: v-raf oncogene converts Emu-myc transgenic B cells into macrophages. Cell53, 857–867.
-
(1988)
Cell
, vol.53
, pp. 857-867
-
-
Klinken, S.P.1
Alexander, W.S.2
Adams, J.M.3
-
55
-
-
0034699390
-
Cell-fate conversion of lymphoid-committed progenitors by instructive actions of cytokines
-
Kondo, M., Scherer, D. C., Miyamoto, T., et al. (2000). Cell-fate conversion of lymphoid-committed progenitors by instructive actions of cytokines. Nature407, 383–386.
-
(2000)
Nature
, vol.407
, pp. 383-386
-
-
Kondo, M.1
Scherer, D.C.2
Miyamoto, T.3
-
56
-
-
33846593911
-
A two-step, pu.1-dependent mechanism for developmentally regulated chromatin remodeling and transcription of the c-fms gene
-
Krysinska, H., Hoogenkamp, M., Ingram, R., et al. (2007). A two-step, PU.1-dependent mechanism for developmentally regulated chromatin remodeling and transcription of the c-fms gene. Mol. Cell Biol.27, 878–887.
-
(2007)
Mol. Cell Biol
, vol.27
, pp. 878-887
-
-
Krysinska, H.1
Hoogenkamp, M.2
Ingram, R.3
-
57
-
-
33846257739
-
Reprogramming of committed t cell progenitors to macrophages and dendritic cells by c/ebp alpha and pu.1 transcription factors
-
Laiosa, C. V., Stadtfeld, M., Xie, H., de Andres-Aguayo, L. & Graf, T. (2006). Reprogramming of committed T cell progenitors to macrophages and dendritic cells by C/EBP alpha and PU.1 transcription factors. Immunity25, 731–744.
-
(2006)
Immunity
, vol.25
, pp. 731-744
-
-
Laiosa, C.V.1
Stadtfeld, M.2
Xie, H.3
De Andres-Aguayo, L.4
Graf, T.5
-
58
-
-
33747196725
-
Multilineage transcriptional priming and determination of alternate hematopoietic cell fates
-
Laslo, P., Spooner, C. J., Warmflash, A., et al. (2006). Multilineage transcriptional priming and determination of alternate hematopoietic cell fates. Cell126, 755–766.
-
(2006)
Cell
, vol.126
, pp. 755-766
-
-
Laslo, P.1
Spooner, C.J.2
Warmflash, A.3
-
59
-
-
33646397850
-
Genetic toggle switch without cooperative binding
-
Lipshtat, A., Loinger, A., Balaban, N. Q. & Biham, O. (2006). Genetic toggle switch without cooperative binding. Phys. Rev. Lett.96, 188101.
-
(2006)
Phys. Rev. Lett
, vol.96
, pp. 188101
-
-
Lipshtat, A.1
Loinger, A.2
Balaban, N.Q.3
Biham, O.4
-
60
-
-
33646167129
-
Plasticity of the cis-regulatory input function of a gene
-
Mayo, A. E., Setty, Y., Shavit, S., Zaslaver, A. & Alon, U. (2006). Plasticity of the cis-regulatory input function of a gene. PLoS Biol. 4, 555–561.
-
(2006)
Plos Biol
, vol.4
, pp. 555-561
-
-
Mayo, A.E.1
Setty, Y.2
Shavit, S.3
Zaslaver, A.4
Alon, U.5
-
61
-
-
5044249424
-
Assembling a gene regulatory network for specification of the b cell fate
-
Medina, K. L., Pongubala, J. M. R., Reddy, K. L., et al. (2004). Assembling a gene regulatory network for specification of the B cell fate. Dev. Cell7, 607–617.
-
(2004)
Dev. Cell
, vol.7
, pp. 607-617
-
-
Medina, K.L.1
Pongubala, J.M.R.2
Reddy, K.L.3
-
62
-
-
14544270028
-
Gene regulatory networks orchestrating b cell fate specification, commitment, and differentiation
-
Medina, K. L. & Singh, H. (2005). Gene regulatory networks orchestrating B cell fate specification, commitment, and differentiation. Curr. Top. Microbiol. Immunol.290, 1–14.
-
(2005)
Curr. Top. Microbiol. Immunol
, vol.290
, pp. 1-14
-
-
Medina, K.L.1
Singh, H.2
-
63
-
-
33646540711
-
Predicting stochastic gene expression dynamics in single cells
-
Mettetal, J. T., Muzzey, D., Pedraza, J. M., Ozbudak, E. M. & van Oudenaarden, A. (2006). Predicting stochastic gene expression dynamics in single cells. Proc. Natl. Acad. Sci. USA103, 7304–7309.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 7304-7309
-
-
Mettetal, J.T.1
Muzzey, D.2
Pedraza, J.M.3
Ozbudak, E.M.4
Van Oudenaarden, A.5
-
64
-
-
0036070180
-
Myeloid or lymphoid promiscuity as a critical step in hematopoietic lineage commitment
-
Miyamoto, T., Iwasaki, H., Reizis, B., et al. (2002). Myeloid or lymphoid promiscuity as a critical step in hematopoietic lineage commitment. Dev. Cell3, 137–147.
-
(2002)
Dev. Cell
, vol.3
, pp. 137-147
-
-
Miyamoto, T.1
Iwasaki, H.2
Reizis, B.3
-
65
-
-
33747189803
-
When it comes to decisions, myeloid progenitors crave positive feedback
-
Muzzey, D. & van Oudenaarden, A. (2006). When it comes to decisions, myeloid progenitors crave positive feedback. Cell126, 650–652.
-
(2006)
Cell
, vol.126
, pp. 650-652
-
-
Muzzey, D.1
Van Oudenaarden, A.2
-
66
-
-
33745220278
-
Single-cell proteomic analysis of
-
Newman, J. R. S., Ghaemmaghami, S., Ihmels, J., et al. (2006). Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature441, 840–846.
-
(2006)
Nature
, vol.441
, pp. 840-846
-
-
Newman, J.R.S.1
Ghaemmaghami, S.2
Ihmels, J.3
-
67
-
-
0001389945
-
Enzyme induction as an all-or-none phenomenon
-
Novick, A. & Weiner, M. (1957). Enzyme induction as an all-or-none phenomenon. Proc. Natl. Acad. Sci. USA43, 553–566.
-
(1957)
Proc. Natl. Acad. Sci. USA
, vol.43
, pp. 553-566
-
-
Novick, A.1
Weiner, M.2
-
68
-
-
0034303586
-
Diversification of haematopoietic stem cells to specific lineages
-
Orkin, S. H. (2000). Diversification of haematopoietic stem cells to specific lineages. Nat. Rev. Genet.1, 57–64.
-
(2000)
Nat. Rev. Genet
, vol.1
, pp. 57-64
-
-
Orkin, S.H.1
-
69
-
-
1442354192
-
Multistability in the lactose utilization network of
-
Ozbudak, E. M., Thattai, M., Lim, H. N., Shraiman, B. I. & van Oudenaarden, A. (2004). Multistability in the lactose utilization network of Escherichia coli. Nature427, 737–740.
-
(2004)
Nature
, vol.427
, pp. 737-740
-
-
Ozbudak, E.M.1
Thattai, M.2
Lim, H.N.3
Shraiman, B.I.4
Van Oudenaarden, A.5
-
70
-
-
0842285841
-
Summing up the noise in genetic networks
-
Paulsson, J. (2004). Summing up the noise in genetic networks. Nature427, 415–418.
-
(2004)
Nature
, vol.427
, pp. 415-418
-
-
Paulsson, J.1
-
71
-
-
15544388848
-
Noise propagation in genetic networks
-
Pedraza, J. & van Oudenaarden, A. (2005). Noise propagation in genetic networks. Science307, 1965–1969.
-
(2005)
Science
, vol.307
, pp. 1965-1969
-
-
Pedraza, J.1
Van Oudenaarden, A.2
-
72
-
-
0004194541
-
-
Cambridge, MA: Blackwell Scientific Publications
-
Ptashne, M. (1992). A Genetic Switch. Cambridge, MA: Blackwell Scientific Publications.
-
(1992)
A Genetic Switch
-
-
Ptashne, M.1
-
73
-
-
0942279178
-
Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method
-
Rathinam, M., Petzold, L. R., Cao, Y. & Gillespie, D. T. (2003). Stiffness in stochastic chemically reacting systems: the implicit tau-leaping method. J. Chem. Phys.119, 12784–12794.
-
(2003)
J. Chem. Phys
, vol.119
, pp. 12784-12794
-
-
Rathinam, M.1
Petzold, L.R.2
Cao, Y.3
Gillespie, D.T.4
-
74
-
-
33747871080
-
Quantitative models of developmental pattern formation
-
Reeves, G. T., Muratov, C. B., Schüpbach, T. & Shvartsman, S. Y. (2006). Quantitative models of developmental pattern formation. Dev. Cell11, 289–300.
-
(2006)
Dev. Cell
, vol.11
, pp. 289-300
-
-
Reeves, G.T.1
Muratov, C.B.2
Schüpbach, T.3
Shvartsman, S.Y.4
-
75
-
-
41349084732
-
Optimal path to epigenetic switching
-
Roma, D. M., O’Flanagan, R. A., Ruckenstein, A. E., Sengupta, A. M. & Mukhopadhyay, R. (2005). Optimal path to epigenetic switching. Phys. Rev. E71, 011902.
-
(2005)
Phys. Rev. E
, vol.71
, pp. 011902
-
-
Roma, D.M.1
O’Flanagan, R.A.2
Ruckenstein, A.E.3
Sengupta, A.M.4
Mukhopadhyay, R.5
-
76
-
-
15544371346
-
Gene regulation at the single-cell level
-
Rosenfield, N., Young, W., Alon, U., Swain, P. S. & Elowitz, M. B. (2005). Gene regulation at the single-cell level. Science307, 1962–1965.
-
(2005)
Science
, vol.307
, pp. 1962-1965
-
-
Rosenfield, N.1
Young, W.2
Alon, U.3
Swain, P.S.4
Elowitz, M.B.5
-
77
-
-
17444396980
-
Molecular genetics of t cell development
-
Rothenberg, E. V. & Taghon, T. (2005). Molecular genetics of T cell development. Annu. Rev. Immunol.23, 601–649.
-
(2005)
Annu. Rev. Immunol
, vol.23
, pp. 601-649
-
-
Rothenberg, E.V.1
Taghon, T.2
-
78
-
-
22944451159
-
Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions
-
Salis, H. & Kaznessis, Y. (2005a). Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions. J. Chem. Phys.122, 54103.
-
(2005)
J. Chem. Phys
, vol.122
, pp. 54103
-
-
Salis, H.1
Kaznessis, Y.2
-
79
-
-
33645463036
-
An equation-free probabilistic steady-state approximation: Dynamic application to the stochastic simulation of biochemical reaction networks
-
Salis, H. & Kaznessis, Y. N. (2005b). An equation-free probabilistic steady-state approximation: dynamic application to the stochastic simulation of biochemical reaction networks. J. Chem. Phys.123, 214106.
-
(2005)
J. Chem. Phys
, vol.123
, pp. 214106
-
-
Salis, H.1
Kaznessis, Y.N.2
-
80
-
-
0346688719
-
Why the lysogenic state of phage lambda is so stable: A mathematical modeling approach
-
Santillan, M. & Mackey, M. C. (2004). Why the lysogenic state of phage lambda is so stable: a mathematical modeling approach. Biophys. J.86, 75–84.
-
(2004)
Biophys. J
, vol.86
, pp. 75-84
-
-
Santillan, M.1
Mackey, M.C.2
-
81
-
-
19344375742
-
Transcriptional control in the segmentation gene network of drosophila
-
Schroeder, M. D., Pearce, M., Fak, J., et al. (2004). Transcriptional control in the segmentation gene network of Drosophila. PLoS Biol. 2, e271.
-
(2004)
Plos Biol
, vol.2
-
-
Schroeder, M.D.1
Pearce, M.2
Fak, J.3
-
82
-
-
33747133955
-
Graded levels of interferon regulatory factor-4 coordinate isotype switching with plasma cell differentiation
-
Sciammas, R., Shaffer, A. L., Schatz, J. J., et al. (2006). Graded levels of interferon regulatory factor-4 coordinate isotype switching with plasma cell differentiation. Immunity25, 225–236.
-
(2006)
Immunity
, vol.25
, pp. 225-236
-
-
Sciammas, R.1
Shaffer, A.L.2
Schatz, J.J.3
-
83
-
-
3042693975
-
Early b cell factor promotes b lymphopoiesis with reduced interleukin 7 responsiveness in the absence of e2a
-
Seet, C. S., Brumbaugh, R. L. & Kee, B. L. (2004). Early B cell factor promotes B lymphopoiesis with reduced interleukin 7 responsiveness in the absence of E2A. J. Exp. Med.199, 1689–1700.
-
(2004)
J. Exp. Med
, vol.199
, pp. 1689-1700
-
-
Seet, C.S.1
Brumbaugh, R.L.2
Kee, B.L.3
-
84
-
-
0038610819
-
Detailed map of a
-
Setty, Y., Mayo, A. E., Surette, M. G. & Alon, U. (2003). Detailed map of a cis-regulatory input function. Proc. Natl. Acad. Sci. USA100, 7702–7707.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 7702-7707
-
-
Setty, Y.1
Mayo, A.E.2
Surette, M.G.3
Alon, U.4
-
85
-
-
32044445540
-
Efficient computation of the first passage time distribution of the generalized master equation by steady-state relaxation
-
Shalloway, D. & Faradjian, A. K. (2006). Efficient computation of the first passage time distribution of the generalized master equation by steady-state relaxation. J. Chem. Phys.124, 054112.
-
(2006)
J. Chem. Phys
, vol.124
, pp. 054112
-
-
Shalloway, D.1
Faradjian, A.K.2
-
86
-
-
33845257870
-
Variability and memory of protein levels in human cells
-
Sigal, A., Milo, R., Cohen, A., et al. (2006). Variability and memory of protein levels in human cells. Nature444, 643–646.
-
(2006)
Nature
, vol.444
, pp. 643-646
-
-
Sigal, A.1
Milo, R.2
Cohen, A.3
-
87
-
-
17044440153
-
Contingent gene regulatory networks and b cell fate specification
-
Singh, H., Medina, K. L. & Pongubala, J. M. R. (2005). Contingent gene regulatory networks and B cell fate specification. Proc. Natl. Acad. Sci. USA102, 4949–4953.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 4949-4953
-
-
Singh, H.1
Medina, K.L.2
Pongubala, J.M.R.3
-
88
-
-
84934439502
-
Gene regulatory networks that orchestrate the development of b lymphocyte precursors
-
Singh, H., Pongubala, J. M. R. & Medina, K. L. (2007). Gene regulatory networks that orchestrate the development of B lymphocyte precursors. Adv. Exp. Med. Biol.596, 57–62.
-
(2007)
Adv. Exp. Med. Biol
, vol.596
, pp. 57-62
-
-
Singh, H.1
Pongubala, J.M.R.2
Medina, K.L.3
-
90
-
-
33645293152
-
An excitable gene regulatory circuit induces transient cellular differentiation
-
Suel, G. M., Garcia-Ojalvo, J., Liberman, L. M. & Elowitz, M. B. (2006). An excitable gene regulatory circuit induces transient cellular differentiation. Nature440, 545–550.
-
(2006)
Nature
, vol.440
, pp. 545-550
-
-
Suel, G.M.1
Garcia-Ojalvo, J.2
Liberman, L.M.3
Elowitz, M.B.4
-
91
-
-
34047118521
-
Tunability and noise dependence in differentiation dynamics
-
Suel, G. M., Kulkarni, R. P., Dworkin, J., Garcia-Ojalvo, J. & Elowitz, M. B. (2007). Tunability and noise dependence in differentiation dynamics. Science315, 1716–1719.
-
(2007)
Science
, vol.315
, pp. 1716-1719
-
-
Suel, G.M.1
Kulkarni, R.P.2
Dworkin, J.3
Garcia-Ojalvo, J.4
Elowitz, M.B.5
-
92
-
-
34250217913
-
Mast cell lineage diversion of t lineage precursors by the essential t cell transcription factor gata-3
-
Taghon, T., Yui, M. A. & Rothenberg, E. V. (2007). Mast cell lineage diversion of T lineage precursors by the essential T cell transcription factor GATA-3. Nat. Immunol.8, 845–855.
-
(2007)
Nat. Immunol
, vol.8
, pp. 845-855
-
-
Taghon, T.1
Yui, M.A.2
Rothenberg, E.V.3
-
93
-
-
1542400036
-
A multi-algorithm, multi-timescale method for cell simulation
-
Takahashi, K., Kaizu, K., Hu, B. & Tomita, M. (2004). A multi-algorithm, multi-timescale method for cell simulation. Bioinformatics20, 538–546.
-
(2004)
Bioinformatics
, vol.20
, pp. 538-546
-
-
Takahashi, K.1
Kaizu, K.2
Hu, B.3
Tomita, M.4
-
94
-
-
33746869356
-
Signal detection, modularity, and the correlation between extrinsic and intrinsic noise in biochemical networks
-
Tanase-Nicola, S., Warren, P. B. & ten Wolde, P. R. (2006). Signal detection, modularity, and the correlation between extrinsic and intrinsic noise in biochemical networks. Phys. Rev. Lett.97, 068102.
-
(2006)
Phys. Rev. Lett
, vol.97
, pp. 068102
-
-
Tanase-Nicola, S.1
Warren, P.B.2
Ten Wolde, P.R.3
-
96
-
-
34748813013
-
Computing stationary distributions in equilibrium and nonequilibrium systems with forward flux sampling
-
Valeriani, C., Allen, R. J., Morellia, M. J., Frenkel, D. & ten Wolde, P. R. (2007). Computing stationary distributions in equilibrium and nonequilibrium systems with forward flux sampling. J. Chem. Phys.127, 114109.
-
(2007)
J. Chem. Phys
, vol.127
, pp. 114109
-
-
Valeriani, C.1
Allen, R.J.2
Morellia, M.J.3
Frenkel, D.4
Ten Wolde, P.R.5
-
97
-
-
36849102835
-
Monte carlo estimation of the free energy by multistage sampling
-
Valleau, J. P. & Card, D. N. (1972). Monte Carlo estimation of the free energy by multistage sampling. J. Chem. Phys.57, 5457–5462.
-
(1972)
J. Chem. Phys
, vol.57
, pp. 5457-5462
-
-
Valleau, J.P.1
Card, D.N.2
-
98
-
-
0038515443
-
A novel path sampling method for the calculation of rate constants
-
van Erp, T. S., Moroni, D. & Bolhuis, P. G. (2003). A novel path sampling method for the calculation of rate constants. J. Chem. Phys.118, 7762–7774.
-
(2003)
J. Chem. Phys
, vol.118
, pp. 7762-7774
-
-
Van Erp, T.S.1
Moroni, D.2
Bolhuis, P.G.3
-
100
-
-
0037197850
-
Mechanisms of noise resistance in genetic oscillators
-
Vilar, J. M., Kueh, H. Y., Barkai, N. & Leibler, S. (2002). Mechanisms of noise resistance in genetic oscillators. Proc. Natl. Acad. Sci. USA99, 5988–5992.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 5988-5992
-
-
Vilar, J.M.1
Kueh, H.Y.2
Barkai, N.3
Leibler, S.4
-
101
-
-
39349093381
-
Umbrella sampling for nonequilibrium processes
-
Warmflash, A., Bhimalapuram, P. & Dinner, A. R. (2007). Umbrella sampling for nonequilibrium processes. J. Chem. Phys.127, 154112.
-
(2007)
J. Chem. Phys
, vol.127
, pp. 154112
-
-
Warmflash, A.1
Bhimalapuram, P.2
Dinner, A.R.3
-
102
-
-
56249093501
-
Signatures of combinational regulation in intrinsic biological noise
-
press
-
Warmflash, A. & Dinner, A. R. (2008). Signatures of combinational regulation in intrinsic biological noise. Proc. Natl. Acad. Sci. USA, in press.
-
(2008)
Proc. Natl. Acad. Sci. USA
-
-
Warmflash, A.1
Dinner, A.R.2
-
103
-
-
33749995740
-
Exact results for noise power spectra in linear biochemical reaction networks
-
Warren, P. B., Tanase-Nicola, S. & ten Wolde, P. R. (2006). Exact results for noise power spectra in linear biochemical reaction networks. J. Chem. Phys.125, 144904.
-
(2006)
J. Chem. Phys
, vol.125
, pp. 144904
-
-
Warren, P.B.1
Tanase-Nicola, S.2
Ten Wolde, P.R.3
-
104
-
-
2342464752
-
Enhancement of the stability of genetic switches by overlapping upstream regulatory domains
-
Warren, P. B. & ten Wolde, P. R. (2004). Enhancement of the stability of genetic switches by overlapping upstream regulatory domains. Phys. Rev. Lett.92, 128101.
-
(2004)
Phys. Rev. Lett
, vol.92
, pp. 128101
-
-
Warren, P.B.1
Ten Wolde, P.R.2
-
105
-
-
17444408518
-
Chemical models of genetic toggle switches
-
Warren, P. B. & ten Wolde, P. R. (2005). Chemical models of genetic toggle switches. J. Phys. Chem. B109, 6812–6823.
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 6812-6823
-
-
Warren, P.B.1
Ten Wolde, P.R.2
-
106
-
-
33746516694
-
A hybrid deterministic-stochastic algorithm for modeling cell signaling dynamics in spatially inhomogeneous environments and under the influence of external fields
-
Wylie, D. C., Hori, Y., Dinner, A. R. & Chakraborty, A. K. (2006). A hybrid deterministic-stochastic algorithm for modeling cell signaling dynamics in spatially inhomogeneous environments and under the influence of external fields. J. Phys. Chem. B110, 12749–12765.
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 12749-12765
-
-
Wylie, D.C.1
Hori, Y.2
Dinner, A.R.3
Chakraborty, A.K.4
-
107
-
-
2542455620
-
Stepwise reprogramming of b cells into macrophages
-
Xie, H., Ye, M., Feng, R. & Graf, T. (2004). Stepwise reprogramming of B cells into macrophages. Cell117, 663–676.
-
(2004)
Cell
, vol.117
, pp. 663-676
-
-
Xie, H.1
Ye, M.2
Feng, R.3
Graf, T.4
-
108
-
-
0345359924
-
A positive-feedback-based bi-stable ‘memory module’ that governs a cell fate decision
-
Xiong, W. & Ferrell, J. E. (2003). A positive-feedback-based bi-stable ‘memory module’ that governs a cell fate decision. Nature426, 460–465.
-
(2003)
Nature
, vol.426
, pp. 460-465
-
-
Xiong, W.1
Ferrell, J.E.2
-
109
-
-
33645033645
-
Probing gene expression in live cells, one protein molecule at a time
-
Yu, J., Xiao, J., Ren, X., Lao, K. & Xie, X. S. (2006). Probing gene expression in live cells, one protein molecule at a time. Science311, 1600–1603.
-
(2006)
Science
, vol.311
, pp. 1600-1603
-
-
Yu, J.1
Xiao, J.2
Ren, X.3
Lao, K.4
Xie, X.S.5
|