-
1
-
-
0037079054
-
Computational systems biology
-
H. Kitano (2002a) Computational systems biology. Nature 420: 206-210.
-
(2002)
Nature
, vol.420
, pp. 206-210
-
-
Kitano, H.1
-
2
-
-
0036500993
-
Systems biology: A brief overview
-
H. Kitano (2002b): Systems biology: a brief overview. Science 295: 1662-1664.
-
(2002)
Science
, vol.295
, pp. 1662-1664
-
-
Kitano, H.1
-
4
-
-
34548168571
-
The effects of molecular noise and size control on variability in the budding yeast cell cycle
-
S. Di Talia, J.M. Skotheim, J.M. Bean, E.D. Siggia and F.R. Cross (2007) The effects of molecular noise and size control on variability in the budding yeast cell cycle. Nature 448: 947-951.
-
(2007)
Nature
, vol.448
, pp. 947-951
-
-
Di Talia, S.1
Skotheim, J.M.2
Bean, J.M.3
Siggia, E.D.4
Cross, F.R.5
-
5
-
-
67449152160
-
Computational systems biology of the cell cycle
-
A. Csikasz-Nagy (2009) Computational systems biology of the cell cycle. Briefings in Bioinformatics 10(4): 424-434.
-
(2009)
Briefings in Bioinformatics
, vol.10
, Issue.4
, pp. 424-434
-
-
Csikasz-Nagy, A.1
-
6
-
-
0024349002
-
Do the laws of chemistry apply to living cells?
-
P.J. Halling (1989) Do the laws of chemistry apply to living cells? Trends Biochem Sci. 14(8): 317-8.
-
(1989)
Trends Biochem Sci.
, vol.14
, Issue.8
, pp. 317-318
-
-
Halling, P.J.1
-
7
-
-
0033083733
-
It's a noisy business! Genetic regulation at the nanomolar scale
-
H.H. McAdams and A. Arkin (1999) It's a noisy business! Genetic regulation at the nanomolar scale. Trends Genet. 15(2): 65-9.
-
(1999)
Trends Genet.
, vol.15
, Issue.2
, pp. 65-69
-
-
McAdams, H.H.1
Arkin, A.2
-
8
-
-
0026862118
-
Induction mechanism of a single gene molecule: Stochastic or deterministic?
-
M.S.H. Ko (1992) Induction mechanism of a single gene molecule: stochastic or deterministic? Bioessays 14(5): 341-6.
-
(1992)
Bioessays
, vol.14
, Issue.5
, pp. 341-346
-
-
Ko, M.S.H.1
-
9
-
-
0031982512
-
Origins of individual swimming behavior in bacteria
-
M.D. Levin, C.J. Morton-Firth, W.N. Abouhamad, R.B. Beurret and D. Bray (1998) Origins of individual swimming behavior in bacteria. Biophys. 74(1): 175-81.
-
(1998)
Biophys.
, vol.74
, Issue.1
, pp. 175-181
-
-
Levin, M.D.1
Morton-Firth, C.J.2
Abouhamad, W.N.3
Beurret, R.B.4
Bray, D.5
-
10
-
-
0031029852
-
Stochastic mechanisms in gene expression
-
H.H. McAdams and A. Arkin (1997) Stochastic mechanisms in gene expression. Proc Natl Acad Sci U S A. 94(3): 814-9.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, Issue.3
, pp. 814-819
-
-
McAdams, H.H.1
Arkin, A.2
-
11
-
-
0035896577
-
The effect of transcription and translation initiation frequencies on the stochastic fluctuations in prokaryotic gene expression
-
A.M. Kierzek, J. Zaim and P. Zielenkiewicz (2001) The effect of transcription and translation initiation frequencies on the stochastic fluctuations in prokaryotic gene expression. J Biol Chem. 276(11): 8165-72.
-
(2001)
J Biol Chem.
, vol.276
, Issue.11
, pp. 8165-8172
-
-
Kierzek, A.M.1
Zaim, J.2
Zielenkiewicz, P.3
-
12
-
-
0036578645
-
Regulation of noise in the expression of a single gene
-
E.M. Ozbudak, M. Thattai, I. Kurtser, A.D. Grossman and A. van Oudenaarden (2002) Regulation of noise in the expression of a single gene. Nat Genet. 31(1): 69-73.
-
(2002)
Nat Genet.
, vol.31
, Issue.1
, pp. 69-73
-
-
Ozbudak, E.M.1
Thattai, M.2
Kurtser, I.3
Grossman, A.D.4
Van Oudenaarden, A.5
-
13
-
-
0037119587
-
Stochastic gene expression in a single cell
-
M.B. Elowitz, A.J. Levine, E.D. Siggia and P.S. Swain (2002) Stochastic gene expression in a single cell. Science 297(5584): 1183-6.
-
(2002)
Science
, vol.297
, Issue.5584
, pp. 1183-1186
-
-
Elowitz, M.B.1
Levine, A.J.2
Siggia, E.D.3
Swain, P.S.4
-
14
-
-
0037078982
-
Control, exploitation and tolerance of intracellular noise
-
C.V. Rao, D.M. Wolf and A.P. Arkin (2002) Control, exploitation and tolerance of intracellular noise. Nature 420(6912): 231-7.
-
(2002)
Nature
, vol.420
, Issue.6912
, pp. 231-237
-
-
Rao, C.V.1
Wolf, D.M.2
Arkin, A.P.3
-
15
-
-
67049143968
-
Algorithmic systems biology
-
C. Priami (2009) Algorithmic systems biology. Communications of the ACM 52: 80-88.
-
(2009)
Communications of the ACM
, vol.52
, pp. 80-88
-
-
Priami, C.1
-
16
-
-
84991305533
-
Process calculi abstractions for biology
-
(A. Condon, D. Harel, J.N. Kok, A. Salomaa, and E. Winfree, Eds.), Springer
-
M.L. Guerriero, D. Prandi, C. Priami and P. Quaglia (2009) Process Calculi Abstractions for Biology. In Algorithmic Bioprocesses (A. Condon, D. Harel, J.N. Kok, A. Salomaa, and E. Winfree, Eds.), Springer 463-486.
-
(2009)
Algorithmic Bioprocesses
, pp. 463-486
-
-
Guerriero, M.L.1
Prandi, D.2
Priami, C.3
Quaglia, P.4
-
17
-
-
84974715948
-
Stochastic pi-calculus
-
C. Priami (1995) Stochastic pi-calculus. The Computer Journal 38(7): 578-589.
-
(1995)
The Computer Journal
, vol.38
, Issue.7
, pp. 578-589
-
-
Priami, C.1
-
18
-
-
0035888407
-
Application of a stochastic name-passing calculus to representation and simulation of molecular processes
-
C. Priami, A. Regev, E. Shapiro and W. Silverman (2001) Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Information Processing Letters 80: 25-31.
-
(2001)
Information Processing Letters
, vol.80
, pp. 25-31
-
-
Priami, C.1
Regev, A.2
Shapiro, E.3
Silverman, W.4
-
21
-
-
4444383325
-
BioAmbients: An abstraction for biological compartments
-
A. Regev, E. Panina, W. Silverman, L. Cardelli and E. Shapiro (2004) BioAmbients: an abstraction for biological compartments. Theoretical Computer Science 325(1): 141-167.
-
(2004)
Theoretical Computer Science
, vol.325
, Issue.1
, pp. 141-167
-
-
Regev, A.1
Panina, E.2
Silverman, W.3
Cardelli, L.4
Shapiro, E.5
-
25
-
-
38649133815
-
Bio-PEPA: An extension of the process algebra PEPA for biochemical networks
-
F. Ciocchetta and J. Hillstone (2008) Bio-PEPA: An Extension of the Process Algebra PEPA for Biochemical Networks. Proc. of FBTC 2007, (ENTCS, 2008) 194(3): 103-117.
-
(2008)
Proc. of FBTC 2007, (ENTCS, 2008)
, vol.194
, Issue.3
, pp. 103-117
-
-
Ciocchetta, F.1
Hillstone, J.2
-
26
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
D. Gillespie (1977) Exact stochastic simulation of coupled chemical reactions. Journal of Physical Chemistry 81(25): 2340-2361.
-
(1977)
Journal of Physical Chemistry
, vol.81
, Issue.25
, pp. 2340-2361
-
-
Gillespie, D.1
-
27
-
-
0000870544
-
Kinetics of invertase action
-
L. Michaelis and M. L. Menten (1913) Kinetics of invertase action. Biochem. Z. 49, 333.
-
(1913)
Biochem. Z.
, vol.49
, pp. 333
-
-
Michaelis, L.1
Menten, M.L.2
-
29
-
-
0030768931
-
The hill equation revisited: Uses and misuses
-
J.N. Weiss (1997) The Hill equation revisited: uses and misuses. The FASEB Journal 11: 835-841.
-
(1997)
The FASEB Journal
, vol.11
, pp. 835-841
-
-
Weiss, J.N.1
-
30
-
-
56749160113
-
Design principles of biochemical oscillators
-
B. Novak and J.J. Tyson (2008) Design principles of biochemical oscillators. Nat Rev Mol Cell Biol. 9: 981-991.
-
(2008)
Nat Rev Mol Cell Biol.
, vol.9
, pp. 981-991
-
-
Novak, B.1
Tyson, J.J.2
-
31
-
-
33644524741
-
Cell signalling dynamics in time and space
-
B.N. Kholodenko (2006) Cell signalling dynamics in time and space. Nat Rev Mol Cell Biol. 7(3): 165-176.
-
(2006)
Nat Rev Mol Cell Biol.
, vol.7
, Issue.3
, pp. 165-176
-
-
Kholodenko, B.N.1
-
32
-
-
34250834115
-
A compositional approach to the stochastic dynamics of gene networks
-
Springer-Verlag
-
R. Blossey, L. Cardelli and A. Phillips (2006) A Compositional Approach to the Stochastic Dynamics of Gene Networks. Lecture Notes in Computer Science, Springer-Verlag 3939: 99-122.
-
(2006)
Lecture Notes in Computer Science
, vol.3939
, pp. 99-122
-
-
Blossey, R.1
Cardelli, L.2
Phillips, A.3
-
33
-
-
67650657139
-
A programming language for composable DNA circuits
-
A. Phillips and L. Cardelli (2009) A programming language for composable DNA circuits. J. R. Soc. Interface 6: 419-S436.
-
(2009)
J. R. Soc. Interface
, vol.6
, pp. S419-S436
-
-
Phillips, A.1
Cardelli, L.2
-
35
-
-
45749113795
-
Hybrid systems and biology - Continuous and discrete modeling for systems biology
-
Springer-Verlag
-
L. Bortolussi and A. Policriti (2008) Hybrid Systems and Biology - Continuous and Discrete Modeling for Systems Biology. Lecture Notes in Computer Science, Springer-Verlag 5016: 424-448.
-
(2008)
Lecture Notes in Computer Science
, vol.5016
, pp. 424-448
-
-
Bortolussi, L.1
Policriti, A.2
-
37
-
-
0037444724
-
Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the gillespie algorithm
-
C.V. Rao and A.P. Arkin (2003) Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm. J. Chem. Phys. 118(11): 4999-5010.
-
(2003)
J. Chem. Phys.
, vol.118
, Issue.11
, pp. 4999-5010
-
-
Rao, C.V.1
Arkin, A.P.2
-
38
-
-
85020212064
-
Exactness and approximation of the stochastic simulation algorithm
-
I. Mura (2008) Exactness and Approximation of the Stochastic Simulation Algorithm. Tech. Rep. TR-12-2008, CoSBi.
-
(2008)
Tech. Rep. TR-12-2008, CoSBi
-
-
Mura, I.1
-
39
-
-
34047240610
-
Bundschuh02 modeling networks of coupled enzymatic reactions using the total quasi-steady state approximation
-
Bundschuh02 Modeling networks of coupled enzymatic reactions using the total quasi-steady state approximation. PLoS Comput Biol. 3(3): e45.
-
PLoS Comput Biol.
, vol.3
, Issue.3
, pp. e45
-
-
-
40
-
-
0037339442
-
Fluctuations and slow variables in genetic networks
-
R. Bundschuh, F. Hayot and C. Jayaprakash (2003) Fluctuations and Slow Variables in Genetic Networks. Biophysical Journal 84(3): 1606-1615.
-
(2003)
Biophysical Journal
, vol.84
, Issue.3
, pp. 1606-1615
-
-
Bundschuh, R.1
Hayot, F.2
Jayaprakash, C.3
-
41
-
-
85020171967
-
-
CoSBi Lab. http://www.cosbi.eu/index.php/research/prototypes/overview.
-
-
-
-
42
-
-
77952098961
-
Calibration of dynamic models of biological systems with KInfer
-
P. Lecca, A. Palmisano, A. Ihekwaba and C. Priami (2009) Calibration of dynamic models of biological systems with KInfer. Eur Biophys J DOI: 10.1007/s00249-009-0520-3.
-
(2009)
Eur Biophys J
-
-
Lecca, P.1
Palmisano, A.2
Ihekwaba, A.3
Priami, C.4
-
43
-
-
0034691214
-
Stochastic focusing: Fluctuation-enhanced sensitivity of intra-cellular regulation
-
J. Paulsson, O.G. Berg, M. Ehrenberg (2000) Stochastic focusing: fluctuation-enhanced sensitivity of intra-cellular regulation. Proc Natl Acad Sci U S A. 97(13): 7148-53.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, Issue.13
, pp. 7148-7153
-
-
Paulsson, J.1
Berg, O.G.2
Ehrenberg, M.3
-
44
-
-
0037376655
-
Sniffers, buzzers, toggles and blinkers: Dynamics of regulatory and signaling pathways in the cell
-
J.J. Tyson, K.C. Chen and B. Novak (2003) Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol. 15(2): 221-31.
-
(2003)
Curr Opin Cell Biol.
, vol.15
, Issue.2
, pp. 221-231
-
-
Tyson, J.J.1
Chen, K.C.2
Novak, B.3
-
45
-
-
0142027814
-
Structure and function of the feed-forward loop network motif
-
S. Mangan and U. Alon (2003) Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci U S A. 100(21): 11980-5.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, Issue.21
, pp. 11980-11985
-
-
Mangan, S.1
Alon, U.2
-
46
-
-
43049179364
-
Odeling biological systems in stochastic concurrent constraint programming
-
L. Bortolussi and A. Policriti (2008) odeling Biological Systems in Stochastic Concurrent Constraint Programming. Constraints 13(1): 66-90.
-
(2008)
Constraints
, vol.13
, Issue.1
, pp. 66-90
-
-
Bortolussi, L.1
Policriti, A.2
-
47
-
-
28844502722
-
Circadian clocks - The fall and rise of physiology
-
T. Roenneberg and M. Merrow (2005) Circadian clocks - the fall and rise of physiology. Nat Rev Mol Cell Biol. 6(12): 965-71.
-
(2005)
Nat Rev Mol Cell Biol.
, vol.6
, Issue.12
, pp. 965-971
-
-
Roenneberg, T.1
Merrow, M.2
-
48
-
-
34047240610
-
Modeling networks of coupled enzymatic reactions using the total quasi-steady state approximation
-
A. Ciliberto, F. Capuani and J.J. Tyson (2007) Modeling networks of coupled enzymatic reactions using the total quasi-steady state approximation. PLoS Comput Biol. 3(3): e45.
-
(2007)
PLoS Comput Biol.
, vol.3
, Issue.3
, pp. e45
-
-
Ciliberto, A.1
Capuani, F.2
Tyson, J.J.3
-
49
-
-
36348978774
-
Antagonism and bistability in protein interaction networks
-
M. Sabouri-Ghomi, A. Ciliberto, S. Kar, B. Novak, J.J. Tyson (2007) Antagonism and bistability in protein interaction networks. J Theor Biol. 250(1): 209-18.
-
(2007)
J Theor Biol.
, vol.250
, Issue.1
, pp. 209-218
-
-
Sabouri-Ghomi, M.1
Ciliberto, A.2
Kar, S.3
Novak, B.4
Tyson, J.J.5
-
50
-
-
0017833657
-
A model for the statistical fluctuations of protein numbers in a microbial population
-
O.G. Berg (1978) A model for the statistical fluctuations of protein numbers in a microbial population. J Theor Biol. 71(4): 587-603.
-
(1978)
J Theor Biol.
, vol.71
, Issue.4
, pp. 587-603
-
-
Berg, O.G.1
-
51
-
-
0013863816
-
Comparison of experimental binding data and theoretical models in proteins containing subunits
-
D.E. Koshland Jr, G. Nemethy and D. Filmer (1966) Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 5(1): 365-85.
-
(1966)
Biochemistry
, vol.5
, Issue.1
, pp. 365-385
-
-
Koshland, D.E.1
Nemethy, G.2
Filmer, D.3
-
52
-
-
78651189765
-
On the nature of allosteric transitions: A plausible model
-
J. Monod, J. Wyman and J.P. Changeux (1965) On the nature of allosteric transitions: a plausible model. J Mol Biol. 12: 88-118.
-
(1965)
J Mol Biol.
, vol.12
, pp. 88-118
-
-
Monod, J.1
Wyman, J.2
Changeux, J.P.3
-
53
-
-
38349185928
-
Effects of molecular memory and bursting on fluctuations in gene expression
-
J.M. Pedraza and J. Paulsson (2008) Effects of molecular memory and bursting on fluctuations in gene expression. Science 319(5861): 339-43.
-
(2008)
Science
, vol.319
, Issue.5861
, pp. 339-343
-
-
Pedraza, J.M.1
Paulsson, J.2
-
54
-
-
33845270990
-
Regulating the p53 pathway: In vitro hypotheses, in vivo veritas
-
F. Toledo, G.M. Wahl (2006) Regulating the p53 pathway: in vitro hypotheses, in vivo veritas. Nat Rev Cancer 6(12): 909-23.
-
(2006)
Nat Rev Cancer
, vol.6
, Issue.12
, pp. 909-923
-
-
Toledo, F.1
Wahl, G.M.2
-
55
-
-
0001424903
-
An amplified sensitivity arising from covalent modification in biological systems
-
A. Goldbeter and D.E. Koshland Jr (1981) An amplified sensitivity arising from covalent modification in biological systems. Proc Natl Acad Sci U S A. 78(11): 6840-4.
-
(1981)
Proc Natl Acad Sci USA
, vol.78
, Issue.11
, pp. 6840-6844
-
-
Goldbeter, A.1
Koshland, D.E.2
-
56
-
-
52949098296
-
Frequency-modulated nuclear localization bursts coordinate gene regulation
-
L. Cai, C.K. Dalal and M.B. Elowitz (2008) Frequency-modulated nuclear localization bursts coordinate gene regulation. Nature 455(7212): 485-90.
-
(2008)
Nature
, vol.455
, Issue.7212
, pp. 485-490
-
-
Cai, L.1
Dalal, C.K.2
Elowitz, M.B.3
-
57
-
-
36148997654
-
Computational analysis of mammalian cell division gated by a circadian clock: Quantized cell cycles and cell size control
-
J. Zamborszky, C.I. Hong and A. Csikasz-Nagy (2007) Computational analysis of mammalian cell division gated by a circadian clock: quantized cell cycles and cell size control. J Biol Rhythms 22(6): 542-53.
-
(2007)
J Biol Rhythms
, vol.22
, Issue.6
, pp. 542-553
-
-
Zamborszky, J.1
Hong, C.I.2
Csikasz-Nagy, A.3
-
58
-
-
13844294211
-
The casein kinase 1 family: Participation in multiple cellular processes in eukaryotes
-
U. Knippschilda, A. Gochtb, S. Wolffa, N. Hubera, J. Loehlerc and M. Stoetera (2005) The casein kinase 1 family: participation in multiple cellular processes in eukaryotes. Cellular Signalling 17(6): 675-689.
-
(2005)
Cellular Signalling
, vol.17
, Issue.6
, pp. 675-689
-
-
Knippschilda, U.1
Gochtb, A.2
Wolffa, S.3
Hubera, N.4
Loehlerc, J.5
Stoetera, M.6
-
59
-
-
51849166317
-
Compositionality, stochasticity, and cooperativity in dynamic models of gene regulation
-
R. Blossey, L. Cardelli and A. Phillips (2007) Compositionality, stochasticity, and cooperativity in dynamic models of gene regulation. HFSP Journal 2(1): 17-28.
-
(2007)
HFSP Journal
, vol.2
, Issue.1
, pp. 17-28
-
-
Blossey, R.1
Cardelli, L.2
Phillips, A.3
|