-
1
-
-
20044373640
-
Transcription-based prediction of response to IFNbeta using supervised computational methods
-
Baranzini SE, Mousavi P, Rio J, Caillier SJ, Stillman A, et al. Transcription-based prediction of response to IFNbeta using supervised computational methods. PLoS Biol 2005, 3:e2.
-
(2005)
PLoS Biol
, vol.3
-
-
Baranzini, S.E.1
Mousavi, P.2
Rio, J.3
Caillier, S.J.4
Stillman, A.5
-
2
-
-
0031915896
-
Large-scale temporal gene expression mapping of central nervous system development
-
Wen X, Fuhrman S, Michaels GS, Carr DB, Smith S, et al. Large-scale temporal gene expression mapping of central nervous system development. Proc Natl Acad Sci U S A 1998, 95:334-339.
-
(1998)
Proc Natl Acad Sci U S A
, vol.95
, pp. 334-339
-
-
Wen, X.1
Fuhrman, S.2
Michaels, G.S.3
Carr, D.B.4
Smith, S.5
-
3
-
-
2142808278
-
Tracking operator state fluctuations in gene expression in single cells
-
Banerjee B, Balasubramanian S, Ananthakrishna G, Ramakrishnan TV, Shivashankar GV. Tracking operator state fluctuations in gene expression in single cells. Biophys J 2004, 86:3052-3059.
-
(2004)
Biophys J
, vol.86
, pp. 3052-3059
-
-
Banerjee, B.1
Balasubramanian, S.2
Ananthakrishna, G.3
Ramakrishnan, T.V.4
Shivashankar, G.V.5
-
4
-
-
0037119587
-
Stochastic gene expression in a single cell
-
Elowitz MB, Levine AJ, Siggia ED, Swain PS. Stochastic gene expression in a single cell. Science 2002, 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
-
5
-
-
0742305866
-
Network biology: understanding the cell's functional organization
-
Barabasi AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5:101-113.
-
(2004)
Nat Rev Genet
, vol.5
, pp. 101-113
-
-
Barabasi, A.L.1
Oltvai, Z.N.2
-
8
-
-
0036207347
-
Modeling and simulation of genetic regulatory systems: a literature review
-
De Jong H. Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol 2002, 9:67-103.
-
(2002)
J Comput Biol
, vol.9
, pp. 67-103
-
-
De Jong, H.1
-
9
-
-
0842309206
-
Inferring gene networks from time series microarray data using dynamic Bayesian networks
-
Kim SY, Imoto S, Miyano S. Inferring gene networks from time series microarray data using dynamic Bayesian networks. Brief Bioinform 2003, 4:228-235.
-
(2003)
Brief Bioinform
, vol.4
, pp. 228-235
-
-
Kim, S.Y.1
Imoto, S.2
Miyano, S.3
-
11
-
-
0000042837
-
Evaluating functional network inference using simulations of complex biological systems
-
Smith VA, Jarvis ED, Hartemink AJ. Evaluating functional network inference using simulations of complex biological systems. Bioinformatics 2002, 18(suppl 1):S216-S224.
-
(2002)
Bioinformatics
, vol.18
, Issue.1 SUPPL
-
-
Smith, V.A.1
Jarvis, E.D.2
Hartemink, A.J.3
-
12
-
-
0041627865
-
Influence of network topology and data collection on network inference
-
Smith VA, Jarvis ED, Hartemink AJ. Influence of network topology and data collection on network inference. Pac Symp Biocomput 2003, 11:164-175.
-
(2003)
Pac Symp Biocomput
, vol.11
, pp. 164-175
-
-
Smith, V.A.1
Jarvis, E.D.2
Hartemink, A.J.3
-
13
-
-
85024429815
-
A new approach to linear filtering and prediction problems
-
Kalman RE. A new approach to linear filtering and prediction problems. J Basic Eng 1960, 82:35-45.
-
(1960)
J Basic Eng
, vol.82
, pp. 35-45
-
-
Kalman, R.E.1
-
14
-
-
4143058645
-
Gene networks inference using dynamic Bayesian networks
-
Perrin BE, Ralaivola L, Mazurie A, Bottani S, Mallet J, et al. Gene networks inference using dynamic Bayesian networks. Bioinformatics 2003, 19(suppl 2):II138-II148.
-
(2003)
Bioinformatics
, vol.19
, Issue.2 SUPPL
-
-
Perrin, B.E.1
Ralaivola, L.2
Mazurie, A.3
Bottani, S.4
Mallet, J.5
-
15
-
-
0033723743
-
A new approach for the nonlinear transformation of means and covariances in filters and estimators
-
Julier S, Uhlmann J, Durrant-Whyte HF. A new approach for the nonlinear transformation of means and covariances in filters and estimators. IEEE Trans Autom Control 2000, 45:477-482.
-
(2000)
IEEE Trans Autom Control
, vol.45
, pp. 477-482
-
-
Julier, S.1
Uhlmann, J.2
Durrant-Whyte, H.F.3
-
16
-
-
0041815593
-
Nonlinear dynamical system identification from uncertain and indirect measurements
-
Voss HU, Timmer J, Kurths J. Nonlinear dynamical system identification from uncertain and indirect measurements. Int J Bifurcat Chaos 2004, 14:1905-1933.
-
(2004)
Int J Bifurcat Chaos
, vol.14
, pp. 1905-1933
-
-
Voss, H.U.1
Timmer, J.2
Kurths, J.3
-
17
-
-
33644555826
-
Hybrid grammar-based approach to nonlinear dynamical system identification from biological time series
-
Mckinney BA, Crowe JE, Voss HU, Crooke PS, Barney N, et al. Hybrid grammar-based approach to nonlinear dynamical system identification from biological time series. Phys Rev E Stat Nonlin Soft Matter Phys 2006, 73:021912.
-
(2006)
Phys Rev E Stat Nonlin Soft Matter Phys
, vol.73
, pp. 021912
-
-
Mckinney, B.A.1
Crowe, J.E.2
Voss, H.U.3
Crooke, P.S.4
Barney, N.5
-
18
-
-
56749164843
-
Grammatical immune system evolution for reverse engineering dynamic Bayesian models
-
Mckinney BA, Tian D. Grammatical immune system evolution for reverse engineering dynamic Bayesian models. Cancer Informatics 2008, 6:433-447.
-
(2008)
Cancer Informatics
, vol.6
, pp. 433-447
-
-
Mckinney, B.A.1
Tian, D.2
-
19
-
-
0003932731
-
Temporal Organization in Cells
-
New York: Academic Press
-
Goodwin BC Temporal Organization in Cells. New York: Academic Press; 1963.
-
(1963)
-
-
Goodwin, B.C.1
-
20
-
-
0002275384
-
The dynamics of feedback control circuits in biochemical pathways
-
Tyson JJ, Othmer HG. The dynamics of feedback control circuits in biochemical pathways. Prog Theor Biol 1978, 5:1-62.
-
(1978)
Prog Theor Biol
, vol.5
, pp. 1-62
-
-
Tyson, J.J.1
Othmer, H.G.2
-
21
-
-
0014649230
-
Biochemical systems analysis.I. Some mathematical properties of the rate law for the component enzymatic reactions
-
Savageau MA. Biochemical systems analysis. I. Some mathematical properties of the rate law for the component enzymatic reactions. J Theor Biol 1969, 25:365-369.
-
(1969)
J Theor Biol
, vol.25
, pp. 365-369
-
-
Savageau, M.A.1
-
22
-
-
0015231849
-
Parameter sensitivity as a criterion for evaluating and comparing the performance of biochemical systems
-
Savageau MA. Parameter sensitivity as a criterion for evaluating and comparing the performance of biochemical systems. Nature 1971, 229:542-544.
-
(1971)
Nature
, vol.229
, pp. 542-544
-
-
Savageau, M.A.1
-
23
-
-
0003735335
-
Biochemical Systems Analysis: a Study of Function and Design inMolecular Biology
-
Reading, MA: Addison-Wesley
-
Savageau MA Biochemical Systems Analysis: a Study of Function and Design inMolecular Biology. Reading, MA: Addison-Wesley; 1976.
-
(1976)
-
-
Savageau, M.A.1
-
24
-
-
0004151462
-
Computational Analysis of Biochemical Systems: a Practical Guide for Biochemists and Molecular Biologists
-
Cambridge: Cambridge University Press
-
Voit EO Computational Analysis of Biochemical Systems: a Practical Guide for Biochemists and Molecular Biologists. Cambridge: Cambridge University Press; 2000.
-
(2000)
-
-
Voit, E.O.1
-
25
-
-
4444351989
-
Decoupling dynamical systems for pathway identification from metabolic profiles
-
Voit EO, Almeida J. Decoupling dynamical systems for pathway identification from metabolic profiles. Bioinformatics 2004, 20:1670-1681.
-
(2004)
Bioinformatics
, vol.20
, pp. 1670-1681
-
-
Voit, E.O.1
Almeida, J.2
-
26
-
-
0037461033
-
Dynamic modeling of genetic networks using genetic algorithm and S-system
-
Kikuchi S, Tominaga D, Arita M, Takahashi K, Tomita M. Dynamic modeling of genetic networks using genetic algorithm and S-system. Bioinformatics 2003, 19:643-650.
-
(2003)
Bioinformatics
, vol.19
, pp. 643-650
-
-
Kikuchi, S.1
Tominaga, D.2
Arita, M.3
Takahashi, K.4
Tomita, M.5
-
27
-
-
14944363706
-
Construction of genetic network using evolutionary algorithm and combined fitness function
-
Shin A, Iba H. Construction of genetic network using evolutionary algorithm and combined fitness function. Genome Inform 2003, 14:94-103.
-
(2003)
Genome Inform
, vol.14
, pp. 94-103
-
-
Shin, A.1
Iba, H.2
-
28
-
-
3142617691
-
Mathematical and computational techniques to deduce complex biochemical reaction mechanisms
-
Crampin EJ, Schnell S, McSharry PE. Mathematical and computational techniques to deduce complex biochemical reaction mechanisms. Prog Biophys Mol Biol 2004, 86:77-112.
-
(2004)
Prog Biophys Mol Biol
, vol.86
, pp. 77-112
-
-
Crampin, E.J.1
Schnell, S.2
McSharry, P.E.3
-
29
-
-
84880012186
-
Identifiability of parameters in the output least square formulation
-
In: Walter E: ed. Identifiability of Parametric Models. Tarrtown, NY: Pergamon
-
Chavent G Identifiability of parameters in the output least square formulation. In: Walter E: ed. Identifiability of Parametric Models. Tarrytown, NY: Pergamon; 1987.
-
-
-
Chavent, G.1
-
30
-
-
0003577917
-
Statistical Power Analysis for the Behavioral Sciences
-
2nd ed. Mahwah, NJ: Lawrence Erlbaum Associates
-
Cohen J Statistical Power Analysis for the Behavioral Sciences. 2nd ed. Mahwah, NJ: Lawrence Erlbaum Associates; 1988.
-
(1988)
-
-
Cohen, J.1
-
31
-
-
0003478714
-
Robinson DK Data Reduction and Error Analysis for the Physical Sciences
-
2nd ed. New York: Mcgraw-Hill
-
Bevington PR, Robinson DK Data Reduction and Error Analysis for the Physical Sciences. 2nd ed. New York: Mcgraw-Hill; 1992.
-
(1992)
-
-
Bevington, P.R.1
-
32
-
-
0033736476
-
Genetic network inference: from co-expression clustering to reverse engineering
-
D'haeseleer P, Liang S, Somogui R. Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics 2000, 16:707-726.
-
(2000)
Bioinformatics
, vol.16
, pp. 707-726
-
-
D'haeseleer, P.1
Liang, S.2
Somogui, R.3
-
34
-
-
4644301730
-
A benchmark for methods in reverse engineering and model discrimination: problem formulation and solutions
-
Kremling A, Fischer S, Gadkar K, Doyle FJ, Sauter T, et al. A benchmark for methods in reverse engineering and model discrimination: problem formulation and solutions. Genome Res 2004, 14:1773-1785.
-
(2004)
Genome Res
, vol.14
, pp. 1773-1785
-
-
Kremling, A.1
Fischer, S.2
Gadkar, K.3
Doyle, F.J.4
Sauter, T.5
-
35
-
-
5044229817
-
The challenges of modeling mammalian biocomplexity
-
Nicholson JK, Holmes E, Lindon JC, Wilson ID. The challenges of modeling mammalian biocomplexity. Nat Biotechnol 2004, 22:1268-1274.
-
(2004)
Nat Biotechnol
, vol.22
, pp. 1268-1274
-
-
Nicholson, J.K.1
Holmes, E.2
Lindon, J.C.3
Wilson, I.D.4
-
36
-
-
0003684449
-
The Elements of Statistical Learning
-
Data Mining, Inference, and Prediction: New York: Springer-Verlag
-
Hastie T, Tibshirani R, Friedman J The Elements of Statistical Learning: Data Mining, Inference, and Prediction: New York: Springer-Verlag; 2003.
-
(2003)
-
-
Hastie, T.1
Tibshirani, R.2
Friedman, J.3
-
37
-
-
33747603487
-
Integrated mechanistic and data-driven modelling for multivariate analysis of signalling pathways
-
Hua F, Hautaniemi S, Yokoo R, Lauffenburger DA. Integrated mechanistic and data-driven modelling for multivariate analysis of signalling pathways. J R Soc Interface 2006, 3:515-526.
-
(2006)
J R Soc Interface
, vol.3
, pp. 515-526
-
-
Hua, F.1
Hautaniemi, S.2
Yokoo, R.3
Lauffenburger, D.A.4
-
38
-
-
23244467882
-
Rewiring of the yeast transcriptional network through the evolution of motif usage
-
Ihmels J, Bergmann S, Gerami-Nejad M, Yanai I, McClellan M, et al. Rewiring of the yeast transcriptional network through the evolution of motif usage. Science 2005, 309:938-940.
-
(2005)
Science
, vol.309
, pp. 938-940
-
-
Ihmels, J.1
Bergmann, S.2
Gerami-Nejad, M.3
Yanai, I.4
McClellan, M.5
-
39
-
-
0034644270
-
The segment polarity network is a robust developmental module
-
VonDassow G, Meir E, Munro EM, Odell GM. The segment polarity network is a robust developmental module. Nature 2000, 406:188-192.
-
(2000)
Nature
, vol.406
, pp. 188-192
-
-
VonDassow, G.1
Meir, E.2
Munro, E.M.3
Odell, G.M.4
-
40
-
-
0043069489
-
Drug research: myths, hype and reality
-
Kubinyi H. Drug research: myths, hype and reality. Nat Rev Drug Discov 2003, 2:665-668.
-
(2003)
Nat Rev Drug Discov
, vol.2
, pp. 665-668
-
-
Kubinyi, H.1
-
41
-
-
33746778387
-
Cytokine expression patterns associated with systemic adverse events following smallpox immunization
-
McKinney BA, Reif DM, Rock MT, Edwards KM, Kingsmore SF, et al. Cytokine expression patterns associated with systemic adverse events following smallpox immunization. J Infect Dis 2006, 194:444-453.
-
(2006)
J Infect Dis
, vol.194
, pp. 444-453
-
-
McKinney, B.A.1
Reif, D.M.2
Rock, M.T.3
Edwards, K.M.4
Kingsmore, S.F.5
-
44
-
-
15544371346
-
Gene regulation at the single-cell level
-
Rosenfeld N, Young JW, Alon U, Swain PS, Elowitz MB. Gene regulation at the single-cell level. Science 2005, 307:1962-1965.
-
(2005)
Science
, vol.307
, pp. 1962-1965
-
-
Rosenfeld, N.1
Young, J.W.2
Alon, U.3
Swain, P.S.4
Elowitz, M.B.5
-
45
-
-
19544379881
-
Stochasticity in gene expression: from theories to phenotypes
-
Kaern M, Elston TC, Blake WJ, Collins JJ. Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet 2005, 6:451-464.
-
(2005)
Nat Rev Genet
, vol.6
, pp. 451-464
-
-
Kaern, M.1
Elston, T.C.2
Blake, W.J.3
Collins, J.J.4
-
46
-
-
0035193294
-
Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations
-
Kepler T, Elston TC. Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations. Biophys J 2001, 81:3116-3136.
-
(2001)
Biophys J
, vol.81
, pp. 3116-3136
-
-
Kepler, T.1
Elston, T.C.2
-
48
-
-
4544321024
-
Modeling and simulation of intracellular dynamics: choosing an appropriate framework
-
Wolkenhauer O, Ullah M, Kolch W, Cho K-W.Modeling and simulation of intracellular dynamics: choosing an appropriate framework. IEEE Trans Nanobiosci 2004, 3:200-207.
-
(2004)
IEEE Trans Nanobiosci
, vol.3
, pp. 200-207
-
-
Wolkenhauer, O.1
Ullah, M.2
Kolch, W.3
Cho, K.-W.4
-
49
-
-
44049109914
-
A rigorous derivation of the chemical master equation
-
Gillespie DT. A rigorous derivation of the chemical master equation. Physica A 1992, 188:404-425.
-
(1992)
Physica A
, vol.188
, pp. 404-425
-
-
Gillespie, D.T.1
-
50
-
-
0033083733
-
It's a noisy business! Genetic regulation at the nanomolar scale
-
McAdams HH, Arkin A. It's a noisy business! Genetic regulation at the nanomolar scale. Trends Genet 1999, 15:65-69.
-
(1999)
Trends Genet
, vol.15
, pp. 65-69
-
-
McAdams, H.H.1
Arkin, A.2
-
51
-
-
0032428151
-
Modeling stochastic gene expression: implications for haploinsufficiency
-
Cook DL, Gerber AN, Tapscott SJ. Modeling stochastic gene expression: implications for haploinsufficiency. Proc Natl Acad Sci U S A 1998, 95:15641-15646.
-
(1998)
Proc Natl Acad Sci U S A
, vol.95
, pp. 15641-15646
-
-
Cook, D.L.1
Gerber, A.N.2
Tapscott, S.J.3
-
52
-
-
0037108809
-
Increased noise as an effect of haploinsufficiency of the tumor-suppressor gene neurofibromatosis type 1 in vitro
-
Kemkemer R, Schrank S, Vogel W, Gruler H, Kaufmann D. Increased noise as an effect of haploinsufficiency of the tumor-suppressor gene neurofibromatosis type 1 in vitro. Proc Natl Acad Sci U S A 2002, 99:13783-13788.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 13783-13788
-
-
Kemkemer, R.1
Schrank, S.2
Vogel, W.3
Gruler, H.4
Kaufmann, D.5
-
53
-
-
33749022748
-
How lifetimes shape epigenotype within and across generations
-
Whitelaw NC, Whitelaw E. How lifetimes shape epigenotype within and across generations. Hum Mol Genet 2006, 15(Spec No 2):R131-R137.
-
(2006)
Hum Mol Genet
, vol.15
, Issue.SPEC. NO 2
-
-
Whitelaw, N.C.1
Whitelaw, E.2
|