-
1
-
-
33847377573
-
A robustness-based approach to systems-oriented drug design
-
Kitano H. A robustness-based approach to systems-oriented drug design. Nat Rev Drug Discov 2007; 6: 202-210.
-
(2007)
Nat Rev Drug Discov
, vol.6
, pp. 202-210
-
-
Kitano, H.1
-
2
-
-
33751238890
-
Computational Biology and Drug Discovery: From Single-Target to Network Drugs
-
Ambesi-Impiombato A, di Bernardo D. Computational Biology and Drug Discovery: From Single-Target to Network Drugs. Current Bioinform 2007; 1: 3-13.
-
(2007)
Current Bioinform
, vol.1
, pp. 3-13
-
-
Ambesi-Impiombato, A.1
di Bernardo, D.2
-
3
-
-
12344259602
-
Advances to Bayesian network inference for generating causal networks from observational biological data
-
Yu J, Smith VA, Wang PP, Hartemink AJ, Jarvis ED. Advances to Bayesian network inference for generating causal networks from observational biological data. Bioinformatics 2004; 20: 3594-3603.
-
(2004)
Bioinformatics
, vol.20
, pp. 3594-3603
-
-
Yu, J.1
Smith, V.A.2
Wang, P.P.3
Hartemink, A.J.4
Jarvis, E.D.5
-
4
-
-
0033655775
-
Mutual information relevance networks: Functional genomic clustering using pairwise entropy measurements
-
Butte A, Kohane I. Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac Symp Biocomp 2000; 5: 418-429.
-
(2000)
Pac Symp Biocomp
, vol.5
, pp. 418-429
-
-
Butte, A.1
Kohane, I.2
-
5
-
-
16844376909
-
Reverse engineering of regulatory networks in human B cells
-
Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A. Reverse engineering of regulatory networks in human B cells. Nat Genet 2005; 37: 382-390.
-
(2005)
Nat Genet
, vol.37
, pp. 382-390
-
-
Basso, K.1
Margolin, A.A.2
Stolovitzky, G.3
Klein, U.4
Dalla-Favera, R.5
Califano, A.6
-
8
-
-
0036207347
-
Modelling and Simulation of Genetic Regulatory Systems: A Literature Review
-
De Jong H. Modelling 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
-
-
85195236502
-
-
Wessels LFA, Van Someren EP, Reinders, MJT. A Comparison of Genetic Network Models. Pac Symp Biocomput 2001; 6: 508-519.
-
Wessels LFA, Van Someren EP, Reinders, MJT. A Comparison of Genetic Network Models. Pac Symp Biocomput 2001; 6: 508-519.
-
-
-
-
10
-
-
0033736476
-
Genetic network inference: From co-expression clustering to reverse engineering
-
D'haeseleer P, Liang S, Somogyi 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
Somogyi, R.3
-
13
-
-
0002054202
-
Modeling the complexity of genetic networks: Understanding multigenic and pleiotropic regulation
-
Somogyi R, Sniegoski CA. Modeling the complexity of genetic networks: Understanding multigenic and pleiotropic regulation. Complexity 1996; 1: 45-63.
-
(1996)
Complexity
, vol.1
, pp. 45-63
-
-
Somogyi, R.1
Sniegoski, C.A.2
-
14
-
-
85195240392
-
-
Liang S, Fuhrman S, Somogyi R. REVEAL, A general reverse engineering algorithm for inference of genetic network architectures. Pac Symp Biocomput 1998; 3: 18-29.
-
Liang S, Fuhrman S, Somogyi R. REVEAL, A general reverse engineering algorithm for inference of genetic network architectures. Pac Symp Biocomput 1998; 3: 18-29.
-
-
-
-
15
-
-
0031630211
-
Genomic regulation modeled as a network with basins of attraction
-
Wuensche A. Genomic regulation modeled as a network with basins of attraction. Pac Symp Biocomput 1998; 3: 89-102.
-
(1998)
Pac Symp Biocomput
, vol.3
, pp. 89-102
-
-
Wuensche, A.1
-
16
-
-
0032616683
-
Identification of genetic networks from a small number of gene expression patterns under the Boolean network model
-
Akutsu T, Miyano S, Kuhara S. Identification of genetic networks from a small number of gene expression patterns under the Boolean network model. Pac Symp Biocomput 1999; 4: 17-28.
-
(1999)
Pac Symp Biocomput
, vol.4
, pp. 17-28
-
-
Akutsu, T.1
Miyano, S.2
Kuhara, S.3
-
17
-
-
0033707333
-
Algorithms for identify Boolean Networks and related biological networks based on Matrix Multiplication and fingerprint function
-
Tokyo, Japan
-
Akutsu T., Miyano S, Kuhara, S. Algorithms for identify Boolean Networks and related biological networks based on Matrix Multiplication and fingerprint function Pro 4th Ann Int Conf Res Comput Mol Biol, Tokyo, Japan, 2000; pp: 8-14.
-
(2000)
Pro 4th Ann Int Conf Res Comput Mol Biol
, pp. 8-14
-
-
Akutsu, T.1
Miyano, S.2
Kuhara, S.3
-
19
-
-
0038048325
-
Inferring genetic networks and identifying compound mode of action via expression profiling
-
Gardner TS, di Bernardo D, Lorenz D, Collins JJ. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 2003; 301: 102-105.
-
(2003)
Science
, vol.301
, pp. 102-105
-
-
Gardner, T.S.1
di Bernardo, D.2
Lorenz, D.3
Collins, J.J.4
-
21
-
-
0032611513
-
Modeling Gene Expression with Differential Equations
-
Chen T, He HL, Church GM. Modeling Gene Expression with Differential Equations. Pac Symp Biocomput 1999; 4: 29-40.
-
(1999)
Pac Symp Biocomput
, vol.4
, pp. 29-40
-
-
Chen, T.1
He, H.L.2
Church, G.M.3
-
22
-
-
0043130707
-
Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data of Bacillus Subtilis Using Differential Equations
-
de Hoon MJL, Imoto S, Kobayashi K, Ogasawara N, Miyano S. Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data of Bacillus Subtilis Using Differential Equations. Pac Symp Biocomput 2003; 8: 17-28.
-
(2003)
Pac Symp Biocomput
, vol.8
, pp. 17-28
-
-
de Hoon, M.J.L.1
Imoto, S.2
Kobayashi, K.3
Ogasawara, N.4
Miyano, S.5
-
23
-
-
0032612220
-
Linear Modeling of mRNA Expression Levels during CNS Development and Injury
-
D'haeseleer P, Wen X, Fuhrman S, Somogyi R. Linear Modeling of mRNA Expression Levels during CNS Development and Injury. Pac Symp Biocomput 1999; 4: 41-52.
-
(1999)
Pac Symp Biocomput
, vol.4
, pp. 41-52
-
-
D'haeseleer, P.1
Wen, X.2
Fuhrman, S.3
Somogyi, R.4
-
25
-
-
2442691914
-
Modeling gene expression from microarray expression data with state-space equations
-
Wu FX, Zhang WJ, Kusalik AJ. Modeling gene expression from microarray expression data with state-space equations. Pac Symp Biocomput 2004; 9: 581-592.
-
(2004)
Pac Symp Biocomput
, vol.9
, pp. 581-592
-
-
Wu, F.X.1
Zhang, W.J.2
Kusalik, A.J.3
-
26
-
-
0000120766
-
Estimating the dimension of a model
-
Schwarz G. Estimating the dimension of a model. Ann Statist 1978; 6: 461-464.
-
(1978)
Ann Statist
, vol.6
, pp. 461-464
-
-
Schwarz, G.1
-
27
-
-
34250232348
-
EM algorithms fro ML factor analysis
-
Bubin DB, Thayer DT. EM algorithms fro ML factor analysis. Psychometrika 1982; 47: 69-76.
-
(1982)
Psychometrika
, vol.47
, pp. 69-76
-
-
Bubin, D.B.1
Thayer, D.T.2
-
28
-
-
0038959172
-
Probabilistic principal component analysis
-
Tipping ME, Bishop CM. Probabilistic principal component analysis. J R Statist Soc B 1999; 61: 611-622.
-
(1999)
J R Statist Soc B
, vol.61
, pp. 611-622
-
-
Tipping, M.E.1
Bishop, C.M.2
-
29
-
-
0034730140
-
Singular value decomposition for genome-wide expression data processing and modeling
-
Alter O, Brown PO, Botstein D. Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci USA 2000; 97: 10101-10106.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 10101-10106
-
-
Alter, O.1
Brown, P.O.2
Botstein, D.3
-
30
-
-
0035852785
-
Dynamic modeling of gene expression data
-
Holter NS, Maritan A, Cieplak M, Fedoroff NV, Banavar JR. Dynamic modeling of gene expression data. Proc. Natl. Acad. Sci. USA 2001; 98: 1693-1698.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 1693-1698
-
-
Holter, N.S.1
Maritan, A.2
Cieplak, M.3
Fedoroff, N.V.4
Banavar, J.R.5
-
32
-
-
84936421967
-
Choosing models for cross-classification
-
Raftery AE. Choosing models for cross-classification. Amer Sociol Rev 1986; 51: 145-146.
-
(1986)
Amer Sociol Rev
, vol.51
, pp. 145-146
-
-
Raftery, A.E.1
-
33
-
-
0004168026
-
-
2nd Edition, Cambridge, MA: The MIT Press
-
Harvey AC. Time Series Models. 2nd Edition, Cambridge, MA: The MIT Press 1993.
-
(1993)
Time Series Models
-
-
Harvey, A.C.1
-
35
-
-
0004161838
-
-
2nd edition, Cambridge, UK: Cambridge University Press
-
Press WH, Flannery BP, Teukolsky SA, Vetterling WT. Numerical Recipes in C: The Art of Scientific Computing. 2nd edition, Cambridge, UK: Cambridge University Press 1992.
-
(1992)
Numerical Recipes in C: The Art of Scientific Computing
-
-
Press, W.H.1
Flannery, B.P.2
Teukolsky, S.A.3
Vetterling, W.T.4
-
36
-
-
12144277948
-
State-Space Model with Time Delays for Gene Regulatory Networks
-
Wu FX, Zhang WJ, Kusalik AJ. State-Space Model with Time Delays for Gene Regulatory Networks. J Biol Syst 2004; 12: 483-500.
-
(2004)
J Biol Syst
, vol.12
, pp. 483-500
-
-
Wu, F.X.1
Zhang, W.J.2
Kusalik, A.J.3
-
37
-
-
2442687038
-
A Mixed Integer Linear Programming (MILP) Framework for Inferring Time Delay in Gene Regulatory Networks
-
Dasika M, Dasika MS, Gupta A, et al. A Mixed Integer Linear Programming (MILP) Framework for Inferring Time Delay in Gene Regulatory Networks. Pac Symp Biocompu 2004; 9: 474-485.
-
(2004)
Pac Symp Biocompu
, vol.9
, pp. 474-485
-
-
Dasika, M.1
Dasika, M.S.2
Gupta, A.3
-
38
-
-
22144466898
-
Inferring Gene Regulatory Networks with Time Delays Using Genetic Algorithm
-
Wu FX, Poirier GG, Zhang W J. Inferring Gene Regulatory Networks with Time Delays Using Genetic Algorithm. Syst Biol 2005; 2: 67-74.
-
(2005)
Syst Biol
, vol.2
, pp. 67-74
-
-
Wu, F.X.1
Poirier, G.G.2
Zhang, W.J.3
-
39
-
-
3142744689
-
Modelling T cell activation using gene expression profiling and state space models
-
Rangel C, Angus J, Ghahramani Z, et al. Modelling T cell activation using gene expression profiling and state space models. Bioinformatics, 2004; 20: 1361-1372.
-
(2004)
Bioinformatics
, vol.20
, pp. 1361-1372
-
-
Rangel, C.1
Angus, J.2
Ghahramani, Z.3
-
40
-
-
85195242462
-
Gene regulatory network modelling: A state-space approach
-
in press
-
Wu FX. Gene regulatory network modelling: A state-space approach. Int J Data Mining Bioinform 2007; 2: in press.
-
(2007)
Int J Data Mining Bioinform
, pp. 2
-
-
Wu, F.X.1
-
41
-
-
3142671295
-
Modeling genetic regulatory networks using gene expression profiling and state space models
-
D. Husmeier, S. Roberts, and R. Dybowski eds, Springer-Verla
-
Rangel C, Angus J, Ghahramani Z, et al. Modeling genetic regulatory networks using gene expression profiling and state space models. In D. Husmeier, S. Roberts, and R. Dybowski (eds), Prob Model Bioinform Med Informat. Springer-Verla, 2006; pp: 269-293.
-
(2006)
Prob Model Bioinform Med Informat
, pp. 269-293
-
-
Rangel, C.1
Angus, J.2
Ghahramani, Z.3
-
42
-
-
28344441080
-
Modelling and identification of transcription factor motifs in human chondrogenesis
-
Liu Y, Yokota H. Modelling and identification of transcription factor motifs in human chondrogenesis, Syst Biol 2004; 1: 85-92.
-
(2004)
Syst Biol
, vol.1
, pp. 85-92
-
-
Liu, Y.1
Yokota, H.2
-
43
-
-
0346801873
-
The Gene Ontology (GO) database and informatics resource
-
Harris MA. The Gene Ontology (GO) database and informatics resource. Nucl Acids Res 2004; 3: D258-61.
-
(2004)
Nucl Acids Res
, vol.3
-
-
Harris, M.A.1
-
44
-
-
85195242535
-
-
Hu X, Sokhansanj B, Wu D, Tang Y. A Novel Approach for Mining and Dynamic Fuzzy Simulation of Biomolecular Network. Accepted to be published in IEEE Trans Fuzzy Syst.
-
Hu X, Sokhansanj B, Wu D, Tang Y. A Novel Approach for Mining and Dynamic Fuzzy Simulation of Biomolecular Network. Accepted to be published in IEEE Trans Fuzzy Syst.
-
-
-
-
45
-
-
33746639801
-
Mining and Analyzing Scale-free Protein-Protein Interaction Network
-
Hu X. Mining and Analyzing Scale-free Protein-Protein Interaction Network. Int J Bioinform Res Appl 2005; 1: 81-101.
-
(2005)
Int J Bioinform Res Appl
, vol.1
, pp. 81-101
-
-
Hu, X.1
|