-
1
-
-
34249079154
-
Network motifs: Theory and experimental approaches
-
Alon, U. 2007. Network motifs: theory and experimental approaches. Nat. Rev. Genet. 8, 450-461.
-
(2007)
Nat. Rev. Genet
, vol.8
, pp. 450-461
-
-
Alon, U.1
-
2
-
-
33847015674
-
Computational analysis of the synergy among multiple interacting genes
-
Anastassiou, D. 2007. Computational analysis of the synergy among multiple interacting genes. Mol. Syst. Biol. 3, 83.
-
(2007)
Mol. Syst. Biol
, vol.3
, pp. 83
-
-
Anastassiou, D.1
-
3
-
-
33745449162
-
Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast
-
Balaji, S., Babu, M.M., Iyer, L.M., et al. 2006. Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. J. Mol. Biol. 360, 213-227.
-
(2006)
J. Mol. Biol
, vol.360
, pp. 213-227
-
-
Balaji, S.1
Babu, M.M.2
Iyer, L.M.3
-
4
-
-
16844376909
-
Reverse engineering of regulatory networks in human B cells
-
Basso, K., Margolin, A.A., Stolovitzky, G., et al. 2005. Reverse engineering of regulatory networks in human B cells. Nat. Genet. 37, 382-390.
-
(2005)
Nat. Genet
, vol.37
, pp. 382-390
-
-
Basso, K.1
Margolin, A.A.2
Stolovitzky, G.3
-
5
-
-
12344269924
-
GO::termfinder - open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes
-
Boyle, E.I., Weng, S., Gollub, J., et al. 2004. GO::termfinder - open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes. Bioinformatics 20, 3710-3715.
-
(2004)
Bioinformatics
, vol.20
, pp. 3710-3715
-
-
Boyle, E.I.1
Weng, S.2
Gollub, J.3
-
6
-
-
27744552572
-
Inferring gene networks from steady-state response to single-gene perturbations
-
Brazhnik, P. 2005. Inferring gene networks from steady-state response to single-gene perturbations. J. Theor. Biol. 237, 427-440.
-
(2005)
J. Theor. Biol
, vol.237
, pp. 427-440
-
-
Brazhnik, P.1
-
7
-
-
0036683181
-
Linking the genes: Inferring quantitative gene networks from microarray data
-
De la Fuente, A., Brazhnik, P., and Mendes, P. 2002. Linking the genes: inferring quantitative gene networks from microarray data. Trends Genet. 18, 395-398.
-
(2002)
Trends Genet
, vol.18
, pp. 395-398
-
-
De la Fuente, A.1
Brazhnik, P.2
Mendes, P.3
-
8
-
-
34547788797
-
Bayesian approaches to reverse engineer cellular systems: A simulation study on nonlinear Gaussian networks
-
Ferrazzi, F., Sebastiani, P., Ramoni, M., et al. 2007. Bayesian approaches to reverse engineer cellular systems: a simulation study on nonlinear Gaussian networks. BMC Bioinform. 8, S2.
-
(2007)
BMC Bioinform
, vol.8
-
-
Ferrazzi, F.1
Sebastiani, P.2
Ramoni, M.3
-
9
-
-
0842288337
-
Inferring cellular networks using probabilistic graphical models
-
Friedman, N. 2004. Inferring cellular networks using probabilistic graphical models. Science 303, 799-805.
-
(2004)
Science
, vol.303
, pp. 799-805
-
-
Friedman, N.1
-
10
-
-
0038048325
-
Inferring genetic networks and identifying compound mode of action via expression profiling
-
Gardner, T.S., di Bernardo, D., Lorenz, D., et al. 2003. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301, 102-105.
-
(2003)
Science
, vol.301
, pp. 102-105
-
-
Gardner, T.S.1
di Bernardo, D.2
Lorenz, D.3
-
11
-
-
0033518234
-
From molecular to modular cell biology
-
Hartwell, L.H., Hopfield, J.J., Leibler, S., et al. 1999. From molecular to modular cell biology. Nature 402, C47-C52.
-
(1999)
Nature
, vol.402
-
-
Hartwell, L.H.1
Hopfield, J.J.2
Leibler, S.3
-
12
-
-
38549123363
-
Gene ontology annotations at SGD: New data sources and annotation methods
-
Hong, E.L., Balakrishnan, R., Dong, Q., et al. 2008. Gene ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 36, D577-D581.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Hong, E.L.1
Balakrishnan, R.2
Dong, Q.3
-
13
-
-
0036789922
-
Untangling the wires: A strategy to trace functional interactions in signaling and gene networks
-
Kholodenko, B.N., Kiyatkin, A., Bruggeman, F.J., et al. 2002. Untangling the wires: a strategy to trace functional interactions in signaling and gene networks. Proc. Natl. Acad. Sci. USA 99, 12841-12846.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 12841-12846
-
-
Kholodenko, B.N.1
Kiyatkin, A.2
Bruggeman, F.J.3
-
14
-
-
4644301730
-
A benchmark for methods in reverse engineering and model discrimination: Problem formulation and solutions
-
Kremling, A., Fischer, S., Gadkar, K., et al. 2004. A benchmark for methods in reverse engineering and model discrimination: problem formulation and solutions. Genome Res. 14, 1773-1785.
-
(2004)
Genome Res
, vol.14
, pp. 1773-1785
-
-
Kremling, A.1
Fischer, S.2
Gadkar, K.3
-
15
-
-
13244264814
-
Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach
-
Ma, H., Buer, J., and Zeng, A. 2004. Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach. BMC Bioinform. 5, 199.
-
(2004)
BMC Bioinform
, vol.5
, pp. 199
-
-
Ma, H.1
Buer, J.2
Zeng, A.3
-
16
-
-
59649096341
-
Replaying the evolutionary tape: Biomimetic reverse engineering of gene networks
-
to appear
-
Marbach, D., Mattiussi, C., and Floreano, D. 2009. Replaying the evolutionary tape: biomimetic reverse engineering of gene networks. Ann. NY Acad. Sci. (to appear).
-
(2009)
Ann. NY Acad. Sci
-
-
Marbach, D.1
Mattiussi, C.2
Floreano, D.3
-
17
-
-
2942694772
-
Artificial gene networks for objective comparison of analysis algorithms
-
Mendes, P., Sha, W., and Ye, K. 2003. Artificial gene networks for objective comparison of analysis algorithms. Bioinformatics 19, Suppl 2, ii122-ii129.
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 2
-
-
Mendes, P.1
Sha, W.2
Ye, K.3
-
18
-
-
1542287343
-
Superfamilies of evolved and designed networks
-
Milo, R., Itzkovitz, S., Kashtan, N., et al. 2004. Superfamilies of evolved and designed networks. Science 303, 1538-1542.
-
(2004)
Science
, vol.303
, pp. 1538-1542
-
-
Milo, R.1
Itzkovitz, S.2
Kashtan, N.3
-
19
-
-
55749093996
-
Network inference using informative priors
-
Mukherjee, S., and Speed, T.P. 2008. Network inference using informative priors. Proc. Natl. Acad. Sci. USA 105, 14313-14318.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 14313-14318
-
-
Mukherjee, S.1
Speed, T.P.2
-
20
-
-
33749468596
-
Finding community structure in networks using the eigenvectors of matrices
-
Newman, M.E.J. 2006. Finding community structure in networks using the eigenvectors of matrices. Phys. Rev. E, 74 (3 Pt 2): 036104.
-
(2006)
Phys. Rev. E
, vol.74
, Issue.3 PART 2
, pp. 036104
-
-
Newman, M.E.J.1
-
21
-
-
33749117778
-
Simulation of microarray data with realistic characteristics
-
Nykter, M., Aho, T., Andesmäk, M., et al. 2006. Simulation of microarray data with realistic characteristics. BMC Bioinform. 7, 349.
-
(2006)
BMC Bioinform
, vol.7
, pp. 349
-
-
Nykter, M.1
Aho, T.2
Andesmäk, M.3
-
22
-
-
33646901020
-
Reverse engineering the gap gene network of Drosophila melanogaster
-
Perkins, T.J., Jaeger, J., Reinitz, J., et al. 2006. Reverse engineering the gap gene network of Drosophila melanogaster. PLoS Comput. Biol. 2, e51.
-
(2006)
PLoS Comput. Biol
, vol.2
-
-
Perkins, T.J.1
Jaeger, J.2
Reinitz, J.3
-
23
-
-
0037199968
-
Hierarchical organization of modularity in metabolic networks
-
Ravasz, E., Somera, A.L., Mongru, D.A., et al. 2002. Hierarchical organization of modularity in metabolic networks. Science 297, 1551-1555.
-
(2002)
Science
, vol.297
, pp. 1551-1555
-
-
Ravasz, E.1
Somera, A.L.2
Mongru, D.A.3
-
24
-
-
33847064282
-
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
-
Reguly, T., Breitkreutz, A., Boucher, L., et al. 2006. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J. Biol. 5, 11.
-
(2006)
J. Biol
, vol.5
, pp. 11
-
-
Reguly, T.1
Breitkreutz, A.2
Boucher, L.3
-
25
-
-
13144283679
-
Modular analysis of the transcriptional regulatory network of E. coli
-
Resendis-Antonio, O., Freyre-González, J.A., Menchaca- Méndez, R., et al. 2005. Modular analysis of the transcriptional regulatory network of E. coli. Trends Genet. 21, 16-20.
-
(2005)
Trends Genet
, vol.21
, pp. 16-20
-
-
Resendis-Antonio, O.1
Freyre-González, J.A.2
Menchaca- Méndez, R.3
-
26
-
-
15944367731
-
Reconstructing biological networks using conditional correlation analysis
-
Rice, J.J., Tu, Y., and Stolovitzky, G. 2005. Reconstructing biological networks using conditional correlation analysis. Bioinformatics 21, 765-773.
-
(2005)
Bioinformatics
, vol.21
, pp. 765-773
-
-
Rice, J.J.1
Tu, Y.2
Stolovitzky, G.3
-
27
-
-
43349102320
-
A system for generating transcription regulatory networks with combinatorial control of transcription
-
Roy, S., Werner-Washburne, M., and Lane, T. 2008. A system for generating transcription regulatory networks with combinatorial control of transcription. Bioinformatics 24, 1318-1320.
-
(2008)
Bioinformatics
, vol.24
, pp. 1318-1320
-
-
Roy, S.1
Werner-Washburne, M.2
Lane, T.3
-
28
-
-
0036578795
-
Network motifs in the transcriptional regulation network of Escherichia coli
-
Shen-Orr, S.S., Milo, R., Mangan, S., et al. 2002. Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 31, 64-68.
-
(2002)
Nat. Genet
, vol.31
, pp. 64-68
-
-
Shen-Orr, S.S.1
Milo, R.2
Mangan, S.3
-
29
-
-
36249019789
-
Dialogue on reverse-engineering assessment and methods: The dream of high-throughput pathway inference
-
Stolovitzky, G., Monroe, D., and Califano, A. 2007. Dialogue on reverse-engineering assessment and methods: the dream of high-throughput pathway inference. Ann. NY Acad. Sci. 1115, 1-22.
-
(2007)
Ann. NY Acad. Sci
, vol.1115
, pp. 1-22
-
-
Stolovitzky, G.1
Monroe, D.2
Califano, A.3
-
30
-
-
0037687416
-
Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling
-
Tegner, J., Yeung, M.K.S., Hasty, J., et al. 2003. Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling. Proc. Natl. Acad. Sci. USA 100, 5944-5949.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 5944-5949
-
-
Tegner, J.1
Yeung, M.K.S.2
Hasty, J.3
-
31
-
-
33144486498
-
SynTReN: A generator of synthetic gene expression data for design and analysis of structure learning algorithms
-
Van den Bulcke, T., van Leemput, K., Naudts, B., et al. 2006. SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms. BMC Bioinform. 7, 43.
-
(2006)
BMC Bioinform
, vol.7
, pp. 43
-
-
Van den Bulcke, T.1
van Leemput, K.2
Naudts, B.3
-
32
-
-
0034644270
-
The segment polarity network is a robust developmental module
-
Von Dassow, G., Meir, E., Munro, E.M., et al. 2000. The segment polarity network is a robust developmental module. Nature 406, 188-192.
-
(2000)
Nature
, vol.406
, pp. 188-192
-
-
Von Dassow, G.1
Meir, E.2
Munro, E.M.3
-
33
-
-
33746602343
-
Reconstructing gene regulatory networks: From random to scale-free connectivity
-
Wildenhain, J., and Crampin, E.J. 2006. Reconstructing gene regulatory networks: from random to scale-free connectivity. Syst. Biol. 153, 247-256.
-
(2006)
Syst. Biol
, vol.153
, pp. 247-256
-
-
Wildenhain, J.1
Crampin, E.J.2
-
34
-
-
0242490789
-
Importance of input perturbations and stochastic gene expression in the reverse engineering of genetic regulatory networks: Insights from an identifiability analysis of an in silico network
-
Zak, D.E., Gonye, G.E., Schwaber, J.S., et al. 2003. Importance of input perturbations and stochastic gene expression in the reverse engineering of genetic regulatory networks: insights from an identifiability analysis of an in silico network. Genome Res. 13, 2396-2405.
-
(2003)
Genome Res
, vol.13
, pp. 2396-2405
-
-
Zak, D.E.1
Gonye, G.E.2
Schwaber, J.S.3
|