-
2
-
-
31544482407
-
Mapping pathways and phenotypes by systematic gene overexpression
-
Sopko, R., Huang, D., Preston, N. et al. (2006) Mapping pathways and phenotypes by systematic gene overexpression. Mol. Cell, 21, 319-330.
-
(2006)
Mol. Cell
, vol.21
, pp. 319-330
-
-
Sopko, R.1
Huang, D.2
Preston, N.3
-
3
-
-
34247629588
-
Genetic reconstruction of a functional transcriptional regulatory network
-
Hu, Z., Killion, P.J. and Iyer, V.R. (2007) Genetic reconstruction of a functional transcriptional regulatory network. Nat. Genet., 39, 683-687.
-
(2007)
Nat. Genet.
, vol.39
, pp. 683-687
-
-
Hu, Z.1
Killion, P.J.2
Iyer, V.R.3
-
4
-
-
0034704248
-
Genome-wide location and function of DNA binding proteins
-
Ren, B., Robert, F., Wyrick, J.J. et al. (2000) Genome-wide location and function of DNA binding proteins. Science, 290, 2306.
-
(2000)
Science
, vol.290
, pp. 2306
-
-
Ren, B.1
Robert, F.2
Wyrick, J.J.3
-
5
-
-
67650663220
-
Backup in gene regulatory networks explains differences between binding and knockout results
-
Gitter, A., Siegfried, Z., Klutstein, M. et al. (2009) Backup in gene regulatory networks explains differences between binding and knockout results. Mol. Syst. Biol., 5, 276.
-
(2009)
Mol. Syst. Biol.
, vol.5
, pp. 276
-
-
Gitter, A.1
Siegfried, Z.2
Klutstein, M.3
-
6
-
-
84864930280
-
Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data
-
Yang, T.-H. and Wu, W.-S. (2012) Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data. BMC Syst. Biol., 6, 102.
-
(2012)
BMC Syst. Biol.
, vol.6
, pp. 102
-
-
Yang, T.-H.1
Wu, W.-S.2
-
7
-
-
78651272522
-
YEASTRACT: Providing a programmatic access to curated transcriptional regulatory associations in saccharomyces cerevisiae through a web services interface
-
Abdulrehman, D., Monteiro, P.T., Teixeira, M.C. et al. (2011) YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface. Nucleic Acids Res., 39, D136-D140.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. D136-D140
-
-
Abdulrehman, D.1
Monteiro, P.T.2
Teixeira, M.C.3
-
8
-
-
84891806965
-
The YEASTRACT database: An upgraded information system for the analysis of gene and genomic transcription regulation in saccharomyces cerevisiae
-
Teixeira, M.C., Monteiro, P.T., Guerreiro, J.F. et al. (2014) The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic Acids Res., 42, D161-D166.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D161-D166
-
-
Teixeira, M.C.1
Monteiro, P.T.2
Guerreiro, J.F.3
-
10
-
-
0013178945
-
-
McGraw-Hill, New York
-
Lee, R.C.T., Tseng, T., Chang, R. et al. (2005) Introduction to the Design and Analysis of Algorithms: A Strategic Approach. McGraw-Hill, New York.
-
(2005)
Introduction to the Design and Analysis of Algorithms: A Strategic Approach
-
-
Lee, R.C.T.1
Tseng, T.2
Chang, R.3
-
11
-
-
0036790999
-
Transitive functional annotation by shortest-path analysis of gene expression data
-
Zhou, X., Kao, M.C.J. and Wong, W.H. (2002) Transitive functional annotation by shortest-path analysis of gene expression data. Proc. Natl Acad. Sci. USA, 99, 12783.
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
-
-
Zhou, X.1
Kao, M.C.J.2
Wong, W.H.3
-
12
-
-
67249148362
-
Exploring network structure, dynamics, and function using NetworkX
-
Varoquaux, G., Vaught, T. and Millman, J. (eds) Pasadena, CA USA
-
Hagberg, A., Swart, P. and Schult, D. (2008) Exploring Network Structure, Dynamics, and Function Using NetworkX. In: Varoquaux, G., Vaught, T. and Millman, J. (eds), Proceedings of the 7th Python in Science conference (SciPy 2008), Pasadena, CA USA. pp. 11-15.
-
(2008)
Proceedings of the 7th Python in Science Conference (SciPy 2008)
, pp. 11-15
-
-
Hagberg, A.1
Swart, P.2
Schult, D.3
-
13
-
-
84867453337
-
Graphviz-open source graph drawing tools
-
Springer, New York
-
Ellson, J., Gansner, E., Koutsofios, L. et al. (2002) Graphviz-open source graph drawing tools. In: Graph Drawing. Springer, New York, pp. 483-485.
-
(2002)
Graph Drawing
, pp. 483-485
-
-
Ellson, J.1
Gansner, E.2
Koutsofios, L.3
-
14
-
-
36448940491
-
New insights into the regulation of the saccharomyces cerevisiae UGA4 gene: Two parallel pathways participate in carbon-regulated transcription
-
Luzzani, C., Cardillo, S.B., Moretti, M.B. et al. (2007) New insights into the regulation of the Saccharomyces cerevisiae UGA4 gene: two parallel pathways participate in carbon-regulated transcription. Microbiology, 153, 3677-3684.
-
(2007)
Microbiology
, vol.153
, pp. 3677-3684
-
-
Luzzani, C.1
Cardillo, S.B.2
Moretti, M.B.3
-
15
-
-
9144257282
-
The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes
-
Ruepp, A., Zollner, A., Maier, D. et al. (2004) The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res., 32, 5539-5545.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 5539-5545
-
-
Ruepp, A.1
Zollner, A.2
Maier, D.3
-
16
-
-
77949477875
-
Characterizing regulatory path motifs in integrated networks using perturbational data
-
Joshi, A., van Parys, T., Peer, Y.V. et al. (2010) Characterizing regulatory path motifs in integrated networks using perturbational data. Genome Biol., 11, R32.
-
(2010)
Genome Biol.
, vol.11
, pp. R32
-
-
Joshi, A.1
Van Parys, T.2
Peer, Y.V.3
-
17
-
-
70350452746
-
Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks
-
Huang, S.C. and Fraenkel, E. (2009) Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks. Sci. Signal., 2, ra40.
-
(2009)
Sci. Signal.
, vol.2
, pp. ra40
-
-
Huang, S.C.1
Fraenkel, E.2
-
18
-
-
34547830859
-
SPINE: A framework for signaling-regulatory pathway inference from cause-effect experiments
-
Ourfali, O., Shlomi, T., Ideker, T. et al. (2007) SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. Bioinformatics, 23, i359-i366.
-
(2007)
Bioinformatics
, vol.23
, pp. i359-i366
-
-
Ourfali, O.1
Shlomi, T.2
Ideker, T.3
-
19
-
-
42949096140
-
EQED: An efficient method for interpreting eQTL associations using protein networks
-
Suthram, S., Beyer, A., Karp, R.M. et al. (2008) eQED: an efficient method for interpreting eQTL associations using protein networks. Mol. Syst. Biol., 4, 162.
-
(2008)
Mol. Syst. Biol.
, vol.4
, pp. 162
-
-
Suthram, S.1
Beyer, A.2
Karp, R.M.3
-
20
-
-
61349114190
-
Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity
-
Yeger-Lotem, E., Riva, L., Su, L.J. et al. (2009) Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity. Nat. Genet., 41, 316-323.
-
(2009)
Nat. Genet.
, vol.41
, pp. 316-323
-
-
Yeger-Lotem, E.1
Riva, L.2
Su, L.J.3
-
22
-
-
79959930131
-
ChIP-array: Combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor
-
Qin, J., Li, M.J., Wang, P. et al. (2011) ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor. Nucleic Acids Res., 39, W430-W436.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. W430-W436
-
-
Qin, J.1
Li, M.J.2
Wang, P.3
-
23
-
-
0035775725
-
A new approach to decoding life: Systems biology
-
Ideker, T., Galitski, T. and Hood, L. (2001) A new approach to decoding life: systems biology. Annu. Rev. Genomics Hum. Genet., 2, 343-372.
-
(2001)
Annu. Rev. Genomics Hum. Genet.
, vol.2
, pp. 343-372
-
-
Ideker, T.1
Galitski, T.2
Hood, L.3
-
24
-
-
28444475160
-
A data integration methodology for systems biology
-
Hwang, D., Rust, A.G., Ramsey, S. et al. (2005) A data integration methodology for systems biology. Proc. Natl Acad. Sci. USA, 102, 17296-17301.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 17296-17301
-
-
Hwang, D.1
Rust, A.G.2
Ramsey, S.3
-
25
-
-
28444498336
-
A data integration methodology for systems biology: Experimental verification
-
Hwang, D., Smith, J.J., Leslie, D.M. et al. (2005) A data integration methodology for systems biology: experimental verification. Proc. Natl Acad. Sci. USA, 102, 17302-17307.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 17302-17307
-
-
Hwang, D.1
Smith, J.J.2
Leslie, D.M.3
-
26
-
-
4644326931
-
Genomic analysis of regulatory network dynamics reveals large topological changes
-
Luscombe, N.M., Babu, M.M., Yu, H. et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature, 431, 308-312.
-
(2004)
Nature
, vol.431
, pp. 308-312
-
-
Luscombe, N.M.1
Babu, M.M.2
Yu, H.3
-
27
-
-
67650093251
-
The yeast GATA factor gat1 occupies a central position in nitrogen catabolite repression-sensitive gene activation
-
Georis, I., Feller, A., Vierendeels, F. et al. (2009) The yeast GATA factor Gat1 occupies a central position in nitrogen catabolite repression-sensitive gene activation. Mol. Cell. Biol., 29, 3803-3815.
-
(2009)
Mol. Cell. Biol.
, vol.29
, pp. 3803-3815
-
-
Georis, I.1
Feller, A.2
Vierendeels, F.3
-
28
-
-
0030944694
-
Cross regulation of four GATA factors that control nitrogen catabolic gene expression in saccharomyces cerevisiae
-
Coffman, J.A., Rai, R., Loprete, D.M. et al. (1997) Cross regulation of four GATA factors that control nitrogen catabolic gene expression in Saccharomyces cerevisiae. J. Bacteriol., 179, 3416-3429.
-
(1997)
J. Bacteriol.
, vol.179
, pp. 3416-3429
-
-
Coffman, J.A.1
Rai, R.2
Loprete, D.M.3
|