-
1
-
-
33745449162
-
Comprehensive Analysis of Combinatorial Regulation using the Transcriptional Regulatory Network of Yeast
-
DOI 10.1016/j.jmb.2006.04.029, PII S0022283606004931
-
Balaji, S., Babu, M. M., Iyer, L. M., Luscombe, N. M. and Aravind, L. (2006) Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. J. Mol. Biol., 360, 213-227. (Pubitemid 43949401)
-
(2006)
Journal of Molecular Biology
, vol.360
, Issue.1
, pp. 213-227
-
-
Balaji, S.1
Babu, M.M.2
Iyer, L.M.3
Luscombe, N.M.4
Aravind, L.5
-
2
-
-
60749102185
-
Attractors and democratic dynamics
-
Bar-Yam, Y., Harmon, D. and de Bivort, B. (2009) Attractors and democratic dynamics. Science, 323, 1016-1017.
-
(2009)
Science
, vol.323
, pp. 1016-1017
-
-
Bar-Yam, Y.1
Harmon, D.2
De Bivort, B.3
-
3
-
-
77951044336
-
Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels
-
Bhardwaj, N., Yan, K. K. and Gerstein, M. B. (2010) Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels. Proc. Natl Acad. Sci. USA, 107, 6841-6846.
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 6841-6846
-
-
Bhardwaj, N.1
Yan, K.K.2
Gerstein, M.B.3
-
4
-
-
77649299348
-
An atlas of combinatorial transcriptional regulation in mouse and man
-
Ravasi, T., Suzuki, H., Cannistraci, C. V., Katayama, S., Bajic, V. B., Tan, K., Akalin, A., Schmeier, S., Kanamori-Katayama, M., Bertin, N. et al. (2010) An atlas of combinatorial transcriptional regulation in mouse and man. Cell, 140, 744-752.
-
(2010)
Cell
, vol.140
, pp. 744-752
-
-
Ravasi, T.1
Suzuki, H.2
Cannistraci, C.3
Katayama, S.4
Bajic, V.5
Tan, K.6
Akalin, A.7
Schmeier, S.8
Kanamori-Katayama, M.9
Bertin, N.10
-
6
-
-
0036500609
-
A genomic regulatory network for development
-
DOI 10.1126/science.1069883
-
Davidson, E. H., Rast, J. P., Oliveri, P., Ransick, A., Calestani, C., Yuh, C. H., Minokawa, T., Amore, G., Hinman, V., Arenas-Mena, C. et al. (2002) A genomic regulatory network for development. Science, 295, 1669-1678. (Pubitemid 34202895)
-
(2002)
Science
, vol.295
, Issue.5560
, pp. 1669-1678
-
-
Davidson, E.H.1
Rast, J.P.2
Oliveri, P.3
Ransick, A.4
Calestani, C.5
Yuh, C.-H.6
Minokawa, T.7
Amore, G.8
Hinman, V.9
Arenas-Mena, C.10
Otim, O.11
Brown, C.T.12
Livi, C.B.13
Lee, P.Y.14
Revilla, R.15
Rust, A.G.16
Pan, Z.J.17
Schilstra, M.J.18
Clarke, P.J.C.19
Arnone, M.I.20
Rowen, L.21
Cameron, R.A.22
McClay, D.R.23
Hood, L.24
Bolouri, H.25
more..
-
7
-
-
17044382973
-
Transcriptional network underlying caenorhabditis elegans vulval development
-
Inoue, T., Wang, M., Ririe, T. O., Fernandes, J. S. and Sternberg, P. W. (2005) Transcriptional network underlying Caenorhabditis elegans vulval development. Proc. Natl Acad. Sci. USA, 102, 4972-4977.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 4972-4977
-
-
Inoue, T.1
Wang, M.2
Ririe, T.3
Fernandes, J.S.4
Sternberg, P.W.5
-
8
-
-
78049507393
-
Rewiring of transcriptional regulatory networks: Hierarchy, rather than connectivity, better reflects the importance of regulators
-
Bhardwaj, N., Kim, P. M. and Gerstein, M. B. (2010) Rewiring of transcriptional regulatory networks: hierarchy, rather than connectivity, better reflects the importance of regulators. Sci. Signal., 3, ra79.
-
(2010)
Sci. Signal.
, vol.3
-
-
Bhardwaj, N.1
Kim, P.M.2
Gerstein, M.B.3
-
9
-
-
34248398455
-
Hierarchy and feedback in the evolution of the Escherichia coli transcription network
-
DOI 10.1073/pnas.0609023104
-
Cosentino Lagomarsino, M., Jona, P., Bassetti, B. and Isambert, H. (2007) Hierarchy and feedback in the evolution of the Escherichia coli transcription network. Proc. Natl Acad. Sci. USA, 104, 5516-5520. (Pubitemid 47175712)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.13
, pp. 5516-5520
-
-
Lagomarsino, M.C.1
Jona, P.2
Bassetti, B.3
Isambert, H.4
-
10
-
-
38549153853
-
Human PAML browser: A database of positive selection on human genes using phylogenetic methods
-
DOI 10.1093/nar/gkm764
-
Nickel, G. C., Tefft, D. and Adams, M. D. (2008) Human PAML browser: a database of positive selection on human genes using phylogenetic methods. Nucleic Acids Res., 36, D800-D808. (Pubitemid 351149826)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.SUPPL. 1
-
-
Nickel, G.C.1
Tefft, D.2
Adams, M.D.3
-
11
-
-
11144358198
-
A gene atlas of the mouse and human protein-encoding transcriptomes
-
DOI 10.1073/pnas.0400782101
-
Su, A. I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K. A., Block, D., Zhang, J., Soden, R., Hayakawa, M., Kreiman, G. et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl Acad. Sci. USA, 101, 6062-6067. (Pubitemid 38520528)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.16
, pp. 6062-6067
-
-
Su, A.I.1
Wiltshire, T.2
Batalov, S.3
Lapp, H.4
Ching, K.A.5
Block, D.6
Zhang, J.7
Soden, R.8
Hayakawa, M.9
Kreiman, G.10
Cooke, M.P.11
Walker, J.R.12
Hogenesch, J.B.13
-
12
-
-
12344280017
-
Summaries of affymetrix genechip probe level data
-
Irizarry, R. A., Bolstad, B. M., Collin, F., Cope, L. M., Hobbs, B. and Speed, T. P. (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res., 31,-e15.
-
(2003)
Nucleic Acids Res.
, vol.31
-
-
Irizarry, R.1
Bolstad, B.2
Collin, F.3
Cope, L.4
Hobbs, B.5
Speed, T.P.6
-
13
-
-
18744369640
-
Use of within-array replicate spots for assessing differential expression in microarray experiments
-
DOI 10.1093/bioinformatics/bti270
-
Smyth, G. K., Michaud, J. and Scott, H. S. (2005) Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics, 21, 2067-2075. (Pubitemid 40668046)
-
(2005)
Bioinformatics
, vol.21
, Issue.9
, pp. 2067-2075
-
-
Smyth, G.K.1
Michaud, J.2
Scott, H.S.3
-
14
-
-
0346888587
-
On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles
-
DOI 10.1002/sim.1548
-
Kendziorski, C. M., Newton, M. A., Lan, H. and Gould, M. N. (2003) On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles. Stat. Med., 22, 3899-3914. (Pubitemid 38008708)
-
(2003)
Statistics in Medicine
, vol.22
, Issue.24
, pp. 3899-3914
-
-
Kendziorski, C.M.1
Newton, M.A.2
Lan, H.3
Gould, M.N.4
-
15
-
-
0001677717
-
Controlling the false discovery rate a practical and powerful approach to multiple testing
-
Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate - a practical and powerful approach to multiple testing. J. Roy. Stat. Soc. B Methodol., 57, 289-300.
-
(1995)
J. Roy. Stat. Soc. B Methodol.
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
16
-
-
84984996500
-
The gene ontology project in 2008.
-
Consortium, T. G. O. (2008) The Gene Ontology project in 2008. Nucleic Acids Res., 36, D440-D444.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Consortium, T.G..O.1
-
17
-
-
46249132982
-
Evolutionary design principles of modules that control cellular differentiation: Consequences for hysteresis and multistationarity
-
DOI 10.1093/bioinformatics/btn229
-
Kim, J., Kim, T. G., Jung, S. H., Kim, J. R., Park, T., Heslop- Harrison, P. and Cho, K. H. (2008) Evolutionary design principles of modules that control cellular differentiation: consequences for hysteresis and multistationarity. Bioinformatics, 24, 1516-1522. (Pubitemid 351911703)
-
(2008)
Bioinformatics
, vol.24
, Issue.13
, pp. 1516-1522
-
-
Kim, J.1
Kim, T.-G.2
Jung, S.H.3
Kim, J.-R.4
Park, T.5
Heslop-Harrison, P.6
Cho, K.-H.7
-
18
-
-
78651449005
-
Evolutionary design principles and functional characteristics based on kingdom-specific network motifs
-
Kim, T. H., Kim, J., Heslop-Harrison, P. and Cho, K. H. (2011) Evolutionary design principles and functional characteristics based on kingdom-specific network motifs. Bioinformatics, 27, 245-251.
-
(2011)
Bioinformatics
, vol.27
, pp. 245-251
-
-
Kim, T.1
Kim, J.2
Heslop-Harrison, P.3
Cho, K.H.4
-
19
-
-
0001844324
-
An overview of genetic algorithms. 1. Fundamentals
-
Beasley, D., Bull, D. R. and Martin, R. R. (1993) An overview of genetic algorithms. 1. Fundamentals. U. Comput., 15, 58-69.
-
(1993)
U. Comput.
, vol.15
, pp. 58-69
-
-
Beasley, D.1
Bull, D.R.2
Martin, R.R.3
-
20
-
-
0036081062
-
The kegg databases at genomenet
-
Kanehisa, M., Goto, S., Kawashima, S. and Nakaya, A. (2002) The KEGG databases at GenomeNet. Nucleic Acids Res., 30, 42-46.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 42-46
-
-
Kanehisa, M.1
Goto, S.2
Kawashima, S.3
Nakaya, A.4
-
21
-
-
0037208166
-
TRANSFAC®: Transcriptional regulation, from patterns to profiles
-
DOI 10.1093/nar/gkg108
-
Matys, V., Fricke, E., Geffers, R., Gossling, E., Haubrock, M., Hehl, R., Hornischer, K., Karas, D., Kel, A. E., Kel-Margoulis, O. V. et al. (2003) TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-378. (Pubitemid 36150406)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.1
, pp. 374-378
-
-
Matys, V.1
Fricke, E.2
Geffers, R.3
Gossling, E.4
Haubrock, M.5
Hehl, R.6
Hornischer, K.7
Karas, D.8
Kel, A.E.9
Kel-Margoulis, O.V.10
Kloos, D.-U.11
Land, S.12
Lewicki-Potapov, B.13
Michael, H.14
Munch, R.15
Reuter, I.16
Rotert, S.17
Saxel, H.18
Scheer, M.19
Thiele, S.20
Wingender, E.21
more..
-
22
-
-
78651299341
-
Regulondb version 7.0: Transcriptional regulation of escherichia coli k-12 integrated within genetic sensory response units (gensor units)
-
Gama-Castro, S., Salgado, H., Peralta-Gil, M., Santos-Zavaleta, A., Muniz-Rascado, L., Solano-Lira, H., Jimenez-Jacinto, V., Weiss, V., Garcia-Sotelo, J. S., Lopez-Fuentes, A. et al. (2011) RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). Nucleic Acids Res., 39, D98-D105.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Gama-Castro, S.1
Salgado, H.2
Peralta-Gil, M.3
Santos-Zavaleta, A.4
Muniz-Rascado, L.5
Solano-Lira, H.6
Jimenez-Jacinto, V.7
Weiss, V.8
Garcia-Sotelo, J.9
Lopez-Fuentes, A.10
-
23
-
-
0037245913
-
BIND: The biomolecular interaction network database
-
DOI 10.1093/nar/gkg056
-
Bader, G. D., Betel, D. and Hogue, C. W. (2003) BIND: the biomolecular interaction network database. Nucleic Acids Res., 31, 248-250. (Pubitemid 36150376)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.1
, pp. 248-250
-
-
Bader, G.D.1
Betel, D.2
Hogue, C.W.V.3
-
24
-
-
0037119587
-
Stochastic gene expression in a single cell
-
DOI 10.1126/science.1070919
-
Elowitz, M. B., Levine, A. J., Siggia, E. D. and Swain, P. S. (2002) Stochastic gene expression in a single cell. Science, 297, 1183-1186. (Pubitemid 36193353)
-
(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
-
25
-
-
0036790975
-
Intrinsic and extrinsic contributions to stochasticity in gene expression
-
Swain, P. S.,-elowitz, M. B. and Siggia, E. D. (2002) Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc. Natl Acad. Sci. USA, 99, 12795-12800.
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 12795-12800
-
-
Swain, P.S.1
Elowitz, M.2
Siggia, E.3
-
26
-
-
77955870492
-
A system-level investigation into the cellular toxic response mechanism mediated by ahr signal transduction pathway
-
Gim, J., Kim, H. S., Kim, J., Choi, M., Kim, J. R., Chung, Y. J. and Cho, K. H. (2010) A system-level investigation into the cellular toxic response mechanism mediated by AhR signal transduction pathway. Bioinformatics, 26, 2169-2175.
-
(2010)
Bioinformatics
, vol.26
, pp. 2169-2175
-
-
Gim, J.1
Kim, H.2
Kim, J.3
Choi, M.4
Kim, J.5
Chung, Y.J.6
Cho, K.H.7
-
27
-
-
21644437234
-
STAT module can function as a biphasic amplitude filter
-
DOI 10.1049/sb:20045037
-
Mayya, V. and Loew, L. M. (2005) STAT module can function as a biphasic amplitude filter. Syst. Biol., 2, 43-52. (Pubitemid 40932497)
-
(2005)
Systems Biology
, vol.2
, Issue.1
, pp. 43-52
-
-
Mayya, V.1
Loew, L.M.2
-
28
-
-
36849048783
-
Biphasic insulin secretion from freshly isolated or cultured, perifused rodent islets: comparative studies with rats and mice
-
DOI 10.1016/j.metabol.2007.07.020, PII S0026049507002892
-
Zawalich, W. S., Yamazaki, H. and Zawalich, K. C. (2008) Biphasic insulin secretion from freshly isolated or cultured, perifused rodent islets: comparative studies with rats and mice. Metabolism, 57, 30-39. (Pubitemid 350234971)
-
(2008)
Metabolism: Clinical and Experimental
, vol.57
, Issue.1
, pp. 30-39
-
-
Zawalich, W.S.1
Yamazaki, H.2
Zawalich, K.C.3
-
29
-
-
79960105112
-
Glycolytic oscillations and limits on robust efficiency
-
Chandra, F. A., Buzi, G. and Doyle, J. C. (2011) Glycolytic oscillations and limits on robust efficiency. Science, 333, 187-192.
-
(2011)
Science
, vol.333
, pp. 187-192
-
-
Chandra, F.1
Buzi, G.2
Doyle, J.C.3
-
30
-
-
33746639260
-
Module-based analysis of robustness tradeoffs in the heat shock response system
-
Kurata, H.,-el-Samad, H., Iwasaki, R., Ohtake, H., Doyle, J. C., Grigorova, I., Gross, C. A. and Khammash, M. (2006) Module-based analysis of robustness tradeoffs in the heat shock response system. PLoS Comput. Biol., 2,-e59.
-
(2006)
PLoS Comput. Biol.
, vol.2
-
-
Kurata, H.1
El-Samad, H.2
Iwasaki, R.3
Ohtake, H.4
Doyle, J.5
Grigorova, I.6
Gross, C.7
Khammash, M.8
-
32
-
-
33749350211
-
Transcriptional dynamics of the embryonic stem cell switch
-
Chickarmane, V., Troein, C., Nuber, U. A., Sauro, H. M. and Peterson, C. (2006) Transcriptional dynamics of the embryonic stem cell switch. PLoS Comput. Biol., 2,-e123.
-
(2006)
PLoS Comput. Biol.
, vol.2
-
-
Chickarmane, V.1
Troein, C.2
Nuber, U.3
Sauro, H.M.4
Peterson, C.5
-
33
-
-
66449090934
-
Reprogramming cell fates: Reconciling rarity with robustness
-
Huang, S. (2009) Reprogramming cell fates: reconciling rarity with robustness. Bioessays, 31, 546-560.
-
(2009)
Bioessays
, vol.31
, pp. 546-560
-
-
Huang, S.1
-
34
-
-
0035983272
-
The nature of robustness in development
-
DOI 10.1002/bies.10093
-
Nijhout, H. F. (2002) The nature of robustness in development. BioEssays, 24, 553-563. (Pubitemid 34629875)
-
(2002)
BioEssays
, vol.24
, Issue.6
, pp. 553-563
-
-
Nijhout, H.F.1
-
35
-
-
58149145777
-
The biphasic behavior of incoherent feed-forward loops in biomolecular regulatory networks
-
Kim, D., Kwon, Y. K. and Cho, K. H. (2008) The biphasic behavior of incoherent feed-forward loops in biomolecular regulatory networks. BioEssays, 30, 1204-1211.
-
(2008)
BioEssays
, vol.30
, pp. 1204-1211
-
-
Kim, D.1
Kwon, Y.K.2
Cho, K.H.3
-
36
-
-
78651092705
-
A hidden incoherent switch regulates rcan1 in the calcineurin-nfat signaling network
-
Shin, S. Y., Yang, H. W., Kim, J. R., Do Heo, W. and Cho, K. H. (2011) A hidden incoherent switch regulates RCAN1 in the calcineurin-NFAT signaling network. J. Cell Sci., 124, 82-90.
-
(2011)
J. Cell Sci.
, vol.124
, pp. 82-90
-
-
Shin, S.1
Yang, H.2
Kim, J.3
Do Heo, W.4
Cho, K.H.5
-
37
-
-
0032485391
-
Structure of the DNA-binding domains from NFAT, Fos and Jun bound specifically to DNA
-
DOI 10.1038/32100
-
Chen, L., Glover, J. N., Hogan, P. G., Rao, A. and Harrison, S. C. (1998) Structure of the DNA-binding domains from NFAT, Fos and Jun bound specifically to DN A. Nature, 392, 42-48. (Pubitemid 28150581)
-
(1998)
Nature
, vol.392
, Issue.6671
, pp. 42-48
-
-
Chen, L.1
Glovert, J.N.M.2
Hogan, P.G.3
Rao, A.4
Harrison, S.C.5
-
38
-
-
0029617947
-
Virus induction of human IFNβ gene expression requires the assembly of an enhanceosome
-
DOI 10.1016/0092-8674(95)90136-1
-
Thanos, D. and Maniatis, T. (1995) Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome. Cell, 83, 1091-1100. (Pubitemid 26007801)
-
(1995)
Cell
, vol.83
, Issue.7
, pp. 1091-1100
-
-
Thanos, D.1
Maniatis, T.2
|