-
1
-
-
70349882120
-
Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses
-
Amit, I. et al. (2009) Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science, 326, 257-263.
-
(2009)
Science
, vol.326
, pp. 257-263
-
-
Amit, I.1
-
2
-
-
67649982744
-
Diversity and complexity in DNA recognition by transcription factors
-
Badis, G. et al. (2009) Diversity and complexity in DNA recognition by transcription factors. Science, 324, 1720-1723.
-
(2009)
Science
, vol.324
, pp. 1720-1723
-
-
Badis, G.1
-
3
-
-
33750238153
-
Stratus not altocumulus: a new view of the yeast protein interaction network
-
Batada, N. et al (2006) Stratus not altocumulus: a new view of the yeast protein interaction network. PLoS Biol., 4, e317.
-
(2006)
PLoS Biol
, vol.4
-
-
Batada, N.1
-
4
-
-
0002460150
-
The ALARM monitoring system: a case study with two probabilistic inference techniques for belief networks
-
Beinlich, I. et al. (1989) The ALARM monitoring system: a case study with two probabilistic inference techniques for belief networks. In Proceedings of the 2nd European Conference on AI in Medicine, 38, 247-256.
-
(1989)
Proceedings of the 2nd European Conference on AI in Medicine
, vol.38
, pp. 247-256
-
-
Beinlich, I.1
-
5
-
-
0002610737
-
On a routing problem
-
Bellman, R. (1958) On a routing problem. Q. Appl. Math., 16, 87-90.
-
(1958)
Q. Appl. Math.
, vol.16
, pp. 87-90
-
-
Bellman, R.1
-
6
-
-
45449115390
-
Variation in homeodomain DNA binding revealed by highresolution analysis of sequence preferences
-
Berger, M. et al. (2008) Variation in homeodomain DNA binding revealed by highresolution analysis of sequence preferences. Cell, 133, 1266-1276.
-
(2008)
Cell
, vol.133
, pp. 1266-1276
-
-
Berger, M.1
-
7
-
-
77953077420
-
Aglobal protein kinase and phosphatase interaction network in yeast
-
Breitkreutz, A. et al (2010)Aglobal protein kinase and phosphatase interaction network in yeast. Science, 328, 1043-1046.
-
(2010)
Science
, vol.328
, pp. 1043-1046
-
-
Breitkreutz, A.1
-
8
-
-
84984933073
-
Structure and function of a transcriptional network activated by the MAPK Hog1
-
Capaldi, A. et al. (2008) Structure and function of a transcriptional network activated by the MAPK Hog1. Nat. Genet., 40, 1300-1306.
-
(2008)
Nat. Genet.
, vol.40
, pp. 1300-1306
-
-
Capaldi, A.1
-
9
-
-
46749127803
-
Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia
-
Chang, L. et al. (2008) Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia. Genome Biol., 9, R38.
-
(2008)
Genome Biol
, vol.9
-
-
Chang, L.1
-
10
-
-
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
-
11
-
-
2942582468
-
Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data
-
Gao, F. et al. (2004) Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. BMC Bioinformatics, 5, 31.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 31
-
-
Gao, F.1
-
12
-
-
1542284074
-
Clb6/Cdc28 and Cdc14 regulate phosphorylation status and cellular localization of Swi6
-
Geymonat, M. et al. (2004) Clb6/Cdc28 and Cdc14 regulate phosphorylation status and cellular localization of Swi6. Mol. Cell Biol., 24, 2277-2285.
-
(2004)
Mol. Cell Biol.
, vol.24
, pp. 2277-2285
-
-
Geymonat, M.1
-
13
-
-
0034721670
-
The Isw2 chromatin remodeling complex represses early meiotic genes upon recruitment by Ume6p
-
Goldmark, J. et al. (2000) The Isw2 chromatin remodeling complex represses early meiotic genes upon recruitment by Ume6p. Cell, 103, 423-433.
-
(2000)
Cell
, vol.103
, pp. 423-433
-
-
Goldmark, J.1
-
14
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
Harbison, C. et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature, 431, 99-104.
-
(2004)
Nature
, vol.431
, pp. 99-104
-
-
Harbison, C.1
-
15
-
-
33847744247
-
How complete are current yeast and human protein-interaction networks?
-
Hart, G. et al. (2006) How complete are current yeast and human protein-interaction networks? Genome Biol., 7, 120.
-
(2006)
Genome Biol
, vol.7
, pp. 120
-
-
Hart, G.1
-
16
-
-
0036366689
-
Combining location and expression data for principled discovery of genetic regulatory network models
-
Hartemink, A.J. et al. (2002) Combining location and expression data for principled discovery of genetic regulatory network models. Pac. Symp. Biocomput., 437-449.
-
(2002)
Pac. Symp. Biocomput.
, pp. 437-449
-
-
Hartemink, A.J.1
-
17
-
-
33745178476
-
Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in saccharomyces cerevisiae
-
Herrgard, M. et al. (2006) Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in saccharomyces cerevisiae. Genome Res., 16, 627-635.
-
(2006)
Genome Res
, vol.16
, pp. 627-635
-
-
Herrgard, M.1
-
18
-
-
0036894656
-
Complex transcriptional circuitry at the G1/S transition in saccharomyces cerevisiae
-
Horak, C. et al. (2002) Complex transcriptional circuitry at the G1/S transition in saccharomyces cerevisiae. Genes Dev., 16, 3017-3033.
-
(2002)
Genes Dev
, vol.16
, pp. 3017-3033
-
-
Horak, C.1
-
19
-
-
34247629588
-
Genetic reconstruction of a functional transcriptional regulatory network
-
Hu, Z. et al. (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
-
20
-
-
0034616930
-
Functional discovery via a compendium of expression profiles
-
Hughes, T. et al. (2000) Functional discovery via a compendium of expression profiles. Cell, 102, 109-126.
-
(2000)
Cell
, vol.102
, pp. 109-126
-
-
Hughes, T.1
-
21
-
-
0000801240
-
Discovering regulatory and signalling circuits in molecular interaction networks
-
Ideker, T. et al. (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics, 18 (Suppl. 1), S233-S240.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Ideker, T.1
-
22
-
-
0030716393
-
Identification of the Saccharomyces cerevisiae genes STB1-STB5 encoding Sin3p binding proteins
-
Kasten, M. and Stillman, D. (1997). Identification of the Saccharomyces cerevisiae genes STB1-STB5 encoding Sin3p binding proteins. Mol. Gen. Genet., 256, 376-386.
-
(1997)
Mol. Gen. Genet.
, vol.256
, pp. 376-386
-
-
Kasten, M.1
Stillman, D.2
-
23
-
-
67749113808
-
Transcriptional regulatory circuits: predicting numbers from alphabets
-
Kim, H. et al. (2009) Transcriptional regulatory circuits: predicting numbers from alphabets. Science, 325, 429-432.
-
(2009)
Science
, vol.325
, pp. 429-432
-
-
Kim, H.1
-
25
-
-
0034612501
-
Forkhead-like transcription factors recruit Ndd1 to the chromatin of G2/M-specific promoters
-
Koranda, M. et al. (2000) Forkhead-like transcription factors recruit Ndd1 to the chromatin of G2/M-specific promoters. Nature, 406, 94-98.
-
(2000)
Nature
, vol.406
, pp. 94-98
-
-
Koranda, M.1
-
26
-
-
57149100949
-
Apredictive model of the oxygen and heme regulatory network in yeast
-
Kundaje, A. et al. (2008)Apredictive model of the oxygen and heme regulatory network in yeast. PLoS Comput. Biol., 4, e1000224.
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Kundaje, A.1
-
27
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
Lee, T. et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 298, 799-804.
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.1
-
28
-
-
33749037129
-
Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification
-
Lee, S-I. et al. (2006) Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification. Proc. Natl Acad. Sci. USA, 103, 14062-14067.
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 14062-14067
-
-
Lee, S.-I.1
-
29
-
-
33645769260
-
An improved map of conserved regulatory sites for Saccharomyces cerevisiae
-
MacIsaac, K. et al. (2006) An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics, 7, 113.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 113
-
-
MacIsaac, K.1
-
30
-
-
0037012880
-
Specificity and stability in topology of protein networks
-
Maslov, S. and Sneppen, K. (2002) Specificity and stability in topology of protein networks. Science, 296, 910-913.
-
(2002)
Science
, vol.296
, pp. 910-913
-
-
Maslov, S.1
Sneppen, K.2
-
31
-
-
4444231731
-
Role of the N-terminal region of Rap1p in the transcriptional activation of glycolytic genes in Saccharomyces cerevisiae
-
Mizuno, T. et al. (2004) Role of the N-terminal region of Rap1p in the transcriptional activation of glycolytic genes in Saccharomyces cerevisiae. Yeast, 21, 851-866.
-
(2004)
Yeast
, vol.21
, pp. 851-866
-
-
Mizuno, T.1
-
32
-
-
3142536716
-
Exploration of essential gene functions via titratable promoter alleles
-
Mnaimneh, S. et al. (2004) Exploration of essential gene functions via titratable promoter alleles. Cell, 118, 31-44.
-
(2004)
Cell
, vol.118
, pp. 31-44
-
-
Mnaimneh, S.1
-
33
-
-
2442718023
-
Using protein-protein interactions for refining gene networks estimated from microarray data by bayesian networks
-
Nariai, N. et al. (2004) Using protein-protein interactions for refining gene networks estimated from microarray data by bayesian networks. Pac. Symp. Biocomput., 336-347.
-
(2004)
Pac. Symp. Biocomput.
, pp. 336-347
-
-
Nariai, N.1
-
34
-
-
0034076869
-
Two regulators of Ste12p inhibit pheromone-responsive transcription by separate mechanisms
-
Olson, K. et al. (2000) Two regulators of Ste12p inhibit pheromone-responsive transcription by separate mechanisms. Mol. Cell Biol., 20, 4199-4209.
-
(2000)
Mol. Cell Biol.
, vol.20
, pp. 4199-4209
-
-
Olson, K.1
-
35
-
-
34547830859
-
SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments
-
Ourfali, O. et al. (2007) SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. Bioinformatics, 23, i359-i366.
-
(2007)
Bioinformatics
, vol.23
-
-
Ourfali, O.1
-
36
-
-
76749100265
-
Network-free inference of knockout effects in yeast
-
Peleg, T. et al. (2010) Network-free inference of knockout effects in yeast. PLoS Comput. Biol., 6, e1000635.
-
(2010)
PLoS Comput. Biol.
, vol.6
-
-
Peleg, T.1
-
37
-
-
33747379083
-
The forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle
-
Pramila, T. et al. (2006) The forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle. Genes Dev., 20, 2266-2278.
-
(2006)
Genes Dev
, vol.20
, pp. 2266-2278
-
-
Pramila, T.1
-
38
-
-
41849123062
-
Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics
-
Ramsey, S.A. et al. (2008) Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics. PLoS Comput. Biol., 4, e1000021.
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Ramsey, S.A.1
-
39
-
-
0037941585
-
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data
-
Segal, E. et al. (2003) Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet., 34, 166-176.
-
(2003)
Nat. Genet.
, vol.34
, pp. 166-176
-
-
Segal, E.1
-
40
-
-
21844455527
-
Learning module networks
-
Segal, E. et al. (2005) Learning module networks. J. Mach. Learn. Res., 6, 557-588.
-
(2005)
J. Mach. Learn. Res.
, vol.6
, pp. 557-588
-
-
Segal, E.1
-
41
-
-
72249103485
-
A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection
-
Shapira, S. et al (2009) A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection. Cell, 139, 1255-1267.
-
(2009)
Cell
, vol.139
, pp. 1255-1267
-
-
Shapira, S.1
-
42
-
-
0029557246
-
UME6 is a central component of a developmental regulatory switch controlling meiosis-specific gene expression
-
Steber, C. and Esposito, R. (1995) UME6 is a central component of a developmental regulatory switch controlling meiosis-specific gene expression. Proc. Natl Acad. Sci. USA, 92, 12490-12494.
-
(1995)
Proc. Natl Acad. Sci. USA
, vol.92
, pp. 12490-12494
-
-
Steber, C.1
Esposito, R.2
-
43
-
-
65149083962
-
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
-
Suzuki, H. et al. (2009) The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat. Genet., 41, 553-562.
-
(2009)
Nat. Genet.
, vol.41
, pp. 553-562
-
-
Suzuki, H.1
-
44
-
-
0036138322
-
How to reconstruct a large genetic network from n gene perturbations in fewer than n2 easy steps
-
Wagner, A. (2001). How to reconstruct a large genetic network from n gene perturbations in fewer than n2 easy steps. Bioinformatics, 17, 1183-1197.
-
(2001)
Bioinformatics
, vol.17
, pp. 1183-1197
-
-
Wagner, A.1
-
45
-
-
3142550630
-
Physical network models
-
Yeang, C. et al. (2004) Physical network models. J. Comput. Biol., 11, 243-262.
-
(2004)
J. Comput. Biol.
, vol.11
, pp. 243-262
-
-
Yeang, C.1
-
46
-
-
61349114190
-
Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity
-
Yeger-Lotem, E. 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
-
47
-
-
62549145762
-
Toward accurate reconstruction of functional protein networks
-
Yosef, N. et al. (2009) Toward accurate reconstruction of functional protein networks. Mol. Syst. Biol., 5, 248.
-
(2009)
Mol. Syst. Biol.
, vol.5
, pp. 248
-
-
Yosef, N.1
-
48
-
-
12744261506
-
A new dynamic bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data
-
Zou, M. and Conzen, S.D. (2005). A new dynamic bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data. Bioinformatics, 21, 71-79.
-
(2005)
Bioinformatics
, vol.21
, pp. 71-79
-
-
Zou, M.1
Conzen, S.D.2
|