-
1
-
-
70350452746
-
Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks
-
S.-s. C. Huang, E. Fraenkel, Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks. Sci. Signal. 2, ra40 (2009).
-
(2009)
Sci. Signal.
, vol.2
-
-
Huang, S.-S.C.1
Fraenkel, E.2
-
2
-
-
66149137998
-
Dynamic signaling in the Hog1 MAPK pathway relies on high basal signal transduction
-
J. Macia, S. Regot, T. Peeters, N. Conde, R. Solé, F. Posas, Dynamic signaling in the Hog1 MAPK pathway relies on high basal signal transduction. Sci. Signal. 2, ra13 (2009).
-
(2009)
Sci. Signal.
, vol.2
-
-
MacIa, J.1
Regot, S.2
Peeters, T.3
Conde, N.4
Solé, R.5
Posas, F.6
-
3
-
-
0000801240
-
Discovering regulatory and signalling circuits in molecular interaction networks
-
T. Ideker, O. Ozier, B. Schwikowski, A. F. Siegel, Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 18, S233-S240 (2002).
-
(2002)
Bioinformatics
, vol.18
-
-
Ideker, T.1
Ozier, O.2
Schwikowski, B.3
Siegel, A.F.4
-
4
-
-
0347473809
-
Gaining confidence in high-throughput protein interaction networks
-
J. S. Bader, A. Chaudhuri, J. Rothberg, J. Chant, Gaining confidence in high-throughput protein interaction networks. Nat. Biotechnol. 22, 78-85 (2004).
-
(2004)
Nat. Biotechnol.
, vol.22
, pp. 78-85
-
-
Bader, J.S.1
Chaudhuri, A.2
Rothberg, J.3
Chant, J.4
-
5
-
-
29044432227
-
An algorithmic framework for the exact solution of the prize-collecting Steiner tree problem
-
I. Ljubic, R. Weiskircher, U. Pferschy, G. W. Klau, P. Mutzel, M. Fischetti, An algorithmic framework for the exact solution of the prize-collecting Steiner tree problem. Math. Program. 105, 427-449 (2006).
-
(2006)
Math. Program.
, vol.105
, pp. 427-449
-
-
Ljubic, I.1
Weiskircher, R.2
Pferschy, U.3
Klau, G.W.4
Mutzel, P.5
Fischetti, M.6
-
6
-
-
46249128543
-
Identifying functional modules in protein-protein interaction networks: An integrated exact approach
-
M. T. Dittrich, G. W. Klau, A. Rosenwald, T. Dandekar, T. Müller, Identifying functional modules in protein-protein interaction networks: An integrated exact approach. Bioinformatics 24, i223-i231 (2008).
-
(2008)
Bioinformatics
, vol.24
-
-
Dittrich, M.T.1
Klau, G.W.2
Rosenwald, A.3
Dandekar, T.4
Müller, T.5
-
7
-
-
33745764032
-
A computational framework for the topological analysis and targeted disruption of signal transduction networks
-
M. S. Dasika, A. Burgard, C. D. Maranas, A computational framework for the topological analysis and targeted disruption of signal transduction networks. Biophys. J. 91, 382-398 (2006).
-
(2006)
Biophys. J.
, vol.91
, pp. 382-398
-
-
Dasika, M.S.1
Burgard, A.2
Maranas, C.D.3
-
8
-
-
33847708336
-
Refinement and expansion of signaling pathways: The osmotic response network in yeast
-
I. Gat-Viks, R. Shamir, Refinement and expansion of signaling pathways: The osmotic response network in yeast. Genome Res. 17, 358-367 (2007).
-
(2007)
Genome Res.
, vol.17
, pp. 358-367
-
-
Gat-Viks, I.1
Shamir, R.2
-
9
-
-
4243148480
-
Authoritative sources in a hyperlinked environment
-
J. M. Kleinberg, Authoritative sources in a hyperlinked environment. JACM 46, 604-632 1999).
-
(1999)
JACM
, vol.46
, pp. 604-632
-
-
Kleinberg, J.M.1
-
10
-
-
0038589165
-
The anatomy of a large-scale hypertextual Web search engine
-
S. Brin, L. Page, The anatomy of a large-scale hypertextual Web search engine. Computer Networks and ISDN Systems 30, 107-117 (1998).
-
(1998)
Computer Networks and ISDN Systems
, vol.30
, pp. 107-117
-
-
Brin, S.1
Page, L.2
-
11
-
-
29144442904
-
Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps
-
E. Nabieva, K. Jim, A. Agarwal, B. Chazelle, M. Singh, Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. Bioinformatics 21, i302-i310 (2005).
-
(2005)
Bioinformatics
, vol.21
-
-
Nabieva, E.1
Jim, K.2
Agarwal, A.3
Chazelle, B.4
Singh, M.5
-
12
-
-
57149103917
-
Finding friends and enemies in an enemies-only network: A graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions
-
Y. Qi, Y. Suhail, Y. Lin, J. Boeke, J. Bader, Finding friends and enemies in an enemies-only network: A graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions. Genome Res. 18, 1991-2004 (2008).
-
(1991)
Genome Res.
, vol.18
, pp. 2008
-
-
Qi, Y.1
Suhail, Y.2
Lin, Y.3
Boeke, J.4
Bader, J.5
-
13
-
-
42949096140
-
EQED: An efficient method for interpreting eQTL associations using protein networks
-
S. Suthram, A. Beyer, R. M. Karp, Y. Eldar, T. Ideker, eQED: An efficient method for interpreting eQTL associations using protein networks. Mol. Syst. Biol. 4, 162 (2008).
-
(2008)
Mol. Syst. Biol.
, vol.4
, pp. 162
-
-
Suthram, S.1
Beyer, A.2
Karp, R.M.3
Eldar, Y.4
Ideker, T.5
-
14
-
-
61349114190
-
Bridging high-throughput genetic and transcriptional data reveals cellular responses to α-synuclein toxicity
-
E. Yeger-Lotem, L. Riva, L. J. Su, A. D. Gitler, A. G. Cashikar, O. D. King, P. K. Auluck, M. L. Geddie, J. S. Valastyan, D. R. Karger, S. Lindquist, E. Fraenkel, Bridging high-throughput genetic and transcriptional data reveals cellular responses to α-synuclein toxicity. Nat. Genet. 41, 316-323 (2009).
-
(2009)
Nat. Genet.
, vol.41
, pp. 316-323
-
-
Yeger-Lotem, E.1
Riva, L.2
Su, L.J.3
Gitler, A.D.4
Cashikar, A.G.5
King, O.D.6
Auluck, P.K.7
Geddie, M.L.8
Valastyan, J.S.9
Karger, D.R.10
Lindquist, S.11
Fraenkel, E.12
-
15
-
-
10944251582
-
Principles of MAP kinase signaling specificity in Saccharomyces cerevisiae
-
M. A. Schwartz, H. D. Madhani, Principles of MAP kinase signaling specificity in Saccharomyces cerevisiae. Annu. Rev. Genet. 38, 725-748 (2004).
-
(2004)
Annu. Rev. Genet.
, vol.38
, pp. 725-748
-
-
Schwartz, M.A.1
Madhani, H.D.2
-
16
-
-
34047259513
-
A systems-biology analysis of feedback inhibition in the Sho1 osmotic-stress-response pathway
-
N. Hao, M. Behar, S. C. Parnell, M. P. Torres, C. H. Borchers, T. C. Elston, H. G. Dohlman, A systems-biology analysis of feedback inhibition in the Sho1 osmotic-stress-response pathway. Curr. Biol. 17, 659-667 (2007).
-
(2007)
Curr. Biol.
, vol.17
, pp. 659-667
-
-
Hao, N.1
Behar, M.2
Parnell, S.C.3
Torres, M.P.4
Borchers, C.H.5
Elston, T.C.6
Dohlman, H.G.7
-
17
-
-
32444442870
-
The Ste5 scaffold allosterically modulates signaling output of the yeast mating pathway
-
R. P. Bhattacharyya, A. Reményi, M. C. Good, C. J. Bashor, A. M. Falick, W. A. Lim, The Ste5 scaffold allosterically modulates signaling output of the yeast mating pathway. Science 311, 822-826 (2006).
-
(2006)
Science
, vol.311
, pp. 822-826
-
-
Bhattacharyya, R.P.1
Reményi, A.2
Good, M.C.3
Bashor, C.J.4
Falick, A.M.5
Lim, W.A.6
-
18
-
-
33847324364
-
Cross-talk and decision making in MAP kinase pathways
-
M. N. McClean, A. Mody, J. R. Broach, S. Ramanathan, Cross-talk and decision making in MAP kinase pathways. Nat. Genet. 39, 409-414 (2007).
-
(2007)
Nat. Genet.
, vol.39
, pp. 409-414
-
-
McClean, M.N.1
Mody, A.2
Broach, J.R.3
Ramanathan, S.4
-
19
-
-
33847394655
-
MAPK-mediated bimodal gene expression and adaptive gradient sensing in yeast
-
S. Paliwal, P. A. Iglesias, K. Campbell, Z. Hilioti, A. Groisman, A. Levchenko, MAPK-mediated bimodal gene expression and adaptive gradient sensing in yeast. Nature 446, 46-51 (2007).
-
(2007)
Nature
, vol.446
, pp. 46-51
-
-
Paliwal, S.1
Iglesias, P.A.2
Campbell, K.3
Hilioti, Z.4
Groisman, A.5
Levchenko, A.6
-
20
-
-
62649094918
-
Dynamic analysis of MAPK signaling using a high-throughput microfluidic single-cell imaging platform
-
R. J. Taylor, D. Falconnet, A. Niemisto, S. A. Ramsey, S. Prinz, I. Shmulevich, T. Galitski, C. L. Hansen, Dynamic analysis of MAPK signaling using a high-throughput microfluidic single-cell imaging platform. Proc. Natl. Acad. Sci. U.S.A. 106, 3758-3763 (2009).
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 3758-3763
-
-
Taylor, R.J.1
Falconnet, D.2
Niemisto, A.3
Ramsey, S.A.4
Prinz, S.5
Shmulevich, I.6
Galitski, T.7
Hansen, C.L.8
-
21
-
-
0038048325
-
Inferring genetic networks and identifying compound mode of action via expression profiling
-
T. S. Gardner, D. di Bernardo, D. Lorenz, J. J. Collins, Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301, 102-105 (2003).
-
(2003)
Science
, vol.301
, pp. 102-105
-
-
Gardner, T.S.1
Di Bernardo, D.2
Lorenz, D.3
Collins, J.J.4
-
22
-
-
44449100825
-
Signal processing by the HOG MAP kinase pathway
-
P. Hersen, M. N. McClean, L. Mahadevan, S. Ramanathan, Signal processing by the HOG MAP kinase pathway. Proc. Natl. Acad. Sci. U.S.A. 105, 7165-7170 (2008).
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 7165-7170
-
-
Hersen, P.1
McClean, M.N.2
Mahadevan, L.3
Ramanathan, S.4
-
23
-
-
38549084632
-
The frequency dependence of osmoadaptation in Saccharomyces cerevisiae
-
J. T. Mettetal, D. Muzzey, C. Gómez-Uribe, A. Van Oudenaarden, The frequency dependence of osmoadaptation in Saccharomyces cerevisiae. Science 319, 482-484 (2008).
-
(2008)
Science
, vol.319
, pp. 482-484
-
-
Mettetal, J.T.1
Muzzey, D.2
Gómez-Uribe, C.3
Van Oudenaarden, A.4
-
24
-
-
23444449142
-
Integrative model of the response of yeast to osmotic shock
-
E. Klipp, B. Nordlander, R. Krüger, P. Gennemark, S. Hohmann, Integrative model of the response of yeast to osmotic shock. Nat. Biotechnol. 23, 975-982 (2005).
-
(2005)
Nat. Biotechnol.
, vol.23
, pp. 975-982
-
-
Klipp, E.1
Nordlander, B.2
Krüger, R.3
Gennemark, P.4
Hohmann, S.5
-
25
-
-
66349125024
-
Synthetic gene networks that count
-
A. E. Friedland, T. K. Lu, X. Wang, D. Shi, G. Church, J. J. Collins, Synthetic gene networks that count. Science 324, 1199-1202 (2009).
-
(2009)
Science
, vol.324
, pp. 1199-1202
-
-
Friedland, A.E.1
Lu, T.K.2
Wang, X.3
Shi, D.4
Church, G.5
Collins, J.J.6
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