-
1
-
-
0032616683
-
Identification of genetic networks from a small number of gene expression patterns under the Boolean network model
-
Akutsu T., Miyano S., and Kuhara S. Identification of genetic networks from a small number of gene expression patterns under the Boolean network model. Pac. Symp. Biocomput. (1999) 17-28
-
(1999)
Pac. Symp. Biocomput.
, pp. 17-28
-
-
Akutsu, T.1
Miyano, S.2
Kuhara, S.3
-
2
-
-
34249079154
-
Network motifs: theory and experimental approaches
-
Alon U. Network motifs: theory and experimental approaches. Nat. Rev. Genet. 8 (2007) 450-461
-
(2007)
Nat. Rev. Genet.
, vol.8
, pp. 450-461
-
-
Alon, U.1
-
3
-
-
0034730140
-
Singular value decomposition for genome-wide expression data processing and modelling
-
Alter O., Brown P.O., and Botstein D. Singular value decomposition for genome-wide expression data processing and modelling. Proc. Natl. Acad. Sci. U.S.A. 97 (2000) 10101-10106
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, pp. 10101-10106
-
-
Alter, O.1
Brown, P.O.2
Botstein, D.3
-
4
-
-
41549159731
-
Evolutionary approaches for the reverse-engineering of gene regulatory networks: a study on a biologically realistic dataset
-
Auliac C., Frouin V., Gidrol X., and d'Alche-Buc F. Evolutionary approaches for the reverse-engineering of gene regulatory networks: a study on a biologically realistic dataset. BMC Bioinform. 9 (2008) 91
-
(2008)
BMC Bioinform.
, vol.9
, pp. 91
-
-
Auliac, C.1
Frouin, V.2
Gidrol, X.3
d'Alche-Buc, F.4
-
5
-
-
0023003380
-
In vivo half-life of a protein is a function of its amino-terminal residue
-
Bachmair A., Finley D., and Varshavsky A. In vivo half-life of a protein is a function of its amino-terminal residue. Science 234 (1986) 179-186
-
(1986)
Science
, vol.234
, pp. 179-186
-
-
Bachmair, A.1
Finley, D.2
Varshavsky, A.3
-
6
-
-
33645307955
-
Inference of gene regulatory networks and compound mode of action from time course gene expression profiles
-
Bansal M., Gatta G.D., and di Bernardo D. Inference of gene regulatory networks and compound mode of action from time course gene expression profiles. Bioinformatics 22 (2006) 815-822
-
(2006)
Bioinformatics
, vol.22
, pp. 815-822
-
-
Bansal, M.1
Gatta, G.D.2
di Bernardo, D.3
-
8
-
-
0038483826
-
Emergence of scaling in random networks
-
Barabasi A.L., and Albert R. Emergence of scaling in random networks. Science 286 (1999) 509-512
-
(1999)
Science
, vol.286
, pp. 509-512
-
-
Barabasi, A.L.1
Albert, R.2
-
9
-
-
16844376909
-
Reverse engineering of regulatory networks in human B cells
-
Basso K., Margolin A.A., Stolovitzky G., Klein U., Dalla-Favera R., and Califano A. Reverse engineering of regulatory networks in human B cells. Nat. Genet. 37 (2005) 382-390
-
(2005)
Nat. Genet.
, vol.37
, pp. 382-390
-
-
Basso, K.1
Margolin, A.A.2
Stolovitzky, G.3
Klein, U.4
Dalla-Favera, R.5
Califano, A.6
-
10
-
-
13744251104
-
Inferring combinatorial regulation of transcription in silico
-
Bluthgen N., Kielbasa S.M., and Herzel H. Inferring combinatorial regulation of transcription in silico. Nucleic Acids Res. 33 (2005) 272-279
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 272-279
-
-
Bluthgen, N.1
Kielbasa, S.M.2
Herzel, H.3
-
11
-
-
33747813561
-
The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
-
Bonneau R., Reiss D.J., Shannon P., Facciotti M., Hood L., Baliga N.S., and Thorsson V. The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol. 7 (2006) R36
-
(2006)
Genome Biol.
, vol.7
-
-
Bonneau, R.1
Reiss, D.J.2
Shannon, P.3
Facciotti, M.4
Hood, L.5
Baliga, N.S.6
Thorsson, V.7
-
12
-
-
2942544498
-
Protein interaction networks from yeast to human
-
Bork P., Jensen L.J., von Mering C., Ramani A.K., Lee I., and Marcotte E.M. Protein interaction networks from yeast to human. Curr. Opin. Struct. Biol. 14 (2004) 292-299
-
(2004)
Curr. Opin. Struct. Biol.
, vol.14
, pp. 292-299
-
-
Bork, P.1
Jensen, L.J.2
von Mering, C.3
Ramani, A.K.4
Lee, I.5
Marcotte, E.M.6
-
13
-
-
12344288395
-
Effectiveness and limitation of two-dimensional gel electrophoresis in bacterial membrane protein proteomics and perspectives
-
Bunai K., and Yamane K. Effectiveness and limitation of two-dimensional gel electrophoresis in bacterial membrane protein proteomics and perspectives. J. Chromatogr. B Anal. Technol. Biomed. Life Sci. 815 (2005) 227-236
-
(2005)
J. Chromatogr. B Anal. Technol. Biomed. Life Sci.
, vol.815
, pp. 227-236
-
-
Bunai, K.1
Yamane, K.2
-
14
-
-
0033655775
-
Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements
-
Butte A.J., and Kohane I.S. Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac. Symp. Biocomput. (2000) 418-429
-
(2000)
Pac. Symp. Biocomput.
, pp. 418-429
-
-
Butte, A.J.1
Kohane, I.S.2
-
15
-
-
0034710924
-
Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks
-
Butte A.J., Tamayo P., Slonim D., Golub T.R., and Kohane I.S. Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proc. Natl. Acad. Sci. U.S.A. 97 (2000) 12182-12186
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, pp. 12182-12186
-
-
Butte, A.J.1
Tamayo, P.2
Slonim, D.3
Golub, T.R.4
Kohane, I.S.5
-
17
-
-
59649121280
-
Reverse engineering molecular regulatory networks from microarray data with qp-graphs
-
Castelo R., and Roverato A. Reverse engineering molecular regulatory networks from microarray data with qp-graphs. J. Comput. Biol. 16 (2009) 213-227
-
(2009)
J. Comput. Biol.
, vol.16
, pp. 213-227
-
-
Castelo, R.1
Roverato, A.2
-
18
-
-
38349192794
-
Ganoderma lucidum polysaccharides in human monocytic leukemia cells: from gene expression to network construction
-
Cheng K.C., Huang H.C., Chen J.H., Hsu J.W., Cheng H.C., Ou C.H., Yang W.B., Chen S.T., Wong C.H., and Juan H.F. Ganoderma lucidum polysaccharides in human monocytic leukemia cells: from gene expression to network construction. BMC Genomics 8 (2007) 411
-
(2007)
BMC Genomics
, vol.8
, pp. 411
-
-
Cheng, K.C.1
Huang, H.C.2
Chen, J.H.3
Hsu, J.W.4
Cheng, H.C.5
Ou, C.H.6
Yang, W.B.7
Chen, S.T.8
Wong, C.H.9
Juan, H.F.10
-
19
-
-
0032112293
-
A genome-wide transcriptional analysis of the mitotic cell cycle
-
Cho R.J., Campbell M.J., Winzeler E.A., Steinmetz L., Conway A., Wodicka L., Wolfsberg T.G., Gabrielian A.E., Landsman D., Lockhart D.J., and Davis R.W. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell 2 (1998) 65-73
-
(1998)
Mol. Cell
, vol.2
, pp. 65-73
-
-
Cho, R.J.1
Campbell, M.J.2
Winzeler, E.A.3
Steinmetz, L.4
Conway, A.5
Wodicka, L.6
Wolfsberg, T.G.7
Gabrielian, A.E.8
Landsman, D.9
Lockhart, D.J.10
Davis, R.W.11
-
20
-
-
34249740137
-
Reverse engineering of gene regulatory networks
-
Cho K.H., Choo S.M., Jung S.H., Kim J.R., Choi H.S., and Kim J. Reverse engineering of gene regulatory networks. IET Syst. Biol. 1 (2007) 149-163
-
(2007)
IET Syst. Biol.
, vol.1
, pp. 149-163
-
-
Cho, K.H.1
Choo, S.M.2
Jung, S.H.3
Kim, J.R.4
Choi, H.S.5
Kim, J.6
-
21
-
-
0042128797
-
Incorporating biological knowledge into evaluation of causal regulatory hypotheses
-
Chrisman L., Langley P., Bay S., and Pohorille A. Incorporating biological knowledge into evaluation of causal regulatory hypotheses. Pac. Symp. Biocomput. (2003) 128-139
-
(2003)
Pac. Symp. Biocomput.
, pp. 128-139
-
-
Chrisman, L.1
Langley, P.2
Bay, S.3
Pohorille, A.4
-
22
-
-
84883351409
-
A SAT-based approach to decipher Gene Regulatory Networks
-
Paper presented at:, Lyon
-
Corblin, F., Bordeaux, L., Hamadi, Y., Fanchon, E., Trilling, L., 2007. A SAT-based approach to decipher Gene Regulatory Networks. Paper presented at: Integrative Post-Genomics, RIAMS, Lyon.
-
(2007)
Integrative Post-Genomics, RIAMS
-
-
Corblin, F.1
Bordeaux, L.2
Hamadi, Y.3
Fanchon, E.4
Trilling, L.5
-
23
-
-
36249003810
-
Benchmarking of dynamic Bayesian networks inferred from stochastic time-series data
-
David L.A., and Wiggins C.H. Benchmarking of dynamic Bayesian networks inferred from stochastic time-series data. Ann. N. Y. Acad. Sci. 1115 (2007) 90-101
-
(2007)
Ann. N. Y. Acad. Sci.
, vol.1115
, pp. 90-101
-
-
David, L.A.1
Wiggins, C.H.2
-
24
-
-
0036207347
-
Modeling and simulation of genetic regulatory systems: a literature review
-
de Jong H. Modeling and simulation of genetic regulatory systems: a literature review. J. Comput. Biol. 9 (2002) 67-103
-
(2002)
J. Comput. Biol.
, vol.9
, pp. 67-103
-
-
de Jong, H.1
-
25
-
-
12344321571
-
Discovery of meaningful associations in genomic data using partial correlation coefficients
-
de la Fuente A., Bing N., Hoeschele I., and Mendes P. Discovery of meaningful associations in genomic data using partial correlation coefficients. Bioinformatics 20 (2004) 3565-3574
-
(2004)
Bioinformatics
, vol.20
, pp. 3565-3574
-
-
de la Fuente, A.1
Bing, N.2
Hoeschele, I.3
Mendes, P.4
-
26
-
-
57149148250
-
Combinatorial regulation of endothelial gene expression by ets and forkhead transcription factors
-
De Val S., Chi N.C., Meadows S.M., Minovitsky S., Anderson J.P., Harris I.S., Ehlers M.L., Agarwal P., Visel A., Xu S.M., et al. Combinatorial regulation of endothelial gene expression by ets and forkhead transcription factors. Cell 135 (2008) 1053-1064
-
(2008)
Cell
, vol.135
, pp. 1053-1064
-
-
De Val, S.1
Chi, N.C.2
Meadows, S.M.3
Minovitsky, S.4
Anderson, J.P.5
Harris, I.S.6
Ehlers, M.L.7
Agarwal, P.8
Visel, A.9
Xu, S.M.10
-
27
-
-
44849118743
-
Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering
-
Della Gatta G., Bansal M., Ambesi-Impiombato A., Antonini D., Missero C., and di Bernardo D. Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering. Genome Res. 18 (2008) 939-948
-
(2008)
Genome Res.
, vol.18
, pp. 939-948
-
-
Della Gatta, G.1
Bansal, M.2
Ambesi-Impiombato, A.3
Antonini, D.4
Missero, C.5
di Bernardo, D.6
-
28
-
-
22044438132
-
EXAMINE: a computational approach to reconstructing gene regulatory networks
-
Deng X., Geng H., and Ali H. EXAMINE: a computational approach to reconstructing gene regulatory networks. Biosystems 81 (2005) 125-136
-
(2005)
Biosystems
, vol.81
, pp. 125-136
-
-
Deng, X.1
Geng, H.2
Ali, H.3
-
31
-
-
34249932435
-
Probing transcription factor dynamics at the single-molecule level in a living cell
-
Elf J., Li G.W., and Xie X.S. Probing transcription factor dynamics at the single-molecule level in a living cell. Science 316 (2007) 1191-1194
-
(2007)
Science
, vol.316
, pp. 1191-1194
-
-
Elf, J.1
Li, G.W.2
Xie, X.S.3
-
32
-
-
33645294070
-
Oncomirs-microRNAs with a role in cancer
-
Esquela-Kerscher A., and Slack F.J. Oncomirs-microRNAs with a role in cancer. Nat. Rev. Cancer 6 (2006) 259-269
-
(2006)
Nat. Rev. Cancer
, vol.6
, pp. 259-269
-
-
Esquela-Kerscher, A.1
Slack, F.J.2
-
33
-
-
33846400424
-
Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
-
Faith J.J., Hayete B., Thaden J.T., Mogno I., Wierzbowski J., Cottarel G., Kasif S., Collins J.J., and Gardner T.S. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol. 5 (2007) e8
-
(2007)
PLoS Biol.
, vol.5
-
-
Faith, J.J.1
Hayete, B.2
Thaden, J.T.3
Mogno, I.4
Wierzbowski, J.5
Cottarel, G.6
Kasif, S.7
Collins, J.J.8
Gardner, T.S.9
-
34
-
-
70449521865
-
-
Paris
-
Fanchon, E., Corblin, F., Trilling, L., Hermant, B., Gulino, D., 2004. Modeling the molecular network controlling adhesion between human endothelial cells: inference and simulation using constraint logic programming, Paper presented at: Computational Methods in Systems Biology, Paris.
-
(2004)
Modeling the molecular network controlling adhesion between human endothelial cells: Inference and simulation using constraint logic programming, Paper presented at: Computational Methods in Systems Biology
-
-
Fanchon, E.1
Corblin, F.2
Trilling, L.3
Hermant, B.4
Gulino, D.5
-
35
-
-
50949111867
-
Embedding mRNA stability in correlation analysis of time-series gene expression data
-
Farina L., De Santis A., Salvucci S., Morelli G., and Ruberti I. Embedding mRNA stability in correlation analysis of time-series gene expression data. PLoS Comput. Biol. 4 (2008) e1000141
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Farina, L.1
De Santis, A.2
Salvucci, S.3
Morelli, G.4
Ruberti, I.5
-
37
-
-
0036100833
-
Analysis techniques for microarray time-series data
-
Filkov V., Skiena S., and Zhi J.Z. Analysis techniques for microarray time-series data. J. Comput. Biol. 9 (2002) 317-330
-
(2002)
J. Comput. Biol.
, vol.9
, pp. 317-330
-
-
Filkov, V.1
Skiena, S.2
Zhi, J.Z.3
-
39
-
-
0038048325
-
Inferring genetic networks and identifying compound mode of action via expression profiling
-
Gardner T.S., di Bernardo D., Lorenz D., and Collins J.J. Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301 (2003) 102-105
-
(2003)
Science
, vol.301
, pp. 102-105
-
-
Gardner, T.S.1
di Bernardo, D.2
Lorenz, D.3
Collins, J.J.4
-
40
-
-
0033637153
-
Genomic expression programs in the response of yeast cells to environmental changes
-
Gasch A.P., Spellman P.T., Kao C.M., Carmel-Harel O., Eisen M.B., Storz G., Botstein D., and Brown P.O. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11 (2000) 4241-4257
-
(2000)
Mol. Biol. Cell
, vol.11
, pp. 4241-4257
-
-
Gasch, A.P.1
Spellman, P.T.2
Kao, C.M.3
Carmel-Harel, O.4
Eisen, M.B.5
Storz, G.6
Botstein, D.7
Brown, P.O.8
-
41
-
-
0036653675
-
Concomitant determination of absolute values of cellular protein amounts, synthesis rates, and turnover rates by quantitative proteome profiling
-
Gerner C., Vejda S., Gelbmann D., Bayer E., Gotzmann J., Schulte-Hermann R., and Mikulits W. Concomitant determination of absolute values of cellular protein amounts, synthesis rates, and turnover rates by quantitative proteome profiling. Mol. Cell Proteomics 1 (2002) 528-537
-
(2002)
Mol. Cell Proteomics
, vol.1
, pp. 528-537
-
-
Gerner, C.1
Vejda, S.2
Gelbmann, D.3
Bayer, E.4
Gotzmann, J.5
Schulte-Hermann, R.6
Mikulits, W.7
-
42
-
-
58149354385
-
Analysis of combinatorial cis-regulation in synthetic and genomic promoters
-
Gertz J., Siggia E.D., and Cohen B.A. Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature 457 (2009) 215-218
-
(2009)
Nature
, vol.457
, pp. 215-218
-
-
Gertz, J.1
Siggia, E.D.2
Cohen, B.A.3
-
43
-
-
36248991815
-
A framework for elucidating regulatory networks based on prior information and expression data
-
Gevaert O., Van Vooren S., and De Moor B. A framework for elucidating regulatory networks based on prior information and expression data. Ann. N. Y. Acad. Sci. 1115 (2007) 240-248
-
(2007)
Ann. N. Y. Acad. Sci.
, vol.1115
, pp. 240-248
-
-
Gevaert, O.1
Van Vooren, S.2
De Moor, B.3
-
44
-
-
0142215475
-
Global analysis of protein expression in yeast
-
Ghaemmaghami S., Huh W.K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., and Weissman J.S. Global analysis of protein expression in yeast. Nature 425 (2003) 737-741
-
(2003)
Nature
, vol.425
, pp. 737-741
-
-
Ghaemmaghami, S.1
Huh, W.K.2
Bower, K.3
Howson, R.W.4
Belle, A.5
Dephoure, N.6
O'Shea, E.K.7
Weissman, J.S.8
-
45
-
-
34249853738
-
Computational and experimental approaches for modeling gene regulatory networks
-
Goutsias J., and Lee N.H. Computational and experimental approaches for modeling gene regulatory networks. Curr. Pharm. Des. 13 (2007) 1415-1436
-
(2007)
Curr. Pharm. Des.
, vol.13
, pp. 1415-1436
-
-
Goutsias, J.1
Lee, N.H.2
-
46
-
-
0141920354
-
Comparing protein abundance and mRNA expression levels on a genomic scale
-
Greenbaum D., Colangelo C., Williams K., and Gerstein M. Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol. 4 (2003) 117
-
(2003)
Genome Biol.
, vol.4
, pp. 117
-
-
Greenbaum, D.1
Colangelo, C.2
Williams, K.3
Gerstein, M.4
-
47
-
-
0036545614
-
Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae
-
Griffin T.J., Gygi S.P., Ideker T., Rist B., Eng J., Hood L., and Aebersold R. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol. Cell Proteomics 1 (2002) 323-333
-
(2002)
Mol. Cell Proteomics
, vol.1
, pp. 323-333
-
-
Griffin, T.J.1
Gygi, S.P.2
Ideker, T.3
Rist, B.4
Eng, J.5
Hood, L.6
Aebersold, R.7
-
48
-
-
22244454113
-
Synchronous neural activity in scale-free network models versus random network models
-
Grinstein G., and Linsker R. Synchronous neural activity in scale-free network models versus random network models. Proc. Natl. Acad. Sci. U.S.A. 102 (2005) 9948-9953
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 9948-9953
-
-
Grinstein, G.1
Linsker, R.2
-
49
-
-
17444430052
-
Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection
-
Guthke R., Moller U., Hoffmann M., Thies F., and Topfer S. Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection. Bioinformatics 21 (2005) 1626-1634
-
(2005)
Bioinformatics
, vol.21
, pp. 1626-1634
-
-
Guthke, R.1
Moller, U.2
Hoffmann, M.3
Thies, F.4
Topfer, S.5
-
50
-
-
0036366689
-
Combining location and expression data for principled discovery of genetic regulatory network models
-
Hartemink A.J., Gifford D.K., Jaakkola T.S., and Young R.A. Combining location and expression data for principled discovery of genetic regulatory network models. Pac. Symp. Biocomput. (2002) 437-449
-
(2002)
Pac. Symp. Biocomput.
, pp. 437-449
-
-
Hartemink, A.J.1
Gifford, D.K.2
Jaakkola, T.S.3
Young, R.A.4
-
51
-
-
62549091023
-
Benchmarking regulatory network reconstruction with GRENDEL
-
Haynes B.C., and Brent M.R. Benchmarking regulatory network reconstruction with GRENDEL. Bioinformatics 25 (2009) 801-807
-
(2009)
Bioinformatics
, vol.25
, pp. 801-807
-
-
Haynes, B.C.1
Brent, M.R.2
-
52
-
-
33645784574
-
In search of functional association from time-series microarray data based on the change trend and level of gene expression
-
He F., and Zeng A.P. In search of functional association from time-series microarray data based on the change trend and level of gene expression. BMC Bioinform. 7 (2006) 69
-
(2006)
BMC Bioinform.
, vol.7
, pp. 69
-
-
He, F.1
Zeng, A.P.2
-
53
-
-
38349026526
-
Dynamic cumulative activity of transcription factors as a mechanism of quantitative gene regulation
-
He F., Buer J., Zeng A.P., and Balling R. Dynamic cumulative activity of transcription factors as a mechanism of quantitative gene regulation. Genome Biol. 8 (2007) R181
-
(2007)
Genome Biol.
, vol.8
-
-
He, F.1
Buer, J.2
Zeng, A.P.3
Balling, R.4
-
54
-
-
61349180117
-
Gene regulatory network inference: data integration in dynamic models-a review
-
Hecker M., Lambeck S., Toepfer S., van Someren E., and Guthke R. Gene regulatory network inference: data integration in dynamic models-a review. Biosystems 96 (2009) 86-103
-
(2009)
Biosystems
, vol.96
, pp. 86-103
-
-
Hecker, M.1
Lambeck, S.2
Toepfer, S.3
van Someren, E.4
Guthke, R.5
-
55
-
-
0037050004
-
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
-
Ho Y., Gruhler A., Heilbut A., Bader G.D., Moore L., Adams S.L., Millar A., Taylor P., Bennett K., Boutilier K., et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415 (2002) 180-183
-
(2002)
Nature
, vol.415
, pp. 180-183
-
-
Ho, Y.1
Gruhler, A.2
Heilbut, A.3
Bader, G.D.4
Moore, L.5
Adams, S.L.6
Millar, A.7
Taylor, P.8
Bennett, K.9
Boutilier, K.10
-
56
-
-
1642363230
-
Loss of translational control in yeast compromised for the major mRNA decay pathway
-
Holmes L.E., Campbell S.G., De Long S.K., Sachs A.B., and Ashe M.P. Loss of translational control in yeast compromised for the major mRNA decay pathway. Mol. Cell Biol. 24 (2004) 2998-3010
-
(2004)
Mol. Cell Biol.
, vol.24
, pp. 2998-3010
-
-
Holmes, L.E.1
Campbell, S.G.2
De Long, S.K.3
Sachs, A.B.4
Ashe, M.P.5
-
57
-
-
0035852785
-
Dynamic modeling of gene expression data
-
Holter N.S., Maritan A., Cieplak M., Fedoroff N.V., and Banavar J.R. Dynamic modeling of gene expression data. Proc. Natl. Acad. Sci. U.S.A. 98 (2001) 1693-1698
-
(2001)
Proc. Natl. Acad. Sci. U.S.A.
, vol.98
, pp. 1693-1698
-
-
Holter, N.S.1
Maritan, A.2
Cieplak, M.3
Fedoroff, N.V.4
Banavar, J.R.5
-
58
-
-
0344464762
-
Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks
-
Husmeier D. Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks. Bioinformatics 19 (2003) 2271-2282
-
(2003)
Bioinformatics
, vol.19
, pp. 2271-2282
-
-
Husmeier, D.1
-
59
-
-
0035805255
-
Integrated genomic and proteomic analyses of a systematically perturbed metabolic network
-
Ideker T., Thorsson V., Ranish J.A., Christmas R., Buhler J., Eng J.K., Bumgarner R., Goodlett D.R., Aebersold R., and Hood L. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292 (2001) 929-934
-
(2001)
Science
, vol.292
, pp. 929-934
-
-
Ideker, T.1
Thorsson, V.2
Ranish, J.A.3
Christmas, R.4
Buhler, J.5
Eng, J.K.6
Bumgarner, R.7
Goodlett, D.R.8
Aebersold, R.9
Hood, L.10
-
60
-
-
0034609791
-
The large-scale organization of metabolic networks
-
Jeong H., Tombor B., Albert R., Oltvai Z.N., and Barabasi A.L. The large-scale organization of metabolic networks. Nature 407 (2000) 651-654
-
(2000)
Nature
, vol.407
, pp. 651-654
-
-
Jeong, H.1
Tombor, B.2
Albert, R.3
Oltvai, Z.N.4
Barabasi, A.L.5
-
62
-
-
33845476668
-
Reconstructing repressor protein levels from expression of gene targets in Escherichia coli
-
Khanin R., Vinciotti V., and Wit E. Reconstructing repressor protein levels from expression of gene targets in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 18592-18596
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 18592-18596
-
-
Khanin, R.1
Vinciotti, V.2
Wit, E.3
-
63
-
-
34548299801
-
Bayesian Orthogonal Least Squares (BOLS) algorithm for reverse engineering of gene regulatory networks
-
Kim C.S. Bayesian Orthogonal Least Squares (BOLS) algorithm for reverse engineering of gene regulatory networks. BMC Bioinform. 8 (2007) 251
-
(2007)
BMC Bioinform.
, vol.8
, pp. 251
-
-
Kim, C.S.1
-
64
-
-
38349055557
-
Indeterminacy of reverse engineering of Gene Regulatory Networks: the curse of gene elasticity
-
Krishnan A., Giuliani A., and Tomita M. Indeterminacy of reverse engineering of Gene Regulatory Networks: the curse of gene elasticity. PLoS ONE 2 (2007) e562
-
(2007)
PLoS ONE
, vol.2
-
-
Krishnan, A.1
Giuliani, A.2
Tomita, M.3
-
65
-
-
2442492954
-
Functional relationships between gene pairs in oral squamous cell carcinoma
-
Kuo W.P., Mendez E., Chen C., Whipple M.E., Farell G., Agoff N., and Park P.J. Functional relationships between gene pairs in oral squamous cell carcinoma. AMIA Annu. Symp. Proc. (2003) 371-375
-
(2003)
AMIA Annu. Symp. Proc.
, pp. 371-375
-
-
Kuo, W.P.1
Mendez, E.2
Chen, C.3
Whipple, M.E.4
Farell, G.5
Agoff, N.6
Park, P.J.7
-
66
-
-
0038281506
-
Inference of transcriptional regulation relationships from gene expression data
-
Kwon A.T., Hoos H.H., and Ng R. Inference of transcriptional regulation relationships from gene expression data. Bioinformatics 19 (2003) 905-912
-
(2003)
Bioinformatics
, vol.19
, pp. 905-912
-
-
Kwon, A.T.1
Hoos, H.H.2
Ng, R.3
-
67
-
-
10044240790
-
Using prior knowledge to improve genetic network reconstruction from microarray data
-
Le Phillip P., Bahl A., and Ungar L.H. Using prior knowledge to improve genetic network reconstruction from microarray data. In Silico Biol. 4 (2004) 335-353
-
(2004)
In Silico Biol.
, vol.4
, pp. 335-353
-
-
Le Phillip, P.1
Bahl, A.2
Ungar, L.H.3
-
68
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
Lee T.I., Rinaldi N.J., Robert F., Odom D.T., Bar-Joseph Z., Gerber G.K., Hannett N.M., Harbison C.T., Thompson C.M., Simon I., et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298 (2002) 799-804
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
Rinaldi, N.J.2
Robert, F.3
Odom, D.T.4
Bar-Joseph, Z.5
Gerber, G.K.6
Hannett, N.M.7
Harbison, C.T.8
Thompson, C.M.9
Simon, I.10
-
69
-
-
9444239213
-
A probabilistic functional network of yeast genes
-
Lee I., Date S.V., Adai A.T., and Marcotte E.M. A probabilistic functional network of yeast genes. Science 306 (2004) 1555-1558
-
(2004)
Science
, vol.306
, pp. 1555-1558
-
-
Lee, I.1
Date, S.V.2
Adai, A.T.3
Marcotte, E.M.4
-
70
-
-
41549138299
-
An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae
-
Lee I., Li Z., and Marcotte E.M. An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae. PLoS ONE 2 (2007) e988
-
(2007)
PLoS ONE
, vol.2
-
-
Lee, I.1
Li, Z.2
Marcotte, E.M.3
-
72
-
-
58149349958
-
Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information
-
Luo W., Hankenson K.D., and Woolf P.J. Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information. BMC Bioinform. 9 (2008) 467
-
(2008)
BMC Bioinform.
, vol.9
, pp. 467
-
-
Luo, W.1
Hankenson, K.D.2
Woolf, P.J.3
-
73
-
-
27844482652
-
Estimating genomic coexpression networks using first-order conditional independence
-
Magwene P.M., and Kim J. Estimating genomic coexpression networks using first-order conditional independence. Genome Biol. 5 (2004) R100
-
(2004)
Genome Biol.
, vol.5
-
-
Magwene, P.M.1
Kim, J.2
-
74
-
-
0142027814
-
Structure and function of the feed-forward loop network motif
-
Mangan S., and Alon U. Structure and function of the feed-forward loop network motif. Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 11980-11985
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, pp. 11980-11985
-
-
Mangan, S.1
Alon, U.2
-
75
-
-
36248989626
-
Theory and limitations of genetic network inference from microarray data
-
Margolin A.A., and Califano A. Theory and limitations of genetic network inference from microarray data. Ann. N. Y. Acad. Sci. 1115 (2007) 51-72
-
(2007)
Ann. N. Y. Acad. Sci.
, vol.1115
, pp. 51-72
-
-
Margolin, A.A.1
Califano, A.2
-
76
-
-
33947305781
-
ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
-
Margolin A.A., Nemenman I., Basso K., Wiggins C., Stolovitzky G., Dalla Favera R., and Califano A. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinform. 7 Suppl. 1 (2006) S7
-
(2006)
BMC Bioinform.
, vol.7
, Issue.SUPPL. 1
-
-
Margolin, A.A.1
Nemenman, I.2
Basso, K.3
Wiggins, C.4
Stolovitzky, G.5
Dalla Favera, R.6
Califano, A.7
-
77
-
-
38449088751
-
Inferring cellular networks-a review
-
Markowetz F., and Spang R. Inferring cellular networks-a review. BMC Bioinform. 8 Suppl. 6 (2007) S5
-
(2007)
BMC Bioinform.
, vol.8
, Issue.SUPPL. 6
-
-
Markowetz, F.1
Spang, R.2
-
78
-
-
27644446030
-
Molecular biology. P-bodies mark the spot for controlling protein production
-
Marx J. Molecular biology. P-bodies mark the spot for controlling protein production. Science 310 (2005) 764-765
-
(2005)
Science
, vol.310
, pp. 764-765
-
-
Marx, J.1
-
79
-
-
1542287343
-
Superfamilies of evolved and designed networks
-
Milo R., Itzkovitz S., Kashtan N., Levitt R., Shen-Orr S., Ayzenshtat I., Sheffer M., and Alon U. Superfamilies of evolved and designed networks. Science 303 (2004) 1538-1542
-
(2004)
Science
, vol.303
, pp. 1538-1542
-
-
Milo, R.1
Itzkovitz, S.2
Kashtan, N.3
Levitt, R.4
Shen-Orr, S.5
Ayzenshtat, I.6
Sheffer, M.7
Alon, U.8
-
80
-
-
2442718023
-
Using protein-protein interactions for refining gene networks estimated from microarray data by Bayesian networks
-
Nariai N., Kim S., Imoto S., and Miyano S. Using protein-protein interactions for refining gene networks estimated from microarray data by Bayesian networks. Pac. Symp. Biocomput. (2004) 336-347
-
(2004)
Pac. Symp. Biocomput.
, pp. 336-347
-
-
Nariai, N.1
Kim, S.2
Imoto, S.3
Miyano, S.4
-
83
-
-
33645807381
-
Turnover in the Alps: an mRNA perspective. Workshops on mechanisms and regulation of mRNA turnover
-
Newbury S.F., Muhlemann O., and Stoecklin G. Turnover in the Alps: an mRNA perspective. Workshops on mechanisms and regulation of mRNA turnover. EMBO Rep. 7 (2006) 143-148
-
(2006)
EMBO Rep.
, vol.7
, pp. 143-148
-
-
Newbury, S.F.1
Muhlemann, O.2
Stoecklin, G.3
-
84
-
-
33748530630
-
Reverse engineering genetic networks using evolutionary computation
-
Noman N., and Iba H. Reverse engineering genetic networks using evolutionary computation. Genome Inform. 16 (2005) 205-214
-
(2005)
Genome Inform.
, vol.16
, pp. 205-214
-
-
Noman, N.1
Iba, H.2
-
85
-
-
4243144353
-
Certain topics in telegraphic transmission theory
-
(Reprinted from Transactions of the AIEE, pp. 617-644, 1928)
-
Nyquist H. Certain topics in telegraphic transmission theory. Proceedings of the IEEE, vol. 86 (1928/2002) 280-305 (Reprinted from Transactions of the AIEE, pp. 617-644, 1928)
-
(1928)
Proceedings of the IEEE, vol. 86
, pp. 280-305
-
-
Nyquist, H.1
-
86
-
-
0344844807
-
Modelling regulatory pathways in E. coli from time series expression profiles
-
Ong I., Glasner J., and Page D. Modelling regulatory pathways in E. coli from time series expression profiles. Bioinformatics 18 (2002) S241-248
-
(2002)
Bioinformatics
, vol.18
-
-
Ong, I.1
Glasner, J.2
Page, D.3
-
87
-
-
33845306813
-
NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth
-
Palomero T., Lim W.K., Odom D.T., Sulis M.L., Real P.J., Margolin A., Barnes K.C., O'Neil J., Neuberg D., Weng A.P., et al. NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth. Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 18261-18266
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 18261-18266
-
-
Palomero, T.1
Lim, W.K.2
Odom, D.T.3
Sulis, M.L.4
Real, P.J.5
Margolin, A.6
Barnes, K.C.7
O'Neil, J.8
Neuberg, D.9
Weng, A.P.10
-
88
-
-
4143058645
-
Gene networks inference using dynamic Bayesian networks
-
Perrin B.E., Ralaivola L., Mazurie A., Bottani S., Mallet J., and d'Alche-Buc F. Gene networks inference using dynamic Bayesian networks. Bioinformatics 19 Suppl. 2 (2003) ii138-ii148
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 2
-
-
Perrin, B.E.1
Ralaivola, L.2
Mazurie, A.3
Bottani, S.4
Mallet, J.5
d'Alche-Buc, F.6
-
89
-
-
0035861975
-
Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions
-
Qian J., Dolled-Filhart M., Lin J., Yu H., and Gerstein M. Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions. J. Mol. Biol. 314 (2001) 1053-1066
-
(2001)
J. Mol. Biol.
, vol.314
, pp. 1053-1066
-
-
Qian, J.1
Dolled-Filhart, M.2
Lin, J.3
Yu, H.4
Gerstein, M.5
-
90
-
-
0036627676
-
Reverse engineering of regulatory networks: simulation studies on a genetic algorithm approach for ranking hypotheses
-
Repsilber D., Liljenstrom H., and Andersson S.G. Reverse engineering of regulatory networks: simulation studies on a genetic algorithm approach for ranking hypotheses. Biosystems 66 (2002) 31-41
-
(2002)
Biosystems
, vol.66
, pp. 31-41
-
-
Repsilber, D.1
Liljenstrom, H.2
Andersson, S.G.3
-
91
-
-
25144501141
-
A Bayesian regression approach to the inference of regulatory networks from gene expression data
-
Rogers S., and Girolami M. A Bayesian regression approach to the inference of regulatory networks from gene expression data. Bioinformatics 21 (2005) 3131-3137
-
(2005)
Bioinformatics
, vol.21
, pp. 3131-3137
-
-
Rogers, S.1
Girolami, M.2
-
92
-
-
31044433976
-
Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source
-
Ronen M., and Botstein D. Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source. Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 389-394
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 389-394
-
-
Ronen, M.1
Botstein, D.2
-
93
-
-
70449530302
-
Metabolomics for functional genomics, systems biology, and biotechnology
-
Saito K., and Matsuda F. Metabolomics for functional genomics, systems biology, and biotechnology. Annu. Rev. Plant Biol. (2008)
-
(2008)
Annu. Rev. Plant Biol.
-
-
Saito, K.1
Matsuda, F.2
-
94
-
-
0014733809
-
Biochemical systems analysis. 3. Dynamic solutions using a power-law approximation
-
Savageau M.A. Biochemical systems analysis. 3. Dynamic solutions using a power-law approximation. J. Theor. Biol. 26 (1970) 215-226
-
(1970)
J. Theor. Biol.
, vol.26
, pp. 215-226
-
-
Savageau, M.A.1
-
95
-
-
15944364151
-
An empirical Bayes approach to inferring large-scale gene association networks
-
Schafer J., and Strimmer K. An empirical Bayes approach to inferring large-scale gene association networks. Bioinformatics 21 (2005) 754-764
-
(2005)
Bioinformatics
, vol.21
, pp. 754-764
-
-
Schafer, J.1
Strimmer, K.2
-
96
-
-
0028806048
-
Quantitative monitoring of gene expression patterns with a complementary DNA microarray
-
Schena M., Shalon D., Davis R.W., and Brown P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270 (1995) 467-470
-
(1995)
Science
, vol.270
, pp. 467-470
-
-
Schena, M.1
Shalon, D.2
Davis, R.W.3
Brown, P.O.4
-
97
-
-
1642528831
-
Post-translational modifications and their biological functions: proteomic analysis and systematic approaches
-
Seo J., and Lee K.J. Post-translational modifications and their biological functions: proteomic analysis and systematic approaches. J. Biochem. Mol. Biol. 37 (2004) 35-44
-
(2004)
J. Biochem. Mol. Biol.
, vol.37
, pp. 35-44
-
-
Seo, J.1
Lee, K.J.2
-
98
-
-
0031996528
-
Communication in the presence of noise
-
(Reprinted from Proceedings of the IRE, 37, pp. 10-21, 1949)
-
Shannon C.E. Communication in the presence of noise. Proceedings of the IEEE, vol. 86 (1949/1998) 447-457 (Reprinted from Proceedings of the IRE, 37, pp. 10-21, 1949)
-
(1949)
Proceedings of the IEEE, vol. 86
, pp. 447-457
-
-
Shannon, C.E.1
-
99
-
-
34547126444
-
Regulation of transcript elongation through cooperative and ordered recruitment of cofactors
-
Sharma M., George A.A., Singh B.N., Sahoo N.C., and Rao K.V. Regulation of transcript elongation through cooperative and ordered recruitment of cofactors. J. Biol. Chem. 282 (2007) 20887-20896
-
(2007)
J. Biol. Chem.
, vol.282
, pp. 20887-20896
-
-
Sharma, M.1
George, A.A.2
Singh, B.N.3
Sahoo, N.C.4
Rao, K.V.5
-
100
-
-
0036578795
-
Network motifs in the transcriptional regulation network of Escherichia coli
-
Shen-Orr S.S., Milo R., Mangan S., and Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 31 (2002) 64-68
-
(2002)
Nat. Genet.
, vol.31
, pp. 64-68
-
-
Shen-Orr, S.S.1
Milo, R.2
Mangan, S.3
Alon, U.4
-
101
-
-
33751407959
-
Computational inference of neural information flow networks
-
Smith V.A., Yu J., Smulders T.V., Hartemink A.J., and Jarvis E.D. Computational inference of neural information flow networks. PLoS Comput. Biol. 2 (2006) e161
-
(2006)
PLoS Comput. Biol.
, vol.2
-
-
Smith, V.A.1
Yu, J.2
Smulders, T.V.3
Hartemink, A.J.4
Jarvis, E.D.5
-
102
-
-
34547844096
-
Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks: synthetic versus real data
-
Soranzo N., Bianconi G., and Altafini C. Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks: synthetic versus real data. Bioinformatics 23 (2007) 1640-1647
-
(2007)
Bioinformatics
, vol.23
, pp. 1640-1647
-
-
Soranzo, N.1
Bianconi, G.2
Altafini, C.3
-
103
-
-
0031742022
-
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
-
Spellman P.T., Sherlock G., Zhang M.Q., Iyer V.R., Anders K., Eisen M.B., Brown P.O., Botstein D., and Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell. 9 (1998) 3273-3297
-
(1998)
Mol. Biol. Cell.
, vol.9
, pp. 3273-3297
-
-
Spellman, P.T.1
Sherlock, G.2
Zhang, M.Q.3
Iyer, V.R.4
Anders, K.5
Eisen, M.B.6
Brown, P.O.7
Botstein, D.8
Futcher, B.9
-
105
-
-
0141993704
-
A gene-coexpression network for global discovery of conserved genetic modules
-
Stuart J.M., Segal E., Koller D., and Kim S.K. A gene-coexpression network for global discovery of conserved genetic modules. Science 302 (2003) 249-255
-
(2003)
Science
, vol.302
, pp. 249-255
-
-
Stuart, J.M.1
Segal, E.2
Koller, D.3
Kim, S.K.4
-
106
-
-
3242891560
-
Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection
-
Tamada Y., Kim S., Bannai H., Imoto S., Tashiro K., Kuhara S., and Miyano S. Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection. Bioinformatics 19 Suppl. 2 (2003) ii227-236
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 2
-
-
Tamada, Y.1
Kim, S.2
Bannai, H.3
Imoto, S.4
Tashiro, K.5
Kuhara, S.6
Miyano, S.7
-
107
-
-
31044450846
-
Utilizing evolutionary information and gene expression data for estimating gene networks with bayesian network models
-
Tamada Y., Bannai H., Imoto S., Katayama T., Kanehisa M., and Miyano S. Utilizing evolutionary information and gene expression data for estimating gene networks with bayesian network models. J. Bioinform. Comput. Biol. 3 (2005) 1295-1313
-
(2005)
J. Bioinform. Comput. Biol.
, vol.3
, pp. 1295-1313
-
-
Tamada, Y.1
Bannai, H.2
Imoto, S.3
Katayama, T.4
Kanehisa, M.5
Miyano, S.6
-
108
-
-
0037687416
-
Reverse engineering gene networks: integrating genetic perturbations with dynamical modelling
-
Tegner J., Yeung M.K., Hasty J., and Collins J.J. Reverse engineering gene networks: integrating genetic perturbations with dynamical modelling. Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 5944-5949
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, pp. 5944-5949
-
-
Tegner, J.1
Yeung, M.K.2
Hasty, J.3
Collins, J.J.4
-
109
-
-
15944378903
-
Post-translational modifications influence transcription factor activity: a view from the ETS superfamily
-
Tootle T.L., and Rebay I. Post-translational modifications influence transcription factor activity: a view from the ETS superfamily. Bioessays 27 (2005) 285-298
-
(2005)
Bioessays
, vol.27
, pp. 285-298
-
-
Tootle, T.L.1
Rebay, I.2
-
110
-
-
0038492417
-
A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae)
-
Troyanskaya O.G., Dolinski K., Owen A.B., Altman R.B., and Botstein D. A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 8348-8353
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, pp. 8348-8353
-
-
Troyanskaya, O.G.1
Dolinski, K.2
Owen, A.B.3
Altman, R.B.4
Botstein, D.5
-
111
-
-
1342286937
-
Studying the conditions for learning dynamic bayesian networks to discover genetic regulatory networks
-
van Berlo R.J.P., van Someren E.P., and Reinders M.J.T. Studying the conditions for learning dynamic bayesian networks to discover genetic regulatory networks. Simulation 79 (2003) 689-702
-
(2003)
Simulation
, vol.79
, pp. 689-702
-
-
van Berlo, R.J.P.1
van Someren, E.P.2
Reinders, M.J.T.3
-
112
-
-
4644292576
-
The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model
-
van Noort V., Snel B., and Huynen M.A. The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model. EMBO Rep. 5 (2004) 280-284
-
(2004)
EMBO Rep.
, vol.5
, pp. 280-284
-
-
van Noort, V.1
Snel, B.2
Huynen, M.A.3
-
113
-
-
33845410054
-
Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments
-
van Riel N.A. Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments. Brief Bioinform. 7 (2006) 364-374
-
(2006)
Brief Bioinform.
, vol.7
, pp. 364-374
-
-
van Riel, N.A.1
-
115
-
-
42649134526
-
Parameter optimization in S-system models
-
Vilela M., Chou I.C., Vinga S., Vasconcelos A.T., Voit E.O., and Almeida J.S. Parameter optimization in S-system models. BMC Syst. Biol. 2 (2008) 35
-
(2008)
BMC Syst. Biol.
, vol.2
, pp. 35
-
-
Vilela, M.1
Chou, I.C.2
Vinga, S.3
Vasconcelos, A.T.4
Voit, E.O.5
Almeida, J.S.6
-
117
-
-
0034104824
-
Coarse-grained reverse engineering of genetic regulatory networks
-
Wahde M., and Hertz J. Coarse-grained reverse engineering of genetic regulatory networks. Biosystems 55 (2000) 129-136
-
(2000)
Biosystems
, vol.55
, pp. 129-136
-
-
Wahde, M.1
Hertz, J.2
-
118
-
-
33749860977
-
Post-translational modifications in the context of therapeutic proteins
-
Walsh G., and Jefferis R. Post-translational modifications in the context of therapeutic proteins. Nat. Biotechnol. 24 (2006) 1241-1252
-
(2006)
Nat. Biotechnol.
, vol.24
, pp. 1241-1252
-
-
Walsh, G.1
Jefferis, R.2
-
119
-
-
59949103192
-
High-resolution human core-promoter prediction with CoreBoost_HM
-
Wang X., Xuan Z., Zhao X., Li Y., and Zhang M.Q. High-resolution human core-promoter prediction with CoreBoost_HM. Genome Res. 19 (2009) 266-275
-
(2009)
Genome Res.
, vol.19
, pp. 266-275
-
-
Wang, X.1
Xuan, Z.2
Zhao, X.3
Li, Y.4
Zhang, M.Q.5
-
120
-
-
0035106351
-
Large-scale analysis of the yeast proteome by multidimensional protein identification technology
-
Washburn M.P., Wolters D., and Yates III J.R. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19 (2001) 242-247
-
(2001)
Nat. Biotechnol.
, vol.19
, pp. 242-247
-
-
Washburn, M.P.1
Wolters, D.2
Yates III, J.R.3
-
121
-
-
0142040405
-
Metabolomics in systems biology
-
Weckwerth W. Metabolomics in systems biology. Annu. Rev. Plant Biol. 54 (2003) 669-689
-
(2003)
Annu. Rev. Plant Biol.
, vol.54
, pp. 669-689
-
-
Weckwerth, W.1
-
122
-
-
34249774309
-
Reconstructing gene regulatory networks with bayesian networks by combining expression data with multiple sources of prior knowledge
-
(Article 15)
-
Werhli A.V., and Husmeier D. Reconstructing gene regulatory networks with bayesian networks by combining expression data with multiple sources of prior knowledge. Stat. Appl. Genet. Mol. Biol. 6 (2007) (Article 15)
-
(2007)
Stat. Appl. Genet. Mol. Biol.
, vol.6
-
-
Werhli, A.V.1
Husmeier, D.2
-
123
-
-
33749825955
-
Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks
-
Werhli A.V., Grzegorczyk M., and Husmeier D. Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks. Bioinformatics 22 (2006) 2523-2531
-
(2006)
Bioinformatics
, vol.22
, pp. 2523-2531
-
-
Werhli, A.V.1
Grzegorczyk, M.2
Husmeier, D.3
-
124
-
-
63049087845
-
Strategy for surveying the proteome using affinity proteomics and mass spectrometry
-
Wingren C., James P., and Borrebaeck C.A. Strategy for surveying the proteome using affinity proteomics and mass spectrometry. Proteomics 9 (2009) 1511-1517
-
(2009)
Proteomics
, vol.9
, pp. 1511-1517
-
-
Wingren, C.1
James, P.2
Borrebaeck, C.A.3
-
125
-
-
1642586299
-
Control of gene expression by a natural metabolite-responsive ribozyme
-
Winkler W.C., Nahvi A., Roth A., Collins J.A., and Breaker R.R. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428 (2004) 281-286
-
(2004)
Nature
, vol.428
, pp. 281-286
-
-
Winkler, W.C.1
Nahvi, A.2
Roth, A.3
Collins, J.A.4
Breaker, R.R.5
-
126
-
-
61849137222
-
Many roads to maturity: microRNA biogenesis pathways and their regulation
-
Winter J., Jung S., Keller S., Gregory R.I., and Diederichs S. Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat. Cell Biol. 11 (2009) 228-234
-
(2009)
Nat. Cell Biol.
, vol.11
, pp. 228-234
-
-
Winter, J.1
Jung, S.2
Keller, S.3
Gregory, R.I.4
Diederichs, S.5
-
128
-
-
12344257752
-
GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray data
-
Wu C.C., Huang H.C., Juan H.F., and Chen S.T. GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray data. Bioinformatics 20 (2004) 3691-3693
-
(2004)
Bioinformatics
, vol.20
, pp. 3691-3693
-
-
Wu, C.C.1
Huang, H.C.2
Juan, H.F.3
Chen, S.T.4
-
129
-
-
39149104076
-
Structural systems identification of genetic regulatory networks
-
Xiong H., and Choe Y. Structural systems identification of genetic regulatory networks. Bioinformatics 24 (2008) 553-560
-
(2008)
Bioinformatics
, vol.24
, pp. 553-560
-
-
Xiong, H.1
Choe, Y.2
-
130
-
-
1942469444
-
Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction
-
Yeger-Lotem E., Sattath S., Kashtan N., Itzkovitz S., Milo R., Pinter R.Y., Alon U., and Margalit H. Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 5934-5939
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 5934-5939
-
-
Yeger-Lotem, E.1
Sattath, S.2
Kashtan, N.3
Itzkovitz, S.4
Milo, R.5
Pinter, R.Y.6
Alon, U.7
Margalit, H.8
-
131
-
-
0037197936
-
Reverse engineering gene networks using singular value decomposition and robust regression
-
Yeung M.K., Tegner J., and Collins J.J. Reverse engineering gene networks using singular value decomposition and robust regression. Proc. Natl. Acad. Sci. U.S.A. 99 (2002) 6163-6168
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 6163-6168
-
-
Yeung, M.K.1
Tegner, J.2
Collins, J.J.3
-
132
-
-
0042706147
-
Genomic analysis of gene expression relationships in transcriptional regulatory networks
-
Yu H., Luscombe N.M., Qian J., and Gerstein M. Genomic analysis of gene expression relationships in transcriptional regulatory networks. Trends Genet. 19 (2003) 422-427
-
(2003)
Trends Genet.
, vol.19
, pp. 422-427
-
-
Yu, H.1
Luscombe, N.M.2
Qian, J.3
Gerstein, M.4
-
133
-
-
12344259602
-
Advances to Bayesian network inference for generating causal networks from observational biological data
-
Yu J., Smith V.A., Wang P.P., Hartemink A.J., and Jarvis E.D. Advances to Bayesian network inference for generating causal networks from observational biological data. Bioinformatics 20 (2004) 3594-3603
-
(2004)
Bioinformatics
, vol.20
, pp. 3594-3603
-
-
Yu, J.1
Smith, V.A.2
Wang, P.P.3
Hartemink, A.J.4
Jarvis, E.D.5
-
134
-
-
46249109755
-
Discerning static and causal interactions in genome-wide reverse engineering problems
-
Zampieri M., Soranzo N., and Altafini C. Discerning static and causal interactions in genome-wide reverse engineering problems. Bioinformatics 24 (2008) 1510-1515
-
(2008)
Bioinformatics
, vol.24
, pp. 1510-1515
-
-
Zampieri, M.1
Soranzo, N.2
Altafini, C.3
-
135
-
-
38449108806
-
Computational analyses of eukaryotic promoters
-
Zhang M.Q. Computational analyses of eukaryotic promoters. BMC Bioinform. 8 Suppl. 6 (2007) S3
-
(2007)
BMC Bioinform.
, vol.8
, Issue.SUPPL. 6
-
-
Zhang, M.Q.1
-
136
-
-
33748654580
-
Inferring gene regulatory networks from time series data using the minimum description length principle
-
Zhao W., Serpedin E., and Dougherty E.R. Inferring gene regulatory networks from time series data using the minimum description length principle. Bioinformatics 22 (2006) 2129-2135
-
(2006)
Bioinformatics
, vol.22
, pp. 2129-2135
-
-
Zhao, W.1
Serpedin, E.2
Dougherty, E.R.3
-
137
-
-
47649123776
-
Recovering genetic regulatory networks from chromatin immunoprecipitation and steady-state microarray data
-
Zhao W., Serpedin E., and Dougherty E.R. Recovering genetic regulatory networks from chromatin immunoprecipitation and steady-state microarray data. EURASIP J. Bioinform. Syst. Biol. (2008) 248747
-
(2008)
EURASIP J. Bioinform. Syst. Biol.
, pp. 248747
-
-
Zhao, W.1
Serpedin, E.2
Dougherty, E.R.3
-
138
-
-
12744261506
-
A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data
-
Zou M., and Conzen S.D. A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data. Bioinformatics 21 (2005) 71-79
-
(2005)
Bioinformatics
, vol.21
, pp. 71-79
-
-
Zou, M.1
Conzen, S.D.2
|