-
1
-
-
33847055114
-
How to infer gene networks from expression profiles
-
Bansal, M., Belcastro, V., Ambesi-Impiombato, A., et al. 2007. How to infer gene networks from expression profiles. Mol. Syst. Biol. 3, 78.
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 78
-
-
Bansal, M.1
Belcastro, V.2
Ambesi-Impiombato, A.3
-
2
-
-
16844376909
-
Reverse engineering of regulatory networks in human B cells
-
Basso, K., Margolin, A.A., Stolovitzky, G., et al. 2005. Reverse engineering of regulatory networks in human B cells. Nat. Genet. 37, 382-390.
-
(2005)
Nat. Genet.
, vol.37
, pp. 382-390
-
-
Basso, K.1
Margolin, A.A.2
Stolovitzky, G.3
-
3
-
-
68049100110
-
Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli
-
Bennett, B.D., Kimball, E.H., Gao, M., et al. 2009. Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat. Chem. Biol. 5, 593-599.
-
(2009)
Nat. Chem. Biol.
, vol.5
, pp. 593-599
-
-
Bennett, B.D.1
Kimball, E.H.2
Gao, M.3
-
4
-
-
0030804853
-
Flux analysis of underdetermined metabolic networks: The quest for the missing constraints
-
DOI 10.1016/S0167-7799(97)01067-6
-
Bonarius, H., Schmid, G., and Tramper, J. 1997. Flux analysis of underdetermined metabolic networks: The quest for the missing constraints. Trends Biotechnol. 15, 308-314. (Pubitemid 27330626)
-
(1997)
Trends in Biotechnology
, vol.15
, Issue.8
, pp. 308-314
-
-
Bonarius, H.P.J.1
Schmid, G.2
Tramper, J.3
-
6
-
-
34248512719
-
Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry
-
DOI 10.1038/nprot.2007.95, PII NPROT.2007.95
-
De Vos, R.C.H., Moco, S., Lommen, A., et al. 2007. Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry. Nat. Protoc. 2, 778-791. (Pubitemid 46745574)
-
(2007)
Nature Protocols
, vol.2
, Issue.4
, pp. 778-791
-
-
De Vos, R.C.H.1
Moco, S.2
Lommen, A.3
Keurentjes, J.J.B.4
Bino, R.J.5
Hall, R.D.6
-
7
-
-
0034625143
-
The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
-
DOI 10.1073/pnas.97.10.5528
-
Edwards, J.S., and Palsson, B.O. 2000. The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities. Proc. Natl. Acad. Sci. USA 97, 5528-5533. (Pubitemid 30313752)
-
(2000)
Proceedings of the National Academy of Sciences of the United States of America
, vol.97
, Issue.10
, pp. 5528-5533
-
-
Edwards, J.S.1
Palsson, B.O.2
-
8
-
-
0035125986
-
In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
-
DOI 10.1038/84379
-
Edwards, J.S., Ibarra, R.U., and Palsson, B.O. 2001. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat. Biotechnol. 19, 125-130. (Pubitemid 32144439)
-
(2001)
Nature Biotechnology
, vol.19
, Issue.2
, pp. 125-130
-
-
Edwards, J.S.1
Ibarra, R.U.2
Palsson, B.O.3
-
9
-
-
78149440921
-
Towards monitoring real-time cellular response using an integrated microfluidics-matrix assisted laser desorption ionisation/nanoelectrospray ionisation-ion mobility-mass spectrometry platform
-
Enders, J.R., Marasco, C.C., Kole, A., et al. 2010. Towards monitoring real-time cellular response using an integrated microfluidics-matrix assisted laser desorption ionisation/nanoelectrospray ionisation-ion mobility-mass spectrometry platform. IET Syst. Biol. 4, 416.
-
(2010)
IET Syst. Biol.
, vol.4
, pp. 416
-
-
Enders, J.R.1
Marasco, C.C.2
Kole, A.3
-
10
-
-
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., et al. 2007. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol. 5, e8.
-
(2007)
PLoS Biol.
, vol.5
-
-
Faith, J.J.1
Hayete, B.2
Thaden, J.T.3
-
11
-
-
0037313750
-
Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network
-
DOI 10.1101/gr.234503
-
Förster, J., Famili, I., Fu, P., et al. 2003. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 13, 244-253. (Pubitemid 36581837)
-
(2003)
Genome Research
, vol.13
, Issue.2
, pp. 244-253
-
-
Forster, J.1
Famili, I.2
Fu, P.3
Palsson, B.O.4
Nielsen, J.5
-
12
-
-
27144533653
-
Reconstructing the metabolic network of a bacterium from its genome
-
DOI 10.1016/j.tim.2005.09.001, PII S0966842X05002490
-
Francke, C., Siezen, R.J., and Teusink, B. 2005. Reconstructing the metabolic network of a bacterium from its genome. Trends Microbiol. 13, 550-558. (Pubitemid 41506897)
-
(2005)
Trends in Microbiology
, vol.13
, Issue.11
, pp. 550-558
-
-
Francke, C.1
Siezen, R.J.2
Teusink, B.3
-
13
-
-
0842288337
-
Inferring Cellular Networks Using Probabilistic Graphical Models
-
DOI 10.1126/science.1094068
-
Friedman, N. 2004. Inferring cellular networks using probabilistic graphical models. Science 303, 799-805. (Pubitemid 38174650)
-
(2004)
Science
, vol.303
, Issue.5659
, pp. 799-805
-
-
Friedman, N.1
-
14
-
-
33845368513
-
COPASI-A Complex pathway simulator
-
Hoops, S., Sahle, S., Gauges, R., et al. 2006. COPASI-a COmplex PAthway SImulator. Bioinformatics 22, 3067-3074.
-
(2006)
Bioinformatics
, vol.22
, pp. 3067-3074
-
-
Hoops, S.1
Sahle, S.2
Gauges, R.3
-
15
-
-
0035775725
-
A new approach to decoding life: Systems biology
-
DOI 10.1146/annurev.genom.2.1.343
-
Ideker, T., Galitski, T., and Hood, L. 2001. A new approach to decoding life: Systems biology. Annu. Rev. Genomics Hum. Genet. 2, 343-372. (Pubitemid 35265011)
-
(2001)
Annual Review of Genomics and Human Genetics
, vol.2
, pp. 343-372
-
-
Ideker, T.1
Galitski, T.2
Hood, L.3
-
16
-
-
34247612307
-
Multiple high-throughput analyses monitor the response of E. coli to perturbations
-
DOI 10.1126/science.1132067
-
Ishii, N., Nakahigashi, K., Baba, T., et al. 2007. Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science 316, 593-597. (Pubitemid 46683144)
-
(2007)
Science
, vol.316
, Issue.5824
, pp. 593-597
-
-
Ishii, N.1
Nakahigashi, K.2
Baba, T.3
Robert, M.4
Soga, T.5
Kanai, A.6
Hirasawa, T.7
Naba, M.8
Hirai, K.9
Hoque, A.10
Ho, P.Y.11
Kakazu, Y.12
Sugawara, K.13
Igarashi, S.14
Harada, S.15
Masuda, T.16
Sugiyama, N.17
Togashi, T.18
Hasegawa, M.19
Takai, Y.20
Yugi, K.21
Arakawa, K.22
Iwata, N.23
Toya, Y.24
Nakayama, Y.25
Nishioka, T.26
Shimizu, K.27
Mori, H.28
Tomita, M.29
more..
-
17
-
-
11244328060
-
The pathway tools software
-
Karp, P.D., Paley, S., and Romero, P. 2002. The Pathway Tools software. Bioinformatics 18, Suppl 1, S225-S232. (Pubitemid 41185657)
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Karp, P.D.1
Paley, S.2
Romero, P.3
-
18
-
-
0142122303
-
Advances in flux balance analysis
-
DOI 10.1016/j.copbio.2003.08.001
-
Kauffman, K.J., Prakash, P., and Edwards, J.S. 2003. Advances in flux balance analysis. Curr. Opin. Biotechnol. 14, 491-496. (Pubitemid 37298033)
-
(2003)
Current Opinion in Biotechnology
, vol.14
, Issue.5
, pp. 491-496
-
-
Kauffman, K.J.1
Prakash, P.2
Edwards, J.S.3
-
19
-
-
33947305781
-
ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
-
Margolin, A.A., Nemenman, I., Basso, K., et al. 2006a. ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 7, Suppl 1, S7.
-
(2006)
BMC Bioinformatics
, vol.7 SUPPL.1
-
-
Margolin, A.A.1
Nemenman, I.2
Basso, K.3
-
20
-
-
33750353888
-
Reverse engineering cellular networks
-
Margolin, A.A., Wang, K., Lim, W.K., et al. 2006b. Reverse engineering cellular networks. Nat. Protoc. 1, 662-671.
-
(2006)
Nat. Protoc.
, vol.1
, pp. 662-671
-
-
Margolin, A.A.1
Wang, K.2
Lim, W.K.3
-
21
-
-
78149438375
-
Multivariate dependence and genetic networks inference
-
Margolin, A.A., Wang, K., Califano, A., et al. 2010. Multivariate dependence and genetic networks inference. IET Syst. Biol. 4, 428.
-
(2010)
IET Syst. Biol.
, vol.4
, pp. 428
-
-
Margolin, A.A.1
Wang, K.2
Califano, A.3
-
22
-
-
36248940715
-
Reconstruction of metabolic networks from high-throughput metabolite profiling data: In silico analysis of red blood cell metabolism
-
DOI 10.1196/annals.1407.013, Reverse Engineering Biological Networks: Opportunities and Challenges in Computational Methods for Pathway Inference
-
Nemenman, I., Escola, G.S., Hlavacek, W.S., et al. 2007. Reconstruction of metabolic networks from high-throughput metabolite profiling data: In silico analysis of red blood cell metabolism. Ann. N. Y. Acad. Sci. 1115, 102-115. (Pubitemid 350134802)
-
(2007)
Annals of the New York Academy of Sciences
, vol.1115
, pp. 102-115
-
-
Nemenman, I.1
Escola, G.S.2
Hlavacek, W.S.3
Unkefer, P.J.4
Unkefer, C.J.5
Wall, M.E.6
-
23
-
-
0032919364
-
KEGG: Kyoto encyclopedia of genes and genomes
-
DOI 10.1093/nar/27.1.29
-
Ogata, H., Goto, S., Sato, K., et al. 1999. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 27, 29-34. (Pubitemid 29209394)
-
(1999)
Nucleic Acids Research
, vol.27
, Issue.1
, pp. 29-34
-
-
Ogata, H.1
Goto, S.2
Sato, K.3
Fujibuchi, W.4
Bono, H.5
Kanehisa, M.6
-
24
-
-
34247123157
-
Cellular metabolomics of Escherchia coli
-
DOI 10.1586/14789450.4.2.187
-
Rabinowitz, J.D. 2007. Cellular metabolomics of Escherchia coli. Expert Rev. Proteomics 4, 187-198. (Pubitemid 46588455)
-
(2007)
Expert Review of Proteomics
, vol.4
, Issue.2
, pp. 187-198
-
-
Rabinowitz, J.D.1
-
25
-
-
8544253237
-
Assignment of endogenous substrates to enzymes by global metabolite profiling
-
DOI 10.1021/bi0480335
-
Saghatelian, A., Trauger, S.A., Want, E.J., et al. 2004. Assignment of endogenous substrates to enzymes by global metabolite profiling. Biochemistry 43, 14332-14339. (Pubitemid 39491967)
-
(2004)
Biochemistry
, vol.43
, Issue.45
, pp. 14332-14339
-
-
Saghatelian, A.1
Trauger, S.A.2
Want, E.J.3
Hawkins, E.G.4
Siuzdak, G.5
Cravatt, B.F.6
-
26
-
-
0034447725
-
Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems
-
DOI 10.1002/1097-0290(2000)71:4<286::AID-BIT1018>3.0.CO;2-R
-
Schilling, C.H., Edwards, J.S., Letscher, D., et al. 2000. Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems. Biotechnol. Bioeng. 71, 286-306. (Pubitemid 32377286)
-
(2000)
Biotechnology and Bioengineering
, vol.71
, Issue.4
, pp. 286-306
-
-
Schilling, C.H.1
Edwards, J.S.2
Letscher, D.3
Palsson, B.O.4
-
27
-
-
0033080396
-
Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering
-
DOI 10.1016/S0167-7799(98)01290-6, PII S0167779998012906
-
Schuster, S., Dandekar, T., and Fell, D.A. 1999. Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering. Trends Biotechnol. 17, 53-60. (Pubitemid 29332898)
-
(1999)
Trends in Biotechnology
, vol.17
, Issue.2
, pp. 53-60
-
-
Schuster, S.1
Dandekar, T.2
Fell, D.A.3
-
28
-
-
34247842946
-
Methods, applications and concepts of metabolite profiling: Primary metabolism
-
Steinhauser, D., and Kopka, J. 2007. Methods, applications and concepts of metabolite profiling: Primary metabolism. EXS 97, 171-194.
-
(2007)
EXS
, vol.97
, pp. 171-194
-
-
Steinhauser, D.1
Kopka, J.2
-
29
-
-
0033109513
-
Commentary. Metabolic profiling: A Rosetta Stone for genomics?
-
DOI 10.1016/S1369-5266(99)80017-X
-
Trethewey, R.N., Krotzky, A.J., and Willmitzer, L. 1999. Metabolic profiling: A Rosetta Stone for genomics? Curr. Opin. Plant Biol. 2, 83-85. (Pubitemid 29181906)
-
(1999)
Current Opinion in Plant Biology
, vol.2
, Issue.2
, pp. 83-85
-
-
Trethewey, R.N.1
Krotzky, A.J.2
Willmitzer, L.3
-
30
-
-
70249108504
-
Genome-wide identification of post-translational modulators of transcription factor activity in human B cells
-
Wang, K., Saito, M., Bisikirska, B.C., et al. 2009. Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nat. Biotechnol. 27, 829-837.
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 829-837
-
-
Wang, K.1
Saito, M.2
Bisikirska, B.C.3
|