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For: Sanford K, Soucaille P, Whited G, Chotani G. Genomics to fluxomics and physiomics - pathway engineering. Curr Opin Microbiol 2002;5:318-22. [PMID: 12057688 DOI: 10.1016/s1369-5274(02)00318-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Number Cited by Other Article(s)
1
Recent advances in high-throughput 13C-fluxomics. Curr Opin Biotechnol 2016;43:104-109. [PMID: 27838571 DOI: 10.1016/j.copbio.2016.10.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 10/21/2016] [Accepted: 10/25/2016] [Indexed: 12/11/2022]
2
Cuperlovic-Culf M, Culf AS. Applied metabolomics in drug discovery. Expert Opin Drug Discov 2016;11:759-70. [DOI: 10.1080/17460441.2016.1195365] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
3
Wishart DS. Emerging applications of metabolomics in drug discovery and precision medicine. Nat Rev Drug Discov 2016;15:473-84. [PMID: 26965202 DOI: 10.1038/nrd.2016.32] [Citation(s) in RCA: 964] [Impact Index Per Article: 107.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
4
White biotechnology: State of the art strategies for the development of biocatalysts for biorefining. Biotechnol Adv 2015;33:1653-70. [PMID: 26303096 DOI: 10.1016/j.biotechadv.2015.08.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 07/31/2015] [Accepted: 08/17/2015] [Indexed: 12/31/2022]
5
Niedenführ S, Wiechert W, Nöh K. How to measure metabolic fluxes: a taxonomic guide for (13)C fluxomics. Curr Opin Biotechnol 2014;34:82-90. [PMID: 25531408 DOI: 10.1016/j.copbio.2014.12.003] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 11/28/2014] [Accepted: 12/01/2014] [Indexed: 12/24/2022]
6
Zhang Z, Shen T, Rui B, Zhou W, Zhou X, Shang C, Xin C, Liu X, Li G, Jiang J, Li C, Li R, Han M, You S, Yu G, Yi Y, Wen H, Liu Z, Xie X. CeCaFDB: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13C-fluxomics. Nucleic Acids Res 2014;43:D549-57. [PMID: 25392417 PMCID: PMC4383945 DOI: 10.1093/nar/gku1137] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
7
Heux S, Poinot J, Massou S, Sokol S, Portais JC. A novel platform for automated high-throughput fluxome profiling of metabolic variants. Metab Eng 2014;25:8-19. [PMID: 24930895 DOI: 10.1016/j.ymben.2014.06.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 04/07/2014] [Accepted: 06/04/2014] [Indexed: 11/15/2022]
8
Tang KH, Tang YJ, Blankenship RE. Carbon metabolic pathways in phototrophic bacteria and their broader evolutionary implications. Front Microbiol 2011;2:165. [PMID: 21866228 PMCID: PMC3149686 DOI: 10.3389/fmicb.2011.00165] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 07/18/2011] [Indexed: 11/19/2022]  Open
9
Matsuoka Y, Shimizu K. Current status of 13C-metabolic flux analysis and future perspectives. Process Biochem 2010. [DOI: 10.1016/j.procbio.2010.03.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
10
Rühl M, Zamboni N, Sauer U. Dynamic flux responses in riboflavin overproducing Bacillus subtilis to increasing glucose limitation in fed-batch culture. Biotechnol Bioeng 2010;105:795-804. [PMID: 19882734 DOI: 10.1002/bit.22591] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
11
Systems biology of industrial microorganisms. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2010;120:51-99. [PMID: 20503029 DOI: 10.1007/10_2009_59] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
12
Toward systematic metabolic engineering based on the analysis of metabolic regulation by the integration of different levels of information. Biochem Eng J 2009. [DOI: 10.1016/j.bej.2009.06.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
13
From systems biology to fuel—Chlamydomonas reinhardtii as a model for a systems biology approach to improve biohydrogen production. J Biotechnol 2009;142:10-20. [DOI: 10.1016/j.jbiotec.2009.02.008] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Revised: 02/03/2009] [Accepted: 02/09/2009] [Indexed: 11/23/2022]
14
Heinonen M, Rantanen A, Mielikäinen T, Kokkonen J, Kiuru J, Ketola RA, Rousu J. FiD: a software for ab initio structural identification of product ions from tandem mass spectrometric data. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008;22:3043-3052. [PMID: 18763276 DOI: 10.1002/rcm.3701] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
15
van der Werf MJ, Overkamp KM, Muilwijk B, Koek MM, van der Werff-van der Vat BJC, Jellema RH, Coulier L, Hankemeier T. Comprehensive analysis of the metabolome of Pseudomonas putida S12 grown on different carbon sources. MOLECULAR BIOSYSTEMS 2008;4:315-27. [PMID: 18354785 DOI: 10.1039/b717340g] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
16
Predicting gene essentiality using genome-scale in silico models. Methods Mol Biol 2008;416:433-57. [PMID: 18392986 DOI: 10.1007/978-1-59745-321-9_30] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
17
de Graaf AA, Venema K. Gaining insight into microbial physiology in the large intestine: a special role for stable isotopes. Adv Microb Physiol 2007;53:73-168. [PMID: 17707144 DOI: 10.1016/s0065-2911(07)53002-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
18
Nookaew I, Meechai A, Thammarongtham C, Laoteng K, Ruanglek V, Cheevadhanarak S, Nielsen J, Bhumiratana S. Identification of flux regulation coefficients from elementary flux modes: A systems biology tool for analysis of metabolic networks. Biotechnol Bioeng 2007;97:1535-49. [PMID: 17238207 DOI: 10.1002/bit.21339] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
19
Sekiyama Y, Kikuchi J. Towards dynamic metabolic network measurements by multi-dimensional NMR-based fluxomics. PHYTOCHEMISTRY 2007;68:2320-9. [PMID: 17532017 DOI: 10.1016/j.phytochem.2007.04.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Revised: 03/30/2007] [Accepted: 04/08/2007] [Indexed: 05/08/2023]
20
Sauer U. Introduction and Perspectives. EcoSal Plus 2007;2. [PMID: 26443590 DOI: 10.1128/ecosal.3.1.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2007] [Indexed: 06/05/2023]
21
Sauer U. Metabolic networks in motion: 13C-based flux analysis. Mol Syst Biol 2006;2:62. [PMID: 17102807 PMCID: PMC1682028 DOI: 10.1038/msb4100109] [Citation(s) in RCA: 490] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2006] [Accepted: 10/06/2006] [Indexed: 01/08/2023]  Open
22
Schnackenberg LK, Beger RD. Monitoring the health to disease continuum with global metabolic profiling and systems biology. Pharmacogenomics 2006;7:1077-86. [PMID: 17054417 DOI: 10.2217/14622416.7.7.1077] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
23
Lee WNP. Characterizing phenotype with tracer based metabolomics. Metabolomics 2006;2:31-39. [PMID: 25540606 PMCID: PMC4271195 DOI: 10.1007/s11306-006-0017-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2005] [Accepted: 01/25/2006] [Indexed: 01/01/2023]
24
The role of high-throughput transcriptome analysis in metabolic engineering. BIOTECHNOL BIOPROC E 2005. [DOI: 10.1007/bf02989821] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
25
Lee SY, Lee DY, Kim TY. Systems biotechnology for strain improvement. Trends Biotechnol 2005;23:349-58. [PMID: 15923052 DOI: 10.1016/j.tibtech.2005.05.003] [Citation(s) in RCA: 182] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2005] [Revised: 02/28/2005] [Accepted: 05/06/2005] [Indexed: 10/25/2022]
26
van der Werf MJ, Jellema RH, Hankemeier T. Microbial metabolomics: replacing trial-and-error by the unbiased selection and ranking of targets. J Ind Microbiol Biotechnol 2005;32:234-52. [PMID: 15895265 DOI: 10.1007/s10295-005-0231-4] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2004] [Accepted: 03/10/2005] [Indexed: 01/01/2023]
27
Beste DJV, Peters J, Hooper T, Avignone-Rossa C, Bushell ME, McFadden J. Compiling a molecular inventory for Mycobacterium bovis BCG at two growth rates: evidence for growth rate-mediated regulation of ribosome biosynthesis and lipid metabolism. J Bacteriol 2005;187:1677-84. [PMID: 15716438 PMCID: PMC1064002 DOI: 10.1128/jb.187.5.1677-1684.2005] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2004] [Accepted: 11/29/2004] [Indexed: 11/20/2022]  Open
28
Middaugh J, Hamel R, Jean-Baptiste G, Beriault R, Chenier D, Appanna VD. Aluminum triggers decreased aconitase activity via Fe-S cluster disruption and the overexpression of isocitrate dehydrogenase and isocitrate lyase: a metabolic network mediating cellular survival. J Biol Chem 2004;280:3159-65. [PMID: 15548528 DOI: 10.1074/jbc.m411979200] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
29
Patil KR, Akesson M, Nielsen J. Use of genome-scale microbial models for metabolic engineering. Curr Opin Biotechnol 2004;15:64-9. [PMID: 15102469 DOI: 10.1016/j.copbio.2003.11.003] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
30
Herrgård MJ, Covert MW, Palsson BØ. Reconstruction of microbial transcriptional regulatory networks. Curr Opin Biotechnol 2004;15:70-7. [PMID: 15102470 DOI: 10.1016/j.copbio.2003.11.002] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
31
Bro C, Nielsen J. Impact of ‘ome’ analyses on inverse metabolic engineering. Metab Eng 2004;6:204-11. [PMID: 15256210 DOI: 10.1016/j.ymben.2003.11.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2003] [Accepted: 11/04/2003] [Indexed: 10/26/2022]
32
de Vos WM, Hugenholtz J. Engineering metabolic highways in Lactococci and other lactic acid bacteria. Trends Biotechnol 2004;22:72-9. [PMID: 14757041 DOI: 10.1016/j.tibtech.2003.11.011] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
33
Chakrabarti S, Bhattacharya S, Bhattacharya SK. Biochemical engineering: cues from cells. Trends Biotechnol 2003;21:204-9. [PMID: 12727381 DOI: 10.1016/s0167-7799(03)00077-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
34
Bhattacharya S, Chakrabarti S, Nayak A, Bhattacharya SK. Metabolic networks of microbial systems. Microb Cell Fact 2003;2:3. [PMID: 12740044 PMCID: PMC155636 DOI: 10.1186/1475-2859-2-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2003] [Accepted: 04/11/2003] [Indexed: 12/02/2022]  Open
35
A Method for Estimating Metabolic Fluxes from Incomplete Isotopomer Information. ACTA ACUST UNITED AC 2003. [DOI: 10.1007/3-540-36481-1_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2023]
36
Davidov E, Holland J, Marple E, Naylor S. Advancing drug discovery through systems biology. Drug Discov Today 2003;8:175-83. [PMID: 12581712 DOI: 10.1016/s1359-6446(03)02600-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
37
Yeast functional genomics and metabolic engineering: past, present and future. TOPICS IN CURRENT GENETICS 2003. [DOI: 10.1007/3-540-37003-x_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
38
Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2002. [PMCID: PMC2448418 DOI: 10.1002/cfg.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]  Open
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