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The small world inside large metabolic networks.

Proceedings. Biological sciences

Wagner A, Fell DA.
PMID: 11522199
Proc Biol Sci. 2001 Sep 07;268(1478):1803-10. doi: 10.1098/rspb.2001.1711.

The metabolic network of the catabolic, energy and biosynthetic metabolism of Escherichia coli is a paradigmatic case for the large genetic and metabolic networks that functional genomics efforts are beginning to elucidate. To analyse the structure of previously unknown...

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Wagner A, Fell DA. The small world inside large metabolic networks. Proc Biol Sci. 2001;268(1478):1803-10doi: 10.1098/rspb.2001.1711.
Wagner, A., & Fell, D. A. (2001). The small world inside large metabolic networks. Proceedings. Biological sciences, 268(1478), 1803-10. https://doi.org/10.1098/rspb.2001.1711
Wagner, A, and Fell, D A. "The small world inside large metabolic networks." Proceedings. Biological sciences vol. 268,1478 (2001): 1803-10. doi: https://doi.org/10.1098/rspb.2001.1711
Wagner A, Fell DA. The small world inside large metabolic networks. Proc Biol Sci. 2001 Sep 07;268(1478):1803-10. doi: 10.1098/rspb.2001.1711. PMID: 11522199; PMCID: PMC1088812.
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[The aerobic and the anaerobic metabolism of Escherichia coli].

Biochimica et biophysica acta

SZULMAJSTER J, GRUNBERG-MANAGO M, PROUVOST A.
PMID: 13032173
Biochim Biophys Acta. 1952 Dec;9(6):636-44. doi: 10.1016/0006-3002(52)90225-4.

No abstract available.

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SZULMAJSTER J, GRUNBERG-MANAGO M, PROUVOST A. Sur le métabolisme aérobie et anaérobie de E. coli. [The aerobic and the anaerobic metabolism of Escherichia coli]. Biochim Biophys Acta. 1952;9(6):636-44doi: 10.1016/0006-3002(52)90225-4.
SZULMAJSTER, J., GRUNBERG-MANAGO, M., & PROUVOST, A. (1952). Sur le métabolisme aérobie et anaérobie de E. coli. [The aerobic and the anaerobic metabolism of Escherichia coli]. Biochimica et biophysica acta, 9(6), 636-44. https://doi.org/10.1016/0006-3002(52)90225-4
SZULMAJSTER, J, et al. "Sur le métabolisme aérobie et anaérobie de E. coli." [The aerobic and the anaerobic metabolism of Escherichia coli]. Biochimica et biophysica acta vol. 9,6 (1952): 636-44. doi: https://doi.org/10.1016/0006-3002(52)90225-4
SZULMAJSTER J, GRUNBERG-MANAGO M, PROUVOST A. Sur le métabolisme aérobie et anaérobie de E. coli. [The aerobic and the anaerobic metabolism of Escherichia coli]. Biochim Biophys Acta. 1952 Dec;9(6):636-44. doi: 10.1016/0006-3002(52)90225-4. Undetermined. PMID: 13032173.
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Pantothenate studies. III. Description of the extracted pantothenate-synthesizing enzyme of Escherichia coli.

The Journal of biological chemistry

MAAS WK.
PMID: 12999714
J Biol Chem. 1952 Sep;198(1):23-32.

No abstract available.

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MAAS WK. Pantothenate studies. III. Description of the extracted pantothenate-synthesizing enzyme of Escherichia coli. J Biol Chem. 1952;198(1):23-32
MAAS, W. K. (1952). Pantothenate studies. III. Description of the extracted pantothenate-synthesizing enzyme of Escherichia coli. The Journal of biological chemistry, 198(1), 23-32.
MAAS, W K. "Pantothenate studies. III. Description of the extracted pantothenate-synthesizing enzyme of Escherichia coli." The Journal of biological chemistry vol. 198,1 (1952): 23-32.
MAAS WK. Pantothenate studies. III. Description of the extracted pantothenate-synthesizing enzyme of Escherichia coli. J Biol Chem. 1952 Sep;198(1):23-32. PMID: 12999714.
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Kinetically accessible yield (KAY) for redirection of metabolism to produce exo-metabolites.

Metabolic engineering

Lafontaine Rivera JG, Theisen MK, Chen PW, Liao JC.
PMID: 28389394
Metab Eng. 2017 May;41:144-151. doi: 10.1016/j.ymben.2017.03.011. Epub 2017 Apr 05.

The product formation yield (product formed per unit substrate consumed) is often the most important performance indicator in metabolic engineering. Until now, the actual yield cannot be predicted, but it can be bounded by its maximum theoretical value. The...

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Lafontaine Rivera JG, Theisen MK, Chen PW, et al. Kinetically accessible yield (KAY) for redirection of metabolism to produce exo-metabolites. Metab Eng. 2017;41:144-151doi: 10.1016/j.ymben.2017.03.011.
Lafontaine Rivera, J. G., Theisen, M. K., Chen, P. W., & Liao, J. C. (2017). Kinetically accessible yield (KAY) for redirection of metabolism to produce exo-metabolites. Metabolic engineering, 41144-151. https://doi.org/10.1016/j.ymben.2017.03.011
Lafontaine Rivera, Jimmy G, et al. "Kinetically accessible yield (KAY) for redirection of metabolism to produce exo-metabolites." Metabolic engineering vol. 41 (2017): 144-151. doi: https://doi.org/10.1016/j.ymben.2017.03.011
Lafontaine Rivera JG, Theisen MK, Chen PW, Liao JC. Kinetically accessible yield (KAY) for redirection of metabolism to produce exo-metabolites. Metab Eng. 2017 May;41:144-151. doi: 10.1016/j.ymben.2017.03.011. Epub 2017 Apr 05. PMID: 28389394.
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Engineering Escherichia coli Cell Factories for n-Butanol Production.

Advances in biochemical engineering/biotechnology

Dong H, Zhao C, Zhang T, Lin Z, Li Y, Zhang Y.
PMID: 25662903
Adv Biochem Eng Biotechnol. 2016;155:141-63. doi: 10.1007/10_2015_306.

The production of n-butanol, as a widely applied solvent and potential fuel, is attracting much attention. The fermentative production of butanol coupled with the production of acetone and ethanol by Clostridium (ABE fermentation) was once one of the oldest...

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Dong H, Zhao C, Zhang T, et al. Engineering Escherichia coli Cell Factories for n-Butanol Production. Adv Biochem Eng Biotechnol. 2016;155:141-63doi: 10.1007/10_2015_306.
Dong, H., Zhao, C., Zhang, T., Lin, Z., Li, Y., & Zhang, Y. (2016). Engineering Escherichia coli Cell Factories for n-Butanol Production. Advances in biochemical engineering/biotechnology, 155141-63. https://doi.org/10.1007/10_2015_306
Dong, Hongjun, et al. "Engineering Escherichia coli Cell Factories for n-Butanol Production." Advances in biochemical engineering/biotechnology vol. 155 (2016): 141-63. doi: https://doi.org/10.1007/10_2015_306
Dong H, Zhao C, Zhang T, Lin Z, Li Y, Zhang Y. Engineering Escherichia coli Cell Factories for n-Butanol Production. Adv Biochem Eng Biotechnol. 2016;155:141-63. doi: 10.1007/10_2015_306. PMID: 25662903.
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XTMS: pathway design in an eXTended metabolic space.

Nucleic acids research

Carbonell P, Parutto P, Herisson J, Pandit SB, Faulon JL.
PMID: 24792156
Nucleic Acids Res. 2014 Jul;42:W389-94. doi: 10.1093/nar/gku362. Epub 2014 May 03.

As metabolic engineering and synthetic biology progress toward reaching the goal of a more sustainable use of biological resources, the need of increasing the number of value-added chemicals that can be produced in industrial organisms becomes more imperative. Exploring,...

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Carbonell P, Parutto P, Herisson J, et al. XTMS: pathway design in an eXTended metabolic space. Nucleic Acids Res. 2014;42:W389-94doi: 10.1093/nar/gku362.
Carbonell, P., Parutto, P., Herisson, J., Pandit, S. B., & Faulon, J. L. (2014). XTMS: pathway design in an eXTended metabolic space. Nucleic acids research, 42W389-94. https://doi.org/10.1093/nar/gku362
Carbonell, Pablo, et al. "XTMS: pathway design in an eXTended metabolic space." Nucleic acids research vol. 42 (2014): W389-94. doi: https://doi.org/10.1093/nar/gku362
Carbonell P, Parutto P, Herisson J, Pandit SB, Faulon JL. XTMS: pathway design in an eXTended metabolic space. Nucleic Acids Res. 2014 Jul;42:W389-94. doi: 10.1093/nar/gku362. Epub 2014 May 03. PMID: 24792156; PMCID: PMC4086079.
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Reassessing Escherichia coli as a cell factory for biofuel production.

Current opinion in biotechnology

Wang C, Pfleger BF, Kim SW.
PMID: 28292659
Curr Opin Biotechnol. 2017 Jun;45:92-103. doi: 10.1016/j.copbio.2017.02.010. Epub 2017 Mar 11.

Via metabolic engineering, industrial microorganisms have the potential to convert renewable substrates into a wide range of biofuels that can address energy security and environmental challenges associated with current fossil fuels. The user-friendly bacterium, Escherichia coli, remains one of...

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Wang C, Pfleger BF, Kim SW. Reassessing Escherichia coli as a cell factory for biofuel production. Curr Opin Biotechnol. 2017;45:92-103doi: 10.1016/j.copbio.2017.02.010.
Wang, C., Pfleger, B. F., & Kim, S. W. (2017). Reassessing Escherichia coli as a cell factory for biofuel production. Current opinion in biotechnology, 4592-103. https://doi.org/10.1016/j.copbio.2017.02.010
Wang, Chonglong, et al. "Reassessing Escherichia coli as a cell factory for biofuel production." Current opinion in biotechnology vol. 45 (2017): 92-103. doi: https://doi.org/10.1016/j.copbio.2017.02.010
Wang C, Pfleger BF, Kim SW. Reassessing Escherichia coli as a cell factory for biofuel production. Curr Opin Biotechnol. 2017 Jun;45:92-103. doi: 10.1016/j.copbio.2017.02.010. Epub 2017 Mar 11. PMID: 28292659.
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Prediction of dynamic behavior of mutant strains from limited wild-type data.

Metabolic engineering

Song HS, Ramkrishna D.
PMID: 22500302
Metab Eng. 2012 Mar;14(2):69-80. doi: 10.1016/j.ymben.2012.02.003.

Metabolic engineering is the field of introducing genetic changes in organisms so as to modify their function towards synthesizing new products of high impact to society. However, engineered cells frequently have impaired growth rates thus seriously limiting the rate...

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Song HS, Ramkrishna D. Prediction of dynamic behavior of mutant strains from limited wild-type data. Metab Eng. 2012;14(2):69-80doi: 10.1016/j.ymben.2012.02.003.
Song, H. S., & Ramkrishna, D. (2012). Prediction of dynamic behavior of mutant strains from limited wild-type data. Metabolic engineering, 14(2), 69-80. https://doi.org/10.1016/j.ymben.2012.02.003
Song, Hyun-Seob, and Ramkrishna, Doraiswami. "Prediction of dynamic behavior of mutant strains from limited wild-type data." Metabolic engineering vol. 14,2 (2012): 69-80. doi: https://doi.org/10.1016/j.ymben.2012.02.003
Song HS, Ramkrishna D. Prediction of dynamic behavior of mutant strains from limited wild-type data. Metab Eng. 2012 Mar;14(2):69-80. doi: 10.1016/j.ymben.2012.02.003. PMID: 22500302.
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Dispensability of Escherichia coli's latent pathways.

Proceedings of the National Academy of Sciences of the United States of America

Cornelius SP, Lee JS, Motter AE.
PMID: 21300895
Proc Natl Acad Sci U S A. 2011 Feb 22;108(8):3124-9. doi: 10.1073/pnas.1009772108. Epub 2011 Feb 07.

Gene-knockout experiments on single-cell organisms have established that expression of a substantial fraction of genes is not needed for optimal growth. This problem acquired a new dimension with the recent discovery that environmental and genetic perturbations of the bacterium...

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Cornelius SP, Lee JS, Motter AE. Dispensability of Escherichia coli's latent pathways. Proc Natl Acad Sci U S A. 2011;108(8):3124-9doi: 10.1073/pnas.1009772108.
Cornelius, S. P., Lee, J. S., & Motter, A. E. (2011). Dispensability of Escherichia coli's latent pathways. Proceedings of the National Academy of Sciences of the United States of America, 108(8), 3124-9. https://doi.org/10.1073/pnas.1009772108
Cornelius, Sean P, et al. "Dispensability of Escherichia coli's latent pathways." Proceedings of the National Academy of Sciences of the United States of America vol. 108,8 (2011): 3124-9. doi: https://doi.org/10.1073/pnas.1009772108
Cornelius SP, Lee JS, Motter AE. Dispensability of Escherichia coli's latent pathways. Proc Natl Acad Sci U S A. 2011 Feb 22;108(8):3124-9. doi: 10.1073/pnas.1009772108. Epub 2011 Feb 07. PMID: 21300895; PMCID: PMC3044393.
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Time-resolved selected ion flow tube mass spectrometric quantification of the volatile compounds generated by E. coli JM109 cultured in two different media.

Rapid communications in mass spectrometry : RCM

Chippendale TW, Španěl P, Smith D.
PMID: 21710596
Rapid Commun Mass Spectrom. 2011 Aug 15;25(15):2163-72. doi: 10.1002/rcm.5099.

Preliminary measurements have been made of the volatile compounds emitted by the bacterium E. coli JM109 cultured in the commonly used media Dulbecco's modified Eagle's medium (DMEM) and lysogeny broth (LB) using selected ion flow tube mass spectrometry, SIFT-MS,...

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Chippendale TW, Španěl P, Smith D. Time-resolved selected ion flow tube mass spectrometric quantification of the volatile compounds generated by E. coli JM109 cultured in two different media. Rapid Commun Mass Spectrom. 2011;25(15):2163-72doi: 10.1002/rcm.5099.
Chippendale, T. W., Španěl, P., & Smith, D. (2011). Time-resolved selected ion flow tube mass spectrometric quantification of the volatile compounds generated by E. coli JM109 cultured in two different media. Rapid communications in mass spectrometry : RCM, 25(15), 2163-72. https://doi.org/10.1002/rcm.5099
Chippendale, Thomas W E, et al. "Time-resolved selected ion flow tube mass spectrometric quantification of the volatile compounds generated by E. coli JM109 cultured in two different media." Rapid communications in mass spectrometry : RCM vol. 25,15 (2011): 2163-72. doi: https://doi.org/10.1002/rcm.5099
Chippendale TW, Španěl P, Smith D. Time-resolved selected ion flow tube mass spectrometric quantification of the volatile compounds generated by E. coli JM109 cultured in two different media. Rapid Commun Mass Spectrom. 2011 Aug 15;25(15):2163-72. doi: 10.1002/rcm.5099. PMID: 21710596.
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A quantitative metabolomics study of bacterial metabolites in different domains.

Analytica chimica acta

Zhong F, Xu M, Metz P, Ghosh-Dastidar P, Zhu J.
PMID: 30292298
Anal Chim Acta. 2018 Dec 11;1037:237-244. doi: 10.1016/j.aca.2018.02.046. Epub 2018 Feb 23.

Absolute metabolite concentrations are essential information for quantitative metabolomics studies, as concentrations are closely related to metabolic reactions, enzyme kinetics and other important biological activities. A well-performed metabolites extraction procedure, a reliable detection method, and a robust quantitative approach...

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Zhong F, Xu M, Metz P, et al. A quantitative metabolomics study of bacterial metabolites in different domains. Anal Chim Acta. 2018;1037:237-244doi: 10.1016/j.aca.2018.02.046.
Zhong, F., Xu, M., Metz, P., Ghosh-Dastidar, P., & Zhu, J. (2018). A quantitative metabolomics study of bacterial metabolites in different domains. Analytica chimica acta, 1037237-244. https://doi.org/10.1016/j.aca.2018.02.046
Zhong, Fanyi, et al. "A quantitative metabolomics study of bacterial metabolites in different domains." Analytica chimica acta vol. 1037 (2018): 237-244. doi: https://doi.org/10.1016/j.aca.2018.02.046
Zhong F, Xu M, Metz P, Ghosh-Dastidar P, Zhu J. A quantitative metabolomics study of bacterial metabolites in different domains. Anal Chim Acta. 2018 Dec 11;1037:237-244. doi: 10.1016/j.aca.2018.02.046. Epub 2018 Feb 23. PMID: 30292298.
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Isolation of detergent-resistant membranes (DRMs) from Escherichia coli.

Analytical biochemistry

Guzmán-Flores JE, Alvarez AF, Poggio S, Gavilanes-Ruiz M, Georgellis D.
PMID: 27984012
Anal Biochem. 2017 Feb 01;518:1-8. doi: 10.1016/j.ab.2016.10.025. Epub 2016 Oct 29.

Lipid rafts or membrane microdomains have been proposed to compartmentalize cellular processes by spatially organizing diverse molecules/proteins in eukaryotic cells. Such membrane microdomains were recently reported to also exist in a few bacterial species. In this work, we report...

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Guzmán-Flores JE, Alvarez AF, Poggio S, et al. Isolation of detergent-resistant membranes (DRMs) from Escherichia coli. Anal Biochem. 2016;518:1-8doi: 10.1016/j.ab.2016.10.025.
Guzmán-Flores, J. E., Alvarez, A. F., Poggio, S., Gavilanes-Ruiz, M., & Georgellis, D. (2017). Isolation of detergent-resistant membranes (DRMs) from Escherichia coli. Analytical biochemistry, 5181-8. https://doi.org/10.1016/j.ab.2016.10.025
Guzmán-Flores, José E, et al. "Isolation of detergent-resistant membranes (DRMs) from Escherichia coli." Analytical biochemistry vol. 518 (2017): 1-8. doi: https://doi.org/10.1016/j.ab.2016.10.025
Guzmán-Flores JE, Alvarez AF, Poggio S, Gavilanes-Ruiz M, Georgellis D. Isolation of detergent-resistant membranes (DRMs) from Escherichia coli. Anal Biochem. 2017 Feb 01;518:1-8. doi: 10.1016/j.ab.2016.10.025. Epub 2016 Oct 29. PMID: 27984012.
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