107 Works

Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli [Datasets]

Jie Yuan, Christopher D Doucette, William U Fowler, Xiao-Jiang Feng, Matthew Piazza, Herschel A Rabitz, Ned S Wingreen & Joshua D Rabinowitz
Data from the manuscript: Yuan J, Doucette CD, Fowler WU, et al. Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli. Mol Syst Biol. 2009;5:302. doi:10.1038/msb.2009.60

The selective control of glycolysis, gluconeogenesis and glycogenesis by temporal insulin patterns [Datasets]

Rei Noguchi, Hiroyuki Kubota, Katsuyuki Yugi, Yu Toyoshima, Yasunori Komori, Tomoyoshi Soga & Shinya Kuroda
Data from the manuscript: Noguchi R, Kubota H, Yugi K, et al. The selective control of glycolysis, gluconeogenesis and glycogenesis by temporal insulin patterns. Mol Syst Biol. 2013;9:664. Published 2013 May 14. doi:10.1038/msb.2013.19

Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast [Datasets]

Guillermo G Zampar, Anne Kümmel, Jennifer Ewald, Stefan Jol, Bastian Niebel, Paola Picotti, Ruedi Aebersold, Uwe Sauer, Nicola Zamboni & Matthias Heinemann
Data from the manuscript: Zampar GG, Kümmel A, Ewald J, et al. Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast. Mol Syst Biol. 2013;9:651. doi:10.1038/msb.2013.11

Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast [Datasets]

Petri-Jaan Lahtvee, Benjamín J. Sánchez, Agata Smialowska, Sergo Kasvandik, Ibrahim E. Elsemman, Francesco Gatto & Jens Nielsen
Data from the manuscript: Lahtvee PJ, Sánchez BJ, Smialowska A, et al. Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast. Cell Syst. 2017;4(5):495-504.e5. doi:10.1016/j.cels.2017.03.003

Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast [Datasets]

Lars M Blank, Lars Kuepfer & Uwe Sauer
Data from the manuscript: Blank LM, Kuepfer L, Sauer U. Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast. Genome Biol. 2005;6(6):R49. doi:10.1186/gb-2005-6-6-r49

Pseudo-transition Analysis Identifies the Key Regulators of Dynamic Metabolic Adaptations from Steady-State Data [Datasets]

Luca Gerosa, Bart R.B. Haverkorn van Rijsewijk, Dimitris Christodoulou, Karl Kochanowski, Thomas S.B. Schmidt, Elad Noor & Uwe Sauer
Data from the manuscript: Gerosa L, Haverkorn van Rijsewijk BR, Christodoulou D, et al. Pseudo-transition Analysis Identifies the Key Regulators of Dynamic Metabolic Adaptations from Steady-State Data. Cell Syst. 2015;1(4):270-282. doi:10.1016/j.cels.2015.09.008

Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification [Datasets]

Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden & Kazuyuki Shimizu
Data from the manuscript: Kadir TA, Mannan AA, Kierzek AM, McFadden J, Shimizu K. Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification. Microb Cell Fact. 2010;9:88. Published 2010 Nov 19. doi:10.1186/1475-2859-9-88

Dynamic simulation of an in vitro multi-enzyme system [Datasets]

Nobuyoshi Ishii, Yoshihiro Suga, Akiko Hagiya, Hisami Watanabe, Hirotada Mori, Masataka Yoshino & Masaru Tomita
Data from the manuscript: Ishii N, Suga Y, Hagiya A, et al. Dynamic simulation of an in vitro multi-enzyme system. FEBS Lett. 2007;581(3):413-420. doi:10.1016/j.febslet.2006.12.049

Effect of a single-gene knockout on the metabolic regulation in Escherichia coli for D-lactate production under microaerobic condition [Datasets]

Jiangfeng Zhu & Kazuyuki Shimizu
Data from the manuscript: Zhu J, Shimizu K. Effect of a single-gene knockout on the metabolic regulation in Escherichia coli for D-lactate production under microaerobic condition. Metab Eng. 2005;7(2):104-115. doi:10.1016/j.ymben.2004.10.004

Time-dependent regulation of yeast glycolysis upon nitrogen starvation depends on cell history [Datasets]

K. van Eunen, P. Dool, A. B. Canelas, J. Kiewiet, J. Bouwman, W. M. van Gulik, H. V. Westerhoff & B. M. Bakker
Data from the manuscript: van Eunen K, Dool P, Canelas AB, et al. Time-dependent regulation of yeast glycolysis upon nitrogen starvation depends on cell history. IET Syst Biol. 2010;4(2):157-168. doi:10.1049/iet-syb.2009.0025

Analysis of Escherichia coli Anaplerotic Metabolism and Its Regulation Mechanisms From the Metabolic Responses to Altered Dilution Rates and Phosphoenolpyruvate Carboxykinase Knockout [Datasets]

C. Yang, Q. Hua, T. Baba, H. Mori & K. Shimizu
Data from the manuscript: Yang C, Hua Q, Baba T, Mori H, Shimizu K. Analysis of Escherichia coli anaplerotic metabolism and its regulation mechanisms from the metabolic responses to altered dilution rates and phosphoenolpyruvate carboxykinase knockout. Biotechnol Bioeng. 2003;84(2):129-144. doi:10.1002/bit.10692

A multi-level study of recombinant Pichia pastoris in different oxygen conditions [Datasets]

Kristin Baumann, Marc Carnicer, Martin Dragosits, Alexandra B Graf, Johannes Stadlmann, Paula Jouhten, Hannu Maaheimo, Brigitte Gasser, Joan Albiol, Diethard Mattanovich & Pau Ferrer
Data from the manuscript: Baumann K, Carnicer M, Dragosits M, et al. A multi-level study of recombinant Pichia pastoris in different oxygen conditions. BMC Syst Biol. 2010;4:141. Published 2010 Oct 22. doi:10.1186/1752-0509-4-141

Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A [Datasets]

Paula Jouhten, Eija Rintala, Anne Huuskonen, Anu Tamminen, Mervi Toivari, Marilyn Wiebe, Laura Ruohonen, Merja Penttilä & Hannu Maaheimo
Data from the manuscript: Jouhten P, Rintala E, Huuskonen A, et al. Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A. BMC Syst Biol. 2008;2:60. Published 2008 Jul 9. doi:10.1186/1752-0509-2-60

Metabonomic profiles delineate potential role of glutamate-glutamine cycle in db/db mice with diabetes-associated cognitive decline [Datasets]

Yongquan Zheng, Yunjun Yang, Baijun Dong, Hong Zheng, Xiaodong Lin, Du Yao, Xiaokun Li, Liangcai Zhao & Hongchang Gao
Data from the manuscript: Zheng Y, Yang Y, Dong B, et al. Metabonomic profiles delineate potential role of glutamate-glutamine cycle in db/db mice with diabetes-associated cognitive decline. Mol Brain. 2016;9:40. Published 2016 Apr 18. doi:10.1186/s13041-016-0223-5

Metabolic Fluxes during Strong Carbon Catabolite Repression by Malate in Bacillus subtilis [Datasets]

Roelco J. Kleijn, Joerg M. Buescher, Ludovic Le Chat, Matthieu Jules, Stephane Aymerich & Uwe Sauer
Data from the manuscript: Kleijn RJ, Buescher JM, Le Chat L, Jules M, Aymerich S, Sauer U. Metabolic fluxes during strong carbon catabolite repression by malate in Bacillus subtilis. J Biol Chem. 2010;285(3):1587-1596. doi:10.1074/jbc.M109.061747

13C‐metabolic flux analysis for batch culture of Escherichia coli and its pyk and pgi gene knockout mutants based on mass isotopomer distribution of intracellular metabolites [Datasets]

Yoshihiro Toya, Nobuyoshi Ishii, Kenji Nakahigashi, Takashi Hirasawa, Tomoyoshi Soga, Masaru Tomita & Kazuyuki Shimizu
Data from the manuscript: Toya Y, Ishii N, Nakahigashi K, et al. 13C-metabolic flux analysis for batch culture of Escherichia coli and its Pyk and Pgi gene knockout mutants based on mass isotopomer distribution of intracellular metabolites. Biotechnol Prog. 2010;26(4):975-992. doi:10.1002/btpr.420

Generating short-term kinetic responses of primary metabolism of Penicillium chrysogenum through glucose perturbation in the bioscope mini reactor [Datasets]

U. Nasution, W.M. Van Gulik, A. Proell, W.A. van Winden & J.J. Heijnen
Data from the manuscript: Nasution U, van Gulik WM, Proell A, van Winden WA, Heijnen JJ. Generating short-term kinetic responses of primary metabolism of Penicillium chrysogenum through glucose perturbation in the bioscope mini reactor. Metab Eng. 2006;8(5):395-405. doi:10.1016/j.ymben.2006.04.002

Characterization of glucose transport mutants of Saccharomyces cerevisiae during a nutritional upshift reveals a correlation between metabolite levels and glycolytic flux [Datasets]

Daniel Bosch, Mikael Johansson, Cecilia Ferndahl, Carl Johan Franzén, Christer Larsson & Lena Gustafsson
Data from the manuscript: Bosch D, Johansson M, Ferndahl C, Franzén CJ, Larsson C, Gustafsson L. Characterization of glucose transport mutants of Saccharomyces cerevisiae during a nutritional upshift reveals a correlation between metabolite levels and glycolytic flux. FEMS Yeast Res. 2008;8(1):10-25. doi:10.1111/j.1567-1364.2007.00323.x

Data from: Evaluation of novel large cut-off ultrafiltration membranes for adenovirus serotype 5 (Ad5) concentration.

Piergiuseppe Nestola, Duarte Lima Martins, Cristina Peixoto, Susanne Roederstein, Tobias Schleuss, Paula Maria Alves, José Paulo B. Mota & Manuel J. T. Carrondo
The purification of virus particles and viral vectors for vaccine and gene therapy applications is gaining increasing importance in order to deliver a fast, efficient, and reliable production process. Ultrafiltration (UF) is a widely employed unit operation in bioprocessing and its use is present in several steps of the downstream purification train of biopharmaceuticals. However, to date few studies have thoroughly investigated the performance of several membrane materials and cut-offs for virus concentration/diafiltration. The present...

Data from: Evidence for a discrete evolutionary lineage within Equatorial Guinea suggests that the tsetse fly Glossina palpalis palpalis exists as a species complex

Naomi Dyer, Andreia Furtado, Jorge Cano, Filipa Ferreira, M. Odete Afonso, Nicolas Ndong-Mabale, Pedro Ndong-Asumu, Sonia Centeno-Lima, Agustín Benito, David Weetman, Martin Donnelly & Joao Pinto
Tsetse flies of the palpalis group are major vectors of Human African Trypanosomiasis in Africa. Accurate knowledge of species identity is essential for vector control. Here we combine ribosomal internal transcribed spacer 1 (ITS1), mitochondrial Cytochrome Oxidase 1 (COI) and microsatellites to determine the population structure and phylogenetic relations of G. p. palpalis in Equatorial Guinea. COI sequence data suggest that G. p. palpalis in Equatorial Guinea are a distinct subspecies from previously described G....

Metabolic flux analysis for a ppc mutant Escherichia coli based on 13C-labelling experiments together with enzyme activity assays and intracellular metabolite measurements [Datasets]

Lifeng Peng, Marcos J. Arauzo-Bravo & Kazuyuki Shimizu
Data from the manuscript: Peng L, Arauzo-Bravo MJ, Shimizu K. Metabolic flux analysis for a ppc mutant Escherichia coli based on 13C-labelling experiments together with enzyme activity assays and intracellular metabolite measurements. FEMS Microbiol Lett. 2004;235(1):17-23. doi:10.1016/j.femsle.2004.04.003

Latent Pathway Activation and Increased Pathway Capacity Enable Escherichia coli Adaptation to Loss of Key Metabolic Enzymes [Datasets]

Stephen S. Fong, Annik Nanchen, Bernhard O. Palsson & Uwe Sauer
Data from the manuscript: Fong SS, Nanchen A, Palsson BO, Sauer U. Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes. J Biol Chem. 2006;281(12):8024-8033. doi:10.1074/jbc.M510016200

Metabolic and Transcriptional Response to Cofactor Perturbations in Escherichia coli [Datasets]

Anders K. Holm, Lars M. Blank, Marco Oldiges, Andreas Schmid, Christian Solem, Peter R. Jensen & Goutham N. Vemuri
Data from the manuscript: Holm AK, Blank LM, Oldiges M, et al. Metabolic and transcriptional response to cofactor perturbations in Escherichia coli. J Biol Chem. 2010;285(23):17498-17506. doi:10.1074/jbc.M109.095570

Analysis of Escherichia coli Anaplerotic Metabolism and Its Regulation Mechanisms From the Metabolic Responses to Altered Dilution Rates and Phosphoenolpyruvate Carboxykinase Knockout [Datasets]

C. Yang, Q. Hua, T. Baba, H. Mori & K. Shimizu
Data from the manuscript: Yang C, Hua Q, Baba T, Mori H, Shimizu K. Analysis of Escherichia coli anaplerotic metabolism and its regulation mechanisms from the metabolic responses to altered dilution rates and phosphoenolpyruvate carboxykinase knockout. Biotechnol Bioeng. 2003;84(2):129-144. doi:10.1002/bit.10692

Absolute Metabolite Concentrations and Implied Enzyme Active Site Occupancy in Escherichia coli [Datasets]

Bryson D Bennett, Elizabeth H Kimball, Melissa Gao, Robin Osterhout, Stephen J Van Dien & Joshua D Rabinowitz
Data from the manuscript: Bennett BD, Kimball EH, Gao M, Osterhout R, Van Dien SJ, Rabinowitz JD. Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol. 2009;5(8):593-599. doi:10.1038/nchembio.186

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