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Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast
Lars M Blank, Lars Kuepfer, Uwe Sauer
Genome Biol. 2005; 6(6): R49. Published online 2005 May 17. doi: 10.1186/gb-2005-6-6-r49
PMCID:
PMC1175969
Abstract Full Text PDF–404K Supplementary Material
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 Is Cited by the Following 46 Articles in this Archive:
Statistics-based model for prediction of chemical biosynthesis yield from Saccharomyces cerevisiae
Arul M Varman, Yi Xiao, Effendi Leonard, Yinjie J Tang
Microb Cell Fact. 2011; 10: 45. Published online 2011 June 21. doi: 10.1186/1475-2859-10-45
PMCID:
PMC3145561
Abstract Full Text PDF–463K
Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli
Bart R B Haverkorn van Rijsewijk, Annik Nanchen, Sophie Nallet, Roelco J Kleijn, Uwe Sauer
Mol Syst Biol. 2011; 7: 477. Published online 2011 March 29. doi: 10.1038/msb.2011.9
PMCID:
PMC3094070
Abstract Full Text PDF–951K Supplementary Material
Epistatic Interaction Maps Relative to Multiple Metabolic Phenotypes
Evan S. Snitkin, Daniel Segrè
PLoS Genet. 2011 February; 7(2): e1001294. Published online 2011 February 10. doi: 10.1371/journal.pgen.1001294
PMCID:
PMC3037399
Abstract Full Text PDF–2.0M Supplementary Material
Dispensability of Escherichia coli’s latent pathways
Sean P. Cornelius, Joo Sang Lee, Adilson E. Motter
Proc Natl Acad Sci U S A. 2011 February 22; 108(8): 3124–3129. Published online 2011 February 7. doi: 10.1073/pnas.1009772108
PMCID:
PMC3044393
Abstract Full Text PDF–310K Supplementary Material
Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics
Roeland Costenoble, Paola Picotti, Lukas Reiter, Robert Stallmach, Matthias Heinemann, Uwe Sauer, Ruedi Aebersold
Mol Syst Biol. 2011; 7: 464. Published online 2011 February 1. doi: 10.1038/msb.2010.122
PMCID:
PMC3063691
Abstract Full Text PDF–730K Supplementary Material
Metabolic response of Geobacter sulfurreducens towards electron donor/acceptor variation
Tae Hoon Yang, Maddalena V Coppi, Derek R Lovley, Jun Sun
Microb Cell Fact. 2010; 9: 90. Published online 2010 November 22. doi: 10.1186/1475-2859-9-90
PMCID:
PMC3002917
Abstract Full Text PDF–461K Supplementary Material
YEAST DYNAMIC METABOLIC FLUX MEASUREMENT IN NUTRIENT-RICH MEDIA BY HPLC AND ACCELERATOR MASS SPECTROMETRY
Benjamin J. Stewart, Ali Navid, Kenneth W. Turteltaub, Graham Bench
Anal Chem. Author manuscript; available in PMC 2011 December 1.
Published in final edited form as: Anal Chem. 2010 December 1; 82(23): 9812–9817. Published online 2010 November 9. doi: 10.1021/ac102065f
PMCID:
PMC2995814
Abstract Full Text PDF–720K
Functional Compensation of Primary and Secondary Metabolites by Duplicate Genes in Arabidopsis thaliana
Kousuke Hanada, Yuji Sawada, Takashi Kuromori, Romy Klausnitzer, Kazuki Saito, Tetsuro Toyoda, Kazuo Shinozaki, Wen-Hsiung Li, Masami Yokota Hirai
Mol Biol Evol. 2011 January; 28(1): 377–382. Published online 2010 August 24. doi: 10.1093/molbev/msq204
PMCID:
PMC3002239
Abstract Full Text PDF–555K Supplementary Material
13C-Tracer and Gas Chromatography-Mass Spectrometry Analyses Reveal Metabolic Flux Distribution in the Oleaginous Microalga Chlorella protothecoides
Wei Xiong, Lixia Liu, Chao Wu, Chen Yang, Qingyu Wu
Plant Physiol. 2010 October; 154(2): 1001–1011. Published online 2010 August 18. doi: 10.1104/pp.110.158956
PMCID:
PMC2948989
Abstract Full Text PDF–507K Supplementary Material
Prediction of metabolic fluxes by incorporating genomic context and flux-converging pattern analyses
Jong Myoung Park, Tae Yong Kim, Sang Yup Lee
Proc Natl Acad Sci U S A. 2010 August 17; 107(33): 14931–14936. Published online 2010 August 2. doi: 10.1073/pnas.1003740107
PMCID:
PMC2930451
Abstract Full Text PDF–697K Supplementary Material
Tradeoff between enzyme and metabolite efficiency maintains metabolic homeostasis upon perturbations in enzyme capacity
Sarah-Maria Fendt, Joerg Martin Buescher, Florian Rudroff, Paola Picotti, Nicola Zamboni, Uwe Sauer
Mol Syst Biol. 2010; 6: 356. Published online 2010 April 13. doi: 10.1038/msb.2010.11
PMCID:
PMC2872607
Abstract Full Text PDF–1.0M Supplementary Material
Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species
Shiri Freilich, Anat Kreimer, Elhanan Borenstein, Uri Gophna, Roded Sharan, Eytan Ruppin
PLoS Comput Biol. 2010 February; 6(2): e1000690. Published online 2010 February 26. doi: 10.1371/journal.pcbi.1000690
PMCID:
PMC2829043
Abstract Full Text PDF–629K Supplementary Material
Eating at the Table of Another: Metabolomics of Host/Parasite Interactions
Björn F.C. Kafsack, Manuel Llinás
Cell Host Microbe. Author manuscript; available in PMC 2011 February 18.
Published in final edited form as: Cell Host Microbe. 2010 February 18; 7(2): 90–99. doi: 10.1016/j.chom.2010.01.008
PMCID:
PMC2825149
Abstract Full Text PDF–735K
Transcriptional regulation of respiration in yeast metabolizing differently repressive carbon substrates
Sarah-Maria Fendt, Uwe Sauer
BMC Syst Biol. 2010; 4: 12. Published online 2010 February 18. doi: 10.1186/1752-0509-4-12
PMCID:
PMC2847992
Abstract Full Text PDF–550K Supplementary Material
Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks
João F. Matias Rodrigues, Andreas Wagner
PLoS Comput Biol. 2009 December; 5(12): e1000613. Published online 2009 December 18. doi: 10.1371/journal.pcbi.1000613
PMCID:
PMC2785887
Abstract Full Text PDF–785K Supplementary Material
A Genome-Scale Metabolic Model of Arabidopsis and Some of Its Properties
Mark G. Poolman, Laurent Miguet, Lee J. Sweetlove, David A. Fell
Plant Physiol. 2009 November; 151(3): 1570–1581. doi: 10.1104/pp.109.141267
PMCID:
PMC2773075
Abstract Full Text PDF–809K Supplementary Material
Evolutionary constraints permeate large metabolic networks
Andreas Wagner
BMC Evol Biol. 2009; 9: 231. Published online 2009 September 11. doi: 10.1186/1471-2148-9-231
PMCID:
PMC2753571
Abstract Full Text PDF–1.9M
Systems-Level Engineering of Nonfermentative Metabolism in Yeast
Caleb J. Kennedy, Patrick M. Boyle, Zeev Waks, Pamela A. Silver
Genetics. 2009 September; 183(1): 385–397. doi: 10.1534/genetics.109.105254
PMCID:
PMC2746161
Abstract Full Text PDF–2.1M
Understanding the Adaptive Growth Strategy of Lactobacillus plantarum by In Silico Optimisation
Bas Teusink, Anne Wiersma, Leo Jacobs, Richard A. Notebaart, Eddy J. Smid
PLoS Comput Biol. 2009 June; 5(6): e1000410. Published online 2009 June 12. doi: 10.1371/journal.pcbi.1000410
PMCID:
PMC2690837
Abstract Full Text PDF–536K Supplementary Material
Abundant Indispensable Redundancies in Cellular Metabolic Networks
Zhi Wang, Jianzhi Zhang
Genome Biol Evol. 2009; 1: 23–33. Published online 2009 April 30. doi: 10.1093/gbe/evp002
PMCID:
PMC2817398
Abstract Full Text PDF–474K Supplementary Material
Fault Tolerance in Protein Interaction Networks: Stable Bipartite Subgraphs and Redundant Pathways
Arthur Brady, Kyle Maxwell, Noah Daniels, Lenore J. Cowen
PLoS ONE. 2009; 4(4): e5364. Published online 2009 April 28. doi: 10.1371/journal.pone.0005364
PMCID:
PMC2670499
Abstract Full Text PDF–360K
Comparison of Quantitative Metabolite Imaging Tools and Carbon-13 Techniques for Fluxomics
Totte Niittylae, Bhavna Chaudhuri, Uwe Sauer, Wolf B. Frommer
Methods Mol Biol. Author manuscript; available in PMC 2010 December 10.
Published in final edited form as: Methods Mol Biol. 2009; 553: 355–372. doi: 10.1007/978-1-60327-563-7_19
PMCID:
PMC3000467
Abstract Full Text PDF–351K
Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation
Kevin Hannay, Edward M Marcotte, Christine Vogel
BMC Genomics. 2008; 9: 609. Published online 2008 December 16. doi: 10.1186/1471-2164-9-609
PMCID:
PMC2627895
Abstract Full Text PDF–1.7M Supplementary Material
The integrated analysis of metabolic and protein interaction networks reveals novel molecular organizing principles
Pawel Durek, Dirk Walther
BMC Syst Biol. 2008; 2: 100. Published online 2008 November 25. doi: 10.1186/1752-0509-2-100
PMCID:
PMC2607255
Abstract Full Text PDF–1.1M Supplementary Material
Metabolic Network Fluxes in Heterotrophic Arabidopsis Cells: Stability of the Flux Distribution under Different Oxygenation Conditions
Thomas C.R. Williams, Laurent Miguet, Shyam K. Masakapalli, Nicholas J. Kruger, Lee J. Sweetlove, R. George Ratcliffe
Plant Physiol. 2008 October; 148(2): 704–718. doi: 10.1104/pp.108.125195
PMCID:
PMC2556809
Abstract Full Text PDF–591K Supplementary Material
Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions
Evan S Snitkin, Aimée M Dudley, Daniel M Janse, Kaisheen Wong, George M Church, Daniel Segrè
Genome Biol. 2008; 9(9): R140. Published online 2008 September 22. doi: 10.1186/gb-2008-9-9-r140
PMCID:
PMC2592718
Abstract Full Text PDF–692K Supplementary Material
The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism
Intawat Nookaew, Michael C Jewett, Asawin Meechai, Chinae Thammarongtham, Kobkul Laoteng, Supapon Cheevadhanarak, Jens Nielsen, Sakarindr Bhumiratana
BMC Syst Biol. 2008; 2: 71. Published online 2008 August 7. doi: 10.1186/1752-0509-2-71
PMCID:
PMC2542360
Abstract Full Text PDF–1.5M Supplementary Material
Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A
Paula Jouhten, Eija Rintala, Anne Huuskonen, Anu Tamminen, Mervi Toivari, Marilyn Wiebe, Laura Ruohonen, Merja Penttilä, Hannu Maaheimo
BMC Syst Biol. 2008; 2: 60. Published online 2008 July 9. doi: 10.1186/1752-0509-2-60
PMCID:
PMC2507709
Abstract Full Text PDF–491K Supplementary Material
An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments
Ari Rantanen, Juho Rousu, Paula Jouhten, Nicola Zamboni, Hannu Maaheimo, Esko Ukkonen
BMC Bioinformatics. 2008; 9: 266. Published online 2008 June 6. doi: 10.1186/1471-2105-9-266
PMCID:
PMC2430715
Abstract Full Text PDF–529K Supplementary Material
Role of Duplicate Genes in Robustness against Deleterious Human Mutations
Tzu-Lin Hsiao, Dennis Vitkup
PLoS Genet. 2008 March; 4(3): e1000014. Published online 2008 March 14. doi: 10.1371/journal.pgen.1000014
PMCID:
PMC2265532
Abstract Full Text PDF–182K Supplementary Material
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