Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal
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Martin J. Lercher | Balázs Papp | Daniel Hartleb | Claus Fritzemeier | Balázs Szappanos | M. Lercher | B. Papp | Balázs Szappanos | C. Fritzemeier | Daniel Hartleb | Balázs Papp
[1] S. Henry,et al. Revising the Representation of Fatty Acid, Glycerolipid, and Glycerophospholipid Metabolism in the Consensus Model of Yeast Metabolism. , 2013, Industrial biotechnology.
[2] Matthias Heinemann,et al. Systematic assignment of thermodynamic constraints in metabolic network models , 2006, BMC Bioinformatics.
[3] V. Hatzimanikatis,et al. Thermodynamics-based metabolic flux analysis. , 2007, Biophysical journal.
[4] Andreas Wagner,et al. A latent capacity for evolutionary innovation through exaptation in metabolic systems , 2013, Nature.
[5] Neil Swainston,et al. Recon 2.2: from reconstruction to model of human metabolism , 2016, Metabolomics.
[6] J. Russell. The Energy Spilling Reactions of Bacteria and Other Organisms , 2007, Journal of Molecular Microbiology and Biotechnology.
[7] Martin J. Lercher,et al. sybil – Efficient constraint-based modelling in R , 2013, BMC Systems Biology.
[8] Daniel A Beard,et al. Extreme pathways and Kirchhoff's second law. , 2002, Biophysical journal.
[9] Bernhard O Palsson,et al. Extreme pathway analysis of human red blood cell metabolism. , 2002, Biophysical journal.
[10] C. Pál,et al. Adaptive evolution of complex innovations through stepwise metabolic niche expansion , 2016, Nature communications.
[11] Bernhard O. Palsson,et al. BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions , 2010, BMC Bioinformatics.
[12] H. Qian,et al. Thermodynamic constraints for biochemical networks. , 2004, Journal of theoretical biology.
[13] Andreas Hoppe,et al. Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks , 2007, BMC Systems Biology.
[14] Florian Jarre,et al. CycleFreeFlux: efficient removal of thermodynamically infeasible loops from flux distributions , 2015, Bioinform..
[15] Bernhard Ø Palsson,et al. Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints. , 2006, Biophysical journal.
[16] Andreas Wagner,et al. Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks , 2009, PLoS Comput. Biol..
[17] Lake-Ee Quek,et al. Reducing Recon 2 for steady-state flux analysis of HEK cell culture. , 2014, Journal of biotechnology.
[18] Matteo Mori,et al. Counting and Correcting Thermodynamically Infeasible Flux Cycles in Genome-Scale Metabolic Networks , 2013, Metabolites.
[19] Fangfang Xia,et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) , 2013, Nucleic Acids Res..
[20] H. Qian,et al. Energy balance for analysis of complex metabolic networks. , 2002, Biophysical journal.
[21] Rick L. Stevens,et al. High-throughput generation, optimization and analysis of genome-scale metabolic models , 2010, Nature Biotechnology.
[22] Florian Jarre,et al. Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets , 2016, PLoS Comput. Biol..
[23] J. Weber,et al. Accelerated substrate cycling: a new energy-wasting role for leptin in vivo. , 2002, American journal of physiology. Endocrinology and metabolism.
[24] B. Palsson,et al. Elimination of thermodynamically infeasible loops in steady-state metabolic models. , 2011, Biophysical journal.
[25] Edward J. O'Brien,et al. Using Genome-scale Models to Predict Biological Capabilities , 2015, Cell.
[26] Alexander Bockmayr,et al. Fast thermodynamically constrained flux variability analysis , 2013, Bioinform..
[27] B. Palsson,et al. A protocol for generating a high-quality genome-scale metabolic reconstruction , 2010 .
[28] R. Overbeek,et al. Automated genome annotation and metabolic model reconstruction in the SEED and Model SEED. , 2013, Methods in molecular biology.
[29] Soha Hassoun,et al. Discovery of substrate cycles in large scale metabolic networks using hierarchical modularity , 2015, BMC Systems Biology.
[30] R. Heinrich,et al. Metabolic Pathway Analysis: Basic Concepts and Scientific Applications in the Post‐genomic Era , 1999, Biotechnology progress.
[31] R. Nigam,et al. Second Law of Thermodynamics Applied to Metabolic Networks , 2003 .
[32] Thomas Bernard,et al. MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks , 2013, Bioinform..
[33] Joshua A. Lerman,et al. Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments , 2013, Proceedings of the National Academy of Sciences.
[34] Andreas Wagner,et al. Phenotypic innovation through recombination in genome-scale metabolic networks , 2016, Proceedings of the Royal Society B: Biological Sciences.
[35] Adam M. Feist,et al. A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011 , 2011, Molecular systems biology.