FASIMU: flexible software for flux-balance computation series in large metabolic networks
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Andreas Hoppe | Hermann-Georg Holzhütter | Christoph Gille | Andreas Gerasch | Sabrina Hoffmann | C. Gille | H. Holzhütter | A. Hoppe | Sabrina Hoffmann | A. Gerasch
[1] Hiroaki Kitano,et al. CellDesigner: a process diagram editor for gene-regulatory and biochemical networks , 2003 .
[2] Andreas Hoppe,et al. Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis , 2010, BMC Systems Biology.
[3] A. Burgard,et al. Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions. , 2001, Biotechnology and bioengineering.
[4] Matthias König,et al. Fluxviz - Cytoscape plug-in for visualization of flux distributions in networks. , 2010, Genome informatics. International Conference on Genome Informatics.
[5] Markus J. Herrgård,et al. Network-based prediction of human tissue-specific metabolism , 2008, Nature Biotechnology.
[6] Hiroaki Kitano,et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..
[7] Steffen Klamt,et al. Structural and functional analysis of cellular networks with CellNetAnalyzer , 2007, BMC Systems Biology.
[8] G. Stephanopoulos,et al. Metabolic flux analysis: a powerful tool for monitoring tissue function. , 1999, Tissue engineering.
[9] C. Gille,et al. HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology , 2010, Molecular systems biology.
[10] Eiji Oki,et al. GLPK (GNU Linear Programming Kit) , 2012 .
[11] Michael Kaufmann,et al. yFiles - Visualization and Automatic Layout of Graphs , 2001, Graph Drawing Software.
[12] Karthik Raman,et al. A Systems Biology Tool for Flux Analysis of Metabolic Pathways , 2008 .
[13] Miguel Rocha,et al. OptFlux: an open-source software platform for in silico metabolic engineering , 2010, BMC Systems Biology.
[14] James A. Eddy,et al. Accomplishments in genome‐scale in silico modeling for industrial and medical biotechnology , 2009, Biotechnology journal.
[15] Nicola Zamboni,et al. anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data , 2008, BMC Bioinformatics.
[16] B. Palsson,et al. Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states. , 2004, Genome research.
[17] Matthias Heinemann,et al. Systematic assignment of thermodynamic constraints in metabolic network models , 2006, BMC Bioinformatics.
[18] Ronan M. T. Fleming,et al. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 , 2007, Nature Protocols.
[19] Bernhard O. Palsson,et al. Expa: a Program for Calculating Extreme Pathways in Biochemical Reaction Networks , 2005, Bioinform..
[20] Christina Backes,et al. BN++ - A Biological Information System , 2006, J. Integr. Bioinform..
[21] U. Sauer,et al. Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli , 2007, Molecular systems biology.
[22] E. Ruppin,et al. Regulatory on/off minimization of metabolic flux changes after genetic perturbations. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[23] John Boyle,et al. Cytoscape: a community-based framework for network modeling. , 2009, Methods in molecular biology.
[24] Andreas Wagner,et al. The Systems Biology Research Tool: evolvable open-source software , 2008, BMC Systems Biology.
[25] BMC Bioinformatics , 2005 .
[26] David A. Fell,et al. Detection of stoichiometric inconsistencies in biomolecular models , 2008, Bioinform..
[27] H. Holzhütter. The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks. , 2004, European journal of biochemistry.
[28] H. Holzhütter. The generalized flux-minimization method and its application to metabolic networks affected by enzyme deficiencies. , 2006, Bio Systems.
[29] Stefan Schuster,et al. Systems biology Metatool 5.0: fast and flexible elementary modes analysis , 2006 .
[30] G. Church,et al. Analysis of optimality in natural and perturbed metabolic networks , 2002 .
[31] F. Llaneras,et al. An interval approach for dealing with flux distributions and elementary modes activity patterns. , 2007, Journal of theoretical biology.
[32] Hiroaki Kitano,et al. Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration. , 2003, Omics : a journal of integrative biology.
[33] Juan Carlos Nuño,et al. METATOOL: for studying metabolic networks , 1999, Bioinform..
[34] Adam M. Feist,et al. Reconstruction of biochemical networks in microorganisms , 2009, Nature Reviews Microbiology.
[35] D. Fell,et al. Is maximization of molar yield in metabolic networks favoured by evolution? , 2008, Journal of theoretical biology.
[36] Ronan M. T. Fleming,et al. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 , 2007, Nature Protocols.
[37] 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.
[38] B. Palsson,et al. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data , 2001, Nature Biotechnology.
[39] H. Holzhütter,et al. Pruning genome-scale metabolic models to consistent ad functionem networks. , 2007, Genome informatics. International Conference on Genome Informatics.
[40] Hermann-Georg Holzhütter,et al. METANNOGEN: compiling features of biochemical reactions needed for the reconstruction of metabolic networks , 2007, BMC Syst. Biol..
[41] Patrick Lincoln,et al. BioSPICE: access to the most current computational tools for biologists. , 2003, Omics : a journal of integrative biology.