Scalable metabolic pathway analysis
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[1] F. Turroni,et al. Unveiling the gut microbiota composition and functionality associated with constipation through metagenomic analyses , 2017, Scientific Reports.
[2] Daniel Machado,et al. Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism , 2014, PLoS Comput. Biol..
[3] Karsten Zengler,et al. Modelling approaches for studying the microbiome , 2019, Nature Microbiology.
[4] B. Palsson,et al. Elimination of thermodynamically infeasible loops in steady-state metabolic models. , 2011, Biophysical journal.
[5] B. Palsson,et al. Expanded Metabolic Reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an In Silico Genome-Scale Characterization of Single- and Double-Deletion Mutants , 2005, Journal of bacteriology.
[6] Thomas Bernard,et al. MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks , 2013, Bioinform..
[7] A. Burgard,et al. Minimal Reaction Sets for Escherichia coli Metabolism under Different Growth Requirements and Uptake Environments , 2001, Biotechnology progress.
[8] Jens Nielsen,et al. The gut microbiota modulates host amino acid and glutathione metabolism in mice , 2015 .
[9] C. Jungreuthmayer,et al. Toward Genome‐Scale Metabolic Pathway Analysis , 2016 .
[10] Eugénio C. Ferreira,et al. Random sampling of elementary flux modes in large-scale metabolic networks , 2012, Bioinform..
[11] Ronan M. T. Fleming,et al. Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota , 2016, Nature Biotechnology.
[12] T. Preston,et al. Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism , 2016, Gut microbes.
[13] Tom M. Conrad,et al. Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models , 2010, Molecular systems biology.
[14] Philip Miller,et al. BiGG Models: A platform for integrating, standardizing and sharing genome-scale models , 2015, Nucleic Acids Res..
[15] Lixin Zhu,et al. Characterization of gut microbiomes in nonalcoholic steatohepatitis (NASH) patients: A connection between endogenous alcohol and NASH , 2013, Hepatology.
[16] Angel Rubio,et al. Computing the shortest elementary flux modes in genome-scale metabolic networks , 2009, Bioinform..
[17] Avlant Nilsson,et al. Recon3D: A Resource Enabling A Three-Dimensional View of Gene Variation in Human Metabolism , 2018, Nature Biotechnology.
[18] S. Schuster,et al. Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns. , 2009, Genome research.
[20] Iain G. Johnston,et al. The Essential Genome of Escherichia coli K-12 , 2017, mBio.
[21] Adam M. Feist,et al. The biomass objective function. , 2010, Current opinion in microbiology.
[22] Doraiswami Ramkrishna,et al. Sequential computation of elementary modes and minimal cut sets in genome‐scale metabolic networks using alternate integer linear programming , 2017, Bioinform..
[23] Jens Nielsen,et al. Gut microbiota dysbiosis is associated with malnutrition and reduced plasma amino acid levels: Lessons from genome-scale metabolic modeling. , 2018, Metabolic engineering.
[24] J. Stelling,et al. Model-based integration of genomics and metabolomics reveals SNP functionality in Mycobacterium tuberculosis , 2019, Proceedings of the National Academy of Sciences of the United States of America.
[25] Leen Stougie,et al. Enumeration of minimal stoichiometric precursor sets in metabolic networks , 2016, Algorithms for Molecular Biology.
[26] M. Sabater,et al. Elevated circulating levels of succinate in human obesity are linked to specific gut microbiota , 2018, The ISME Journal.
[27] Joshua A. Lerman,et al. COBRApy: COnstraints-Based Reconstruction and Analysis for Python , 2013, BMC Systems Biology.
[28] Daniel C. Zielinski,et al. A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. , 2016, Cell systems.
[29] B. Palsson,et al. Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use , 1994, Bio/Technology.
[30] J. Stelling,et al. Microbial network disturbances in relapsing refractory Crohn’s disease , 2019, Nature Medicine.
[31] Leen Stougie,et al. Modes and cuts in metabolic networks: Complexity and algorithms , 2009, Biosyst..
[32] Piotr Gawron,et al. The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease , 2018, bioRxiv.
[33] Jan Schellenberger,et al. Use of Randomized Sampling for Analysis of Metabolic Networks* , 2009, Journal of Biological Chemistry.
[34] Kristopher A. Hunt,et al. Complete enumeration of elementary flux modes through scalable demand-based subnetwork definition , 2014, Bioinform..
[35] Bernhard O. Palsson,et al. Connecting Extracellular Metabolomic Measurements to Intracellular Flux States in Yeast , 2022 .
[36] Francisco J. Planes,et al. Direct calculation of elementary flux modes satisfying several biological constraints in genome-scale metabolic networks , 2014, Bioinform..
[37] S. Klamt,et al. EColiCore2: a reference network model of the central metabolism of Escherichia coli and relationships to its genome-scale parent model , 2017, Scientific Reports.
[38] Leen Stougie,et al. Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks , 2012, Bioinform..
[39] Steffen Klamt,et al. Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks , 2014, PLoS Comput. Biol..
[40] Ines Thiele,et al. Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework , 2015, Gut microbes.
[41] Adam M. Feist,et al. iML1515, a knowledgebase that computes Escherichia coli traits , 2017, Nature Biotechnology.
[42] J. Stelling,et al. Combinatorial Complexity of Pathway Analysis in Metabolic Networks , 2004, Molecular Biology Reports.
[43] V. de Crécy-Lagard,et al. Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes , 2015, Front. Genet..
[44] R. Urbanczik. Enumerating constrained elementary flux vectors of metabolic networks. , 2007, IET systems biology.
[45] Jörg Stelling,et al. Large-scale computation of elementary flux modes with bit pattern trees , 2008, Bioinform..
[46] Xiaomin Su,et al. Lactobacillus maintains healthy gut mucosa by producing L-Ornithine , 2019, Communications Biology.
[47] U. Sauer,et al. A Novel Metabolic Cycle Catalyzes Glucose Oxidation and Anaplerosis in Hungry Escherichia coli* , 2003, Journal of Biological Chemistry.
[48] R. Mahadevan,et al. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. , 2003, Metabolic engineering.
[49] Adam M. Feist,et al. A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011 , 2011, Molecular systems biology.
[50] S. Peterson,et al. B-Vitamin Sharing Promotes Stability of Gut Microbial Communities , 2019, Front. Microbiol..
[51] Sebastián N. Mendoza,et al. A systematic assessment of current genome-scale metabolic reconstruction tools , 2019, Genome Biology.
[52] Steffen Klamt,et al. From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints , 2017, PLoS Comput. Biol..
[53] Frédéric Cazals,et al. A note on the problem of reporting maximal cliques , 2008, Theor. Comput. Sci..
[54] Zhen Xie,et al. Pooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance , 2018, Nature Communications.
[55] F. Rousset,et al. Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors , 2018, bioRxiv.
[56] H. Mori,et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection , 2006, Molecular systems biology.
[57] Bernhard O. Palsson,et al. Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways , 2015, PLoS Comput. Biol..
[58] Jörg Stelling,et al. System-Level Insights into Yeast Metabolism by Thermodynamic Analysis of Elementary Flux Modes , 2012, PLoS Comput. Biol..
[59] Norman Pavelka,et al. Emerging and evolving concepts in gene essentiality , 2017, Nature Reviews Genetics.
[60] David E. Ruckerbauer,et al. Metabolomics integrated elementary flux mode analysis in large metabolic networks , 2015, Scientific Reports.
[61] Adam M. Feist,et al. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information , 2007, Molecular systems biology.
[62] Rajagopalan Srinivasan,et al. An efficient graph theory based method to identify every minimal reaction set in a metabolic network , 2014, BMC Systems Biology.
[63] Jörg Stelling,et al. Genome-scale metabolic networks in time and space , 2018 .
[64] Christian Jungreuthmayer,et al. regEfmtool: Speeding up elementary flux mode calculation using transcriptional regulatory rules in the form of three-state logic , 2013, Biosyst..