Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis
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T. Van Du Tran | Sébastien Moretti | Marco Pagni | Alix T. Coste | Sara Amorim-Vaz | Dominique Sanglard | M. Pagni | D. Sanglard | S. Moretti | A. Coste | V. D. T. Tran | Sara Amorim-Vaz
[1] Daniel J. Gaffney,et al. A survey of best practices for RNA-seq data analysis , 2016, Genome Biology.
[2] Y. Benjamini,et al. Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .
[3] Andrey Alexeyenko,et al. Network enrichment analysis: extension of gene-set enrichment analysis to gene networks , 2012, BMC Bioinformatics.
[4] Francisco J. Planes,et al. Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0. , 2017, 1710.04038.
[5] Kyoung-Jae Won,et al. Distinct macrophage populations direct inflammatory versus physiological changes in adipose tissue , 2018, Proceedings of the National Academy of Sciences.
[6] Olivier Martin,et al. MetaNetX/MNXref – reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks , 2015, Nucleic Acids Res..
[7] Pablo Tamayo,et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[8] Adam M. Feist,et al. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli , 2008, Nature Biotechnology.
[9] R. Mahadevan,et al. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. , 2003, Metabolic engineering.
[10] N. Price,et al. Genome-scale modeling for metabolic engineering , 2015, Journal of Industrial Microbiology & Biotechnology.
[11] L. W. Parks,et al. Physiological implications of sterol biosynthesis in yeast. , 1995, Annual review of microbiology.
[12] Nathan D. Price,et al. Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE , 2012, BMC Systems Biology.
[13] Pietro Lió,et al. Seeing the wood for the trees: a forest of methods for optimization and omic-network integration in metabolic modelling , 2017, Briefings Bioinform..
[14] Klaus Natter,et al. Optimization of lipid production with a genome-scale model of Yarrowia lipolytica , 2015, BMC Systems Biology.
[15] T. C. White,et al. Zinc Finger Transcription Factors Displaced SREBP Proteins as the Major Sterol Regulators during Saccharomycotina Evolution , 2014, PLoS genetics.
[16] Eytan Ruppin,et al. iMAT: an integrative metabolic analysis tool , 2010, Bioinform..
[17] Bernhard O. Palsson,et al. A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1 , 2010, BMC Systems Biology.
[18] Anne Richelle,et al. A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models. , 2017, Cell systems.
[19] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[20] Nathan D. Price,et al. Data-driven integration of genome-scale regulatory and metabolic network models , 2015, Front. Microbiol..
[21] Bernhard O. Palsson,et al. Context-Specific Metabolic Networks Are Consistent with Experiments , 2008, PLoS Comput. Biol..
[22] Min Kyung Kim,et al. Methods for integration of transcriptomic data in genome-scale metabolic models , 2014, Computational and structural biotechnology journal.
[23] Alfonso Valencia,et al. EnrichNet: network-based gene set enrichment analysis , 2012, Bioinform..
[24] Daniel Machado,et al. Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism , 2014, PLoS Comput. Biol..
[25] Nikos Vlassis,et al. Fast Reconstruction of Compact Context-Specific Metabolic Network Models , 2013, PLoS Comput. Biol..
[26] Areejit Samal,et al. Advances in the integration of transcriptional regulatory information into genome-scale metabolic models , 2016, bioRxiv.
[27] Edward J. O'Brien,et al. Using Genome-scale Models to Predict Biological Capabilities , 2015, Cell.
[28] E. Ruppin,et al. Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism , 2010, Molecular systems biology.
[29] Rodrigo Ledesma-Amaro,et al. Yarrowia lipolytica as a biotechnological chassis to produce usual and unusual fatty acids. , 2016, Progress in lipid research.
[30] C. Chothia,et al. Volume changes in protein evolution. , 1994, Journal of molecular biology.
[31] Adam M. Feist,et al. Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli , 2013, Molecular systems biology.
[32] Natapol Pornputtapong,et al. Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT , 2012, PLoS Comput. Biol..
[33] Jason A. Papin,et al. Applications of genome-scale metabolic reconstructions , 2009, Molecular systems biology.
[34] B. Palsson,et al. Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use , 1994, Bio/Technology.