Metabolic Network Reconstruction and Modeling

Methods and Protocols

Buch | Hardcover

410 Seiten

2017 | 1st ed. 2018
Humana Press Inc. (Verlag)
978-1-4939-7527-3 (ISBN)

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This volume looks at the latest methodologies used to study cellular metabolism with in silico approaches. The chapters in this book are divided into 3 parts: part I discusses tools and methods used for metabolic reconstructions and basic constraint-based metabolic modeling (CBMM); Part II explores protocols for the generation of experimental data for metabolic reconstruction and modeling, including transcriptomics, proteomics, and mutant generations; and Part III cover advanced techniques for quantitative modeling of cellular metabolism, including dynamic Flux Balance Analysis and multi-objective optimization. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and thorough, MetabolicNetwork Reconstruction and Modeling: Methods and Protocols is a valuable resource for qualified investigators studying cellular metabolism, and novice researchers who want to start working with CBMM.

Marco Fondi Department of Biology University of Florence Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy Email: marco.fondi@unifi.it

Reconstructing High-Quality Large-Scale Metabolic Models with merlin.- Analyzing and Designing Cell Factories with OptFlux.- The MONGOOSE Rational Arithmetic Toolbox.- The FASTCORE Family: For the Fast Reconstruction of Compact Context-Specific Metabolic Networks Models.- Reconstruction and Analysis of Central Metabolism in Microbes.- Using PSAMM for the Curation and Analysis of Genome-Scale Metabolic Models.- Integration of Comparative Genomics with Genome-Scale Metabolic Modeling to Investigate Strain-Specific Phenotypical Differences.- Temple-Assisted Metabolic Reconstruction and Assembly of Hybrid Bacterial Models.- Integrated Host-Pathogen Metabolic Reconstruction.- Metabloic Model Reconstruction and Analysis of an Artificial Microbial Ecosystem.- RNA Sequencing and Analysis in Microorganisms for Metabolic Network Reconstruction.- Differential Proteomics Based on 2D-Difference In-Gel Electrophoresis and Tandem Mass Spectrometry for the Elucidation of Biological Processes in Antibiotic-Producer Bacterial Strains.- Techniques for Large-Scale Bacterial Genome Manipulation and Characterization of the Mutants with Respect to In Silico Metabolic Reconstructions.- Computational Prediction of Synthetic Lethals in Genome-Scale Metabolic Models using Fast-SL.- Coupling Fluxes, Enzymes, and Regulation in Genome-Scale Metabolic Models.- Dynamic Flux Balance Analysis using DFBAlab.- Designing Optimized Production Hosts by Metabolic Modeling.- Optimization of Multi-Omic Genome-Scale Models: Methodologies, Hands-On Tutorial and Perspectives.

Erscheinungsdatum	19.01.2018
Reihe/Serie	Methods in Molecular Biology ; 1716
Zusatzinfo	92 Illustrations, color; 11 Illustrations, black and white; XI, 410 p. 103 illus., 92 illus. in color. With online files/update.
Verlagsort	Totowa, NJ
Sprache	englisch
Maße	178 x 254 mm
Themenwelt	Naturwissenschaften ► Biologie ► Mikrobiologie / Immunologie
Themenwelt	Naturwissenschaften ► Biologie ► Zellbiologie
Schlagworte	metabolic landscape • Metabolomics • Phenotype Microarray • Proteomics • Transcriptomics
ISBN-10	1-4939-7527-7 / 1493975277
ISBN-13	978-1-4939-7527-3 / 9781493975273
Zustand	Neuware