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Metabolic Network Reconstruction and Modeling By Marco Fondi

Metabolic Network Reconstruction and Modeling by Marco Fondi

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Metabolic Network Reconstruction and Modeling Summary

Metabolic Network Reconstruction and Modeling: Methods and Protocols by Marco Fondi

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, Metabolic Network 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.

About Marco Fondi

Marco Fondi
Department of Biology
University of Florence
Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy

Table of Contents

Preface...Table of Contents...Contributing Authors...
1. Reconstructing High-Quality Large-Scale Metabolic Models with merlinOscar Dias, Miguel Rocha, Eugenio Campos Ferreira, and Isabel Rocha
2. Analyzing and Designing Cell Factories with OptFluxPaulo Vilaca, Paulo Maia, Hugo Giesteira, Isabel Rocha, and Miguel Rocha
3. The MONGOOSE Rational Arithmetic ToolboxChristopher Le and Leonid Chindelevitch
4. The FASTCORE Family: For the Fast Reconstruction of Compact Context-Specific Metabolic Networks ModelsMaria Pires Pacheco and Thomas Sauter
5. Reconstruction and Analysis of Central Metabolism in MicrobesJanaka N. Edirisinghe, Jose P. Faria, Nomi L. Harris, Benjamin H. Allen, and Christopher S. Henry
6. Using PSAMM for the Curation and Analysis of Genome-Scale Metabolic ModelsKeith Dufault-Thompson, Jon Lund Steffensen, and Ying Zhang
7. Integration of Comparative Genomics with Genome-Scale Metabolic Modeling to Investigate Strain-Specific Phenotypical DifferencesJonathan Monk and Emanuele Bosi
8. Temple-Assisted Metabolic Reconstruction and Assembly of Hybrid Bacterial ModelsTiziano Vignolini, Alessia Mengoni, and Marco Fondi
9. Integrated Host-Pathogen Metabolic ReconstructionAnu Raghunathan and Neema Jamshidi
10. Metabloic Model Reconstruction and Analysis of an Artificial Microbial EcosystemChao Ye, Nan Xu, Xiulai Chen, and Liming Liu
11. RNA Sequencing and Analysis in Microorganisms for Metabolic Network ReconstructionEva Pinatel and Clelia Peano
12. Differential Proteomics Based on 2D-Difference In-Gel Electrophoresis and Tandem Mass Spectrometry for the Elucidation of Biological Processes in Antibiotic-Producer Bacterial StrainsGiuseppe Gallo and Andrea Scaloni
13. Techniques for Large-Scale Bacterial Genome Manipulation and Characterization of the Mutants with respect to In Silico Metabolic ReconstructionsGeorge C. diCenzo and Turlough M. Finan
14. Computational Prediction of Synthetic Lethals in Genome-Scale Metabolic Models using Fast-SLKarthik Raman, Aditya Pratapa, Omkar Mohite, and Shankar Balachandran
15. Coupling Fluxes, Enzymes, and Regulation in Genome-Scale Metabolic ModelsPaul A. Jensen
16. Dynamic Flux Balance Analysis using DFBAlabJose Alberto Gomez and Paul I. Barton
17. Designing Optimized Production Hosts by Metabolic ModelingChristian Jungreuthmayer, Matthias P. Gerstl, David A. Pena Navarro, Michael Hanscho, David E. Ruckerbauer, and Jurgen Zanghellini
18. Optimization of Multi-Omic Genome-Scale Models: Methodologies, Hands-On Tutorial and PerspectivesSupreeta Vijayakumar, Max Conway, Pietro Lio, and Claudio Angione

Additional information

Metabolic Network Reconstruction and Modeling: Methods and Protocols by Marco Fondi
Humana Press Inc.
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