Optimization of multi-omic genome-scale models : methodologies, hands-on tutorial, and perspectives / Supreeta Vijayakumar, Max Conway, Pietro Li o, and Claudio Angione. Analyzing and designing cell factories with OptFlux / Paulo Vilaca, Paulo Maia, Hugo Giesteira, Isabel Rocha, and Miguel Rocha -- MONGOOSE rational arithmetic toolbox / Christopher Le and Leonid Chindelevitch -- FASTCORE family : for the fast reconstruction of compact context-specific metabolic networks models / Maria Pires Pacheco and Thomas Sauter -- Reconstruction and analysis of central metabolism in microbes / Janaka N. Edirisinghe, Jose P. Faria, Nomi L. Harris, Benjamin H. Allen, and Christopher S. Henry -- Using PSAMM for the curation and analysis of genome-scale metabolic models / Keith Dufault-Thompson, Jon Lund Steffensen, and Ying Zhang -- Integration of comparative genomics with genome-scale metabolic modeling to investigate strain-specific phenotypical differences / Jonathan Monk and Emanuele Bosi -- Template-assisted metabolic reconstruction and assembly of hybrid bacterial models / Tiziano Vignolini, Alessio Mengoni, and Marco Fondi -- Integrated host-pathogen metabolic reconstructions / Anu Raghunathan and Neema Jamshidi -- Metabolic model reconstruction and analysis of an artificial microbial ecosystem / Chao Ye, Nan Xu, Xiulai Chen, and Liming Liu -- RNA sequencing and analysis in microorganisms for metabolic network reconstruction / Eva Pinatel and Clelia Peano -- Differential proteomics based on 2D-difference in-gel electrophoresis and tandem mass spectrometry for the elucidation of biological processes in antibiotic-producer bacterial strains / Giuseppe Gallo and Andrea Scaloni -- Techniques for large-scale bacterial genome manipulation and characterization of the mutants with respect to in silico metabolic reconstructions / George C. diCenzo and Turlough M. Finan -- Computational prediction of synthetic lethals in genome-scale metabolic models using fast-SL / Karthik Raman, Aditya Pratapa, Omkar Mohite, and Shankar Balachandran -- Coupling fluxes, enzymes, and regulation in genome-scale metabolic models / Paul A. Jensen -- Dynamic flux balance analysis using DFBAlab / Jose Alberto Gomez and Paul I. Barton -- Designing optimized production hosts by metabolic modeling / Christian Jungreuthmayer, Matthias P. Gerstl, David A. Pena Navarro, Michael Hanscho, David E. Ruckerbauer, and J€urgen Zanghellini -- Optimization of multi-omic genome-scale models : methodologies, hands-on tutorial, and perspectives / Supreeta Vijayakumar, Max Conway, Pietro Li o, and Claudio Angione.
Summary:
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.
This resource is supported by the Institute of Museum and Library Services under the provisions of the Library Services and Technology Act as administered by State Library of Iowa.