Navid A. (ed.) Microbial systems biology: methods and protocols

New York: Humana Press, 2021. — 391 p.Although we have advanced the field of microbial systems biology significantly during the last decade, our foray into analyzing exciting and evermore complex systems such as gut microbiome or autotroph-bacterial interactions requires examining all available data at our disposal. Systems biology analyses today usually use multiple types of omics data for each study. This of course is a pleasant byproduct of the revolutionary advances in technologies that allow rapid and relatively cheap collection of system-level data.
To combine and analyze these data requires the use of increasingly complex computational models and state-of-the-art bioinformatics tools. Fortunately, the field of computational biology has kept up with technological advances. New and exciting tools are being developed that allow for detailed analyses of disparate types of omics data. The results of these studies can then be used to quickly generate system-level models and conduct analyses that at times can only be achieved in silico.
In this edition of the book I have tried to introduce the reader to powerful and easy-to-use computational biology databases and tools (e.g., MetaFlux, Kbase, COBRA toolbox) that can significantly help researchers examine their system-level data. There are also chapters that deal with annotating genomes and using the collected information to conduct network analyses of the system. The book also introduces the reader to a number of
specialized analytic tools (e.g., NanoSIP and PAMMS) that can significantly improve and add to the data that is available for systems biology studies. It is my hope that the information provided by the authors will inspire researchers to explore innovative analytical methods, examine their problem from multiple angles, and generate novel hypotheses that will lead to new scientific discoveries.