This volume addresses the latest state-of-the-art systems biology-oriented approaches that--driven by big data and bioinformatics--are utilized by Computational Systems Biology, an interdisciplinary field that bridges experimental tools with computational tools to tackle complex questions at the frontiers of knowledge in medicine and biotechnology. The chapters in this book are organized into six parts: systems biology of the genome, epigenome, and redox proteome; metabolic networks; aging and longevity; systems biology of diseases; spatiotemporal patterns of rhythms, morphogenesis, and complex dynamics; and genome scale metabolic modeling in biotechnology. In every chapter, readers will find varied methodological approaches applied at different levels, from molecular, cellular, organ to organisms, genome to phenome, and health and disease. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics; criteria utilized for applying specific methodologies; lists of the necessary materials, reagents, software, databases, algorithms, mathematical models, and dedicated analytical procedures; step-by-step, readily reproducible laboratory, bioinformatics, and computational protocols all delivered in didactic and clear style and abundantly illustrated with express case studies and tutorials; and tips on troubleshooting and advice for achieving reproducibility while avoiding mistakes and misinterpretations. The overarching goal driving this volume is to excite the expert and stimulate the newcomer to the field of Computational Systems Biology.Cutting-edge and authoritative, Computational Systems Biology in Medicine and Biotechnology: Methods and Protocols is a valuable resource for pre- and post-graduate students in medicine and biotechnology, and in diverse areas ranging from microbiology to cellular and organismal biology, as well as computational and experimental biologists, and researchers interested in utilizing comprehensive systems biology oriented methods.
Preface...Dedication...Table of Contents...Contributing Authors...Introduction1. Computational Systems Biology and Artificial IntelligenceMiguel A. AonPart I Systems Biology of the Genome, Epigenome, and Redox Proteome2. Bioinformatic Analysis of CircRNA from RNA-seq DatasetsKyle R. Cochran, Myriam Gorospe, and Supriyo De3. Single-Cell Analysis of the Transcriptome and EpigenomeKrystyna Mazan-Mamczarz, Jisu Ha, Supriyo De, and Payel Sen4. Automatic Assignment, Quantitation, and Biological Annotation of Redox Proteomics Datasets with ProteoSushiSjoerd van der Post, Robert W. Seymour, Arshag D. Mooradian, and Jason M. HeldPart II Systems Biology of Metabolic Networks5. A Practical Guide to Integrating Multimodal Machine Learning and Metabolic ModelingSupreeta Vijayakumar, Giuseppe Magazzu, Pradip Moon, Annalisa Occhipinti, and Claudio Angione6. MITODYN: An Open Source Software for Quantitative Modeling of Mitochondrial and Cellular Energy Metabolic Flux Dynamics in Health and DiseaseVitaly A. Selivanov, Olga A. Zagubnaya, Carles Foguet, Yaroslav R. Nartsissov, and Marta Cascante 7. Integrated Multi-Omics, Bioinformatics, and Computational Modeling Approaches to Central Metabolism in OrgansSonia Cortassa, Pierre Villon, Steven J. Sollott, and Miguel A. AonPart III Systems Biology of Aging and Longevity8. Understanding the Human Aging Proteome using Epidemiological ModelsCeereena Ubaida-Mohien, Ruin Moaddel, Zenobia Moore, Pei-Lun Kuo, Ravi Tharakan, Toshiko Tanaka, and Luigi Ferrucci9. Unraveling Pathways of Health and Lifespan with Integrated Multi-Omics ApproachesMiguel A. Aon, Michel Bernier, and Rafael de CaboPart IV Systems Biology of Disease10. UT-Heart: A Finite Element Model Designed for the Multi-Scale and Multi-Physics Integration of Our Knowledge on the Human HeartSeiryo Sugiura, Jun-ichi Okada, Takumi Washio, and Toshiaki Hisada11. Multiscale Modeling of the Mitochondrial Origin of Cardiac Reentrant and Fibrillatory ArrhythmiasSoroosh Sohljoo, Seulhee Kim, Gernot Plank, Brian O'Rourke, and Lufang Zhou12. Automated Quantification and Network Analysis of Redox Dynamics in Neuronal MitochondriaFelix T. Kurz and Michael O. BreckwoldtPart V Systems Biology of Rhythms, Morphogenesis, and Complex Dynamics13. Computational Approaches and Tools as Applied to the Study of Rhythms and Chaos in BiologyAna Georgina Flesia, Paula Sofia Nieto, Miguel A. Aon, Jackelyn Melissa Kembro14. Computational Systems Biology of MorphogenesisJason Ko, Reza Mousavi, and Daniel Lobo15. Agent-Based Modeling of Complex Molecular SystemsMike Holcombe and Eva QwarnstromPart VI Systems Biology in Biotechnology16. Metabolic Modeling of Wine Fermentation at Genome ScalesSebastian N. Mendoza, Pedro Saa, Bas Teusink, and Eduardo Agosin 17. Modeling Approaches to Microbial MetabolismAndreas Kremling