Computational Systems Biology in Medicine and Biotechnology

Methods and Protocols
1. Auflage 2022
ISBN: 978-1-0716-1830-1
Verlag: Springer

Buch, Englisch, 493 Seiten, Book w. online files / update, Format (B × H): 183 mm x 260 mm, Gewicht: 1150 g

Reihe: Methods in Molecular Biology

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. 

Zielgruppe

Professional/practitioner

Autoren/Hrsg.

Cortassa, Sonia

Aon, Miguel A.

Fachgebiete

• Naturwissenschaften Biowissenschaften Angewandte Biologie Bioinformatik
• Technische Wissenschaften Verfahrenstechnik | Chemieingenieurwesen | Biotechnologie Biotechnologie

Inhaltsverzeichnis

Preface…
Dedication…
Table of Contents…
Contributing Authors…

Introduction

1. Computational Systems Biology and Artificial Intelligence
Miguel A. Aon

Part I Systems Biology of the Genome, Epigenome, and Redox Proteome

2. Bioinformatic Analysis of CircRNA from RNA-seq Datasets
Kyle R. Cochran, Myriam Gorospe, and Supriyo De

3. Single-Cell Analysis of the Transcriptome and Epigenome
Krystyna Mazan-Mamczarz, Jisu Ha, Supriyo De, and Payel Sen

4. Automatic Assignment, Quantitation, and Biological Annotation of Redox Proteomics Datasets with ProteoSushi
Sjoerd van der Post, Robert W. Seymour, Arshag D. Mooradian, and Jason M. Held

Part II Systems Biology of Metabolic Networks

5. A Practical Guide to Integrating Multimodal Machine Learning and Metabolic Modeling
Supreeta Vijayakumar, Giuseppe Magazzù, Pradip Moon, Annalisa Occhipinti, and Claudio Angione

6. MITODYN: An Open Source Software for Quantitative Modeling of Mitochondrial and Cellular Energy Metabolic Flux Dynamics in Health and Disease
Vitaly 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 Organs
Sonia Cortassa, Pierre Villon, Steven J. Sollott, and Miguel A. Aon

Part III Systems Biology of Aging and Longevity

8. Understanding the Human Aging Proteome using Epidemiological Models
Ceereena Ubaida-Mohien, Ruin Moaddel, Zenobia Moore, Pei-Lun Kuo, Ravi Tharakan, Toshiko Tanaka, and Luigi Ferrucci

9. Unraveling Pathways of Health and Lifespan with Integrated Multi-Omics Approaches
Miguel A. Aon, Michel Bernier, and Rafael de Cabo

Part IV Systems Biology of Disease

10. UT-Heart: A Finite Element Model Designed for the Multi-Scale and Multi-Physics Integration of Our Knowledge on the Human Heart
Seiryo Sugiura, Jun-ichi Okada, Takumi Washio, and Toshiaki Hisada

11. Multiscale Modeling of the Mitochondrial Origin of Cardiac Reentrant and Fibrillatory Arrhythmias
Soroosh Sohljoo, Seulhee Kim, Gernot Plank, Brian O’Rourke, and Lufang Zhou

12. Automated Quantification and Network Analysis of Redox Dynamics in Neuronal Mitochondria
Felix T. Kurz and Michael O. Breckwoldt

Part V Systems Biology of Rhythms, Morphogenesis, and Complex Dynamics

13. Computational Approaches and Tools as Applied to the Study of Rhythms and Chaos in Biology
Ana Georgina Flesia, Paula Sofia Nieto, Miguel A. Aon, Jackelyn Melissa Kembro

14. Computational Systems Biology of Morphogenesis
Jason Ko, Reza Mousavi, and Daniel Lobo

15. Agent-Based Modeling of Complex Molecular Systems
Mike Holcombe and Eva Qwarnstrom

Part VI Systems Biology in Biotechnology

16. Metabolic Modeling of Wine Fermentation at Genome Scales
Sebastián N. Mendoza, Pedro Saa, Bas Teusink, and Eduardo Agosin 

17. Modeling Approaches to Microbial Metabolism
Andreas Kremling