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Computational Systems Biology in Medicine and Biotechnology

Methods and Protocols

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2399)

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-xiv
  2. Systems Biology of the Genome, Epigenome, and Redox Proteome

    1. Front Matter

      Pages 7-7
    2. Bioinformatic Analysis of CircRNA from RNA-seq Datasets

      • Kyle R. Cochran, Myriam Gorospe, Supriyo De
      Pages 9-19
    3. Single-Cell Analysis of the Transcriptome and Epigenome

      • Krystyna Mazan-Mamczarz, Jisu Ha, Supriyo De, Payel Sen
      Pages 21-60
    4. Automating Assignment, Quantitation, and Biological Annotation of Redox Proteomics Datasets with ProteoSushi

      • Sjoerd van der Post, Robert W. Seymour, Arshag D. Mooradian, Jason M. Held
      Pages 61-84
  3. Systems Biology of Metabolic Networks

    1. Front Matter

      Pages 85-85
    2. A Practical Guide to Integrating Multimodal Machine Learning and Metabolic Modeling

      • Supreeta Vijayakumar, Giuseppe Magazzù, Pradip Moon, Annalisa Occhipinti, Claudio Angione
      Pages 87-122
    3. 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, Marta Cascante
      Pages 123-149
    4. Integrated Multiomics, Bioinformatics, and Computational Modeling Approaches to Central Metabolism in Organs

      • Sonia Cortassa, Pierre Villon, Steven J. Sollott, Miguel A. Aon
      Pages 151-170
  4. Systems Biology of Aging and Longevity

    1. Front Matter

      Pages 171-171
    2. Understanding the Human Aging Proteome Using Epidemiological Models

      • Ceereena Ubaida-Mohien, Ruin Moaddel, Zenobia Moore, Pei-Lun Kuo, Ravi Tharakan, Toshiko Tanaka et al.
      Pages 173-192
    3. Unraveling Pathways of Health and Lifespan with Integrated Multiomics Approaches

      • Miguel A. Aon, Michel Bernier, Rafael de Cabo
      Pages 193-218
  5. Systems Biology of Disease

    1. Front Matter

      Pages 219-219
    2. Multiscale Modeling of the Mitochondrial Origin of Cardiac Reentrant and Fibrillatory Arrhythmias

      • Soroosh Solhjoo, Seulhee Kim, Gernot Plank, Brian O’Rourke, Lufang Zhou
      Pages 247-259
  6. Systems Biology of Rhythms, Morphogenesis, and Complex Dynamics

    1. Front Matter

      Pages 275-275
    2. 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
      Pages 277-341
    3. Computational Systems Biology of Morphogenesis

      • Jason M. Ko, Reza Mousavi, Daniel Lobo
      Pages 343-365

About this book

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. 



Editors and Affiliations

  • Laboratory of Cardiovascular Science, National Institute on Aging, NIH, Baltimore, USA

    Sonia Cortassa

  • Translational Gerontology Branch, Laboratory of Cardiovascular Science, National Institute on Aging, NIH, Baltimore, USA

    Miguel A. Aon

Bibliographic Information

  • Book Title: Computational Systems Biology in Medicine and Biotechnology

  • Book Subtitle: Methods and Protocols

  • Editors: Sonia Cortassa, Miguel A. Aon

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-1831-8

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply 2022

  • Hardcover ISBN: 978-1-0716-1830-1Published: 24 May 2022

  • Softcover ISBN: 978-1-0716-1833-2Published: 25 May 2023

  • eBook ISBN: 978-1-0716-1831-8Published: 23 May 2022

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIV, 493

  • Number of Illustrations: 21 b/w illustrations, 143 illustrations in colour

  • Topics: Bioinformatics, Biotechnology

Buy it now

Buying options

eBook USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Other ways to access