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Systems Biology

  • Book
  • © 2024

Overview

Editors:
  1. Mariano Bizzarri

    1. Department of Experimental Medicine, Sapienza University, Rome, Italy

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    You can also search for this editor in PubMed   Google Scholar

  • 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 2745)

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Table of contents (15 protocols)

  1. Front Matter

    Pages i-xvi
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  2. Models in Systems Biology and Parameters Identification

    1. Front Matter

      Pages 1-1
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    2. Identifying Key In Silico Knockout for Enhancement of Limonene Yield Through Dynamic Metabolic Modelling

      • Jasmeet Kaur Khanijou, Yan Ting Hee, Kumar Selvarajoo
      Pages 3-19

    3. The Search for System’s Parameters: Statistical and Dynamical Description from Complex Network Analysis

      • Alessandro Giuliani
      Pages 21-30

    4. Untargeted Analysis of Short-Chain Peptides in Urine Samples Short Peptides Analysis

      • SaraElsa Aita, Andrea Cerrato, Aldo Laganà, Carmela Maria Montone, Enrico Taglioni, Anna Laura Capriotti
      Pages 31-43

    5. Metastasis Models: Thermodynamics and Complexity

      • A. Guerra, J. A. Betancourt-Mar, J. A. Llanos-Pérez, R. Mansilla, J. M. Nieto-Villar
      Pages 45-75

    6. Metabolomics: Challenges and Opportunities in Systems Biology Studies

      • Ahmed Mediani, Syarul Nataqain Baharum
      Pages 77-90

    7. Optical Estimation of Bioelectric Patterns in Living Embryos

      • Patrick McMillen, Michael Levin
      Pages 91-102

  3. Computational Methods

    1. Front Matter

      Pages 103-103
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    2. Mathematical Modeling in the Study of Organisms and Their Parts

      • Maël Montévil
      Pages 105-119

    3. Systems Biology Modeling of Cancer Nonlinear Dynamics

      • Abdallah Alameddine
      Pages 121-134

  4. Critical Transition States Across Waddington’s Like Landscapes

    1. Front Matter

      Pages 135-135
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    2. From Cell States to Cell Fates: Control of Cell State Transitions

      • Masa Tsuchiya, Alessandro Giuliani, Paul Brazhnik
      Pages 137-162

    3. Understanding Cell Differentiation Through Single-Cell Approaches: Conceptual Challenges of the Systemic Approach

      • Laëtitia Racine, Andras Paldi
      Pages 163-176

    4. Modeling Mammary Organogenesis from Biological First Principles: A Systems Biology Approach

      • Cheryl M. Schaeberle, Victoria A. Bouffard, Carlos Sonnenschein, Ana M. Soto
      Pages 177-188

  5. Specific Fields of Investigation

    1. Front Matter

      Pages 189-189
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    2. Systems Biology and Inborn Error of Metabolism: Analytical Strategy in Investigating Different Biochemical/Genetic Parameters

      • Aurora Piombarolo, Cristiano Ialongo, Mariano Bizzarri, Antonio Angeloni
      Pages 191-210

    3. System Biology Approach in Investigating Epithelial-Mesenchymal Transition (EMT)

      • Noemi Monti, Alessandro Querqui, Guglielmo Lentini, Marco Tafani, Mariano Bizzarri
      Pages 211-225

    4. An Enhanced Quantitative Reverse Transcription-PCR Approach for Measuring Circulating MicroRNAs

      • Mahmoud Tavallaie, Mostafa Khafaei
      Pages 227-231

    5. Systems Biology Approaches to Understanding COVID-19 Spread in the Population

      • Sofija Marković, Igor Salom, Marko Djordjevic
      Pages 233-253
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Keywords

About this book

This second edition volume expands on the previous edition with discussions of the latest advancements and methods used by scientists to study systems biology. The chapters in this book are organized into four parts. Part One looks at models in systems biology and parameters identification such as short peptide analysis, metastasis models, and metabolomics. Part Two covers computational methods in the study of organisms, and cancer non-linear dynamics. Part Three discusses critical transition states across Waddington’s like landscapes such as understanding cell differentiation through single-cell approaches and modeling mammary organogenesis from biological first principles. Part Four talks about specific fields of investigation including inborn errors of metabolism, system biology approach in epithelial-mesenchymal transition, and an approach to understanding how COVID-19 spreads in the population. 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 comprehensive, Systems Biology, Second Edition is a valuable tool for any researcher looking to learn more about this important and developing field.


Editors and Affiliations

  • Department of Experimental Medicine, Sapienza University, Rome, Italy

    Mariano Bizzarri

Bibliographic Information

  • Book Title: Systems Biology

  • Editors: Mariano Bizzarri

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-3577-3

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2024

  • Hardcover ISBN: 978-1-0716-3576-6Published: 08 December 2023

  • Softcover ISBN: 978-1-0716-3579-7Due: 08 January 2024

  • eBook ISBN: 978-1-0716-3577-3Published: 07 December 2023

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: XVI, 256

  • Number of Illustrations: 10 b/w illustrations, 43 illustrations in colour

  • Topics: Bioinformatics

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