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Computational Stem Cell Biology

Methods and Protocols

  • Book
  • © 2019

Overview

Editors:
  1. Patrick Cahan

    1. Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA

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  • 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 1975)

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Table of contents (20 protocols)

  1. Front Matter

    Pages i-xi
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  2. Modeling

    1. Front Matter

      Pages 1-1
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    2. Agent-Based Modelling to Delineate Spatiotemporal Control Mechanisms of the Stem Cell Niche

      • Robert Mines, Kai-Yuan Chen, Xiling Shen
      Pages 3-35

    3. Modeling Cellular Differentiation and Reprogramming with Gene Regulatory Networks

      • András Hartmann, Srikanth Ravichandran, Antonio del Sol
      Pages 37-51

    4. Cell Population Model to Track Stochastic Cellular Decision-Making During Differentiation

      • Keith Task, Ipsita Banerjee
      Pages 53-77

    5. Automated Formal Reasoning to Uncover Molecular Programs of Self-Renewal

      • Sara-Jane Dunn
      Pages 79-105

    6. Mathematical Modelling of Clonal Stem Cell Dynamics

      • Philip Greulich
      Pages 107-129

    7. Computational Tools for Quantifying Concordance in Single-Cell Fate

      • J. A. Cornwell, R. E. Nordon
      Pages 131-156

    8. Quantitative Modelling of the Waddington Epigenetic Landscape

      • Atefeh Taherian Fard, Mark A. Ragan
      Pages 157-171

    9. Modeling Gene Networks to Understand Multistability in Stem Cells

      • David Menn, Xiao Wang
      Pages 173-189

  3. Single Cell Approaches

    1. Front Matter

      Pages 191-191
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    2. Trajectory Algorithms to Infer Stem Cell Fate Decisions

      • Edroaldo Lummertz da Rocha, Mohan Malleshaiah
      Pages 193-209

    3. Gene Regulatory Networks from Single Cell Data for Exploring Cell Fate Decisions

      • Thalia E. Chan, Michael P. H. Stumpf, Ann C. Babtie
      Pages 211-238

    4. Reconstructing Gene Regulatory Networks That Control Hematopoietic Commitment

      • Fiona K. Hamey, Berthold Göttgens
      Pages 239-249

    5. Investigating Cell Fate Decisions with ICGS Analysis of Single Cells

      • Nathan Salomonis
      Pages 251-275

    6. Lineage Inference and Stem Cell Identity Prediction Using Single-Cell RNA-Sequencing Data

      • Sagar, Dominic Grün
      Pages 277-301

  4. Metabolism

    1. Front Matter

      Pages 303-303
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    2. Dynamic Network Modeling of Stem Cell Metabolism

      • Fangzhou Shen, Camden Cheek, Sriram Chandrasekaran
      Pages 305-320

    3. Metabolomics in Stem Cell Biology Research

      • Zhen Sun, Jing Zhao, Hua Yu, Chenyang Zhang, Hu Li, Zhongda Zeng et al.
      Pages 321-330

  5. Assessing and Improving Cell Fate Engineering

    1. Front Matter

      Pages 331-331
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Keywords

About this book

This volume details methods and protocols to further the study of stem cells within the computational stem cell biology (CSCB) field. Chapters are divided into four sections covering the theory and practice of modeling of stem cell behavior, analyzing single cell genome-scale measurements, reconstructing gene regulatory networks, and metabolomics. 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.



Authoritative and cutting-edge, Computational Stem Cell Biology: Methods and Protocols will be an invaluable guide to researchers as they explore stem cells from the perspective of computational biology.


Editors and Affiliations

  • Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA

    Patrick Cahan

Bibliographic Information

  • Book Title: Computational Stem Cell Biology

  • Book Subtitle: Methods and Protocols

  • Editors: Patrick Cahan

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-9224-9

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2019

  • Hardcover ISBN: 978-1-4939-9223-2Published: 07 May 2019

  • Softcover ISBN: 978-1-4939-9226-3Published: 28 October 2020

  • eBook ISBN: 978-1-4939-9224-9Published: 06 May 2019

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 456

  • Number of Illustrations: 12 b/w illustrations, 95 illustrations in colour

  • Topics: Stem Cells, Computer Appl. in Life Sciences, Computational Biology/Bioinformatics

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