Computational Stem Cell Biology: Methods and Protocols

ISBN-13: 9781493992232 / Angielski / Twarda / 2019 / 456 str.

Cahan, Patrick

Opis

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.

Spis treści

Preface…

Table of Contents…

Contributing Authors…

Part I Modeling

1. Agent-Based Modeling to Delineate Spatiotemporal Control Mechanisms of the Stem Cell Niche

Robert Mines, Kai-Yuan Chen, and Xiling Shen

2. Modeling Cellular Differentiation and Reprogramming with Gene Regulatory Networks

András Hartmann, Srikanth Ravichandran, and Antonio del Sol

3. Cell Population Model to Track Stochastic Cellular Decision-Making during Differentiation 

Keith Task and Ipsita Banerjee

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

Sara-Jane Dunn 

5. Mathematical Modeling of Clonal Stem Cell Dynamics

Philip Greulich

6. Computational Tools for Quantifying Concordance in Single Cell Fate

J.A. Cornwell and R.E. Nordon

7. Quantitative Modeling of the Waddington Epigenetic Landscape

Atefeh Taherian Fard and Mark A. Ragan

8. Modeling Gene Networks to Understand Multistability in Stem Cells

David Menn and Xiao Wang

Part II Single Cell Approaches

9. Trajectory Algorithms to Infer Stem Cell Fate Decisions

Edroaldo Lummertz da Rocha and Mohan Malleshaiah

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

Thalia E. Chan, Michael P.H. Stumpf, and Ann C. Babtie

11. Reconstructing Gene Regulatory Networks that Control Hematopoietic Commitment

Fiona K. Hamey and Berthold Göttgens

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

Nathan Salomonis

13. Lineage Inference and Stem Cell Identity Prediction using Single Cell RNA-Sequencing Data

Sagar and Dominic Grün

Part III Metabolism 

14. Dynamic Network Modeling of Stem Cell Metabolism

Fangzhou Shen, Camden Cheek, and Sriram Chandrasekaran

15. Metabolomics in Stem Cell Biology Research

Sun Zhen, Jing Zhao, Hua Yu, Chenyang Zhang, Hu Li, Zhongda Zeng, and Jin Zhang

Part IV Assessing and Improving Cell Fate Engineering

16. Molecular Interaction Networks to Select Factors for Cell Conversion

John F. Ouyang, Uma S. Kamaraj, Jose M. Polo, Julian Gough, and Owen J. L. Rackham

17. A Computational Approach for Cell Fate Reprogramming

Hussein M. Abdallah and Domitilla Del Vecchio 

18. Computational Analysis of Aneuploidy in Pluripotent Stem Cells

Uri Weissbein

19. Cell Fate Engineering Tools for iPSC Disease Modeling

Emily K. W. Lo and Patrick Cahan