Computational Stem Cell Biology: Methods and Protocols

Preface...Table of Contents...Contributing Authors...
Part I Modeling
1. Agent-Based Modeling to Delineate Spatiotemporal Control Mechanisms of the Stem Cell NicheRobert Mines, Kai-Yuan Chen, and Xiling Shen
2. Modeling Cellular Differentiation and Reprogramming with Gene Regulatory NetworksAndr?s 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-RenewalSara-Jane Dunn
5. Mathematical Modeling of Clonal Stem Cell DynamicsPhilip Greulich
6. Computational Tools for Quantifying Concordance in Single Cell FateJ.A. Cornwell and R.E. Nordon
7. Quantitative Modeling of the Waddington Epigenetic LandscapeAtefeh Taherian Fard and Mark A. Ragan
8. Modeling Gene Networks to Understand Multistability in Stem CellsDavid Menn and Xiao Wang
Part II Single Cell Approaches
9. Trajectory Algorithms to Infer Stem Cell Fate DecisionsEdroaldo Lummertz da Rocha and Mohan Malleshaiah
10. Gene Regulatory Networks from Single Cell Data for Exploring Cell Fate DecisionsThalia E. Chan, Michael P.H. Stumpf, and Ann C. Babtie
11. Reconstructing Gene Regulatory Networks that Control Hematopoietic CommitmentFiona K. Hamey and Berthold G?ttgens
12. Investigating Cell Fate Decisions with ICGS Analysis of Single CellsNathan Salomonis
13. Lineage Inference and Stem Cell Identity Prediction using Single Cell RNA-Sequencing DataSagar and Dominic Gr?n
Part III Metabolism
14. Dynamic Network Modeling of Stem Cell MetabolismFangzhou Shen, Camden Cheek, and Sriram Chandrasekaran
15. Metabolomics in Stem Cell Biology ResearchSun 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 ConversionJohn F. Ouyang, Uma S. Kamaraj, Jose M. Polo, Julian Gough, and Owen J. L. Rackham
17. A Computational Approach for Cell Fate ReprogrammingHussein M. Abdallah and Domitilla Del Vecchio
18. Computational Analysis of Aneuploidy in Pluripotent Stem CellsUri Weissbein
19. Cell Fate Engineering Tools for iPSC Disease ModelingEmily K. W. Lo and Patrick Cahan