Computational Stem Cell Biology: Methods and Protocols

Front Matter ....Pages i-xi
Front Matter ....Pages 1-1
 Agent-Based Modelling to Delineate Spatiotemporal Control Mechanisms of the Stem Cell Niche  (Robert Mines, Kai-Yuan Chen, Xiling Shen)....Pages 3-35
 Modeling Cellular Differentiation and Reprogramming with Gene Regulatory Networks  (András Hartmann, Srikanth Ravichandran, Antonio del Sol)....Pages 37-51
 Cell Population Model to Track Stochastic Cellular Decision-Making During Differentiation  (Keith Task, Ipsita Banerjee)....Pages 53-77
 Automated Formal Reasoning to Uncover Molecular Programs of Self-Renewal  (Sara-Jane Dunn)....Pages 79-105
 Mathematical Modelling of Clonal Stem Cell Dynamics  (Philip Greulich)....Pages 107-129
 Computational Tools for Quantifying Concordance in Single-Cell Fate  (J. A. Cornwell, R. E. Nordon)....Pages 131-156
 Quantitative Modelling of the Waddington Epigenetic Landscape  (Atefeh Taherian Fard, Mark A. Ragan)....Pages 157-171
 Modeling Gene Networks to Understand Multistability in Stem Cells  (David Menn, Xiao Wang)....Pages 173-189
Front Matter ....Pages 191-191
 Trajectory Algorithms to Infer Stem Cell Fate Decisions  (Edroaldo Lummertz da Rocha, Mohan Malleshaiah)....Pages 193-209
 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
 Reconstructing Gene Regulatory Networks That Control Hematopoietic Commitment  (Fiona K. Hamey, Berthold Göttgens)....Pages 239-249
 Investigating Cell Fate Decisions with ICGS Analysis of Single Cells  (Nathan Salomonis)....Pages 251-275
 Lineage Inference and Stem Cell Identity Prediction Using Single-Cell RNA-Sequencing Data  ( Sagar, Dominic Grün)....Pages 277-301
Front Matter ....Pages 303-303
 Dynamic Network Modeling of Stem Cell Metabolism  (Fangzhou Shen, Camden Cheek, Sriram Chandrasekaran)....Pages 305-320
 Metabolomics in Stem Cell Biology Research  (Zhen Sun, Jing Zhao, Hua Yu, Chenyang Zhang, Hu Li, Zhongda Zeng et al.)....Pages 321-330
Front Matter ....Pages 331-331
 Molecular Interaction Networks to Select Factors for Cell Conversion  (John F. Ouyang, Uma S. Kamaraj, Jose M. Polo, Julian Gough, Owen J. L. Rackham)....Pages 333-361
 Computational Analysis of Altering Cell Fate  (Hussein M. Abdallah, Domitilla Del Vecchio)....Pages 363-405
 Computational Analysis of Aneuploidy in Pluripotent Stem Cells  (Uri Weissbein)....Pages 407-426
 Cell Fate Engineering Tools for iPSC Disease Modeling  (Emily K. W. Lo, Patrick Cahan)....Pages 427-454
 Correction to: Molecular Interaction Networks to Select Factors for Cell Conversion  (John F. Ouyang, Uma S. Kamaraj, Jose M. Polo, Julian Gough, Owen J. L. Rackham)....Pages C1-C1
Back Matter ....Pages 455-456