ENGLISH

Computational Stem Cell Biology: Methods and Protocols

By Patrick Cahan

Book information

Publisher
Springer New York; Humana
Year
2019
ISBN
978-1-4939-9223-2;978-1-4939-9224-9
Language
english
Format
PDF
Filesize
22 MB (23376541 bytes)
Series
Methods in Molecular Biology 1975
Edition
1st ed.
Pages
XI, 456\450
Time added
2019-09-18 12:16:59
Life Sciences; Stem Cells; Computer Appl. in Life

Description

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. 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

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