Computational Biology for Stem Cell Research is an invaluable guide for researchers as they explore HSCs and MSCs in computational biology. With the growing advancement of technology in the field of biomedical sciences, computational approaches have reduced the financial and experimental burden of the experimental process. In the shortest span, it has established itself as an integral component of any biological research activity. HSC informatics (in silico) techniques such as machine learning, genome network analysis, data mining, complex genome structures, docking, system biology, mathematical modeling, programming (R, Python, Perl, etc.) help to analyze, visualize, network constructions, and protein-ligand or protein-protein interactions. This book is aimed at beginners with an exact correlation between the biomedical sciences and in silico computational methods for HSCs transplantation and translational research and provides insights into methods targeting HSCs properties like proliferation, self-renewal, differentiation, and apoptosis. Modeling Stem Cell Behavior: Explore stem cell behavior through animal models, bridging laboratory studies to real-world clinical allogeneic HSC transplantation (HSCT) scenarios. Bioinformatics-Driven Translational Research: Navigate a path from bench to bedside with cutting-edge bioinformatics approaches, translating computational insights into tangible advancements in stem cell research and medical applications. Interdisciplinary Resource: Discover a single comprehensive resource catering to biomedical sciences, life sciences, and chemistry fields, offering essential insights into computational tools vital for modern research.

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.

"Computational biology in combination with large-scale biology has played a critical role in exploring the great potentials of embryonic stem cells, resulting in significant discoveries. This e-book brings together reviews and essays from different aspects"

The study of stem cell biology is under intensive investigations. Because stem cells have the unique capability to self-renew and differentiate into one or several cell types, they play a critical role in development, tissue homeostasis and regeneration. Stem cells also constitute promising cell candidates for cell therapy. The aim of this book is to provide an accurate knowledge on stem cell biology and regenerative medicine. This book will cover many topics in the field and is based on seminars given by recognized scientists involved the international master program on stem cell biology at the University Pierre and Marie Curie (UPMC) in Paris. Content Preface. Pierre Charbord and Charles Durand. 1) General concepts 1.Stem cell concepts. Charles Durand and Pierre Charbord. 2.Transcriptional regulation in stem cells. Eric Soler and Frank Grosveld. 3.DNA repair in stem cells. Leyla Vahidi Ferdousi and Miria Ricchetti. 4. Stem cells and epigenetic regulation. Emma L. Walton and Claire Francastel. 5. Hydra and the evolution of stem cells. Alexander Klimovich, Anna Marei Böhm and Thomas C.G. Bosch. 6. Ontogeny of stem cells. Thierry Jaffredo. 7. Regeneration in anamniotic vertebrates. Dunja Knapp. 8. Computational models of spatio-temporal stem cell organization. Peter Buske and Joerg Galle. 2) Pluripotent stem cells 9. X chromosome inactivation in stem cells and development. Agnese Loda, Friedemann Loos and Joost Gribnau. 10. Molecular machinery of reprogramming. Romain Desprat, Ollivier Milhavet and Jean-Marc Lemaitre. 11. Modeling human genetic disorders using induced pluripotent stem cells. Franck Lebrin. 3) Adult stem cells 12. Developmental biology of hematopoietic stem cells : Cellular aspects. Laurent Yvernogeau, Jean-Charles Boisset and Catherine Robin. 13. Developmental biology of haematopoietic stem cells: Cell intrinsic and extrinsic regulators of their emergence. Katrin Ottersbach. 14. Biology of hematopoietic stem cells in the adult. Marie-Laure Arcangeli, Rima Haddad, Francoise Pflumio. 15. Epithelial stem cells in the skin. Romain Fontaine, Mathieu Castela and Selim Aractingi. 16. Skeletal muscle stem cells. Elisa Negroni, Maximilien Bencze, Stéphanie Duguez, Gillian Butler-Browne and Vincent Mouly. 17. Mammary stem cells. Marie-Ange Deugnier, Marisa M. Faraldo and Marina A. Glukhova. 18. Intestinal stem cells. Silvia Fre. 19. Neural stem cells. Nathalie Kubis and Martin Catala. 20. Dental stem cells. Anne Poliard. 21. Bone marrow Mesenchymal Stem Cells: from stemness to stromal property of hematopoietic support. Pierre Charbord and Bruno Delorme. 22. Retinal stem cells. Olivier Goureau, Angélique Terray, Katherine S. Matho, Sacha Reichman, and Gael Orieux. 4) Stem cell-related diseases and therapy using stem cells 23. Leukemic stem cells: what the concept brings to disease and patient management. Berent Lunden and Christine Chomienne. 24. Stem cells for cardiac repair. Philippe Menasché. 25. Stem cells for red blood cell production. Christelle Mazurier, Guillaume F Rousseau, Luc Douay and Hélène Lapillonne. 26. Prospectives for therapy with stem cells in skeletal muscular diseases. Maximilien Bencze, Elisa Negroni, Vincent Mouly and Gillian Butler-Browne. 5) Regulatory and philosophical aspects 27. Legal framework for research on Human Embryonic Stem Cells in France and in Europe. Arnaud de Guerra, Emmanuelle Prada-Bordenave 28. Stem cell epistemological issues. Lucie Laplane. 29. Future outlook. Pierre Charbord and Charles Durand.

This book describes a global assessment of stem cell engineering research, achieved through site visits by a panel of experts to leading institutes, followed by dedicated workshops. The assessment made clear that engineers and the engineering approach with its quantitative, system-based thinking can contribute much to the progress of stem cell research and development. The increased need for complex computational models and new, innovative technologies, such as high-throughput screening techniques, organ-on-a-chip models and in vitro tumor models require an increasing involvement of engineers and physical scientists. Additionally, this book will show that although the US is still in a leadership position in stem cell engineering, Asian countries such as Japan, China and Korea, as well as European countries like the UK, Germany, Sweden and the Netherlands are rapidly expanding their investments in the field. Strategic partnerships between countries could lead to major advances of the field and scalable expansion and differentiation of stem cells. This study was funded by the National Science Foundation (NSF), the National Institutes of Health (NIH) and the National Institute of Standards and Technology (NIST).

The advances of live cell video imaging and high-throughput technologies for functional and chemical genomics provide unprecedented opportunities to understand how biological processes work in subcellularand multicellular systems. The interdisciplinary research field of Video Bioinformatics is defined by BirBhanu as the automated processing, analysis, understanding, data mining, visualization, query-basedretrieval/storage of biological spatiotemporal events/data and knowledge extracted from dynamic imagesand microscopic videos. Video bioinformatics attempts to provide a deeper understanding of continuousand dynamic life processes.Genome sequences alone lack spatial and temporal information, and video imaging of specific moleculesand their spatiotemporal interactions, using a range of imaging methods, are essential to understandhow genomes create cells, how cells constitute organisms, and how errant cells cause disease. The bookexamines interdisciplinary research issues and challenges with examples that deal with organismal dynamics,intercellular and tissue dynamics, intracellular dynamics, protein movement, cell signaling and softwareand databases for video bioinformatics.Topics and Features• Covers a set of biological problems, their significance, live-imaging experiments, theory andcomputational methods, quantifiable experimental results and discussion of results.• Provides automated methods for analyzing mild traumatic brain injury over time, identifying injurydynamics after neonatal hypoxia-ischemia and visualizing cortical tissue changes during seizureactivity as examples of organismal dynamics• Describes techniques for quantifying the dynamics of human embryonic stem cells with examplesof cell detection/segmentation, spreading and other dynamic behaviors which are important forcharacterizing stem cell health• Examines and quantifies dynamic processes in plant and fungal systems such as cell trafficking,growth of pollen tubes in model systems such as Neurospora Crassa and Arabidopsis• Discusses the dynamics of intracellular molecules for DNA repair and the regulation of cofilintransport using video analysis• Discusses software, system and database aspects of video bioinformatics by providing examples of5D cell tracking by FARSIGHT open source toolkit, a survey on available databases and software,biological processes for non-verbal communications and identification and retrieval of moth imagesThis unique text will be of great interest to researchers and graduate students of Electrical Engineering,Computer Science, Bioengineering, Cell Biology, Toxicology, Genetics, Genomics, Bioinformatics, ComputerVision and Pattern Recognition, Medical Image Analysis, and Cell Molecular and Developmental Biology.The large number of example applications will also appeal to application scientists and engineers.Dr. Bir Bhanu is Distinguished Professor of Electrical & C omputer Engineering, Interim Chair of theDepartment of Bioengineering, Cooperative Professor of Computer Science & Engineering, and MechanicalEngineering and the Director of the Center for Research in Intelligent Systems, at the University of California,Riverside, California, USA.Dr. Prue Talbot is Professor of Cell Biology & Neuroscience and Director of the Stem Cell Center and Core atthe University of California Riverside, California, USA.

This textbook describes the biology of different adult stem cell types and outlines the current level of knowledge in the field. It clearly explains the basics of hematopoietic, mesenchymal and cord blood stem cells and also covers induced pluripotent stem cells. Further, it includes a chapter on ethical aspects of human stem cell research, which promotes critical thinking and responsible handling of the material. Based on the international masters program Molecular and Developmental Stem Cell Biology taught at Ruhr-University Bochum and Tongji University Shanghai, the book is a valuable source for postdocs and researchers working with stems cells and also offers essential insights for physicians and dentists wishing to expand their knowledge. This textbook is a valuable complement to Concepts and Applications of Stem Cell Biology, also published in the Learning Materials in Biosciences textbook series.