Computational Biology Of Embryonic Stem Cells

"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"

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.

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.

The rapidly developing field of systems biology is influencing many aspects of biological research and is expected to transform biomedicine. Some emerging offshoots and specialized branches in systems biology are receiving particular attention and are becoming highly active areas of research. This collection of invited reviews describes some of the latest cutting-edge experimental and computational advances in these emerging sub-fields of systems biology. In particular, this collection focuses on the study of mammalian embryonic stem cells; new technologies involving mass-spectrometry proteomics; single cell measurements; methods for modeling complex stochastic systems; network-based classification algorithms; and the revolutionary emerging field of systems pharmacology.

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).

Advances in stem cell biology and biotechnology have sparked hopes that therapies will soon be available for maladies which were considered incurable before. However, realization of the clinical potential of stem cells will require better understanding of stem cell physiology and the development of advanced technologies for their efficient differentiation in medically relevant quantities. Resolving these issues necessitates synergistic approaches from multiple fields. Systems biology can be employed to dissect the mechanisms regulating the genome and proteome of stem cells during self-renewal and commitment. Microfluidic platforms can be used to recreate aspects of the stem cell niche and obtain a better understanding of the interactions among stem cells and with their environment. The milieu of stem cells and their progeny can be shaped with appropriately designed biomaterials for the engineering of tissues to replace, reconstitute or regenerate damaged organs. To that end, enabling bioreactor technologies will be necessary for the generation of large quantities of stem cells and their derivatives in a robust and cost-efficient manner. This book invites world-renowned experts in the above fields to discuss the latest advances in their respective areas and to provide insights on the future challenges and achievements in the area of stem cells.

Advances in stem cell biology and biotechnology have sparked hopes that therapies will soon be available for maladies which were considered incurable before. However, realization of the clinical potential of stem cells will require better understanding of stem cell physiology and the development of advanced technologies for their efficient differentiation in medically relevant quantities. Resolving these issues necessitates synergistic approaches from multiple fields. Systems biology can be employed to dissect the mechanisms regulating the genome and proteome of stem cells during self-renewal and commitment. Microfluidic platforms can be used to recreate aspects of the stem cell niche and obtain a better understanding of the interactions among stem cells and with their environment. The milieu of stem cells and their progeny can be shaped with appropriately designed biomaterials for the engineering of tissues to replace, reconstitute or regenerate damaged organs. To that end, enabling bioreactor technologies will be necessary for the generation of large quantities of stem cells and their derivatives in a robust and cost-efficient manner. This book invites world-renowned experts in the above fields to discuss the latest advances in their respective areas and to provide insights on the future challenges and achievements in the area of stem cells.

The first volume of Stem Cells deals with the fundamental principles that govern embryonic and somatic stem cell biology. Historically, the identification and characterization of such pathways and general rules of stemness occurred during embryonic development and Volume I reflects this with topics spanning cell cycle regulation, epigenetics, and asymmetric cell division in a number of organ systems from planarian to human. Three specific sections discuss i) Basic Stem Cell Biology, ii) Tissue Formation During Development, and iii) Model Organisms with particular emphasis on those more relevant for biomedical research and, thus, leading to the topics addressed in Volume II.