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Full Description
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 andPattern 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.
Contents
Part I: Video Bioinformatics: An Introduction.- Live Imaging and Video Bioinformatics.- Video Bioinformatics Methods for Analyzing Cell Dynamics.- Part II: Organismal Dynamics: Analyzing Brain Injury and Disease.- High and Low Level Contextual Modeling for the Detection of Mild-Traumatic Brain Injury.- Automated Identification of Injury Dynamics after Neonatal Hypoxia-Ischemia.- A Real-Time Analysis of Traumatic Brain Injury from T2 Weighted Magnetic Resonance Images using a Symmetry-Based Algorithm.- Visualizing Cortical Tissue Optical Changes during Seizure Activity with Optical Coherence Tomography.- Part III: Dynamics of Stem Cells.- Bio-Inspired Segmentation and Detection Methods for Human Embryonic Stem Cells.- A Video Bioinformatics Method to Quantify Cell Spreading and Its Application to Cells Treated with Rho-associated Protein Kinase and Blebbistatin.- Evaluation of Dynamic Cell Processes and Behavior Using Video Bioinformatics Tools.- Part IV: Dynamic Processes in Plant and Fungal Systems.- Video Bioinformatics: A New Dimension in Quantifying Plant Cell Dynamics.- Understanding Growth of Pollen Tube in Video.- Automatic Image Analysis Pipeline for Studying Growth in Arabidopsis.- Quantitative Analyses using Video Bioinformatics and Image Analysis Tools During Growth and Development in the Multicellular Fungus.- Part V: Dynamics of Intracellular Molecules.- Quantification of the Dynamics of DNA Repair to Ionizing Radiatio
n via Colocalization of 53BP1 and H2AX.- A Method to Regulate Cofilin Transport Using Optogenetics and Live Video Analysis.- Part VI: Software, Systems and Databases.- Integrated 5-D Cell Tracking and Linked Analytics in the FARSIGHT Open Source Toolkit.- Video Bioinformatics Databases and Software.- Understanding of the Biological Process of Non-Verbal Communication.- Identification and Retrieval of Moth Images Based on Wing Patterns.
