CiNii 図書 - Video bioinformatics : from live imaging to knowledge

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.

Part I: Video Bioinformatics: An Introduction Live Imaging and Video Bioinformatics Bir Bhanu and Prue Talbot Video Bioinformatics Methods for Analyzing Cell Dynamics: A Survey Nirmalya Ghosh Part II: Organismal Dynamics: Analyzing Brain Injury and Disease High and Low Level Contextual Modeling for the Detection of Mild-Traumatic Brain Injury Anthony Bianchi, Bir Bhanu and Andre Obenaus Automated Identification of Injury Dynamics after Neonatal Hypoxia-Ischemia Nirmalya Ghosh, Stephen Ashwal and Andre Obenaus A Real-Time Analysis of Traumatic Brain Injury from T2 Weighted Magnetic Resonance Images using a Symmetry-Based Algorithm Ehsan T. Esfahani, Devin W. McBride, Somayeh B. Shafiei and Andre Obenaus Visualizing Cortical Tissue Optical Changes during Seizure Activity with Optical Coherence Tomography Melissa M. Eberle, Carissa L. Rodriguez, Jenny I. Szu, Yan Wang, Mike S. Hsu, Devin K. Binder and B. Hyle Park Part III: Dynamics of Stem Cells Bio-Inspired Segmentation and Detection Methods for Human Embryonic Stem Cells Benjamin X. Guan, Bir Bhanu, Prue Talbot and Jo-Hao Weng A Video Bioinformatics Method to Quantify Cell Spreading and Its Application to Cells Treated with Rho-associated Protein Kinase and Blebbistatin Jo-Hao Weng, Rattapol Phandthong and Prue Talbot Evaluation of Dynamic Cell Processes an d Behavior Using Video Bioinformatics Tools Sabrina C. Lin, Henry Yip, Rattapol Phandthong, Barbara Davis and Prue Talbot Part IV: Dynamic Processes in Plant and Fungal Systems Video Bioinformatics: A New Dimension in Quantifying Plant Cell Dynamics Nolan Ung and Natasha V Raikhel Understanding Growth of Pollen Tube in Video Asongu L. Tambo, Bir Bhanu, Nan Luo and Zhenbiao Yang Automatic Image Analysis Pipeline for Studying Growth in Katya Mkrtchyan, Anirban Chakraborty, Min Liu and Amit Roy-Chowdhury Quantitative Analyses using Video Bioinformatics and Image Analysis Tools During Growth and Development in the Multicellular Fungus Neurospora Crassa Ilva E. Cabrera, Asongu L. Tambo, Alberto C. Cruz, Benjamin X. Guan, Bir Bhanu and Katherine A. Borkovich Part V: Dynamics of Intracellular Molecules Quantification of the Dynamics of DNA Repair to Ionizing Radiation via Colocalization of 53BP1 and H2AX Torsten Groesser, Gerald Fontenay, Ju Han, Hang Chang and Bahram Parvin A Method to Regulate Cofilin Transport Using Optogenetics and Live Video Analysis Atena Zahedi, Vincent On and Irnya Ethell Part VI: Software, Systems and Databases Integrated 5-D Cell Tracking and Linked Analytics in the FARSIGHT Open Source Toolkit Amine Merouane, Arunchalam Narayanaswamy and Badrinath Roysam Video Bioinfo rmatics Databases and Software Ninad S. Thakoor, Alberto C. Cruz and Bir Bhanu Understanding of the Biological Process of Non-Verbal Communication: Facial Emotion and Expression Recognition Alberto C. Cruz, Bir Bhanu and Ninad S. Thakoor Identification and Retrieval of Moth Images Based on Wing Patterns Linan Feng, Bir Bhanu and John Heraty

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Video bioinformatics : from live imaging to knowledge

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