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Video Bioinformatics

From Live Imaging to Knowledge

  • Bir Bhanu
  • Prue Talbot

Part of the Computational Biology book series (COBO, volume 22)

Table of contents

  1. Front Matter
    Pages i-xliii
  2. Video Bioinformatics: An Introduction

    1. Front Matter
      Pages 1-1
    2. Bir Bhanu, Prue Talbot
      Pages 3-12
  3. Organismal Dynamics: Analyzing Brain Injury and Disease

    1. Front Matter
      Pages 57-57
    2. Nirmalya Ghosh, Stephen Ashwal, Andre Obenaus
      Pages 77-97
    3. Ehsan T. Esfahani, Devin W. McBride, Somayeh B. Shafiei, Andre Obenaus
      Pages 99-117
    4. M. M. Eberle, C. L. Rodriguez, J. I. Szu, Y. Wang, M. S. Hsu, D. K. Binder et al.
      Pages 119-132
  4. Dynamics of Stem Cells

    1. Front Matter
      Pages 133-133
    2. Benjamin X. Guan, Bir Bhanu, Prue Talbot, Nikki Jo-Hao Weng
      Pages 135-150
    3. Sabrina C. Lin, Henry Yip, Rattapol Phandthong, Barbara Davis, Prue Talbot
      Pages 167-186
  5. Dynamic Processes in Plant and Fungal Systems

    1. Front Matter
      Pages 187-187
    2. Asongu L. Tambo, Bir Bhanu, Nan Luo, Zhenbiao Yang
      Pages 201-213
    3. Katya Mkrtchyan, Anirban Chakraborty, Min Liu, Amit Roy-Chowdhury
      Pages 215-236
    4. Ilva E. Cabrera, Asongu L. Tambo, Alberto C. Cruz, Benjamin X. Guan, Bir Bhanu, Katherine A. Borkovich
      Pages 237-250
  6. Dynamics of Intracellular Molecules

    1. Front Matter
      Pages 251-251
    2. Torsten Groesser, Gerald V Fontenay, Ju Han, Hang Chang, Janice Pluth, Bahram Parvin
      Pages 253-263
    3. Atena Zahedi, Vincent On, Iryna Ethell
      Pages 265-279
  7. Software, Systems and Databases

    1. Front Matter
      Pages 281-281
    2. Amine Merouane, Arunachalam Narayanaswamy, Badrinath Roysam
      Pages 283-311
    3. Ninad S. Thakoor, Alberto C. Cruz, Bir Bhanu
      Pages 313-328
    4. Linan Feng, Bir Bhanu, John Heraty
      Pages 349-369
  8. Back Matter
    Pages 371-381

About this book

Introduction

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 subcellular and multicellular systems. The interdisciplinary research field of Video Bioinformatics is defined by Bir Bhanu as the automated processing, analysis, understanding, data mining, visualization, query-based retrieval/storage of biological spatiotemporal events/data and knowledge extracted from dynamic images and microscopic videos. Video bioinformatics attempts to provide a deeper understanding of continuous and dynamic life processes.

Genome sequences alone lack spatial and temporal information, and video imaging of specific molecules and their spatiotemporal interactions, using a range of imaging methods, are essential to understand how genomes create cells, how cells constitute organisms, and how errant cells cause disease. The book examines interdisciplinary research issues and challenges with examples that deal with organismal dynamics, intercellular and tissue dynamics, intracellular dynamics, protein movement, cell signaling and software and databases for video bioinformatics.

 

Topics and Features

  • ·        Covers a set of biological problems, their significance, live-imaging experiments, theory and computational methods, quantifiable experimental results and discussion of results.
  • ·        Provides automated methods for analyzing mild traumatic brain injury over time, identifying injury dynamics after neonatal hypoxia-ischemia and visualizing cortical tissue changes during seizure activity as examples of organismal dynamics
  • ·        Describes techniques for quantifying the dynamics of human embryonic stem cells with examples of cell detection/segmentation, spreading and other dynamic behaviors which are important for characterizing 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 cofilin transport using video analysis
  • ·        Discusses software, system and database aspects of video bioinformatics by providing examples of 5D 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 images

This unique text will be of great interest to researchers and graduate students of Electrical Engineering, Computer Science, Bioengineering, Cell Biology, Toxicology, Genetics, Genomics, Bioinformatics, Computer Vision 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 & Computer Engineering, Interim Chair of the Department of Bioengineering, Cooperative Professor of Computer Science & Engineering, and Mechanical Engineering 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 at the University of California Riverside, California, USA.


Keywords

Analyzing Injury and Disease Cell Motility Cell Signaling Computational Biology Image and Video Informatics Intercellular and Tissue Dynamics Intracellular Dynamics Morphogenesis Organismal Dynamics Protein Movement Segmentation, Detection, Tracking and Recognition Spatiotemporal Events

Editors and affiliations

  • Bir Bhanu
    • 1
  • Prue Talbot
    • 2
  1. 1.University of CaliforniaRiversideUSA
  2. 2.University of CaliforniaRiversideUSA

Bibliographic information

  • DOI https://doi.org/10.1007/978-3-319-23724-4
  • Copyright Information Springer International Publishing Switzerland 2015
  • Publisher Name Springer, Cham
  • eBook Packages Computer Science
  • Print ISBN 978-3-319-23723-7
  • Online ISBN 978-3-319-23724-4
  • Series Print ISSN 1568-2684
  • Buy this book on publisher's site