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Bioinformatics and the Cell

Modern Computational Approaches in Genomics, Proteomics and Transcriptomics

  • Book
  • © 2018

Overview

Authors:
  1. Xuhua Xia

    1. University of Ottawa CAREG and Biology Department, Ottawa, Canada

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  • First book with comprehensive numerical illustration of mathematical techniques and computational algorithms used in bioinformatics to convert the rapidly increasing molecular data into organized biological knowledge
  • Focus on interactions among DNA, RNA and proteins in the cell
  • This book should appeal not only to biologists, but also to mathematicians, biostatisticians, and computational scientists, especially those younger ones with an ambition to conquer the rough terrain of bioinformatics

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Table of contents (19 chapters)

  1. Front Matter

    Pages i-xiii
    Download chapter PDF

  2. String Mathematics, BLAST, and FASTA

    • Xuhua Xia
    Pages 1-31

  3. Sequence Alignment

    • Xuhua Xia
    Pages 33-75

  4. Position weight matrix and Perceptron

    • Xuhua Xia
    Pages 77-98

  5. Gibbs sampler

    • Xuhua Xia
    Pages 99-111

  6. Transcriptomics and RNA-Seq Data Analysis

    • Xuhua Xia
    Pages 113-128

  7. Self-Organizing Map and Other Clustering Methods in Transcriptomics

    • Xuhua Xia
    Pages 129-144

  8. Hidden Markov Models and Protein Secondary Structure Prediction

    • Xuhua Xia
    Pages 145-172

  9. Bioinformatics and Translation Initiation

    • Xuhua Xia
    Pages 173-195

  10. Bioinformatics and Translation Elongation

    • Xuhua Xia
    Pages 197-238

  11. Bioinformatics and Translation Termination in Bacteria

    • Xuhua Xia
    Pages 239-254

  12. Genomic Features: Content Sensors, Nucleotide Skew Plot, Strand Asymmetry, and DNA Methylation

    • Xuhua Xia
    Pages 255-268

  13. Nucleotide Substitution Models and Evolutionary Distances

    • Xuhua Xia
    Pages 269-314

  14. Protein Substitution Model and Evolutionary Distance

    • Xuhua Xia
    Pages 315-326

  15. Maximum Parsimony Method in Phylogenetics

    • Xuhua Xia
    Pages 327-341

  16. Distance-Based Phylogenetic Methods

    • Xuhua Xia
    Pages 343-379

  17. Maximum Likelihood in Molecular Phylogenetics

    • Xuhua Xia
    Pages 381-395

  18. Protein Isoelectric Point and Helicobacter pylori

    • Xuhua Xia
    Pages 397-412

  19. Bioinformatics and In Silico 2D Gel Electrophoresis

    • Xuhua Xia
    Pages 413-420

  20. Fundamentals of Proteomics

    • Xuhua Xia
    Pages 421-436
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Keywords

About this book

This second edition integrates the more technical and mathematical aspects of bioinformatics with concrete examples of their application to current research problems in molecular, cellular and evolutionary biology. This broad, unified approach is made possible, in large part, by the very wide scope of Dr. Xia’s own research experience. The integration of genomics, proteomics and transcriptomics into a single volume makes this book required reading for anyone entering the new and emerging fields of Systems Biology and Evolutionary Bioinformatics.

Authors and Affiliations

  • University of Ottawa CAREG and Biology Department, Ottawa, Canada

    Xuhua Xia

About the author

Dr. Xuhua Xia obtained his PhD in population biology at University of Western Ontario in 1990 and made his entry into molecular evolution and phylogenetics at University of Washington in 1993. He was recruited by University of Hong Kong in 1996 as an assistant professor, and served as a senior scientist and the founding head of the Bioinformatics Laboratory of HKU-Pasteur Research Centre. Dr. Xia joined University of Ottawa in 2002 where he is cross-appointed to both Biology Department and the School of Information Technology Engineering. He is an active member in the Center for Advanced Research in Environmental Genomics and the Ottawa Institute of Systems Biology. 

Bibliographic Information

  • Book Title: Bioinformatics and the Cell

  • Book Subtitle: Modern Computational Approaches in Genomics, Proteomics and Transcriptomics

  • Authors: Xuhua Xia

  • DOI: https://doi.org/10.1007/978-3-319-90684-3

  • Publisher: Springer Cham

  • eBook Packages: Biomedical and Life Sciences, Biomedical and Life Sciences (R0)

  • Copyright Information: Springer Science+Business Media LLC 2018

  • Hardcover ISBN: 978-3-319-90682-9Published: 16 July 2018

  • Softcover ISBN: 978-3-030-08073-0Published: 30 January 2019

  • eBook ISBN: 978-3-319-90684-3Published: 05 July 2018

  • Edition Number: 2

  • Number of Pages: XIII, 489

  • Number of Illustrations: 63 b/w illustrations, 59 illustrations in colour

  • Topics: Bioinformatics, Proteomics, Cell Biology, Evolutionary Biology

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