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  • Book
  • © 2015

Fundamentals of Bioinformatics and Computational Biology

Methods and Exercises in MATLAB

Authors:

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  • Clearly presents core bioinformatics principles with “hands-on” examples

  • Illustrates the use of MATLAB bioinformatics toolbox™ for solving complex bioinformatics problems

  • Synthetizes concepts in databases, machine learning, statistics and visualization for bioinformatics research

  • Mainly written for computer scientists and engineers

Part of the book series: Modeling and Optimization in Science and Technologies (MOST, volume 6)

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eBook
USD 169.00
Price excludes VAT (USA)
  • ISBN: 978-3-319-11403-3
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Softcover Book
USD 219.99
Price excludes VAT (USA)
Hardcover Book
USD 219.99
Price excludes VAT (USA)

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Table of contents (17 chapters)

  1. Front Matter

    Pages 1-14
  2. Background

    1. Front Matter

      Pages 1-1
    2. Introduction to Bioinformatics

      • Gautam B. Singh
      Pages 3-10
    3. Introduction to Molecular Biology

      • Gautam B. Singh
      Pages 11-35
    4. Biological Databases

      • Gautam B. Singh
      Pages 37-76
    5. Processing Biological Sequences with MATLAB

      • Gautam B. Singh
      Pages 77-93
  3. Information Retrieval from Biological Databases

    1. Front Matter

      Pages 95-96
    2. Sequence Homology

      • Gautam B. Singh
      Pages 97-125
    3. Protein Alignments

      • Gautam B. Singh
      Pages 127-142
    4. Multiple Sequence Alignment

      • Gautam B. Singh
      Pages 143-158
    5. Alignment Tools

      • Gautam B. Singh
      Pages 159-170
    6. Biolinguistic Methods

      • Gautam B. Singh
      Pages 171-188
  4. Biological Sequence Analysis

    1. Front Matter

      Pages 189-191
    2. Sequence Models

      • Gautam B. Singh
      Pages 193-206
    3. Subsequence Pattern Models

      • Gautam B. Singh
      Pages 207-220
    4. Gene Models

      • Gautam B. Singh
      Pages 221-231
  5. Phylogenetics and Systems Biology

    1. Front Matter

      Pages 233-233
    2. Introduction to Phylogenetic Reconstruction

      • Gautam B. Singh
      Pages 235-252
    3. Distance Based Methods

      • Gautam B. Singh
      Pages 253-260
    4. Character Based Methods: Parsimony

      • Gautam B. Singh
      Pages 261-271

About this book

This book offers comprehensive coverage of all the core topics of bioinformatics, and includes practical examples completed using the MATLAB bioinformatics toolbox™. It is primarily intended as a textbook for engineering and computer science students attending advanced undergraduate and graduate courses in bioinformatics and computational biology. The book develops bioinformatics concepts from the ground up, starting with an introductory chapter on molecular biology and genetics. This chapter will enable physical science students to fully understand and appreciate the ultimate goals of applying the principles of information technology to challenges in biological data management, sequence analysis, and systems biology. The first part of the book also includes a survey of existing biological databases, tools that have become essential in today’s biotechnology research. The second part of the book covers methodologies for retrieving biological information, including fundamental algorithms for sequence comparison, scoring, and determining evolutionary distance. The main focus of the third part is on modeling biological sequences and patterns as Markov chains. It presents key principles for analyzing and searching for sequences of significant motifs and biomarkers. The last part of the book, dedicated to systems biology, covers phylogenetic analysis and evolutionary tree computations, as well as gene expression analysis with microarrays. In brief, the book offers the ideal hands-on reference guide to the field of bioinformatics and computational biology.

 

Keywords

  • Alignment functions in MATLAB
  • Bioinformatics with Perl
  • Biolinguistic methods
  • Biological databases
  • DNA patterns
  • Hidden Markov Models
  • Information retrieval
  • MATLAB for microarrays
  • Phylogenetic Analysis in MATLAB
  • Phylogenetic Trees

Reviews

“As this area of study has grown, textbooks such as this one are appearing for undergraduate or graduate courses in bioinformatics and computational biology. … This book is an introduction to the use of computational techniques to analyze biological data. … The book is logically organized, understandable, and clearly written … . the book offers a competent overview of the core topics of bioinformatics.” (G. R. Mayforth, Computing Reviews, September, 2015)

“This work, a recent addition to the introductory textbook arena, differentiates itself by utilizing MATLAB for sequence analysis and experimentation. … the book offers one more good choice for introductory bioinformatics courses and can be especially valuable to students who are already familiar with MATLAB. Summing Up: Recommended. Upper-division undergraduates and graduate students.” (D. Papamichail, Choice, Vol. 52 (9), May, 2015)

“The author accomplishes his declared objective: to contribute to the creation of educational resources for undergraduate students in computer engineering who are interested in specializing in the new field of bioinformatics. Responding to this need, every chapter includes many examples using MATLAB bioinformatics tools and some proposed exercises.” (Valentin V. Inceu, Computing Reviews, March, 2015)

“This book is built as an introductory textbook (structured for students with computing background) for the rapidly developing, interdisciplinary field of bioinformatics. … although written for students (undergraduate and post-graduate) with a background in computing, the book can be adapted for students with a background in biology or chemistry. This book is a timely addition to the recently emerged and quickly developing field of computational biology.” (Irina Ioana Mohorianu, zbMATH 1306.92001, 2015)

Authors and Affiliations

  • Department of Computer Science and Engineering, Oakland University, Rochester, USA

    Gautam B. Singh

Bibliographic Information

Buying options

eBook
USD 169.00
Price excludes VAT (USA)
  • ISBN: 978-3-319-11403-3
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Softcover Book
USD 219.99
Price excludes VAT (USA)
Hardcover Book
USD 219.99
Price excludes VAT (USA)