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© 2015

Fundamentals of Bioinformatics and Computational Biology

Methods and Exercises in MATLAB

  • 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

Book

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

Table of contents

  1. Front Matter
    Pages 1-14
  2. Background

    1. Front Matter
      Pages 1-1
    2. Gautam B. Singh
      Pages 3-10
    3. Gautam B. Singh
      Pages 11-35
    4. Gautam B. Singh
      Pages 37-76
    5. Gautam B. Singh
      Pages 77-93
  3. Information Retrieval from Biological Databases

    1. Front Matter
      Pages 95-96
    2. Gautam B. Singh
      Pages 97-125
    3. Gautam B. Singh
      Pages 127-142
    4. Gautam B. Singh
      Pages 143-158
    5. Gautam B. Singh
      Pages 159-170
    6. Gautam B. Singh
      Pages 171-188
  4. Biological Sequence Analysis

    1. Front Matter
      Pages 189-191
    2. Gautam B. Singh
      Pages 193-206
    3. Gautam B. Singh
      Pages 207-220
    4. Gautam B. Singh
      Pages 221-231
  5. Phylogenetics and Systems Biology

    1. Front Matter
      Pages 233-233
    2. Gautam B. Singh
      Pages 235-252
    3. Gautam B. Singh
      Pages 253-260
    4. Gautam B. Singh
      Pages 261-271

About this book

Introduction

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

Authors and affiliations

  1. 1.Department of Computer Science and EngineeringOakland UniversityRochesterUSA

Bibliographic information

  • Book Title Fundamentals of Bioinformatics and Computational Biology
  • Book Subtitle Methods and Exercises in MATLAB
  • Authors Gautam B. Singh
  • Series Title Modeling and Optimization in Science and Technologies
  • Series Abbreviated Title Modeling and Optimization in Science and Technologies
  • DOI https://doi.org/10.1007/978-3-319-11403-3
  • Copyright Information Springer International Publishing Switzerland 2015
  • Publisher Name Springer, Cham
  • eBook Packages Engineering Engineering (R0)
  • Hardcover ISBN 978-3-319-11402-6
  • Softcover ISBN 978-3-319-38313-2
  • eBook ISBN 978-3-319-11403-3
  • Series ISSN 2196-7326
  • Series E-ISSN 2196-7334
  • Edition Number 1
  • Number of Pages XVI, 339
  • Number of Illustrations 97 b/w illustrations, 9 illustrations in colour
  • Topics Computational Intelligence
    Computational Biology/Bioinformatics
    Bioinformatics
  • Buy this book on publisher's site
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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)