Tools and Applications

  • David Edwards
  • Jason  Stajich
  • David Hansen

Table of contents

  1. Front Matter
    Pages i-xii
  2. David Edwards, David Hansen, Jason E. Stajich
    Pages 1-11
  3. Michael Imelfort
    Pages 13-37
  4. Sheldon McKay, Scott Cain
    Pages 39-63
  5. Laura A. Kavanaugh, Uwe Ohler
    Pages 65-97
  6. William H. Majoros, Ian Korf, Uwe Ohler
    Pages 99-119
  7. Laurens Wilming, Jennifer Harrow
    Pages 121-136
  8. Alan Moses, Saurabh Sinha
    Pages 137-163
  9. Chris Duran, David Edwards, Jacqueline Batley
    Pages 165-189
  10. Lakshmi K. Matukumalli, Steven G. Schroeder
    Pages 191-207
  11. Terry Clark
    Pages 209-223
  12. Sitao Wu, Yang Zhang
    Pages 225-242
  13. Amandeep S. Sidhu, Matthew I. Bellgard, Tharam S. Dillon
    Pages 243-258
  14. Christopher M. Gowen, Stephen S. Fong
    Pages 279-292
  15. Stephen A. Chervitz, Helen Parkinson, Jennifer M. Fostel, Helen C. Causton, Susanna-Assunta Sanson, Eric W. Deutsch et al.
    Pages 293-329
  16. J. Lynn Fink
    Pages 331-345
  17. Pierre Zweigenbaum, Dina Demner-Fushman
    Pages 347-380
  18. Daniel Damian
    Pages 381-401
  19. John Boyle
    Pages 403-440
  20. Back Matter
    Pages 441-451

About this book


Biology has progressed tremendously in the last decade due in part to the increased automation in the generation of data from sequences to genotypes to phenotypes. Biology is now very much an information science and bioinformatics provides the means to connect biological data to hypotheses. Bioinformatics: Tools and Applications provides up-to-date descriptions of the various areas of applied bioinformatics, from the analysis of sequence, literature, and functional data to the function and evolution of organisms. The ability to process and interpret large volumes of data is essential with the application of new high throughput DNA sequencers providing an overload of sequence data. Initial chapters provide an introduction to the analysis of DNA and protein sequences, from motif detection to gene prediction and annotation, with specific chapters on DNA and protein databases as well as data visualization. Additional chapters focus on gene expression analysis from the perspective of traditional microarrays and more recent sequence based approaches, followed by an introduction to the evolving field of phenomics, with specific chapters detailing advances in plant and microbial phenome analysis and a chapter dealing with the important issue of standards for functional genomics. Further chapters present the area of literature databases and associated mining tools which are becoming increasingly essential to interpret the vast volume of published biological information, while the final chapters present bioinformatics purely from a developers point of view, describing the various data and databases as well as common programming languages used for bioinformatics applications. These chapters provide an introduction and motivation to further avenues for implementation. Together, this volume aims to provide a resource for biology students wanting a greater understanding of the encroaching area of bioinformatics, as well as computer scientists who are interested learning more about the field of applied bioinformatics.

David Edwards gained an Honours degree in agriculture from the University of Nottingham in 1989 and a PhD from the Department of Plant Science, University of Cambridge, UK in 1997. He has held positions within academia (University of Adelaide, Australia; University of Cambridge, UK; and McGill University, Canada), government (Long Ashton Research Centre, UK, Department of Primary Industries, Victoria, Australia) and industry (ICI seeds, UK). David is currently a Principle Research Fellow at the University of Queensland, Australia and leads the bioinformatics group within the Australian Centre for Plant Functional Genomics. David’s areas of interest include applied agricultural biotechnology; the structure and expression of plant genomes; the discovery and application of molecular genetic markers; and applied bioinformatics, with a focus on wheat, barley and Brassica crops.

David Hansen has a Bachelor of Science in Chemistry from the University of Queensland, Brisbane and a PhD in statistical physics from Australian National University. After developing bioinformatics tools at the Wiezmann Institute of Science, Israel and European Bioinformatics Institute, Cambridge, David led the research and development of the SRS genomic data and tool integration software at LION bioscience in Cambridge from 1998 to 2004. David is now a Principal Research Scientist at the CSIRO Australian E-Health Research Centre and leads many research projects in e-Health aimed at improving the collection and use of information relevant to patient health. These research projects are in the areas of health data integration and clinical terminologies, biomedical imaging and remote patient monitoring.

Jason Stajich earned a Bachelor of Science in Computer Science from Duke University in Durham, NC in 1999 and worked as a programmer for the Center for Human Genetics at Duke University Medical Center for two years assisting in building systems supporting human disease gene mapping research. He completed a PhD in Genetics and Genomics from Duke University in 2006 followed by postdoctoral training at the University of California, Berkeley on fellowship from the Miller Institute for Basic Research in Science. Jason is currently an Assistant Professor of Bioinformatics in the Department of Plant Pathology and Microbiology at the University of California, Riverside. Jason’s research focuses on the evolution of fungi studying change at gene and genome scale among populations and across the kingdom employing computational and comparative approaches. He is interested in the emergence and evolution of pathogens and the evolution of development and forms in multicellular fungi.


Annotation DNA DNA sequencing Evolution Translation bioinformatics computer systems currentjks databases gene expression genes genome

Editors and affiliations

  • David Edwards
    • 1
  • Jason  Stajich
    • 2
  • David Hansen
    • 3
  1. 1.Inst. Molecular BioscienceUniversity of QueenslandSt.LuciaAustralia
  2. 2.Dept. Plant & Microbial BiologyUniversity of California, BerkeleyBerkeleyU.S.A.
  3. 3.e-Health Research CentreBrisbaneAustralia

Bibliographic information