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Bioinformatics and the Cell

Modern Computational Approaches in Genomics, Proteomics and Transcriptomics

  • Book
  • © 2007

Overview

Authors:
  1. Xuhua Xia

    1. CAREG and Biology Department, University of Ottawa, K1N 6N5, 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
  • Includes supplementary material: sn.pub/extras

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Table of contents (14 chapters)

  1. Front Matter

    Pages i-xv
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  2. Blast and Fasta

    Pages 1-22

  3. Sequence alignment

    Pages 23-48

  4. Contig assembly

    Pages 49-61

  5. DNA replication and viral evolution

    Pages 62-77

  6. Gene and motif prediction

    Pages 78-108

  7. Hidden Markov Models

    Pages 109-132

  8. Gibbs Sampler

    Pages 133-147

  9. Bioinformatics and vertebrate mitochondria

    Pages 148-172

  10. Characterizing translation efficiency

    Pages 173-206

  11. Protein isoelectric point

    Pages 207-219

  12. Bioinformatics and Two-Dimensional Protein Separation

    Pages 220-230

  13. Self-Organizing Map and other clustering Algorithms

    Pages 231-250

  14. Molecular Phylogenetics

    Pages 251-292

  15. Fundamentals of Proteomics

    Pages 293-308

  16. Back Matter

    Pages 309-349
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Keywords

About this book

Biological and biomedical sciences are becoming more interdisciplinary, and scientists of the future need inte rdisciplinary training instead of the conventional disciplinary training. Just as Sean Eddy (2005) wiselypointed out that sending monolingual diplomats to the United Nations maynot enhance international collaborations, combining strictly disciplinary scientists trained in either mathematics, computational science or molecular biology will not create a productive inte rdisciplinary team ready to solve interdisciplinary problems. Molecular biology is an interdiscip linary science back in its heyday, and founders of molecular biology were ofte n interdisciplinary scientists. Indeed, Francis Crick considered himself as “a mixture of crystallographer, biophysicist, biochemist, and geneticist” (Crick, 1965). Because it was too cumbersome to explain to people that he was such a mixture, the term “molecular biologist” came handy. To get the crystallographer, biophysicist, biochemist,and geneticist within hi mself to collaborate with each other probably worked better than a team with a crystallographer, a biophysicist, a biochemist and a geneticist who maynot even be interested in each other’s problems.

Reviews

From the reviews:

"In this book the author makes an ‘effort to render both mathematical equations and biology to numbers’. … he works out a lot of illustrative examples to make biologists understand the mathematics and computational scientists understand the biology of a wide range of problems in bioinformatics. … The book is addressed to graduate students majoring in sciences and software engineering. Biologists with a sound knowledge of computer programming should be able to implement the presented algorithms in their own programs." (Wiebke Werft, Zentralblatt MATH, Vol. 1166, 2009)

Authors and Affiliations

  • CAREG and Biology Department, University of Ottawa, K1N 6N5, 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. His web site is at http://dambe.bio.uottawa.ca.

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