Bioinformatics and the Cell: Modern Computational Approaches in Genomics, Proteomics and Transcriptomics

ISBN-13: 9781441943910 / Angielski / Miękka / 2010 / 350 str.

Xuhua Xia

Opis

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."

Recenzje

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)

Spis treści

Blast and Fasta.- Sequence alignment.- Contig assembly.- DNA replication and viral evolution.- Gene and motif prediction.- Hidden Markov Models.- Gibbs Sampler.- Bioinformatics and vertebrate mitochondria.- Characterizing translation efficiency.- Protein isoelectric point.- Bioinformatics and Two-Dimensional Protein Separation.- Self-Organizing Map and other clustering Algorithms.- Molecular Phylogenetics.- Fundamentals of Proteomics.

O autorze

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.

Blurb

"Xuhua Xia’s Bioinformatics and the Cell is a welcome addition to the bourgeoning field of bioinformatics text books. Xia stakes out a too-often neglected middle ground in bioinformatics by presenting a work that emphasizes methods’ biological utility without eschewing algorithmic formalism. Readers will find a well-rounded presentation of bioinformatics techniques employed in genomics, transcriptomics and proteomics – unified throughout by the common theme of molecular evolution."

- I. King Jordan, School of Biology, Georgia Institute of Technology

"Bioinformatics and the Cell is a remarkable book because it integrates the more technical and mathematical aspects of bioinformatics with concrete examples of their application to current research problems in molecular and cellular biology. I believe that 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 students entering the new and emerging field of Systems Biology. This is truly a path breaking book."

- Donal Hickey, Concordia University, Montreal, Quebec, Canada

Bioinformatics and the Cell is the 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, with a focus on interactions among DNA, RNA and proteins in the cell. A sample of the illustrated algorithms includes:

• String matching algorithms with associated statistics
• Sequence alignment with the affine function and profile alignment for multiple sequence alignment
• Contig assembly algorithms
• Perceptrons
• Hidden Markov models
• Gibbs sampler
• Self-organizing map
• Algorithms in molecular phylogenetics
• EM algorithm for maximum likelihood calculation
• Monte Carlo integration and Markov chain Monte Carlo algorithms for Bayesian inference
• Mass deconvolution and computational methods for peptide mass fingerprinting

By rendering both mathematics and biology to numbers, 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.

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.