Computing for Comparative Microbial Genomics

Computational Biology

Book 8
Springer Science & Business Media
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Overview and Goals This book describes how to visualize and compare bacterial genomes. Sequencing technologies are becoming so inexpensive that soon going for a cup of coffee will be more expensive than sequencing a bacterial genome. Thus, there is a very real and pressing need for high-throughput computational methods to compare hundreds and thousands of bacterial genomes. It is a long road from molecular biology to systems biology, and in a sense this text can be thought of as a path bridging these ? elds. The goal of this book is to p- vide a coherent set of tools and a methodological framework for starting with raw DNA sequences and producing fully annotated genome sequences, and then using these to build up and test models about groups of interacting organisms within an environment or ecological niche. Organization and Features The text is divided into four main parts: Introduction, Comparative Genomics, Transcriptomics and Proteomics, and ? nally Microbial Communities. The ? rst ? ve chapters are introductions of various sorts. Each of these chapters represents an introduction to a speci? c scienti? c ? eld, to bring all readers up to the same basic level before proceeding on to the methods of comparing genomes. First, a brief overview of molecular biology and of the concept of sequences as biological inf- mation are given.
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Additional Information

Publisher
Springer Science & Business Media
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Published on
Dec 16, 2008
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Pages
270
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ISBN
9781848002555
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Language
English
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Genres
Computers / Computer Science
Computers / Programming / General
Medical / Genetics
Science / Life Sciences / General
Science / Life Sciences / Microbiology
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Content Protection
This content is DRM protected.
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The biological interactions of living organisms, and protein-protein interactions in particular, are astonishingly diverse and present numerous challenges to modern biomolecular research because of their complexity. Analysis of patterns and principles governing these interactions has prompted a rapid development of computational methods to identify protein interaction partners and to understand the roles of individual components of protein interaction networks in cell functions.

This book integrates different approaches from bioinformatics, biochemistry, computational analysis and systems biology to offer the reader a comprehensive global view of the diverse data on protein-protein interactions and protein interaction networks. It brings together the descriptions of experimental techniques and expounds on different computational algorithms for protein network analysis and prediction of protein and domain interactions, with each chapter containing a description of the problem, a review of methods and algorithms, a list of resources and current conclusions.

Features

• Reviews experimental techniques for identification of protein interactions

• Discusses protein interaction databases and methods of integrating data from diverse sources

• Describes computational methods to predict protein and domain interaction partners

• Explores the properties of interaction interfaces and highlights approaches to model the assembly of protein complexes

• Examines the topological and dynamical properties of protein interaction networks and presents the tools for comparative analysis of these networks

Written by leading experts, Protein-protein Interactions and Networks provides a broad, thorough and multidisciplinary coverage of this field. It will be invaluable to researchers from academia and the bioinformatics industry, as well as an excellent auxiliary text for graduate students studying the topic.

Today, as hundreds of genomes have been sequenced and thousands of proteins and more than ten thousand metabolites have been identi?ed, navigating safely through this wealth of information without getting completely lost has become crucial for research in, and teaching of, molecular biology. Consequently, a considerable number of tools have been developed and put on the market in the last two decades that describe the multitude of potential/putative interactions between genes, proteins, metabolites, and other biologically relevant compounds in terms of metabolic, genetic, signaling, and other networks, their aim being to support all sorts of explorations through bio-data bases currently called Systems Biology. As a result, navigating safely through this wealth of information-processing tools has become equally crucial for successful work in molecular biology. To help perform such navigation tasks successfully, this book starts by providing an extremely useful overview of existing tools for ?nding (or designing) and inv- tigating metabolic, genetic, signaling, and other network databases, addressing also user-relevant practical questions like • Is the database viewable through a web browser? • Is there a licensing fee? • What is the data type (metabolic, gene regulatory, signaling, etc. )? • Is the database developed/maintained by a curator or a computer? • Is there any software for editing pathways? • Is it possible to simulate the pathway? It then goes on to introduce a speci?c such tool, that is, the fabulous “Cell - lustrator 3. 0” tool developed by the authors.
Biological and biomedical studies have entered a new era over the past two decades thanks to the wide use of mathematical models and computational approaches. A booming of computational biology, which sheerly was a theoretician’s fantasy twenty years ago, has become a reality. Obsession with computational biology and theoretical approaches is evidenced in articles hailing the arrival of what are va- ously called quantitative biology, bioinformatics, theoretical biology, and systems biology. New technologies and data resources in genetics, such as the International HapMap project, enable large-scale studies, such as genome-wide association st- ies, which could potentially identify most common genetic variants as well as rare variants of the human DNA that may alter individual’s susceptibility to disease and the response to medical treatment. Meanwhile the multi-electrode recording from behaving animals makes it feasible to control the animal mental activity, which could potentially lead to the development of useful brain–machine interfaces. - bracing the sheer volume of genetic, genomic, and other type of data, an essential approach is, ?rst of all, to avoid drowning the true signal in the data. It has been witnessed that theoretical approach to biology has emerged as a powerful and st- ulating research paradigm in biological studies, which in turn leads to a new - search paradigm in mathematics, physics, and computer science and moves forward with the interplays among experimental studies and outcomes, simulation studies, and theoretical investigations.
Innate immunity is one the most evolutionally conserved systems, designed to protect the organism from viruses and bacterial infections, stress and many other types of attacks from the outside world. During the past decade, the capacity of molecular biology and information technology to produce and analyse data have grown exponentially, rapidly reforming many aspects of immunology research in the post-genomics era. As a result, scientific understanding of signalling networks governing the innate immunity response in human tissues and other organisms has evolved beyond recognition, compared to even just a decade ago. Many strategies have been designed over the years to identify novel proteins, which have a crucial role in innate immunity responses by regulating particular signalling pathways. These projects had many advantages, including the definition of novel drug targets, as exemplified by the recent success of anti-TNF therapy, as well as leading to a better, system-wide understanding of the molecular control of innate immunity. In the past few years, a new concept, Immunomics, has been adopted to define an emerging, multidisciplinary field of research (Schonbach, 2003). Although rapid progress has been made to identify the proteins playing pivotal roles in the innate immunity–related signalling pathways (for example, TIR signalling pathways), the catalogue of proteins with a key regulatory function identified and studied is far from completed. Novel proteins need to be char- terised to gain a more comprehensive picture of how signalling networks are regulated.
The biological interactions of living organisms, and protein-protein interactions in particular, are astonishingly diverse and present numerous challenges to modern biomolecular research because of their complexity. Analysis of patterns and principles governing these interactions has prompted a rapid development of computational methods to identify protein interaction partners and to understand the roles of individual components of protein interaction networks in cell functions.

This book integrates different approaches from bioinformatics, biochemistry, computational analysis and systems biology to offer the reader a comprehensive global view of the diverse data on protein-protein interactions and protein interaction networks. It brings together the descriptions of experimental techniques and expounds on different computational algorithms for protein network analysis and prediction of protein and domain interactions, with each chapter containing a description of the problem, a review of methods and algorithms, a list of resources and current conclusions.

Features

• Reviews experimental techniques for identification of protein interactions

• Discusses protein interaction databases and methods of integrating data from diverse sources

• Describes computational methods to predict protein and domain interaction partners

• Explores the properties of interaction interfaces and highlights approaches to model the assembly of protein complexes

• Examines the topological and dynamical properties of protein interaction networks and presents the tools for comparative analysis of these networks

Written by leading experts, Protein-protein Interactions and Networks provides a broad, thorough and multidisciplinary coverage of this field. It will be invaluable to researchers from academia and the bioinformatics industry, as well as an excellent auxiliary text for graduate students studying the topic.

"[Kolata] is a gifted storyteller. Her account of the Baxleys... is both engrossing and distressing... Kolata's book raises crucial questions about knowledge that can be both vital and fatal, both pallative and dangerous." —Andrew Solomon, The New York Review of Books

New York Times science reporter Gina Kolata follows a family through genetic illness and one courageous daughter who decides her fate shall no longer be decided by a genetic flaw.

The phone rings. The doctor from California is on the line. “Are you ready Amanda?” The two people Amanda Baxley loves the most had begged her not to be tested—at least, not now. But she had to find out.

If your family carried a mutated gene that foretold a brutal illness and you were offered the chance to find out if you’d inherited it, would you do it? Would you walk toward the problem, bravely accepting whatever answer came your way? Or would you avoid the potential bad news as long as possible?

In Mercies in Disguise, acclaimed New York Times science reporter and bestselling author Gina Kolata tells the story of the Baxleys, an almost archetypal family in a small town in South Carolina. A proud and determined clan, many of them doctors, they are struck one by one with an inscrutable illness. They finally discover the cause of the disease after a remarkable sequence of events that many saw as providential. Meanwhile, science, progressing for a half a century along a parallel track, had handed the Baxleys a resolution—not a cure, but a blood test that would reveal who had the gene for the disease and who did not. And science would offer another dilemma—fertility specialists had created a way to spare the children through an expensive process.

A work of narrative nonfiction, Mercies in Disguise is the story of a family that took matters into its own hands when the medical world abandoned them. It’s a story of a family that had to deal with unspeakable tragedy and yet did not allow it to tear them apart. And it is the story of a young woman—Amanda Baxley—who faced the future head on, determined to find a way to disrupt her family’s destiny.

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