Computational Methods For Understanding Bacterial And Archaeal Genomes

Author : Ying Xu,J. Peter Gogarten
Publisher : World Scientific
Page : 494 pages
File Size : 49,8 Mb
Release : 2008
Category : Medical
ISBN : 9781860949821

Get Book

Computational Methods for Understanding Bacterial and Archaeal Genomes by Ying Xu,J. Peter Gogarten Pdf

Over 500 prokaryotic genomes have been sequenced to date, and thousands more have been planned for the next few years. While these genomic sequence data provide unprecedented opportunities for biologists to study the world of prokaryotes, they also raise extremely challenging issues such as how to decode the rich information encoded in these genomes. This comprehensive volume includes a collection of cohesively written chapters on prokaryotic genomes, their organization and evolution, the information they encode, and the computational approaches needed to derive such information. A comparative view of bacterial and archaeal genomes, and how information is encoded differently in them, is also presented. Combining theoretical discussions and computational techniques, the book serves as a valuable introductory textbook for graduate-level microbial genomics and informatics courses.

Author : Ying Xu
Publisher : Imperial College Press
Page : 494 pages
File Size : 41,9 Mb
Release : 2008
Category : Science
ISBN : 9781860949838

Get Book

Computational Methods for Understanding Bacterial and Archaeal Genomes by Ying Xu Pdf

Over 500 prokaryotic genomes have been sequenced to date, and thousands more have been planned for the next few years. While these genomic sequence data provide unprecedented opportunities for biologists to study the world of prokaryotes, they also raise extremely challenging issues such as how to decode the rich information encoded in these genomes. This comprehensive volume includes a collection of cohesively written chapters on prokaryotic genomes, their organization and evolution, the information they encode, and the computational approaches needed to derive such information. A comparative view of bacterial and archaeal genomes, and how information is encoded differently in them, is also presented. Combining theoretical discussions and computational techniques, the book serves as a valuable introductory textbook for graduate-level microbial genomics and informatics courses.

Author : David Wayne Ussery,Trudy M. Wassenaar,Stefano Borini
Publisher : Springer Science & Business Media
Page : 272 pages
File Size : 54,9 Mb
Release : 2009-02-26
Category : Science
ISBN : 9781848002548

Get Book

Computing for Comparative Microbial Genomics by David Wayne Ussery,Trudy M. Wassenaar,Stefano Borini Pdf

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.

Author : Eugene V. Koonin,Michael Galperin
Publisher : Springer Science & Business Media
Page : 482 pages
File Size : 50,9 Mb
Release : 2013-06-29
Category : Science
ISBN : 9781475737837

Get Book

Sequence — Evolution — Function by Eugene V. Koonin,Michael Galperin Pdf

Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis. Sequence - Evolution - Function should help bridge the "digital divide" between biologists and computer scientists, allowing biologists to better grasp the peculiarities of the emerging field of Genome Biology and to learn how to benefit from the enormous amount of sequence data available in the public databases. The book is non-technical with respect to the computer methods for genome analysis and discusses these methods from the user's viewpoint, without addressing mathematical and algorithmic details. Prior practical familiarity with the basic methods for sequence analysis is a major advantage, but a reader without such experience will be able to use the book as an introduction to these methods. This book is perfect for introductory level courses in computational methods for comparative and functional genomics.

Author : Joao Carlos Setubal,Jens Stoye,Bas E. Dutilh
Publisher : Frontiers Media SA
Page : 170 pages
File Size : 55,5 Mb
Release : 2021-02-02
Category : Science
ISBN : 9782889664375

Get Book

Computational Methods for Microbiome Analysis by Joao Carlos Setubal,Jens Stoye,Bas E. Dutilh Pdf

Author : Alessio Mengoni,Giovanni Bacci,Marco Fondi
Publisher : Humana
Page : 268 pages
File Size : 51,6 Mb
Release : 2022-05-21
Category : Science
ISBN : 1071611011

Get Book

Bacterial Pangenomics by Alessio Mengoni,Giovanni Bacci,Marco Fondi Pdf

This completely revised edition explores novel discoveries in bacterial genomic research, with a focus on technical and computational improvements as well as methods used for bacterial pangenome analysis, which relies on microbiome studies and metagenomic data. Beginning with up-to-date sequencing methods, the book continues with sections covering methods for deep phylogenetic analysis, the role of metagenomic data in understanding the genomics of the many yet uncultured bacteria, progress in genome-to-phenome inference, as well as computational genomic tools. Written for the highly successful Methods in Molecular Biology series, chapters include the type of practical detail necessary for reproducible results in the lab. Authoritative and up-to-date, Bacterial Pangenomics: Methods and Protocols, Second Edition serves as an ideal guide for both highly qualified investigators in bacterial genomics and for less experienced researchers, including students and teachers, who could use a reference for approaching genomic analysis and genome data.

Author : National Research Council,Division on Earth and Life Studies,Board on Life Sciences,Committee on Metagenomics: Challenges and Functional Applications
Publisher : National Academies Press
Page : 170 pages
File Size : 49,6 Mb
Release : 2007-06-24
Category : Science
ISBN : 9780309106764

Get Book

The New Science of Metagenomics by National Research Council,Division on Earth and Life Studies,Board on Life Sciences,Committee on Metagenomics: Challenges and Functional Applications Pdf

Although we can't usually see them, microbes are essential for every part of human life-indeed all life on Earth. The emerging field of metagenomics offers a new way of exploring the microbial world that will transform modern microbiology and lead to practical applications in medicine, agriculture, alternative energy, environmental remediation, and many others areas. Metagenomics allows researchers to look at the genomes of all of the microbes in an environment at once, providing a "meta" view of the whole microbial community and the complex interactions within it. It's a quantum leap beyond traditional research techniques that rely on studying-one at a time-the few microbes that can be grown in the laboratory. At the request of the National Science Foundation, five Institutes of the National Institutes of Health, and the Department of Energy, the National Research Council organized a committee to address the current state of metagenomics and identify obstacles current researchers are facing in order to determine how to best support the field and encourage its success. The New Science of Metagenomics recommends the establishment of a "Global Metagenomics Initiative" comprising a small number of large-scale metagenomics projects as well as many medium- and small-scale projects to advance the technology and develop the standard practices needed to advance the field. The report also addresses database needs, methodological challenges, and the importance of interdisciplinary collaboration in supporting this new field.

Author : Eberhard Voit
Publisher : Garland Science
Page : 604 pages
File Size : 46,9 Mb
Release : 2017-09-05
Category : Computers
ISBN : 9781351332934

Get Book

A First Course in Systems Biology by Eberhard Voit Pdf

A First Course in Systems Biology is an introduction for advanced undergraduate and graduate students to the growing field of systems biology. Its main focus is the development of computational models and their applications to diverse biological systems. The book begins with the fundamentals of modeling, then reviews features of the molecular inventories that bring biological systems to life and discusses case studies that represent some of the frontiers in systems biology and synthetic biology. In this way, it provides the reader with a comprehensive background and access to methods for executing standard systems biology tasks, understanding the modern literature, and launching into specialized courses or projects that address biological questions using theoretical and computational means. New topics in this edition include: default modules for model design, limit cycles and chaos, parameter estimation in Excel, model representations of gene regulation through transcription factors, derivation of the Michaelis-Menten rate law from the original conceptual model, different types of inhibition, hysteresis, a model of differentiation, system adaptation to persistent signals, nonlinear nullclines, PBPK models, and elementary modes. The format is a combination of instructional text and references to primary literature, complemented by sets of small-scale exercises that enable hands-on experience, and large-scale, often open-ended questions for further reflection.

Author : Hon Wai Leong
Publisher : Imperial College Press
Page : 145 pages
File Size : 48,5 Mb
Release : 2008
Category : Science
ISBN : 9781848162525

Get Book

Regulatory Genomics by Hon Wai Leong Pdf

Research in the field of gene regulation is evolving rapidly in the ever-changing scientific environment. Advances in microarray techniques and comparative genomics have enabled more comprehensive studies of regulatory genomics. The study of genomic binding locations of transcription factors has enabled a more comprehensive modeling of regulatory networks. In addition, complete genomic sequences and comparison of numerous related species have demonstrated the conservation of non-coding DNA sequences, which often provide evidence for cis-regulatory binding sites. Systematic methods to decipher the regulatory mechanism are also crucial for corroborating these regulatory networks; key to these methods are motif discovery algorithms that can help predict cis-regulatory elements. These DNA-motif discovery programs are becoming more sophisticated and are beginning to leverage evidence from comparative genomics. These topics and more were discussed at the 3rd Annual RECOMB Workshop on Regulatory Genomics, which brought together more than 90 attendees and included about 22 excellent talks from leading researchers in the field. This proceedings volume contains ten selected, original manuscripts that were presented during the workshop.

Author : Wang Ziling,Zhang Lishu
Publisher : World Scientific
Page : 304 pages
File Size : 46,9 Mb
Release : 2013-10-10
Category : Computers
ISBN : 9781848169265

Get Book

Essential Computing Skills for Biologists by Wang Ziling,Zhang Lishu Pdf

This is a handbook of methods and protocols for biologists. It aimed at undergraduate, graduate students and researchers originally trained in biological or medical sciences who need to know how to access the data archives of genomes, proteins, metabolites, gene expression profiles and the questions these data and tools can answer. For each chapter, the conceptual and experimental background is provided, together with specific guidelines for handling raw data, including preprocessing and analysis. The content is structured into three parts. Part one introduces basic knowledge about popular bioinformatics tools, databases and web resources. Part two presents examples of omics bioinformatics applications. Part three provides basic statistical analysis skills and programming skills needed to handle and analyze omics datasets.

Author : Dong Xu,James M Keller,Mihail Popescu,Rajkumar Bondugula
Publisher : World Scientific
Page : 248 pages
File Size : 55,9 Mb
Release : 2008-08-11
Category : Computers
ISBN : 9781908978714

Get Book

Applications of Fuzzy Logic in Bioinformatics by Dong Xu,James M Keller,Mihail Popescu,Rajkumar Bondugula Pdf

Many biological systems and objects are intrinsically fuzzy as their properties and behaviors contain randomness or uncertainty. In addition, it has been shown that exact or optimal methods have significant limitation in many bioinformatics problems. Fuzzy set theory and fuzzy logic are ideal to describe some biological systems/objects and provide good tools for some bioinformatics problems. This book comprehensively addresses several important bioinformatics topics using fuzzy concepts and approaches, including measurement of ontological similarity, protein structure prediction/analysis, and microarray data analysis. It also reviews other bioinformatics applications using fuzzy techniques. Contents:Introduction to BioinformaticsIntroduction to Fuzzy Set Theory and Fuzzy LogicFuzzy Similarities in OntologiesFuzzy Logic in Structural BioinformaticsApplication of Fuzzy Logic in Microarray Data AnalysesOther ApplicationsSummary and Outlook Readership: Postdoctoral fellows, students, senior investigators and professional practitioners/bioinformatics experts. Also used as a textbook for upper undergraduates and graduates in bioinformatics. Keywords:Bioinformatics;Fuzzy Set Theory;Fuzzy Logic;Clustering;Ontology;Protein StructureKey Features:Bridges two important research areas — computational intelligence and bioinformaticsChapters are connected seamlessly through a systematic design of the overall structure of the bookProvides appendices on fundamental biological concepts and online resources related to the bookJames Keller, a renowned scientist in computational intelligence, pioneered a number of methods in fuzzy set theoryDong Xu, a well-known researcher in bioinformatics, developed several widely-used bioinformatics tools

Author : Michel Blot
Publisher : Birkhäuser
Page : 220 pages
File Size : 50,5 Mb
Release : 2013-12-01
Category : Science
ISBN : 9783034889636

Get Book

Prokaryotic Genomics by Michel Blot Pdf

Prokaryotic Genomics provides molecular microbiologists in particular and researchers working with bacteria in general with the most important established recipes needed for their work. The volume covers both revisited classical methods and new tools for global analysis such as genomics or proteomics. It is written for those in need of a bench manual to complete their experiments and for those wanting to understand the modern tools used in microbiology.

Author : Anonim
Publisher : Unknown
Page : 664 pages
File Size : 52,8 Mb
Release : 2009
Category : Biology
ISBN : WISC:89099259947

Get Book

Philosophical Transactions of the Royal Society of London by Anonim Pdf

Author : Diana Marco
Publisher : Caister Academic Press Limited
Page : 0 pages
File Size : 51,6 Mb
Release : 2010
Category : Science
ISBN : 1904455549

Get Book

Metagenomics by Diana Marco Pdf

The book is essential reading for all researchers currently performing metagenomics studies and is highly recommended for all students and scientists wishing to increase their understanding of this field.

Author : Maria Anisimova
Publisher : Unknown
Page : 128 pages
File Size : 46,5 Mb
Release : 2012
Category : Evolutionary genetics
ISBN : 1617795828

Get Book

Evolutionary Genomics by Maria Anisimova Pdf