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Author: David Wayne Ussery
Publisher: Springer Science & Business Media
ISBN: 1848002548
Category : Science
Languages : en
Pages : 272
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Book Description
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: David Wayne Ussery
Publisher: Springer Science & Business Media
ISBN: 1848002548
Category : Science
Languages : en
Pages : 272
Get Book Here
Book Description
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
Publisher: Springer Science & Business Media
ISBN: 1475737831
Category : Science
Languages : en
Pages : 482
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Book Description
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: Ying Xu
Publisher: World Scientific
ISBN: 1860949827
Category : Medical
Languages : en
Pages : 494
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Book Description
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: Linda Bruslind
Publisher:
ISBN:
Category : Biology
Languages : en
Pages : 0
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Book Description
Welcome to the wonderful world of microbiology! Yay! So. What is microbiology? If we break the word down it translates to "the study of small life," where the small life refers to microorganisms or microbes. But who are the microbes? And how small are they? Generally microbes can be divided in to two categories: the cellular microbes (or organisms) and the acellular microbes (or agents). In the cellular camp we have the bacteria, the archaea, the fungi, and the protists (a bit of a grab bag composed of algae, protozoa, slime molds, and water molds). Cellular microbes can be either unicellular, where one cell is the entire organism, or multicellular, where hundreds, thousands or even billions of cells can make up the entire organism. In the acellular camp we have the viruses and other infectious agents, such as prions and viroids. In this textbook the focus will be on the bacteria and archaea (traditionally known as the "prokaryotes,") and the viruses and other acellular agents.
Author: João Carlos Setubal
Publisher: Springer Nature
ISBN: 1071638386
Category :
Languages : en
Pages : 622
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Book Description
Author: Surajit Das
Publisher: Academic Press
ISBN: 0128148500
Category : Science
Languages : en
Pages : 715
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Book Description
Microbial Diversity in the Genomic Era presents insights on the techniques used for microbial taxonomy and phylogeny, along with their applications and respective pros and cons. Though many advanced techniques for the identification of any unknown bacterium are available in the genomics era, a far fewer number of the total microbial species have been discovered and identified to date. The assessment of microbial taxonomy and biosystematics techniques discovered and practiced in the current genomics era with suitable recommendations is the prime focus of this book. - Discusses the techniques used for microbial taxonomy and phylogeny with their applications and respective pros and cons - Reviews the evolving field of bacterial typing and the genomic technologies that enable comparative analysis of multiple genomes and the metagenomes of complex microbial environments - Provides a uniform, standard methodology for species designation
Author: Maria Anisimova
Publisher: Humana Press
ISBN: 9781617795848
Category : Medical
Languages : en
Pages : 556
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Book Description
Together with early theoretical work in population genetics, the debate on sources of genetic makeup initiated by proponents of the neutral theory made a solid contribution to the spectacular growth in statistical methodologies for molecular evolution. Evolutionary Genomics: Statistical and Computational Methods is intended to bring together the more recent developments in the statistical methodology and the challenges that followed as a result of rapidly improving sequencing technologies. Presented by top scientists from a variety of disciplines, the collection includes a wide spectrum of articles encompassing theoretical works and hands-on tutorials, as well as many reviews with key biological insight. Volume 2 begins with phylogenomics and continues with in-depth coverage of natural selection, recombination, and genomic innovation. The remaining chapters treat topics of more recent interest, including population genomics, -omics studies, and computational issues related to the handling of large-scale genomic data. Written in the highly successful Methods in Molecular BiologyTM series format, this work provides the kind of advice on methodology and implementation that is crucial for getting ahead in genomic data analyses. Comprehensive and cutting-edge, Evolutionary Genomics: Statistical and Computational Methods is a treasure chest of state-of the-art methods to study genomic and omics data, certain to inspire both young and experienced readers to join the interdisciplinary field of evolutionary genomics.
Author: Institute of Medicine
Publisher: National Academies Press
ISBN: 0309268192
Category : Science
Languages : en
Pages : 429
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Book Description
Over the past several decades, new scientific tools and approaches for detecting microbial species have dramatically enhanced our appreciation of the diversity and abundance of the microbiota and its dynamic interactions with the environments within which these microorganisms reside. The first bacterial genome was sequenced in 1995 and took more than 13 months of work to complete. Today, a microorganism's entire genome can be sequenced in a few days. Much as our view of the cosmos was forever altered in the 17th century with the invention of the telescope, these genomic technologies, and the observations derived from them, have fundamentally transformed our appreciation of the microbial world around us. On June 12 and 13, 2012, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to discuss the scientific tools and approaches being used for detecting and characterizing microbial species, and the roles of microbial genomics and metagenomics to better understand the culturable and unculturable microbial world around us. Through invited presentations and discussions, participants examined the use of microbial genomics to explore the diversity, evolution, and adaptation of microorganisms in a wide variety of environments; the molecular mechanisms of disease emergence and epidemiology; and the ways that genomic technologies are being applied to disease outbreak trace back and microbial surveillance. Points that were emphasized by many participants included the need to develop robust standardized sampling protocols, the importance of having the appropriate metadata, data analysis and data management challenges, and information sharing in real time. The Science and Applications of Microbial Genomics summarizes this workshop.
Author: Hervé Tettelin
Publisher: Springer Nature
ISBN: 3030382818
Category : Science
Languages : en
Pages : 311
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Book Description
This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes. The book’s respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory. Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics.
Author: Slava S. Epstein
Publisher: Springer Science & Business Media
ISBN: 3540854657
Category : Medical
Languages : en
Pages : 215
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Book Description
In 1898, an Austrian microbiologist Heinrich Winterberg made a curious observation: the number of microbial cells in his samples did not match the number of colonies formed on nutrient media (Winterberg 1898). About a decade later, J. Amann qu- tified this mismatch, which turned out to be surprisingly large, with non-growing cells outnumbering the cultivable ones almost 150 times (Amann 1911). These papers signify some of the earliest steps towards the discovery of an important phenomenon known today as the Great Plate Count Anomaly (Staley and Konopka 1985). Note how early in the history of microbiology these steps were taken. Detecting the Anomaly almost certainly required the Plate. If so, then the period from 1881 to 1887, the years when Robert Koch and Petri introduced their key inventions (Koch 1881; Petri 1887), sets the earliest boundary for the discovery, which is remarkably close to the 1898 observations by H. Winterberg. Celebrating its 111th anniversary, the Great Plate Count Anomaly today is arguably the oldest unresolved microbiological phenomenon. In the years to follow, the Anomaly was repeatedly confirmed by all microb- logists who cared to compare the cell count in the inoculum to the colony count in the Petri dish (cf., Cholodny 1929; Butkevich 1932; Butkevich and Butkevich 1936). By mid-century, the remarkable difference between the two counts became a universally recognized phenomenon, acknowledged by several classics of the time (Waksman and Hotchkiss 1937; ZoBell 1946; Jannasch and Jones 1959).
