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Computational Methods For Understanding Bacterial And Archaeal Genomes
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Book Synopsis Computational Methods for Understanding Bacterial and Archaeal Genomes by : Ying Xu
Download or read book Computational Methods for Understanding Bacterial and Archaeal Genomes written by Ying Xu and published by Imperial College Press. This book was released on 2008 with total page 494 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Computational Methods for Understanding Bacterial and Archaeal Genomes by : Ying Xu
Download or read book Computational Methods for Understanding Bacterial and Archaeal Genomes written by Ying Xu and published by World Scientific. This book was released on 2008 with total page 494 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis A First Course in Systems Biology by : Eberhard Voit
Download or read book A First Course in Systems Biology written by Eberhard Voit and published by Garland Science. This book was released on 2017-09-05 with total page 783 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Regulatory Genomics by : Hon Wai Leong
Download or read book Regulatory Genomics written by Hon Wai Leong and published by Imperial College Press. This book was released on 2008 with total page 145 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Essential Computing Skills For Biologists by : Ziling Wang
Download or read book Essential Computing Skills For Biologists written by Ziling Wang and published by World Scientific. This book was released on 2018-07-02 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Applications Of Fuzzy Logic In Bioinformatics by : Dong Xu
Download or read book Applications Of Fuzzy Logic In Bioinformatics written by Dong Xu and published by World Scientific. This book was released on 2008-08-11 with total page 246 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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./a
Book Synopsis The New Science of Metagenomics by : National Research Council
Download or read book The New Science of Metagenomics written by National Research Council and published by National Academies Press. This book was released on 2007-06-24 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Philosophical Transactions of the Royal Society of London by :
Download or read book Philosophical Transactions of the Royal Society of London written by and published by . This book was released on 2009 with total page 664 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Sequence — Evolution — Function by : Eugene V. Koonin
Download or read book Sequence — Evolution — Function written by Eugene V. Koonin and published by Springer Science & Business Media. This book was released on 2013-06-29 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Prokaryotic Genomics by : Michel Blot
Download or read book Prokaryotic Genomics written by Michel Blot and published by Birkhäuser. This book was released on 2013-12-01 with total page 220 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Natural Genetic Engineering and Natural Genome Editing, Volume 1178 by : Günther Witzany
Download or read book Natural Genetic Engineering and Natural Genome Editing, Volume 1178 written by Günther Witzany and published by Wiley-Blackwell. This book was released on 2009-11-23 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: "This volume presents manuscripts stemming from the conference "Natural Genetic Engineering and Natural Genome Editing" held on July 3-6, 2008 ... Salzburg, Austria"-- page V.
Download or read book Bacteriophages written by David R. Harper and published by Springer Nature. This book was released on 2021-01-30 with total page 1376 pages. Available in PDF, EPUB and Kindle. Book excerpt: This first major reference work dedicated to the mannifold industrial and medical applications of bacteriophages provides both theoretical and practical insights into the emerging field of bacteriophage biotechnology. The book introduces to bacteriophage biology, ecology and history and reviews the latest technologies and tools in bacteriophage detection, strain optimization and nanotechnology. Usage of bacteriophages in food safety, agriculture, and different therapeutic areas is discussed in detail. This book serves as essential guide for researchers in applied microbiology, biotechnology and medicine coming from both academia and industry.
Book Synopsis Computational Structural Biology by : Torsten Schwede
Download or read book Computational Structural Biology written by Torsten Schwede and published by World Scientific. This book was released on 2008 with total page 790 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is a comprehensive introduction to Landau-Lifshitz equations and Landau-Lifshitz-Maxwell equations, beginning with the work by Yulin Zhou and Boling Guo in the early 1980s and including most of the work done by this Chinese group led by Zhou and Guo since. The book focuses on aspects such as the existence of weak solutions in multi dimensions, existence and uniqueness of smooth solutions in one dimension, relations with harmonic map heat flows, partial regularity and long time behaviors. The book is a valuable reference book for those who are interested in partial differential equations, geometric analysis and mathematical physics. It may also be used as an advanced textbook by graduate students in these fields.
Book Synopsis The Social Biology of Microbial Communities by : Institute of Medicine
Download or read book The Social Biology of Microbial Communities written by Institute of Medicine and published by National Academies Press. This book was released on 2013-01-10 with total page 633 pages. Available in PDF, EPUB and Kindle. Book excerpt: Beginning with the germ theory of disease in the 19th century and extending through most of the 20th century, microbes were believed to live their lives as solitary, unicellular, disease-causing organisms . This perception stemmed from the focus of most investigators on organisms that could be grown in the laboratory as cellular monocultures, often dispersed in liquid, and under ambient conditions of temperature, lighting, and humidity. Most such inquiries were designed to identify microbial pathogens by satisfying Koch's postulates.3 This pathogen-centric approach to the study of microorganisms produced a metaphorical "war" against these microbial invaders waged with antibiotic therapies, while simultaneously obscuring the dynamic relationships that exist among and between host organisms and their associated microorganisms-only a tiny fraction of which act as pathogens. Despite their obvious importance, very little is actually known about the processes and factors that influence the assembly, function, and stability of microbial communities. Gaining this knowledge will require a seismic shift away from the study of individual microbes in isolation to inquiries into the nature of diverse and often complex microbial communities, the forces that shape them, and their relationships with other communities and organisms, including their multicellular hosts. On March 6 and 7, 2012, the Institute of Medicine's (IOM's) Forum on Microbial Threats hosted a public workshop to explore the emerging science of the "social biology" of microbial communities. Workshop presentations and discussions embraced a wide spectrum of topics, experimental systems, and theoretical perspectives representative of the current, multifaceted exploration of the microbial frontier. Participants discussed ecological, evolutionary, and genetic factors contributing to the assembly, function, and stability of microbial communities; how microbial communities adapt and respond to environmental stimuli; theoretical and experimental approaches to advance this nascent field; and potential applications of knowledge gained from the study of microbial communities for the improvement of human, animal, plant, and ecosystem health and toward a deeper understanding of microbial diversity and evolution. The Social Biology of Microbial Communities: Workshop Summary further explains the happenings of the workshop.
Book Synopsis Microbial Genomes by : Claire M. Fraser
Download or read book Microbial Genomes written by Claire M. Fraser and published by Humana Press. This book was released on 2010-12-09 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This collection of diverse articles by the pioneers of modern genomics takes stock of the current state of the field and elucidates the contribution that sequencing genomes has made to our understanding of microbial metabolism and evolution. Through twenty-eight thought-provoking chapters, the authors describe some of the most common computational methods and their applications to studying pathogenic microorganisms, show how genomics can be used to reconstruct the history and dynamism of the microbial world, and discuss issues as diverse as reconstruction of metabolic pathways, cell cycle processes, microbial evolution, metagenomics, and vaccine development. Additional chapters deal with microarrays and expression analysis and the role of genomic in drug discovery.
Book Synopsis Microbiome in Human Health and Disease by : Pallaval Veera Bramhachari
Download or read book Microbiome in Human Health and Disease written by Pallaval Veera Bramhachari and published by Springer Nature. This book was released on 2021-10-18 with total page 306 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book provides an overview on how the microbiome contributes to human health and disease. The microbiome has also become a burgeoning field of research in medicine, agriculture & environment. The readers will obtain profound knowledge on the connection between intestinal microbiota and immune defense systems, medicine, agriculture & environment. The book may address several researchers, clinicians and scholars working in biomedicine, microbiology and immunology. The application of new technologies has no doubt revolutionized the research initiatives providing new insights into the dynamics of these complex microbial communities and their role in medicine, agriculture & environment shall be more emphasized. Drawing on broad range concepts of disciplines and model systems, this book primarily provides a conceptual framework for understanding these human-microbe, animal-microbe & plant-microbe, interactions while shedding critical light on the scientific challenges that lie ahead. Furthermore this book explains why microbiome research demands a creative and interdisciplinary thinking—the capacity to combine microbiology with human, animal and plant physiology, ecological theory with immunology, and evolutionary perspectives with metabolic science.This book provides an accessible and authoritative guide to the fundamental principles of microbiome science, an exciting and fast-emerging new discipline that is reshaping many aspects of the life sciences. These microbial partners can also drive ecologically important traits, from thermal tolerance to diet in a typical immune system, and have contributed to animal and plant diversification over long evolutionary timescales. Also this book explains why microbiome research presents a more complete picture of the biology of humans and other animals, and how it can deliver novel therapies for human health and new strategies.
Book Synopsis Biological Sequence Analysis by : Richard Durbin
Download or read book Biological Sequence Analysis written by Richard Durbin and published by Cambridge University Press. This book was released on 1998-04-23 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Probabilistic models are becoming increasingly important in analysing the huge amount of data being produced by large-scale DNA-sequencing efforts such as the Human Genome Project. For example, hidden Markov models are used for analysing biological sequences, linguistic-grammar-based probabilistic models for identifying RNA secondary structure, and probabilistic evolutionary models for inferring phylogenies of sequences from different organisms. This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis. Written by an interdisciplinary team of authors, it aims to be accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time present the state-of-the-art in this new and highly important field.
