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| bacterial rna seq analysis: Next Generation Sequencing Jerzy Kulski, 2016-01-14 Next generation sequencing (NGS) has surpassed the traditional Sanger sequencing method to become the main choice for large-scale, genome-wide sequencing studies with ultra-high-throughput production and a huge reduction in costs. The NGS technologies have had enormous impact on the studies of structural and functional genomics in all the life sciences. In this book, Next Generation Sequencing Advances, Applications and Challenges, the sixteen chapters written by experts cover various aspects of NGS including genomics, transcriptomics and methylomics, the sequencing platforms, and the bioinformatics challenges in processing and analysing huge amounts of sequencing data. Following an overview of the evolution of NGS in the brave new world of omics, the book examines the advances and challenges of NGS applications in basic and applied research on microorganisms, agricultural plants and humans. This book is of value to all who are interested in DNA sequencing and bioinformatics across all fields of the life sciences. |
| bacterial rna seq analysis: Regulating with RNA in Bacteria and Archaea Gisela Storz, Kai Papenfort, 2018-11-01 Revealing the many roles of RNA in regulating gene expression For decades after the discoveries of messenger RNA, transfer RNA, and ribosomal RNA, it was largely assumed that the role of RNA in the cell was limited to shuttling the genomic message, chaperoning amino acids, and toiling in the ribosomes. Eventually, hints that RNA molecules might have regulatory roles began to appear. With the advent of genomics and bioinformatics, it became evident that numerous other RNA forms exist and have specific functions, including small RNAs (sRNA), RNA thermometers, and riboswitches to regulate core metabolic pathways, bacterial pathogenesis, iron homeostasis, quorum sensing, and biofilm formation. All of these functions, and more, are presented in Regulating with RNA in Bacteria and Archaea, written by RNA biologists from around the globe. Divided into eight sections-RNases and Helicases, Cis-Acting RNAs, Cis Encoded Base Pairing RNAs, Trans-Encoded Base Pairing RNAs, Protein Titration and Scaffolding, General Considerations, Emerging Topics, and Resources-this book serves as an excellent resource for established RNA biologists and for the many scientists who are studying regulated cellular systems. It is no longer a fair assumption that gene expression regulation is the provenance of proteins only or that control is exerted primarily at the level of transcription. This book makes clear that regulatory RNAs are key partners along with proteins in controlling the complex interactions and pathways found within prokaryotes. |
| bacterial rna seq analysis: Regulation of Bacterial Virulence Michael L. Vasil, Andrew J. Darwin, 2012-12-05 A comprehensive compendium of scholarly contributions relating to bacterial virulence gene regulation. • Provides insights into global control and the switch between distinct infectious states (e.g., acute vs. chronic). • Considers key issues about the mechanisms of gene regulation relating to: surface factors, exported toxins and export mechanisms. • Reflects on how the regulation of intracellular lifestyles and the response to stress can ultimately have an impact on the outcome of an infection. • Highlights and examines some emerging regulatory mechanisms of special significance. • Serves as an ideal compendium of valuable topics for students, researchers and faculty with interests in how the mechanisms of gene regulation ultimately affect the outcome of an array of bacterial infectious diseases. |
| bacterial rna seq analysis: Applications of RNA-Seq in Biology and Medicine Irina Vlasova-St. Louis, 2021-10-13 This book evaluates and comprehensively summarizes the scientific findings that have been achieved through RNA-sequencing (RNA-Seq) technology. RNA-Seq transcriptome profiling of healthy and diseased tissues allows FOR understanding the alterations in cellular phenotypes through the expression of differentially spliced RNA isoforms. Assessment of gene expression by RNA-Seq provides new insight into host response to pathogens, drugs, allergens, and other environmental triggers. RNA-Seq allows us to accurately capture all subtypes of RNA molecules, in any sequenced organism or single-cell type, under different experimental conditions. Merging genomics and transcriptomic profiling provides novel information underlying causative DNA mutations. Combining RNA-Seq with immunoprecipitation and cross-linking techniques is a clever multi-omics strategy assessing transcriptional, post-transcriptional and post-translational levels of gene expression regulation. |
| bacterial rna seq analysis: Transcriptomics in Health and Disease Geraldo A. Passos, 2015-01-27 After sequencing the human genome a decade ago, researchers have continued their projects, but now to try to better understand how, and when, genes are expressed in health and disease. Efforts have been concentrated on the measurement of the expression of RNA transcripts. In an analogy to the genome, the term transcriptome was created to refer to the complete set of RNAs in a cell type or tissue in a particular situation. Transcriptomics is the science that studies this issue and it is a branch of functional genomics. Transcriptomics in Heath and Disease provides a comprehensive overview of the science of transcriptomics initially in health, focusing on the concept of the transcriptome and the main methods to evaluate it. The authors discuss the concept and use of gene expression signatures and transcriptional biomarkers in normal development and diseased tissues and organs. As the transcriptome changes depending on the pathology, there is also a focus on the variations in the gene expression in different diseases such as autoimmune, inflammation, cancer and infections. This book should be very useful for researchers in molecular biology focusing on gene expression, human genetics, immunology, and genomics. |
| bacterial rna seq analysis: RNA-Seq Analysis: Methods, Applications and Challenges Filippo Geraci, Indrajit Saha, Monica Bianchini, 2020-06-08 |
| bacterial rna seq analysis: Metabolic Pathway Engineering Michael E. Himmel, Yannick J. Bomble, 2020-07-28 This book illustrates experimental and computational methodologies used to achieve cost effective biological processes for the production of fuels and biochemicals through multiple approaches to increasing yield, titers, and productivity in a robust host. The volume includes the most recent and cutting-edge aspects of pathway engineering, flux analysis, and metabolic enzyme engineering. Each chapter highlights the complexity and challenges of the problem as well as the methods used to solve this problem or changes needed in current methods. As a part of the highly successful Methods in Molecular Biology series, chapters include the kind of detailed implementation advice that gives researchers a much needed boost. Authoritative and practical, Metabolic Pathway Engineering benefits not only scientists working on more fundamental aspects of this endeavor but also those in the biochemical industry working on strain engineering for robust industrial processes. |
| bacterial rna seq analysis: RNA-seq Data Analysis Eija Korpelainen, Jarno Tuimala, Panu Somervuo, Mikael Huss, Garry Wong, 2014-09-19 The State of the Art in Transcriptome AnalysisRNA sequencing (RNA-seq) data offers unprecedented information about the transcriptome, but harnessing this information with bioinformatics tools is typically a bottleneck. RNA-seq Data Analysis: A Practical Approach enables researchers to examine differential expression at gene, exon, and transcript le |
| bacterial rna seq analysis: Photochemistry Angelo Albini, E. Fasani, 2013 Annotation 'Photochemistry' reviews photo-induced processes that have relevance to the wide-ranging academic and commercial disciplines, and interests in chemistry, physics, biology and technology. |
| bacterial rna seq analysis: Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing Ana M. Aransay, José Luis Lavín Trueba, 2016-06-02 High throughput sequencing (HTS) technologies have conquered the genomics and epigenomics worlds. The applications of HTS methods are wide, and can be used to sequence everything from whole or partial genomes, transcriptomes, non-coding RNAs, ribosome profiling, to single-cell sequencing. Having such diversity of alternatives, there is a demand for information by research scientists without experience in HTS that need to choose the most suitable methodology or combination of platforms and to define their experimental designs to achieve their specific objectives. Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing aims to collect in a single volume all aspects that should be taken into account when HTS technologies are being incorporated into a research project and the reasons behind them. Moreover, examples of several successful strategies will be analyzed to make the point of the crucial features. This book will be of use to all scientist that are unfamiliar with HTS and want to incorporate such technologies to their research. |
| bacterial rna seq analysis: RNA Chaperones Tilman Heise, 2020 This book provides a wide spectrum of methods to study RNA chaperones in vitro, at the single molecule level, and protocols useful for cell-based assays. Beginning with a section on a number of bacterial proteins for study, the volume also explores proteins from eukaryotic cells and how to delve into the complex interactions between RNA chaperones and the folding and unfolding of proteins. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, RNA Chaperones: Methods and Protocols serves as an ideal guide for scientists and students interested in RNA biology and RNA chaperones. Chapter 3 is available Open Access under a CC-BY 4.0 license via link.springer.com. |
| bacterial rna seq analysis: Molecular Microbial Ecology of the Rhizosphere, 2 Volume Set Frans J. de Bruijn, 2013-06-04 Molecular Microbial Ecology of the Rhizosphere covers current knowledge on the molecular basis of plant-microbe interactions in the rhizosphere. Also included in the book are both reviews and research-based chapters describing experimental materials and methods. Edited by a leader in the field, with contributions from authors around the world, Molecular Microbial Ecology of the Rhizosphere brings together the most up-to-date research in this expanding area, and will be a valuable resource for molecular microbiologists and plant soil scientists, as well as upper level students in microbiology, ecology, and agriculture. |
| bacterial rna seq analysis: Invertebrate Immunity Kenneth Söderhäll, 2011-06-28 It can be seen that the insects are the still attracting most research and researchers. However, an increasing interest is emerging to study new invertebrate groups, especially those where the genome is known. Even though Drosophila has been and still is an excellent model for immune studies, it is now clear that there are great differences between immune responses in Drosophila and that of several other invertebrates, which indeed calls for more research on other invertebrates |
| bacterial rna seq analysis: Molecular Infection Biology Jörg Hinrich Hacker, Jürgen Heesemann, 2002-10-03 This comprehensive volume focuses on molecular methods and principles of prokaryotic and eukaryotic pathogens. The authors present the molecular and cellular aspects by focusing on the interactions between pathogenic microorganisms and their hosts. The publication begins with an overview of the most important and dangerous causative agents of infectious diseases. Next are discussions of how microbial weapons, pathogenicity factors, protein secretion machines, and surface variation systems work, presenting the molecular and genetic methods that are used by scientists for their discovery and analysis. Furthermore, infectious diseases are discussed in light of the newly formed research areas of evolutionary and cellular microbiology and genomics. Future aspects on diagnostic techniques, therapy, and vaccine development are also presented. |
| bacterial rna seq analysis: Bacterial Regulatory RNA Veronique Arluison, Claudio Valverde, 2018 |
| bacterial rna seq analysis: Quantitative Real-Time PCR Roberto Biassoni, Alessandro Raso, 2014-04-17 Quantitative Real-Time PCR: Methods and Protocols focuses on different applications of qPCR ranging from microbiological detections (both viral and bacterial) to pathological applications. Several chapters deal with quality issues which regard the quality of starting material, the knowledge of the minimal information required to both perform an assay and to set the experimental plan, while the others focus on translational medicine applications that are ordered following an approximate logical order of their medical application. The last part of the book gives you an idea of an emerging digital PCR technique that is a unique qPCR approach for measuring nucleic acid, particularly suited for low level detection and to develop non-invasive diagnosis. Written for the Methods in Molecular Biology series, most chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, laboratory protocols and tips on troubleshooting and avoiding known pitfalls. Practical and authoritative, Quantitative Real-Time PCR: Methods and Protocols aims to aid researchers seeking to devise new qPCR-based approaches related to his or her area of investigation. |
| bacterial rna seq analysis: The Pangenome Hervé Tettelin, Duccio Medini, 2020-04-30 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. |
| bacterial rna seq analysis: Soil Ecology and Ecosystem Services Diana H. Wall, Richard D. Bardgett, 2013-07-18 This multi-contributor, international volume synthesizes contributions from the world's leading soil scientists and ecologists, describing cutting-edge research that provides a basis for the maintenance of soil health and sustainability. The book covers these advances from a unique perspective of examining the ecosystem services produced by soil biota across different scales - from biotic interactions at microscales to communities functioning at regional and global scales. The book leads the user towards an understanding of how the sustainability of soils, biodiversity, and ecosystem services can be maintained and how humans, other animals, and ecosystems are dependent on living soils and ecosystem services. This is a valuable reference book for academic libraries and professional ecologists worldwide as a statement of progress in the broad field of soil ecology. It will also be of interest to both upper level undergraduate and graduate students taking courses in soil ecology, as well as academic researchers and professionals in the field requiring an authoritative, balanced, and up-to-date overview of this fast expanding topic. |
| bacterial rna seq analysis: Methods in Gut Microbial Ecology for Ruminants Harinder P.S. Makkar, Christopher S. McSweeney, 2006-02-23 Asaresultofvarioushumanactivities,suchasincreaseinhumanpopulation,decrease in arable land due to soil degradation, urbanization, industrialization and associated increase in the demand for livestock products, dramatic changes are occurring in the global ruminant livestock sector. These changes includeshift inthesize of regional livestock populations and in the types of management and feeding systems under which ruminant livestock are held, and increased demand of a wider range of quality attributes from animal agriculture, not just of the products themselves but also of the methods used in their production. The livestock sector will need to respond to newchallengesofincreasinglivestockproductivitywhileprotectingenvironmentand human health and conservingbiodiversity and natural resources. The micro-organisms in the digestive tracts of ruminant livestock have a profound in?uence on the conversion offeedinto end products, which can impact on the- imal and theenvironment. As the livestock sector grows particularly in developing countries, there will be an increasing need to understand these processes for b- ter management and use ofbothfeed and other natural resources that underpinthe development of sustainable feeding systems. |
| bacterial rna seq analysis: Microbiome Analysis Robert G. Beiko, Will Hsiao, John Parkinson, 2018 |
| bacterial rna seq analysis: The Kiwifruit Genome Raffaele Testolin, Hong-Wen Huang, Allan Ross Ferguson, 2016-05-02 This book describes the basic botanical features of kiwifruit and its wild relatives, reports on the steps that led to its genome sequencing, and discusses the results obtained with the assembly and annotation. The core chapters provide essential insights into the main gene families that characterize this species as a crop, including the genes controlling sugar and starch metabolism, pigment biosynthesis and degradation, the ascorbic-acid pathway, fruit softening and postharvest metabolism, allergens, and resistance to pests and diseases. The book offers a valuable reference guide for taxonomists, geneticists and horticulturists. Further, since information gained from the genome sequence is extraordinarily useful in assessing the breeding value of individuals based on whole-genome scans, it will especially benefit plant breeders. Accordingly, chapters are included that focus on gene introgression from wild relatives and genome-based breeding. |
| bacterial rna seq analysis: Bayesian Inference for Gene Expression and Proteomics Kim-Anh Do, Peter Müller, Marina Vannucci, 2006-07-24 Expert overviews of Bayesian methodology, tools and software for multi-platform high-throughput experimentation. |
| bacterial rna seq analysis: Molecular Biology of the Cell , 2002 |
| bacterial rna seq analysis: Bacterial Regulatory RNA Véronique Arluison, Claudio Valverde, 2024-01-13 This second edition details new and updated methods used for studying prokaryotic non-coding RNAs and their protein accomplices. Chapters detail discovery of ncRNAs, characterization of their structure, functions, and their interactomes. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Bacterial Regulatory RNA: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field. |
| bacterial rna seq analysis: Genomics in the Cloud Geraldine A. Van der Auwera, Brian D. O'Connor, 2020-04-02 Data in the genomics field is booming. In just a few years, organizations such as the National Institutes of Health (NIH) will host 50+ petabytesâ??or over 50 million gigabytesâ??of genomic data, and theyâ??re turning to cloud infrastructure to make that data available to the research community. How do you adapt analysis tools and protocols to access and analyze that volume of data in the cloud? With this practical book, researchers will learn how to work with genomics algorithms using open source tools including the Genome Analysis Toolkit (GATK), Docker, WDL, and Terra. Geraldine Van der Auwera, longtime custodian of the GATK user community, and Brian Oâ??Connor of the UC Santa Cruz Genomics Institute, guide you through the process. Youâ??ll learn by working with real data and genomics algorithms from the field. This book covers: Essential genomics and computing technology background Basic cloud computing operations Getting started with GATK, plus three major GATK Best Practices pipelines Automating analysis with scripted workflows using WDL and Cromwell Scaling up workflow execution in the cloud, including parallelization and cost optimization Interactive analysis in the cloud using Jupyter notebooks Secure collaboration and computational reproducibility using Terra |
| bacterial rna seq analysis: Functional Metagenomics: Tools and Applications Trevor C. Charles, Mark R. Liles, Angela Sessitsch, 2017-10-09 In this book, the latest tools available for functional metagenomics research are described.This research enables scientists to directly access the genomes from diverse microbial genomes at one time and study these “metagenomes”. Using the modern tools of genome sequencing and cloning, researchers have now been able to harness this astounding metagenomic diversity to understand and exploit the diverse functions of microorganisms. Leading scientists from around the world demonstrate how these approaches have been applied in many different settings, including aquatic and terrestrial habitats, microbiomes, and many more environments. This is a highly informative and carefully presented book, providing microbiologists with a summary of the latest functional metagenomics literature on all specific habitats. |
| bacterial rna seq analysis: Transcriptome Data Analysis Rajeev K. Azad, |
| bacterial rna seq analysis: High-Throughput Next Generation Sequencing Young Min Kwon, Steven C. Ricke, 2011-03-22 Due to their novel concepts and extraordinary high-throughput sequencing capacity, the “next generation sequencing” methods allow scientists to grasp system-wide landscapes of the complex molecular events taking place in various biological systems, including microorganisms and microbial communities. These methods are now being recognized as essential tools for a more comprehensive and deeper understanding of the mechanisms underlying many biological processes. In High-Throughput Next Generation Sequencing: Methods and Applications, experts in the field explore the most recent advances in the applications of next generation sequencing technologies with an emphasis on microorganisms and their communities; however, the methods described in this book will also offer general applications relevant to the study of any living organisms. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, High-Throughput Next Generation Sequencing: Methods and Applications is an excellent collection of chapters to aid all scientists who wish to apply these innovative research tools to enhance their own pursuits in microbiology and also biology in general. |
| bacterial rna seq analysis: Biological Sequence Analysis Richard Durbin, Sean R. Eddy, Anders Krogh, Graeme Mitchison, 1998-04-23 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. |
| bacterial rna seq analysis: Microbial Genomes Claire M. Fraser, Timothy Read, Karen E. Nelson, 2010-12-09 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. |
| bacterial rna seq analysis: Deep Sequencing Data Analysis Noam Shomron, 2013-07-20 The new genetic revolution is fuelled by Deep Sequencing (or Next Generation Sequencing) apparatuses which, in essence, read billions of nucleotides per reaction. Effectively, when carefully planned, any experimental question which can be translated into reading nucleic acids can be applied.In Deep Sequencing Data Analysis, expert researchers in the field detail methods which are now commonly used to study the multi-facet deep sequencing data field. These included techniques for compressing of data generated, Chromatin Immunoprecipitation (ChIP-seq), and various approaches for the identification of sequence variants. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of necessary materials and reagents, step-by-step, readily reproducible protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Deep Sequencing Data Analysis seeks to aid scientists in the further understanding of key data analysis procedures for deep sequencing data interpretation. |
| bacterial rna seq analysis: Sequence — Evolution — Function Eugene V. Koonin, Michael Galperin, 2013-06-29 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. |
| bacterial rna seq analysis: The Social Biology of Microbial Communities Institute of Medicine, Board on Global Health, Forum on Microbial Threats, 2013-01-10 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. |
| bacterial rna seq analysis: Bacterial Pangenomics Alessio Mengoni, Marco Galardini, Marco Fondi, 2015 |
| bacterial rna seq analysis: Fungal Genomics Ronald P. de Vries, Adrian Tsang, Igor V. Grigoriev, 2019-06-21 This volume details protocols covering nearly all aspects of fungal genomics. New and updated chapters guide the reader through experimental genomics, biotechnologies, and the analysis and processing of data. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Fungal Genomics : Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field. |
| bacterial rna seq analysis: Manipulating the Mouse Embryo Andras Nagy, 2003 Provides background information and detailed protocols for developing a mouse colony and using the animals in transgenic and gene-targeting experiments. The protocols list the animals, equipment, and reagents required and step-by-step procedures. Topics include in vitro culture of preimplantation embryos, surgical procedures, the production of chimeras, and the analysis of genome alterations. The third edition adds protocols for cloning mice, modifying embryonic stem cells, intracytoplasmic sperm injection, and cryopreservation of embryos. |
| bacterial rna seq analysis: Genome Analysis: Current Procedures and Applications Maria S. Poptsova, 2019-04-28 In recent years there have been tremendous achievements made in DNA sequencing technologies and corresponding innovations in data analysis and bioinformatics that have revolutionized the field of genome analysis.In this book, an impressive array of expert authors highlight and review current advances in genome analysis. This volume provides an invaluable, up-to-date and comprehensive overview of the methods currently employed for next-generation sequencing (NGS) data analysis, highlights their problems and limitations, demonstrates the applications and indicates the developing trends in various fields of genome research. The first part of the book is devoted to the methods and applications that arose from, or were significantly advanced by, NGS technologies: the identification of structural variation from DNA-seq data; whole-transcriptome analysis and discovery of small interfering RNAs (siRNAs) from RNA-seq data; motif finding in promoter regions, enhancer prediction and nucleosome sequence code discovery from ChiP-Seq data; identification of methylation patterns in cancer from MeDIP-seq data; transposon identification in NGS data; metagenomics and metatranscriptomics; NGS of viral communities; and causes and consequences of genome instabilities. The second part is devoted to the field of RNA biology with the last three chapters devoted to computational methods of RNA structure prediction including context-free grammar applications.An essential book for everyone involved in sequence data analysis, next-generation sequencing, high-throughput sequencing, RNA structure prediction, bioinformatics and genome analysis. |
| bacterial rna seq analysis: Bioinformatics for Biomedical Science and Clinical Applications K-H Liang, 2013-07-31 Contemporary biomedical and clinical research is undergoing constant development thanks to the rapid advancement of various high throughput technologies at the DNA, RNA and protein levels. These technologies can generate vast amounts of raw data, making bioinformatics methodologies essential in their use for basic biomedical and clinical applications. Bioinformatics for biomedical science and clinical applications demonstrates what these cutting-edge technologies can do and examines how to design an appropriate study, including how to deal with data and address specific clinical questions. The first two chapters consider Bioinformatics and analysis of the human genome. The subsequent three chapters cover the introduction of Transcriptomics, Proteomics and Systems biomedical science. The remaining chapters move on to critical developments, clinical information and conclude with domain knowledge and adaptivity. |
| bacterial rna seq analysis: Post-Transcriptional Gene Regulation Erik Dassi, 2022-11-09 This volume presents the most recent advances in techniques for studying the post-transcriptional regulation of gene expression (PTR). With sections on bioinformatics approaches, expression profiling, the protein and RNA interactome, the mRNA lifecycle, and RNA modifications, the book guides molecular biologists toward harnessing the power of this new generation of techniques, while also introducing the data analysis skills that these high-throughput techniques require. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and up-to-date, Post-Transcriptional Gene Regulation, Third Edition serves as a versatile resource for researchers studying post-transcriptional regulation by both introducing the most recent techniques and providing a comprehensive guide to their implementation. Chapter 6 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com. |
| bacterial rna seq analysis: Transcriptome Data Analysis Yejun Wang, Ming-an Sun, 2019-03-20 This detailed volume provides comprehensive practical guidance on transcriptome data analysis for a variety of scientific purposes. Beginning with general protocols, the collection moves on to explore protocols for gene characterization analysis with RNA-seq data as well as protocols on several new applications of transcriptome studies. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and useful, Transcriptome Data Analysis: Methods and Protocols serves as an ideal guide to the expanding purposes of this field of study. |
Bacteria - Wikipedia
Bacteria (/ bækˈtɪəriə / ⓘ; sg.: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a …
Bacteria | Cell, Evolution, & Classification | Britannica
3 days ago · bacteria, any of a group of microscopic single-celled organisms that live in enormous numbers in almost every environment on Earth, …
Bacterial Infection: Causes, Symptoms, Treatment & Prev…
Sep 20, 2022 · Bacterial infections are diseases that can affect your skin, lungs, brain, blood and other parts of your body. You get them from single …
Bacteria - Definition, Shapes, Characteristics, Types & Exam…
Oct 4, 2019 · Bacteria are single-celled microorganisms with prokaryotic cells, which are single cells that do not have organelles or a true nucleus and are …
Bacteria: Definition & Characteristics With Example…
Feb 2, 2023 · Bacteria are disease-causing, microscopic, single-celled organisms with prokaryotic cell structures. They do not have …
Bacteria - Wikipedia
Bacteria (/ bækˈtɪəriə / ⓘ; sg.: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. …
Bacteria | Cell, Evolution, & Classification | Britannica
3 days ago · bacteria, any of a group of microscopic single-celled organisms that live in enormous numbers in almost every environment on Earth, from deep-sea vents to deep below Earth’s …
Bacterial Infection: Causes, Symptoms, Treatment & Prevention
Sep 20, 2022 · Bacterial infections are diseases that can affect your skin, lungs, brain, blood and other parts of your body. You get them from single-celled organisms multiplying or releasing …
Bacteria - Definition, Shapes, Characteristics, Types & Examples
Oct 4, 2019 · Bacteria are single-celled microorganisms with prokaryotic cells, which are single cells that do not have organelles or a true nucleus and are less complex than eukaryotic cells. …
Bacteria: Definition & Characteristics With Examples & Diagram
Feb 2, 2023 · Bacteria are disease-causing, microscopic, single-celled organisms with prokaryotic cell structures. They do not have membrane-bound organelles, including a true nucleus. Being …
Bacteria: Names, Shapes, Behavior, Which Are Helpful?
Oct 13, 2024 · Bacteria are classified into different groups depending on their shape. There are five distinct bacterial shapes: spherical, rod, spiral, comma, and corkscrew.
What are Bacteria? - Microbiology Society
Bacteria are microbes with a much simpler cell structure than many other organisms, but they are by no means simple. The more scientists look, the more they understand about how complex …
