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| bacterial rna-seq analysis pipeline: 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 pipeline: 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 pipeline: 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 pipeline: 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 pipeline: RNA-Seq Analysis: Methods, Applications and Challenges Filippo Geraci, Indrajit Saha, Monica Bianchini, 2020-06-08 |
| bacterial rna-seq analysis pipeline: 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 pipeline: 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 pipeline: 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 pipeline: 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 pipeline: Gene Quantification Francois Ferre, 2012-12-06 Geneticists and molecular biologists have been interested in quantifying genes and their products for many years and for various reasons (Bishop, 1974). Early molecular methods were based on molecular hybridization, and were devised shortly after Marmur and Doty (1961) first showed that denaturation of the double helix could be reversed - that the process of molecular reassociation was exquisitely sequence dependent. Gillespie and Spiegelman (1965) developed a way of using the method to titrate the number of copies of a probe within a target sequence in which the target sequence was fixed to a membrane support prior to hybridization with the probe - typically a RNA. Thus, this was a precursor to many of the methods still in use, and indeed under development, today. Early examples of the application of these methods included the measurement of the copy numbers in gene families such as the ribosomal genes and the immunoglo bulin family. Amplification of genes in tumors and in response to drug treatment was discovered by this method. In the same period, methods were invented for estimating gene num bers based on the kinetics of the reassociation process - the so-called Cot analysis. This method, which exploits the dependence of the rate of reassociation on the concentration of the two strands, revealed the presence of repeated sequences in the DNA of higher eukaryotes (Britten and Kohne, 1968). An adaptation to RNA, Rot analysis (Melli and Bishop, 1969), was used to measure the abundance of RNAs in a mixed population. |
| bacterial rna-seq analysis pipeline: 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 pipeline: 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 pipeline: 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 pipeline: 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 pipeline: Microbiome in Human Health and Disease Pallaval Veera Bramhachari, 2021-10-18 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. |
| bacterial rna-seq analysis pipeline: Microbiome Analysis Robert G. Beiko, Will Hsiao, John Parkinson, 2018 |
| bacterial rna-seq analysis pipeline: 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 pipeline: 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 pipeline: The Rhizobiaceae Herman P. Spaink, Adam Kondorosi, Paul J.J. Hooykaas, 2012-12-06 The Rhizobiaceae, Molecular Biology of Model Plant-Associated Bacteria. This book gives a comprehensive overview on our present molecular biological knowledge about the Rhizobiaceae, which currently can be called the best-studied family of soil bacteria. For many centuries they have attracted the attention of scientists because of their capacity to associate with plants and as a consequence also to specifically modify plant development. Some of these associations are beneficial for the plant, as is the case for the Rhizobiaceae subgroups collectively called rhizobia, which are able to fix nitrogen in a symbiosis with the plant hosts. This symbiosis results in the fonnation of root or stem nodules, as illustrated on the front cover. In contrast, several Rhizobiaceae subgroups can negatively affect plant development and evoke plant diseases. Examples are Agrobacterium tumefaciens andA. rhizogenes which induce the formation of crown galls or hairy roots on the stems of their host plants, respectively (bottom panels on front cover). In addition to the obvious importance of studies on the Rhizobiaceae for agronomy, this research field has resulted in the discovery of many fundamental scientific principles of general interest, which are highlighted in this book. To mention three examples: (i) the discovery of DNA transfer of A. |
| bacterial rna-seq analysis pipeline: 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 pipeline: Biometry Robert R. Sokal, F. James Rohlf, 1995 Offers students with little background in statistical analysis an introduction to a variety of statistical concepts and methods. In addition to the incorporation of computer calculation, this new edition expands on a number of important topics, including the revised Kolmogrov-Smirnov test. |
| bacterial rna-seq analysis pipeline: Metagenomics and Its Applications in Agriculture, Biomedicine and Environmental Studies Robert W. Li, 2013 Metagenomics is the study of microbial communities sampled directly from their natural environment, without prior culturing. DNA sequencing (or alternatively, an assay of functional properties) is applied to the culture-independent analyses of complex and diverse (meta) populations of microbes. The rapid growth of metagenomics entails an expanded focus on microbes in a wide range of basic and applied research fields, ranging from microbiology to agriculture, biomedicine to bioenergy, and from veterinary to clinical medicine. This book is an insightful and inclusive study on metagenomics and its applications. |
| bacterial rna-seq analysis pipeline: Bacteria and Intracellularity Pascale Cossart, Craig R. Roy, Philippe Sansonetti, 2019-12-24 Bacteria and Intracellularity clearly demonstrates that cellular microbiology as a field has reached maturity, extending beyond the strictly cellular level to infections of various organs and tissues. Decades of intense investigation into host-bacterial pathogen interactions have highlighted common concepts in intracellularity but also very diverse mechanisms underlying the various infections produced by bacteria. This book offers a wide-ranging look at the latest studies, including: foodborne pathogens, including how, when, and where bacteria interact with the gut and its microbiota infections of the urogenital tract, endothelial barriers, and the nervous system major advances in work with Mycobacterium tuberculosis and M. leprae subcellular microbiology, including metabolism of infected cells, nuclear biology, and microRNAs endosymbionts, in particular the latest work with Wolbachia and its effect on insect transmission of viral pathogens research into cell autonomous defense pathways that has led to major insights into immunology and innate immunity the latest developments in technology, for the next steps in the study of intracellularity All facets of cellular physiology, within the entire scope of cells and host tissues, can be targeted by pathogens. This book offers to researchers, students, and laboratorians a valuable overview of the state of current research into the cellular microbiology of host-pathogen interactions. |
| bacterial rna-seq analysis pipeline: 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. |
| bacterial rna-seq analysis pipeline: 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 pipeline: 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 pipeline: The Oil Palm Genome Maizura Ithnin, Ahmad Kushairi, 2020-06-12 This book compiles the fundamental advances resulting from of oil-palm genome and transcriptome sequencing, and describes the challenges faced and strategies applied in sequencing, assembling and annotating oil palm genome sequences. The availability of genome and transcriptome data has made the mining of a high number of new molecular markers useful for genetic diversity as well as marker-trait association studies and the book presents high-throughput genotyping platforms, which allow the detection of QTL regions associated with interesting oil palm traits such as oil unsaturation and yield components using classical genetic and association mapping approaches. Lastly, it also presents the discovery of major genes governing economically important traits of the oil palm. Covering the history of oil palm expansion, classical and molecular cytogenetics, improvements based on wild and advanced genetic materials, and the science of oil palm breeding, the book is a valuable resource for scientists involved in plant genetic research. |
| bacterial rna-seq analysis pipeline: Computational Immunology Josep Bassaganya-Riera, 2015-10-21 Computational Immunology: Models and Tools encompasses the methodological framework and application of cutting-edge tools and techniques to study immunological processes at a systems level, along with the concept of multi-scale modeling. The book's emphasis is on selected cases studies and application of the most updated technologies in computational modeling, discussing topics such as computational modeling and its usage in immunological research, bioinformatics infrastructure, ODE based modeling, agent based modeling, and high performance computing, data analytics, and multiscale modeling. There are also modeling exercises using recent tools and models which lead the readers to a thorough comprehension and applicability. The book is a valuable resource for immunologists, computational biologists, bioinformaticians, biotechnologists, and computer scientists, as well as all those who wish to broaden their knowledge in systems modeling. - Offers case studies with different levels of complexity - Provides a detailed view on cutting-edge tools for modeling that are useful to experimentalists with limited computational skills - Explores the usage of simulation for hypothesis generation, helping the reader to understand the most valuable points on experimental setting |
| bacterial rna-seq analysis pipeline: Data Mining for Systems Biology Hiroshi Mamitsuka, 2019-08-04 This fully updated book collects numerous data mining techniques, reflecting the acceleration and diversity of the development of data-driven approaches to the life sciences. The first half of the volume examines genomics, particularly metagenomics and epigenomics, which promise to deepen our knowledge of genes and genomes, while the second half of the book emphasizes metabolism and the metabolome as well as relevant medicine-oriented subjects. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that is useful for getting optimal results. Authoritative and practical, Data Mining for Systems Biology: Methods and Protocols, Second Edition serves as an ideal resource for researchers of biology and relevant fields, such as medical, pharmaceutical, and agricultural sciences, as well as for the scientists and engineers who are working on developing data-driven techniques, such as databases, data sciences, data mining, visualization systems, and machine learning or artificial intelligence that now are central to the paradigm-altering discoveries being made with a higher frequency. |
| bacterial rna-seq analysis pipeline: Small RNAs: Wolfgang Nellen, Christian Hammann, 2007-11-10 In recent years, the discovery of functional small RNAs has brought about an unprecedented revolution within the field of molecular biology. This volume describes strategies for the discovery and validation of small RNAs. It provides a snapshot of our current understanding of the different mechanisms triggered by small RNAs and the variations encountered in different organisms. |
| bacterial rna-seq analysis pipeline: Microbial Environmental Genomics (MEG) Francis Martin, Stephane Uroz, 2022-12-15 This volume guides researchers on how to characterize, image rare, and hitherto unknown taxa and their interactions, to identify new functions and biomolecules and to understand how environmental changes condition the activity and the response of the organisms living with us and in our environment. Chapters cover different organism types (i.e., archaea, bacteria, fungi, protest, microfauna and microeukaryotes) and propose detailed protocols to produce high quality DNA, to analyse active microbial communities directly involved in complex interactions or processes through stable isotope probing, to identify and characterize of new functional genes, to image in situ interactions and to apply bioinformatics analysis tools to complex metagenomic or RNAseq sequence data. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Microbial Environmental Genomics (MEG): Methods and Protocols, Second Edition aims to serve as a primary research reference for researchers in microbiology working to in the expanding field of molecular ecology and environmental genomics. |
| bacterial rna-seq analysis pipeline: The Good, The Bad and The Ugly: Multiple Roles of Bacteria in Human Life Tatiana Venkova, Chew Chieng Yeo, Manuel Espinosa, 2018-10-17 Bacteria are among the earliest forms of life on Earth. Notwithstanding their small size and primitive origin, bacteria still have a tremendous impact on everyday human life. Over the centuries, research into bacteria have provided and enriched the fundamental biological knowledge due to their readily measured processes and effects on higher organisms. Although molecular genetics and microbiology were among the scientific fields that have mostly benefited from the discoveries made in bacteria, our current state of knowledge has gone beyond what anyone could have ever imagined. The present Research Topic aims to cover new and exciting broad aspects of the importance of bacteria to human life, both positive and negative influences. Regulation of bacterial gene expression, replication and segregation control mechanisms, cell to cell communication via quorum sensors, and the relatively recent finding of bacterial immunity via CRISPR, have led to the development of many, and very important new tools in biotechnology and the emerging field of molecular medicine. The battle against infectious diseases has also benefited from the genetic approaches that have been developed in the quest for finding new targets and novel drugs against pathogenic bacteria. At the next level, the human microbiome project has opened up new avenues in understanding the role of bacteria in human health and wellbeing. Finally, the relationship between bacterial infections and human cancers will also be covered, a subject that is still under verification through rigorous experimental approaches. Special emphasis will be given to the bacterial accessory genome, i.e the mobilome, as the primary cause of health-threatening antimicrobial resistance and the production of toxins and virulence factors. Taking into account the evolutionary importance of horizontal gene transfer and the additional beneficial roles of certain bacterial mobile genetic elements, they help project best “the Good, the Bad and the Ugly” outline of this topic. At the time this eBook is about to be published, our Research Topic has registered nearly 55, 000 views. |
| bacterial rna-seq analysis pipeline: 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 pipeline: Advances in microbial ecology K. C. Marshall, 1988 |
| bacterial rna-seq analysis pipeline: Gene Expression Analysis Nalini Raghavachari, Natàlia Garcia-Reyero, 2018-05-17 This volume provides experimental and bioinformatics approaches related to different aspects of gene expression analysis. Divided in three sections chapters detail wet-lab protocols, bioinformatics approaches, single-cell gene expression, highly multiplexed amplicon sequencing, multi-omics techniques, and targeted sequencing. 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, Gene Expression Analysis: Methods and Protocols aims provide useful information to researchers worldwide. |
| bacterial rna-seq analysis pipeline: Bioinformatics David Edwards, Jason Stajich, David Hansen, 2010-04-29 Bioinformatics is a relatively new field of research. It evolved from the requirement to process, characterize, and apply the information being produced by DNA sequencing technology. The production of DNA sequence data continues to grow exponentially. At the same time, improved bioinformatics such as faster DNA sequence search methods have been combined with increasingly powerful computer systems to process this information. Methods are being developed for the ever more detailed quantification of gene expression, providing an insight into the function of the newly discovered genes, while molecular genetic tools provide a link between these genes and heritable traits. Genetic tests are now available to determine the likelihood of suffering specific ailments and can predict how plant cultivars may respond to the environment. The steps in the translation of the genetic blueprint to the observed phenotype is being increasingly understood through proteome, metabolome and phenome analysis, all underpinned by advances in bioinformatics. Bioinformatics is becoming increasingly central to the study of biology, and a day at a computer can often save a year or more in the laboratory. The volume is intended for graduate-level biology students as well as researchers who wish to gain a better understanding of applied bioinformatics and who wish to use bioinformatics technologies to assist in their research. The volume would also be of value to bioinformatics developers, particularly those from a computing background, who would like to understand the application of computational tools for biological research. Each chapter would include a comprehensive introduction giving an overview of the fundamentals, aimed at introducing graduate students and researchers from diverse backgrounds to the field and bring them up-to-date on the current state of knowledge. To accommodate the broad range of topics in applied bioinformatics, chapters have been grouped into themes: gene and genome analysis, molecular genetic analysis, gene expression analysis, protein and proteome analysis, metabolome analysis, phenome data analysis, literature mining and bioinformatics tool development. Each chapter and theme provides an introduction to the biology behind the data describes the requirements for data processing and details some of the methods applied to the data to enhance biological understanding. |
| bacterial rna-seq analysis pipeline: Hi-C Data Analysis Silvio Bicciato, Francesco Ferrari, 2022-09-04 This volume details a comprehensive set of methods and tools for Hi-C data processing, analysis, and interpretation. Chapters cover applications of Hi-C to address a variety of biological problems, with a specific focus on state-of-the-art computational procedures adopted for the data analysis. 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, Hi-C Data Analysis: Methods and Protocols aims to help computational and molecular biologists working in the field of chromatin 3D architecture and transcription regulation. |
| bacterial rna-seq analysis pipeline: Bioinformatics and Biomedical Engineering Ignacio Rojas, Olga Valenzuela, Fernando Rojas, Luis Javier Herrera, Francisco Ortuño, 2022-06-07 This volume constitutes the proceedings of the 9th International Work-Conference on IWBBIO 2020, held in Maspalomas, Gran Canaria, Spain, in June 2022. The total of 75 papers presented in the proceedings, was carefully reviewed and selected from 212 submissions. The papers cover the latest ideas and realizations in the foundations, theory, models, and applications for interdisciplinary and multidisciplinary research encompassing disciplines of computer science, mathematics, statistics, biology, bioinformatics, and biomedicine. |
| bacterial rna-seq analysis pipeline: Gene Prediction Martin Kollmar, 2019-05-19 This volume introduces software used for gene prediction with focus on eukaryotic genomes. The chapters in this book describe software and web server usage as applied in common use-cases, and explain ways to simplify re-annotation of long available genome assemblies. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary computational requirements, step-by-step, readily reproducible computational protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Gene Prediction: Methods and Protocols is a valuable resource for researchers and research groups working on the assembly and annotation of single species or small groups of species. Chapter 3 is available open access under a CC BY 4.0 license via link.springer.com. |
| bacterial rna-seq analysis pipeline: 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. |
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 …
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 …
