Hidden Treasures In Contemporary Rna Sequencing

Author : Serghei Mangul
Publisher :
ISBN 13 : 9783030139742
Total Pages : 93 pages
Book Rating : 4.43/5 ( download)

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Download or read book Hidden Treasures in Contemporary RNA Sequencing written by Serghei Mangul and published by . This book was released on 2019 with total page 93 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in RNA-sequencing (RNA-seq) technologies have provided an unprecedented opportunity to explore the gene expression landscape across individuals, tissues, and environments by efficiently profiling the RNA sequences present in the samples. When a reference genome sequence or a transcriptome of the sample is available, mapping-based RNA-seq analysis protocols align the RNA-seq reads to the reference sequences, identify novel transcripts, and quantify the abundance of expressed transcripts. The reads that fail to map to the human reference, known as unmapped reads, are a large and often overlooked output of standard RNA-seq analyses. Even in carefully executed experiments, the unmapped reads can comprise a considerable fraction of the complete set of reads produced, and can arise due to technical sequencing produced by low-quality and error-prone copies of the nascent RNA sequence being sampled. Reads can also remain unmapped due to unknown transcripts, recombined B and T cell receptor sequences, A-to-G mismatches from A-to-I RNA editing, trans-splicing, gene fusion, circular RNAs, and the presence of non-host RNA sequences (e.g. bacterial, fungal, and viral organisms). Unmapped reads represent a rich resource for the study of B and T cell receptor repertoires and the human microbiome system--without incurring the expense of additional targeted sequencing. This book introduces and describes the Read Origin Protocol (ROP), a tool that identifies the origin of both mapped and unmapped reads. The protocol first identifies human reads using a standard high-throughput algorithm to map them onto a reference genome and transcriptome. After alignment, reads are grouped into genomic (e.g. CDS, UTRs, introns) and repetitive (e.g. SINEs, LINEs, LTRs) categories. The rest of the ROP protocol characterizes the remaining unmapped reads, which failed to map to the human reference sequences.

Author : Serghei Mangul
Publisher : Springer
ISBN 13 : 3030139735
Total Pages : 93 pages
Book Rating : 4.35/5 ( download)

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Download or read book Hidden Treasures in Contemporary RNA Sequencing written by Serghei Mangul and published by Springer. This book was released on 2019-03-01 with total page 93 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in RNA-sequencing (RNA-seq) technologies have provided an unprecedented opportunity to explore the gene expression landscape across individuals, tissues, and environments by efficiently profiling the RNA sequences present in the samples. When a reference genome sequence or a transcriptome of the sample is available, mapping-based RNA-seq analysis protocols align the RNA-seq reads to the reference sequences, identify novel transcripts, and quantify the abundance of expressed transcripts.The reads that fail to map to the human reference, known as unmapped reads, are a large and often overlooked output of standard RNA-seq analyses. Even in carefully executed experiments, the unmapped reads can comprise a considerable fraction of the complete set of reads produced, and can arise due to technical sequencing produced by low-quality and error-prone copies of the nascent RNA sequence being sampled. Reads can also remain unmapped due to unknown transcripts, recombined B and T cell receptor sequences, A-to-G mismatches from A-to-I RNA editing, trans-splicing, gene fusion, circular RNAs, and the presence of non-host RNA sequences (e.g. bacterial, fungal, and viral organisms). Unmapped reads represent a rich resource for the study of B and T cell receptor repertoires and the human microbiome system—without incurring the expense of additional targeted sequencing.This book introduces and describes the Read Origin Protocol (ROP), a tool that identifies the origin of both mapped and unmapped reads. The protocol first identifies human reads using a standard high-throughput algorithm to map them onto a reference genome and transcriptome. After alignment, reads are grouped into genomic (e.g. CDS, UTRs, introns) and repetitive (e.g. SINEs, LINEs, LTRs) categories. The rest of the ROP protocol characterizes the remaining unmapped reads, which failed to map to the human reference sequences.

Author : Fabio Marchi
Publisher : BoD – Books on Demand
ISBN 13 : 9535135031
Total Pages : 330 pages
Book Rating : 4.36/5 ( download)

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Download or read book Applications of RNA-Seq and Omics Strategies written by Fabio Marchi and published by BoD – Books on Demand. This book was released on 2017-09-13 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: The large potential of RNA sequencing and other "omics" techniques has contributed to the production of a huge amount of data pursuing to answer many different questions that surround the science's great unknowns. This book presents an overview about powerful and cost-efficient methods for a comprehensive analysis of RNA-Seq data, introducing and revising advanced concepts in data analysis using the most current algorithms. A holistic view about the entire context where transcriptome is inserted is also discussed here encompassing biological areas with remarkable technological advances in the study of systems biology, from microorganisms to precision medicine.

Author : National Academies of Sciences Engineering and Medicine
Publisher :
ISBN 13 : 9780309706957
Total Pages : 0 pages
Book Rating : 4.55/5 ( download)

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Download or read book Charting a Future for Sequencing RNA and Its Modifications written by National Academies of Sciences Engineering and Medicine and published by . This book was released on 2024-11-21 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Concerted efforts to deepen understanding of RNA modifications and their role in living systems hold the potential to advance human health, improve crop yields, and address other pressing societal challenges. RNA, which carries the information encoded by DNA to the places where it is needed, is amazingly diverse and dynamic. RNA is processed and modified through natural biological pathways, giving rise to hundreds, in some cases thousands, of distinct RNA molecules for each gene, thereby diversifying genetic information. RNA modifications are known to be pivotal players in nearly all biological processes, and their dysregulation has been implicated in a wide range of human diseases and disorders. Yet, our knowledge of RNA modifications remains incomplete, hindered by current technological limitations. Existing methods cannot discover all RNA modifications, let alone comprehensively sequence them on every RNA molecule. Nonetheless, what is known about RNA modifications has already been leveraged in the development of vaccines that helped saved millions of lives worldwide during the COVID-19 pandemic. RNA modifications also have applications beyond health, for example, enhancing agricultural productivity. Charting a Future for Sequencing RNA and Its Modifications: A New Era for Biology and Medicine calls for a focused, large-scale effort to accelerate technological innovation to harness the full potential of RNA modifications to address pressing societal challenges in health, agriculture, and beyond. This report assesses the scientific and technological breakthroughs, workforce, and infrastructure needs to sequence RNA and its modifications, and ultimately understand the roles RNA modifications play in biological processes and disease. It proposes a roadmap of innovation that will make it possible for any RNA from any biological system to be sequenced end-to-end with all of its modifications - a capability that could lead to more personalized and targeted treatments and instigate transformative changes across various sectors beyond health and medicine.

Author : Dóra Szakonyi
Publisher : Frontiers Media SA
ISBN 13 : 2889630250
Total Pages : 167 pages
Book Rating : 4.57/5 ( download)

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Download or read book Plant RNA Biology written by Dóra Szakonyi and published by Frontiers Media SA. This book was released on 2019-11-18 with total page 167 pages. Available in PDF, EPUB and Kindle. Book excerpt: Discoveries from the past decades revealed that RNA molecules are much more than inert intermediates between the coding DNA sequences and their functional products, proteins. Today, RNAs are recognized as active regulatory molecules influencing gene expression, chromatin organization and genome stability, thus impacting all aspects of plant life including development, growth, reproduction and stress tolerance. Innovations in methodologies, the expanding application of next-generation sequencing technologies, and the creation of public datasets and databases have exposed a new universe of RNA-based mechanisms and led to the discovery of new families of non-coding RNAs, uncovered the large extent of alternative splicing events, and highlighted the potential roles of RNA modifications and RNA secondary structures. Furthermore, considerable advances have been made in identifying RNA-binding and processing factors involved in the synthesis and maturation of different forms of RNA molecules as well as in RNA processing, biochemical modifications or degradation. This Research Topic showcases the broad biological significance of RNAs in plant systems and contains eight original research articles, one review and four mini-reviews, covering various RNA-based mechanisms in higher plants. Emerging new technologies and novel multidisciplinary approaches are empowering the scientific community and will expectedly bring novel insights into our understanding of the mechanisms through which RNA is regulated and regulates biological processes in plant cells.

Author : Jose Victor Lopez
Publisher : Elsevier
ISBN 13 : 0128241136
Total Pages : 264 pages
Book Rating : 4.34/5 ( download)

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Download or read book Assessments and Conservation of Biological Diversity from Coral Reefs to the Deep Sea written by Jose Victor Lopez and published by Elsevier. This book was released on 2023-11-30 with total page 264 pages. Available in PDF, EPUB and Kindle. Book excerpt: Assessments and Conservation of Biological Diversity from Coral Reefs to the Deep Sea: Uncovering Buried Treasures and the Value of the Benthos examines marine benthic habitats around the world that are linked by their physical location at the bottom of the oceans. The book approaches deep sea marine biodiversity with perspectives on genetics, microbiology and evolution, weaving a narrative of vital expert linkages with the goal of protecting something that most people cannot witness or experience. It provides a full assessment of biological diversity within benthic habitats, from coral reefs to plankton and fish species, and offers global case studies. It is the ideal resource for marine conservationists and biologists aiming to expand their knowledge and efforts to the rarely seen, yet equally important, realms of the ocean and respective benthic species. As these deep-sea ecosystems and their species face unprecedented threats of destruction and extinction due to factors including climate change, this book provides the most current knowledge of this undersea world along with solutions for its conservation. Compares and contrasts between shallow and marine habitats to reveal revolutionary connections and continuity Analyzes modern threats and gaps in biological knowledge regarding benthic communities Examines benthic biodiversity through vertical vs. horizontal gradients Poses possible solutions for the conservation of benthic habitats and organisms

Author : DR. AURORA MARTIN
Publisher : INTERDISCIPLINARY INSTITUTE OF HUMAN SECURITY & GOVERNANCE
ISBN 13 : 9354575676
Total Pages : 402 pages
Book Rating : 4.79/5 ( download)

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Download or read book Changing Dimensions of Human Security in Contemporary World written by DR. AURORA MARTIN and published by INTERDISCIPLINARY INSTITUTE OF HUMAN SECURITY & GOVERNANCE. This book was released on 2023-09-11 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: The world turned topsy-turvy after Covid‑19 pandemic. The whole equation and thrust of global politics and economics is now at a new verge. The main question is now – how we can secure human race and humanity. This is the main thrust of the book, Changing Dimensions of Human Security in Contemporary World. This book is an outcome of collective research work done by erudite scholars from different parts of world, like USA, Russia, Japan, Australia, Romania, Nigeria, Nepal, Bangladesh and India, who has come together in search of new trends of human security. They touched upon different milieu as well as dimensions of human security and pandemic in contemporary world scenario. In thirty-two essays, forty-seven authors collectively explored situation of human security in several domains including international politics, law, economy, labour force, sustainable development, education, gender and may more. I believe that this collection of essays can become a benchmark for the future as well as spur new research agendas and projects that will put the region into a much-needed conversation on the recent trends of human security in contemporary world. This book will try to reimagining this changing dimension of Human Security in the Pandemic situation. The goal of this book is to improve the standards of the international community of academicians, researchers, scholars, and scientists by exposing them to the latest trends, developments, and challenges in the field. The volume is essential reading for social scientists, bureaucrats and non-governmental political activists interested in human security. It will also appeal to public policy analysts and scholars who have yet to adopt the contribution of critical security and development studies in the analysis of different dimensions of human security.

Author : K. Ramesh Reddy
Publisher : CRC Press
ISBN 13 : 1498764568
Total Pages : 734 pages
Book Rating : 4.68/5 ( download)

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Download or read book Biogeochemistry of Wetlands written by K. Ramesh Reddy and published by CRC Press. This book was released on 2022-09-10 with total page 734 pages. Available in PDF, EPUB and Kindle. Book excerpt: The globally important nature of wetland ecosystems has led to their increased protection and restoration as well as their use in engineered systems. Underpinning the beneficial functions of wetlands are a unique suite of physical, chemical, and biological processes that regulate elemental cycling in soils and the water column. This book provides an in-depth coverage of these wetland biogeochemical processes related to the cycling of macroelements including carbon, nitrogen, phosphorus, and sulfur, secondary and trace elements, and toxic organic compounds. In this synthesis, the authors combine more than 100 years of experience studying wetlands and biogeochemistry to look inside the black box of elemental transformations in wetland ecosystems. This new edition is updated throughout to include more topics and provide an integrated view of the coupled nature of biogeochemical cycles in wetland systems. The influence of the elemental cycles is discussed at a range of scales in the context of environmental change including climate, sea level rise, and water quality. Frequent examples of key methods and major case studies are also included to help the reader extend the basic theories for application in their own system. Some of the major topics discussed are: Flooded soil and sediment characteristics Aerobic-anaerobic interfaces Redox chemistry in flooded soil and sediment systems Anaerobic microbial metabolism Plant adaptations to reducing conditions Regulators of organic matter decomposition and accretion Major nutrient sources and sinks Greenhouse gas production and emission Elemental flux processes Remediation of contaminated soils and sediments Coupled C-N-P-S processes Consequences of environmental change in wetlands# The book provides the foundation for a basic understanding of key biogeochemical processes and its applications to solve real world problems. It is detailed, but also assists the reader with box inserts, artfully designed diagrams, and summary tables all supported by numerous current references. This book is an excellent resource for senior undergraduates and graduate students studying ecosystem biogeochemistry with a focus in wetlands and aquatic systems.

Author : Essam Halim Houssein
Publisher : Springer Nature
ISBN 13 : 3030990796
Total Pages : 501 pages
Book Rating : 4.94/5 ( download)

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Download or read book Integrating Meta-Heuristics and Machine Learning for Real-World Optimization Problems written by Essam Halim Houssein and published by Springer Nature. This book was released on 2022-06-04 with total page 501 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book collects different methodologies that permit metaheuristics and machine learning to solve real-world problems. This book has exciting chapters that employ evolutionary and swarm optimization tools combined with machine learning techniques. The fields of applications are from distribution systems until medical diagnosis, and they are also included different surveys and literature reviews that will enrich the reader. Besides, cutting-edge methods such as neuroevolutionary and IoT implementations are presented in some chapters. In this sense, the book provides theory and practical content with novel machine learning and metaheuristic algorithms. The chapters were compiled using a scientific perspective. Accordingly, the book is primarily intended for undergraduate and postgraduate students of Science, Engineering, and Computational Mathematics and can be used in courses on Artificial Intelligence, Advanced Machine Learning, among others. Likewise, the material can be helpful for research from the evolutionary computation, artificial intelligence communities.

Author : Huanming Yang
Publisher : World Scientific
ISBN 13 : 9814487171
Total Pages : 168 pages
Book Rating : 4.77/5 ( download)

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Download or read book A Holistic Approach to Rice Research and Genetic Engineering written by Huanming Yang and published by World Scientific. This book was released on 2003-07-14 with total page 168 pages. Available in PDF, EPUB and Kindle. Book excerpt: The aim of this book series is to familiarize scientists, students and the general public with exciting new discoveries and developments in rice genomics. Leading scientists in rice genomics and related fields are invited to write articles in a cohesive format that appeals to both researchers and laypersons with an interest in genomics and biotechnology. The first volume provides the background information and highlights the major achievements in rice genomics; ongoing developments in this exciting field are also discussed. This volume promotes genomics as a holistic approach to rice research and genetic engineering. The chief editor of the series is Prof Huanming Yang of the Beijing Genomics Institute. As one of the most distinguished scientists in rice research today, Prof Yang led a team of researchers who successfully sequenced and analyzed the draft sequence of the indica rice subspecies. In Vol 1 of the series, he co-authors an article entitled “An International Campaign for Agricultural and Livestock Genomics”. Contents:From Human Genome to Rice Genome and Beyond BGI — A Success Story of Jumpstarting Genomic Projects (B Liu et al.)Rice Genomics and the Future of Publicly Funded Rice Research (R P Cantrell)Rice Bioinformatics: From Sequences to Applications (B A Antonio et al.)Rice Microarray Project in Japan (S Kikuchi)Rice Functional Genomics by T-DNA Insertional Mutagenesis (G An)Rice Functional Genomics by Transposon Mutagenesis (C-D Han)Rice Gene Machine: A Vehicle for Finding Functions of Cereal Genes (N M Upadhyaya et al.)Hybrid Rice: The Futute of Rice Cultivation (S S Virmani)Rice Biotech Research at Taiwan Agricultural Research Institute (C-S Wang et al.)An International Campaign for Agricultural and Livestock Genomics (CALG) (J Yu et al.)Retrospective and Advance in Rice Improvement in China (Z-X Sun et al.) Readership: Researchers and university students in rice genomics, genetics, biotechnology and agriculture as well as non-specialist readers. Keywords:Rice;Genomics;Agriculture;Food;Genetics;Biotechnology;Plant