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This detailed book describes some of the most recent advances and up-to-date methodologies to detect, quantify, analyze, and elucidate the biological function of different types of RNA modifications. Importantly, the methodologies and tools described herein can be applied to a wide variety of organisms and can be used to address biological and clinical questions. Beginning with a section on bioinformatics tools, the collection continues with sections on detecting RNA modifications using Nanopore direct RNA sequencing, next-generation sequencing approaches, qPCR- and molecular biology-based methods, mass spectrometry- and NMR-based methods, as well as approaches to assess kinetics, determinants, and functions of RNA modifications. Written for the highly successful Methods in Molecular Biology series style, chapters include introduction 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 Modifications: Methods and Protocols serves as an ideal guide for those working directly in the fields of epitranscriptomics and post-transcriptional gene regulation, as well as for scientists and clinicians interested in bioinformatic tools to study RNA modifications and techniques to dissect their roles in physiology and disease. Chapter 20 is available open access under a CC BY 4.0 license.

Biochemistry. --- Biological chemistry --- Chemical composition of organisms --- Organisms --- Physiological chemistry --- Biology --- Chemistry --- Medical sciences --- Composition

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This detailed book aims to provide an overview of novel bioinformatics resources for exploring diverse aspects of RNA biology. This edition focuses on methods dealing with non-coding RNA (miRNAs, circRNAs or lncRNAs), RNA modifications (m6A or RNA editing), single cell RNA-seq and statistical models to handle count data from RNA-seq experiments. The book also includes chapters based on the classical RNA bioinformatics methods, such as those for deciphering secondary and tertiary RNA structures; however, they are revised to take into account deep sequencing data. Finally, chapters describing methods to analyze RNA sequencing data from emerging third generation sequencing technologies that could provide interesting insights into the transcriptional process and its regulation are also included. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of expert implementation advice that encourages quality results. Comprehensive and up-to-date, RNA Bioinformatics, Second Edition serves as an ideal guide for researchers digging ever-deeper into the depths of the study of RNAs. The chapter 'RNA-Seq Data Analysis in Galaxy' is open access under a CC BY 4.0 license.

Biochemistry. --- Bioinformatics. --- Bio-informatics --- Biological informatics --- Biology --- Information science --- Computational biology --- Systems biology --- Biological chemistry --- Chemical composition of organisms --- Organisms --- Physiological chemistry --- Chemistry --- Medical sciences --- Data processing --- Composition

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Biochemistry. --- Systems biology. --- Computational biology --- Bioinformatics --- Biological systems --- Molecular biology --- Biological chemistry --- Chemical composition of organisms --- Organisms --- Physiological chemistry --- Biology --- Chemistry --- Medical sciences --- Composition

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This book reviews a novel and exciting field of cellular and molecular biology called epitranscriptomics, which focuses on changes in an organism’s cells resulting from the posttranscriptional modification of cellular RNA. RNA-binding proteins (RBPs) play a crucial role in these posttranscriptional modifications and also support several cellular processes necessary for maintaining RNA homeostasis. Exploring the mechanisms underlying RNA modifications and RBP function is an emerging area of biomedical research, taking the study of gene regulation a step beyond epigenetics. This book reveals that the RNA molecule is not just an information-carrying molecule with some secondary structures. Accordingly, how RNA is modified, regulated, packaged, and controlled is an important aspect. Leading experts address questions such as where the over 170 distinct posttranscriptional RNA modifications are located on the genome, what percentage of mRNAs and noncoding RNAs these modifications include, and how an RNA modification impacts a person’s biology. In closing, the book reviews the role of RNA modifications and RBPs in a variety of diseases and their pathogenesis. Addressing some of the most exciting challenges in epitranscriptomics, this book provides a valuable and engaging resource for researchers in academia and industry studying the phenomena of RNA modification.

Epigenetics. --- RNA—Metabolism. --- Biochemistry. --- Bioinformatics. --- RNA Metabolism. --- Biological Chemistry. --- Bio-informatics --- Biological informatics --- Biology --- Information science --- Computational biology --- Systems biology --- Biological chemistry --- Chemical composition of organisms --- Organisms --- Physiological chemistry --- Chemistry --- Medical sciences --- Genetics --- Data processing --- Composition --- Transcripció genètica --- Epigenètica --- Genètica --- Codi genètic --- Factors de transcripció --- RNA --- Metabolism. --- Ribonucleic acid metabolism

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In this sixth edition of Jack Jie Li's seminal "Name Reactions", the author has added three or more synthetic applications of name reactions to reflect the recent advances in organic chemistry. As in previous editions, each reaction is delineated by its detailed step-by-step, electron-pushing mechanism and supplemented with the original and the latest references, especially from review articles. This book is not only an indispensable resource for advanced undergraduate and graduate students for learning and preparing exams, but is also a good reference book for all organic chemists in both industry and academia. Unlike other books on name reactions in organic chemistry, Name Reactions, A Collection of Detailed Reaction Mechanisms and Synthetic Applications focuses on the reaction mechanisms. It covers over 300 classical as well as contemporary name reactions.

Organic chemistry. --- Inorganic chemistry. --- Biochemistry. --- Organic Chemistry. --- Inorganic Chemistry. --- Biochemistry, general. --- Biological chemistry --- Chemical composition of organisms --- Organisms --- Physiological chemistry --- Biology --- Chemistry --- Medical sciences --- Inorganic chemistry --- Inorganic compounds --- Organic chemistry --- Composition --- Chemical reactions. --- Reactions, Chemical --- Chemical processes