Download or read book Visualization and Analysis of RNA Processing written by Sabine Paula Snaar and published by . This book was released on 2003 with total page 160 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Visualizing RNA Dynamics in the Cell written by and published by Academic Press. This book was released on 2016-05-27 with total page 412 pages. Available in PDF, EPUB and Kindle. Book excerpt: Methods in Enzymology: Visualizing RNA Dynamics in the Cell continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods visualizing RNA dynamics in the cell, and includes sections on such topics as identification of RNA cis-regulatory sequences, IRAS, IMAGEtags, MERFISH, plant RNA labeling using MS2, and visualization of 5S dynamics in live cells using photostable corn probe. Continues the legacy of this premier serial with quality chapters authored by leaders in the field Covers research methods in visualizing RNA dynamics in the cell Contains sections on such topics as identification of RNA cis-regulatory sequences, IRAS, IMAGEtags, MERFISH, plant RNA labeling using MS2 and visualization of 5S dynamics in live cells using photostable corn probe
Download or read book RNA Processing written by Gene W. Yeo and published by Springer. This book was released on 2016-06-02 with total page 335 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ribonucleic acid (RNA) binding proteins currently number in the thousands and defects in their function are at the heart of diseases such as cancer and neurodegeneration. RNA binding proteins have become implicated in the intricate control of surprisingly diverse biological settings, such as circadian rhythm, stem cell self-renewal, oncogenesis and germ cell development. This book surveys a range of genome-wide and systems approaches to studying RNA binding proteins, the importance of RNA binding proteins in development, cancer and circadian rhythm.
Download or read book Functional and Computational Analysis of RNA binding Proteins and Their Roles in Cancer written by Yarden Katz and published by . This book was released on 2014 with total page 241 pages. Available in PDF, EPUB and Kindle. Book excerpt: This work is concerned with mRNA processing in mammalian cells and proceeds in two parts. In the first part, I introduce a computational framework for inferring the abundances of mRNA isoforms using high-throughput RNA sequencing data. This framework was applied to study the targets of the ubiquitous splicing factor hnRNP H in human cells. In the second part, I describe an experimental study of the Musashi (hnRNP-like) family of RNA-binding proteins in stem cells and cancer cells, which incorporates computational analyses that rely heavily on the framework developed in part one. In sum, this work provides a computational framework of general use in global analyses of RNA processing and its protein regulators, as well as functional insights into a family of poorly understood RNA-binding proteins. Several related analyses and techniques developed as part of the thesis are described in Appendix A-C. Appendix A describes a study of activity-dependent gene expression and mRNA processing in the mouse olfactory bulb. It uses computational techniques developed in part one of the thesis. Appendix B describes a technique for quantitative visualization of alternative splicing from RNA sequencing data and its integration into a genome browser. Appendix C describes a method for clonal analysis of neural stem cell growth and differentiation in culture using live imaging and `microdot' plates, developed as part of the work presented in part one of the thesis.
Download or read book Computational Genomics with R written by Altuna Akalin and published by CRC Press. This book was released on 2020-12-16 with total page 462 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.
Download or read book RNA protein Interactions written by Kiyoshi Nagai and published by Oxford University Press, USA. This book was released on 1994 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt: The study of RNA-protein interactions is crucial to understanding the mechanisms and control of gene expression and protein synthesis. The realization that RNAs are often far more biologically active than was previously appreciated has stimulated a great deal of new research in this field. Uniquely, in this book, the world's leading researchers have collaborated to produce a comprehensive and current review of RNA-protein interactions for all scientists working in this area. Timely, comprehensive, and authoritative, this new Frontiers title will be invaluable for all researchers in molecular biology, biochemistry and structural biology.
Download or read book RNA Processing written by Steve J. Higgins and published by IRL Press. This book was released on 1994 with total page 232 pages. Available in PDF, EPUB and Kindle. Book excerpt: Post-transcriptional events are increasingly recognized as important sites of regulation of gene expression in eukaryotic cells and so RNA processing has rapidly become an area of intense research activity. These two volumes give detailed practical guidance on all the major aspects of thissubject. Step-by-step practical protocols from leading laboratories are presented for studies of the termination and end-processing, capping, methylation, splicing, and editing of mRNA as well as studies of mRNA stability and processing of rRNA and tRNA. The reader is led through all the key stepsrequired for a successful experimental investigation. This includes full descriptions of the synthesis and purification of RNA substrates for in vitro work, the characterization of specific RNAs, and the isolation and analysis of ribonucleoprotein complexes.RNA processing - A Practical Approach, Volumes I and II, are invaluable laboratory companions for researchers working on mRNA, rRNA, or tRNA gene expression. Their lucid explanatory style and comprehensive coverage of all the key techniques for analysing RNA processing will be welcomed by bothexperienced researchers and
Download or read book RNA Abundance Analysis written by Hailing Jin and published by Humana. This book was released on 2020-09-18 with total page 233 pages. Available in PDF, EPUB and Kindle. Book excerpt: This updated book covers a wide range of techniques on RNA extraction, detection, quantification, visualization, and genome-wide profiling, from conventional methods to state-of-the-art high throughput approaches. It includes detailed techniques to examine mRNAs, small non-coding RNAs, protein-associated small RNAs, organelle RNAs, endosymbiont RNAs, and alternatively spliced RNA variants from various organisms. RNA editing and the computational data processing for genome-wide datasets is also discussed. 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 Abundance Analysis: Methods and Protocols, Second Edition provides a comprehensive set of techniques and methods on isolating and analyzing mRNAs, small RNAs, and other RNA variants, in order to assist researchers in their gene expression studies.
Download or read book RNA Abundance Analysis written by Hailing Jin and published by Humana Press. This book was released on 2016-05-01 with total page 248 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book examines a wide range of techniques on RNA extraction, detection, quantification, visualization, and genome-wide profiling, from conventional methods to state-of-the-art high throughput approaches.
Download or read book Visualization and Analysis of RNA Seq Assembly Graphs written by Fahmi W. Nazarie and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Data Analysis and Visualization in Genomics and Proteomics written by Francisco Azuaje and published by John Wiley & Sons. This book was released on 2005-06-24 with total page 284 pages. Available in PDF, EPUB and Kindle. Book excerpt: Data Analysis and Visualization in Genomics and Proteomics is the first book addressing integrative data analysis and visualization in this field. It addresses important techniques for the interpretation of data originating from multiple sources, encoded in different formats or protocols, and processed by multiple systems. One of the first systematic overviews of the problem of biological data integration using computational approaches This book provides scientists and students with the basis for the development and application of integrative computational methods to analyse biological data on a systemic scale Places emphasis on the processing of multiple data and knowledge resources, and the combination of different models and systems
Download or read book RNA seq Data Analysis written by Eija Korpelainen and published by CRC Press. This book was released on 2014-09-19 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Download or read book Graph Drawing written by Janos Pach and published by Springer. This book was released on 2005-02-10 with total page 547 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the thoroughly refereed post-proceedings of the 12th International Symposium on Graph Drawing, GD 2004, held in New York, NY, USA in September/October 2004. The 39 revised full papers and 12 revised short papers presented together with 4 posters and a report on the graph drawing context were carefully selected during two rounds of reviewing and improvement. All current aspects in graph drawing are addressed ranging from foundational and methodological issues to applications for various classes of graphs in a variety of fields.
Download or read book RNA 3D Structure Analysis and Prediction written by Neocles Leontis and published by Springer Science & Business Media. This book was released on 2012-06-05 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the dramatic increase in RNA 3D structure determination in recent years, we now know that RNA molecules are highly structured. Moreover, knowledge of RNA 3D structures has proven crucial for understanding in atomic detail how they carry out their biological functions. Because of the huge number of potentially important RNA molecules in biology, many more than can be studied experimentally, we need theoretical approaches for predicting 3D structures on the basis of sequences alone. This volume provides a comprehensive overview of current progress in the field by leading practitioners employing a variety of methods to model RNA 3D structures by homology, by fragment assembly, and by de novo energy and knowledge-based approaches.
Download or read book Gene Quantification written by Francois Ferre and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 379 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Ribozymes written by Sabine Müller and published by John Wiley & Sons. This book was released on 2021-07-09 with total page 81 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ribozymes Provides comprehensive coverage of a core field in the molecular biosciences, bringing together decades of knowledge from the world’s top professionals in the field Timely and unique in its breadth of content, this all-encompassing and authoritative reference on ribozymes documents the great diversity of nucleic acid-based catalysis. It integrates the knowledge gained over the past 35 years in the field and features contributions from virtually every leading expert on the subject. Ribozymes is organized into six major parts. It starts by describing general principles and strategies of nucleic acid catalysis. It then introduces naturally occurring ribozymes and includes the search for new catalytic motifs or novel genomic locations of known motifs. Next, it covers the development and design of engineered ribozymes, before moving on to DNAzymes as a close relative of ribozymes. The next part examines the use of ribozymes for medicinal and environmental diagnostics, as well as for therapeutic tools. It finishes with a look at the tools and methods in ribozyme research, including the techniques and assays for structural and functional characterization of nucleic acid catalysts. The first reference to tie together all aspects of the multi-faceted field of ribozymes Features more than 30 comprehensive chapters in two volumes Covers the chemical principles of RNA catalysis; naturally occurring ribozymes, engineered ribozymes; DNAzymes; ribozymes as tools in diagnostics and therapy, and tools and methods to study ribozymes Includes first-hand accounts of concepts, techniques, and applications by a team of top international experts from leading academic institutions Dedicates half of its content to methods and practical applications, ranging from bioanalytical tools to medical diagnostics to therapeutics Ribozymes is an unmatched resource for all biochemists, biotechnologists, molecular biologists, and bioengineers interested in the topic.
Download or read book RNA Processing written by Steve J. Higgins and published by Oxford University Press. This book was released on 1994 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt: This two-volume set provides detailed practical guidance on all major aspects of RNA processing. Each procedure is clearly explained so that the reader can follow all of the key stages of a successful experimental investigation.
