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Dissecting Protein Rna Interaction Network In Human Genome
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Book Synopsis Dissecting Protein-RNA Interaction Network in Human Genome by : Seyedsasan Hashemikhabir
Download or read book Dissecting Protein-RNA Interaction Network in Human Genome written by Seyedsasan Hashemikhabir and published by . This book was released on 2020 with total page 184 pages. Available in PDF, EPUB and Kindle. Book excerpt: In eukaryotes, gene regulation is a complex multilevel process comprising of transcriptional, post-transcriptional, and post-translational control. Although the regulation at transcriptional and post-translational levels is gradually being understood, protein machinery and the mechanisms underlying the post-transcriptional regulation remain to be elucidated. In the first study of this dissertation, I designed and implemented a database of RNA Binding Protein (RBP) Expression and Disease Dynamics (READ-DB: darwin.soic.iupui.edu), a non-redundant, curated database of human RBPs. This RBP knowledge base includes data from different experimental studies providing a one stop portal for understanding the expression, evolutionary trajectories, and disease dynamics of RBPs in the context of post-transcriptional regulatory networks. Despite the existence of several experimental procedures to understand the function of RBPs, a lack of a proper computational method to profile differential occupancy limits the scope of research. In the second study, I built a scalable framework for comparing genome-wide protein occupancy profiles among cell-types data, to uncover alterations in protein-RNA interactomes. diffHunter (github.com/Sasanh/diffHunter), is a window based peak calling and profile comparison method that can efficiently store the base-pair level read information of every given sample in a NoSQL (Not Only SQL) database. It identifies and quantitates the genome-wide binding differences between a pair of samples in two stages: Peak Calling and Differential Binding Identification. Identifying such regions enables us to compare the biologically important regions that differ between two conditions. Finally, I studied A-to- I RNA editing as one of the special functions of an RBPs' family. ADAR family RBPs are the primary driver in the conversion of adenosine to inosine (A-to-I) within mRNA. I developed a Cancer-specific RNA-editing Identification using Somatic variation Pipeline (CRISP: github.com/Sasanh/CRISP) a computational framework for accurate identification of A-to-I editing events contributing to the prognosis and stratification of glioblastoma subtypes as well as the editing events that can serve as molecular classifiers for therapeutic approaches. I proposed two models that explains the cis-regulatory role of A-to-I editing events in noncoding regions in modulating the post-transcriptional regulation of target transcripts in glioblastoma.
Book Synopsis Dissecting Regulatory Interactions of RNA and Protein by : Marvin Jens
Download or read book Dissecting Regulatory Interactions of RNA and Protein written by Marvin Jens and published by Springer. This book was released on 2014-05-20 with total page 115 pages. Available in PDF, EPUB and Kindle. Book excerpt: The work described in this book is an excellent example of interdisciplinary research in systems biology. It shows how concepts and approaches from the field of physics can be efficiently used to answer biological questions and reports on a novel methodology involving creative computer-based analyses of high-throughput biological data. Many of the findings described in the book, which are the result of collaborations between the author (a theoretical scientist) and experimental biologists and between different laboratories, have been published in high-quality peer-reviewed journals such as Molecular Cell and Nature. However, while those publications address different aspects of post-transcriptional gene regulation, this book provides readers with a complete, coherent and logical view of the research project as a whole. The introduction presents post-transcriptional gene regulation from a distinct angle, highlighting aspects of information theory and evolution and laying the groundwork for the questions addressed in the subsequent chapters, which concern the regulation of the transcriptome as the primary functional carrier of active genetic information.
Book Synopsis New Strategies Reveal Key Features of Protein-RNA Networks by : Christopher Lapointe
Download or read book New Strategies Reveal Key Features of Protein-RNA Networks written by Christopher Lapointe and published by . This book was released on 2016 with total page 389 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein-RNA interactions are ubiquitous. They determine where, when, and how much protein is produced from an mRNA. Single RNA-binding proteins often bind to many RNAs. Multiple proteins can simultaneously bind to a single RNA molecule. The particular combination of proteins dictates the fate of that mRNA. Networks of protein-RNA interactions, referred to as 0́−protein-RNA networks0́+, underlie fundamental cellular processes and have well-established connections to disease. The challenges now are to understand how they are formed, how they function, and how they are balanced in vivo. I employed an integrated approach of biochemistry, molecular biology, genomics, genetics, and bioinformatics to develop new strategies for the dissection of protein-RNA networks. I began with structure-function analyses of an RNA-modifying enzyme (Chapter 2), which enabled me to develop a method to identify protein-RNA interactions in vivo, which we termed 0́−RNA Tagging0́+ (Chapter 3). I used RNA Tagging to reveal that while proteins productively bind specific RNAs to control their function, they also 0́−sample0́+ RNAs by binding briefly to them without exerting a regulatory effect. I next integrated RNA Tagging with a different approach to identify RNAs bound by a particular protein called HITS-CLIP. I demonstrated that the two approaches are complementary, and together they defined a core set of mRNAs controlled by an RNA-binding protein (Chapter 4). These studies enabled collaborative multi-omic analyses, which revealed that Saccharomyces cerevisiae Puf3p is a key post-transcriptional repressor of mitochondrial biogenesis factors. In parallel, I employed RNA Tagging to dissect a protein-RNA network controlled by three related RNA-binding proteins 0́3 Puf3p, Puf4p, and Puf5p 0́3 in yeast (Chapter 5). The architecture of the network is controlled by competition among the proteins for mRNAs, which is balanced via an interplay of binding affinity and relative abundance. Together, my thesis research includes the development of a novel method and new strategies to analyze protein-RNA interactions that occur inside living cells. These approaches have several advantages over those previously described, provide new insights into how proteins regulate RNAs, and are widely applicable to protein-RNA networks throughout biology. They provide new opportunities to probe the nature and dynamics of protein-RNA networks in living cells.
Book Synopsis RNA-RNA Interactions by : Frank J. Schmidt
Download or read book RNA-RNA Interactions written by Frank J. Schmidt and published by Humana Press. This book was released on 2014-10-29 with total page 219 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this volume expert researchers in the field detail many of the methods which are now commonly used to study RNA. These methods are presented as a guidebook to scientists who are experienced with RNA research and want to brush up on a new technique. 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 key tips on troubleshooting and avoiding known pitfalls. Thorough and intuitive, RNA-RNA Interactions: Methods and Protocols guides scientists investigating biological systems and studying RNA.
Book Synopsis RNA-protein Interactions by : Kiyoshi Nagai
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.
Book Synopsis Analyzing Microarray Gene Expression Data by : Geoffrey J. McLachlan
Download or read book Analyzing Microarray Gene Expression Data written by Geoffrey J. McLachlan and published by John Wiley & Sons. This book was released on 2005-02-18 with total page 366 pages. Available in PDF, EPUB and Kindle. Book excerpt: A multi-discipline, hands-on guide to microarray analysis of biological processes Analyzing Microarray Gene Expression Data provides a comprehensive review of available methodologies for the analysis of data derived from the latest DNA microarray technologies. Designed for biostatisticians entering the field of microarray analysis as well as biologists seeking to more effectively analyze their own experimental data, the text features a unique interdisciplinary approach and a combined academic and practical perspective that offers readers the most complete and applied coverage of the subject matter to date. Following a basic overview of the biological and technical principles behind microarray experimentation, the text provides a look at some of the most effective tools and procedures for achieving optimum reliability and reproducibility of research results, including: An in-depth account of the detection of genes that are differentially expressed across a number of classes of tissues Extensive coverage of both cluster analysis and discriminant analysis of microarray data and the growing applications of both methodologies A model-based approach to cluster analysis, with emphasis on the use of the EMMIX-GENE procedure for the clustering of tissue samples The latest data cleaning and normalization procedures The uses of microarray expression data for providing important prognostic information on the outcome of disease
Book Synopsis Post-Transcriptional Gene Regulation by : Erik Dassi
Download or read book Post-Transcriptional Gene Regulation written by Erik Dassi and published by Humana. This book was released on 2022-11-09 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents the most recent advances in techniques for studying the post-transcriptional regulation of gene expression (PTR). With sections on bioinformatics approaches, expression profiling, the protein and RNA interactome, the mRNA lifecycle, and RNA modifications, the book guides molecular biologists toward harnessing the power of this new generation of techniques, while also introducing the data analysis skills that these high-throughput techniques require. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and up-to-date, Post-Transcriptional Gene Regulation, Third Edition serves as a versatile resource for researchers studying post-transcriptional regulation by both introducing the most recent techniques and providing a comprehensive guide to their implementation. Chapter 6 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.
Book Synopsis Statistical Models by : David Freedman
Download or read book Statistical Models written by David Freedman and published by Cambridge University Press. This book was released on 2009-04-27 with total page 442 pages. Available in PDF, EPUB and Kindle. Book excerpt: This lively and engaging book explains the things you have to know in order to read empirical papers in the social and health sciences, as well as the techniques you need to build statistical models of your own. The discussion in the book is organized around published studies, as are many of the exercises. Relevant journal articles are reprinted at the back of the book. Freedman makes a thorough appraisal of the statistical methods in these papers and in a variety of other examples. He illustrates the principles of modelling, and the pitfalls. The discussion shows you how to think about the critical issues - including the connection (or lack of it) between the statistical models and the real phenomena. The book is written for advanced undergraduates and beginning graduate students in statistics, as well as students and professionals in the social and health sciences.
Book Synopsis Protein-Protein Interaction Networks by : Stefan Canzar
Download or read book Protein-Protein Interaction Networks written by Stefan Canzar and published by Humana. This book was released on 2019-10-04 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores techniques that study interactions between proteins in different species, and combines them with context-specific data, analysis of omics datasets, and assembles individual interactions into higher-order semantic units, i.e., protein complexes and functional modules. The chapters in this book cover computational methods that solve diverse tasks such as the prediction of functional protein-protein interactions; the alignment-based comparison of interaction networks by SANA; using the RaptorX-ComplexContact webserver to predict inter-protein residue-residue contacts; the docking of alternative confirmations of proteins participating in binary interactions and the visually-guided selection of a docking model using COZOID; the detection of novel functional units by KeyPathwayMiner and how PathClass can use such de novo pathways to classify breast cancer subtypes. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary hardware- and software, step-by-step, readily reproducible computational protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Protein-Protein Interaction Networks: Methods and Protocols is a valuable resource for both novice and expert researchers who are interested in learning more about this evolving field.
Book Synopsis RNA Infrastructure and Networks by : Lesley J. Collins
Download or read book RNA Infrastructure and Networks written by Lesley J. Collins and published by Springer Science & Business Media. This book was released on 2011-09-15 with total page 297 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNAs form complexes with proteins and other RNAs. The RNA‐infrastructure represents the spatiotemporal interaction of these proteins and RNAs in a cell‐wide network. RNA Infrastructure and Networks brings together these ideas to illustrate the scope of RNA‐based biology, and how connecting RNA mechanisms is a powerful tool to investigate regulatory pathways. This book is but a taste of the wide range of RNA‐based mechanisms that connect in the RNA infrastructure.
Book Synopsis Molecular Biology of The Cell by : Bruce Alberts
Download or read book Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Evolution of Translational Omics by : Institute of Medicine
Download or read book Evolution of Translational Omics written by Institute of Medicine and published by National Academies Press. This book was released on 2012-09-13 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt: Technologies collectively called omics enable simultaneous measurement of an enormous number of biomolecules; for example, genomics investigates thousands of DNA sequences, and proteomics examines large numbers of proteins. Scientists are using these technologies to develop innovative tests to detect disease and to predict a patient's likelihood of responding to specific drugs. Following a recent case involving premature use of omics-based tests in cancer clinical trials at Duke University, the NCI requested that the IOM establish a committee to recommend ways to strengthen omics-based test development and evaluation. This report identifies best practices to enhance development, evaluation, and translation of omics-based tests while simultaneously reinforcing steps to ensure that these tests are appropriately assessed for scientific validity before they are used to guide patient treatment in clinical trials.
Book Synopsis Protein-Nucleic Acid Interactions by : Phoebe A. Rice
Download or read book Protein-Nucleic Acid Interactions written by Phoebe A. Rice and published by Royal Society of Chemistry. This book was released on 2008-05-22 with total page 417 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides both in-depth background and up-to-date information in this area. The chapters are organized by general themes and principles, written by experts who illustrate topics with current findings. Topics covered include: - the role of ions and hydration in protein-nucleic acid interactions - transcription factors and combinatorial specificity - indirect readout of DNA sequence - single-stranded nucleic acid binding proteins - nucleic acid junctions and proteins, - RNA protein recognition - recognition of DNA damage. It will be a key reference for both advanced students and established scientists wishing to broaden their horizons.
Book Synopsis Computation in BioInformatics by : S. Balamurugan
Download or read book Computation in BioInformatics written by S. Balamurugan and published by John Wiley & Sons. This book was released on 2021-10-19 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt: COMPUTATION IN BIOINFORMATICS Bioinformatics is a platform between the biology and information technology and this book provides readers with an understanding of the use of bioinformatics tools in new drug design. The discovery of new solutions to pandemics is facilitated through the use of promising bioinformatics techniques and integrated approaches. This book covers a broad spectrum of the bioinformatics field, starting with the basic principles, concepts, and application areas. Also covered is the role of bioinformatics in drug design and discovery, including aspects of molecular modeling. Some of the chapters provide detailed information on bioinformatics related topics, such as silicon design, protein modeling, DNA microarray analysis, DNA-RNA barcoding, and gene sequencing, all of which are currently needed in the industry. Also included are specialized topics, such as bioinformatics in cancer detection, genomics, and proteomics. Moreover, a few chapters explain highly advanced topics, like machine learning and covalent approaches to drug design and discovery, all of which are significant in pharma and biotech research and development. Audience Researchers and engineers in computation biology, information technology, bioinformatics, drug design, biotechnology, pharmaceutical sciences.
Book Synopsis RNA Biochemistry and Biotechnology by : Jan Barciszewski
Download or read book RNA Biochemistry and Biotechnology written by Jan Barciszewski and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 373 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA Biochemistry and Biotechnology describes various aspects of nucleic acid and protein structure, mainly RNA structure and proteins, interacting with specific RNA species. Papers deal with DNA protein interactions, telomerase, aminoacyl-tRNA synthetases, elongation factor Tu, DNA repair, RNA structure, NMR technology, RNA aptamer interaction of biological macromolecules with metal ions. Two papers deal with theoretical aspects of RNA structure production and computer modelling. Many papers describe the possibility of commercial application of RNA biotechnology. One article discusses the impact of direct democracy on basic science supporting biotechnology. Readership: Advanced graduate students, Ph.D. students and young scientists as well as specialists in the field.
Book Synopsis Systems Biology of RNA Binding Proteins by : Gene W. Yeo
Download or read book Systems Biology of RNA Binding Proteins written by Gene W. Yeo and published by Springer. This book was released on 2014-09-08 with total page 474 pages. Available in PDF, EPUB and Kindle. Book excerpt: After transcription in the nucleus, RNA binding proteins (RBPs) recognize cis-regulatory RNA elements within pre-mRNA sequence to form mRNA-protein (mRNP) complexes. Similarly to DNA binding proteins such as transcription factors that regulate gene expression by binding to DNA elements in the promoters of genes, RBPs regulate the fate of target RNAs by interacting with specific sequences or RNA secondary structural features within the transcribed RNA molecule. The set of functional RNA elements recognized by RBPs within target RNAs and which control the temporal, functional and spatial dynamics of the target RNA define a putative “mRNP code”. These cis-regulatory RNA elements can be found in the 5’ and 3’ untranslated regions (UTRs), introns, and exons of all protein-coding genes. RNA elements in 5’ and 3’ UTRs are frequently involved in targeting RNA to specific cellular compartments, affecting 3’ end formation, controlling RNA stability and regulating mRNA translation. RNA elements in introns and exons are known to function as splicing enhancers or silencers during the splicing process from pre-mRNA to mature mRNA. This book provides case studies of RNA binding proteins that regulate aspects of RNA processing that are important for fundamental understanding of diseases and development. Chapters include systems-level perspectives, mechanistic insights into RNA processing and RNA Binding proteins in genetic variation, development and disease. The content focuses on systems biology and genomics of RNA Binding proteins and their relation to human diseases.
Book Synopsis Genomic and Precision Medicine by : Geoffrey S. Ginsburg
Download or read book Genomic and Precision Medicine written by Geoffrey S. Ginsburg and published by Academic Press. This book was released on 2022-04-09 with total page 379 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genomic and Precision Medicine: Oncology, Third Edition focuses on the applications of genome discovery as research points to personalized cancer therapies. Each chapter is organized to cover the application of genomics and personalized medicine tools and technologies to a) Risk Assessment and Susceptibility, b) Diagnosis and Prognosis, c) Pharmacogenomics and Precision Therapeutics, and d) Emerging and Future Opportunities in the field. Provides a comprehensive volume written and edited by oncology genomic specialists for oncology health providers Includes succinct commentary and key learning points that will assist providers with their local needs for implementation of genomic and personalized medicine into practice Presents an up-to-date overview on major opportunities for genomic and personalized medicine in practice Covers case studies that highlight the practical use of genomics in the management of patients
