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Insights In Rna Networks And Biology
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Book Synopsis Insights in RNA Networks and Biology by : André P. Gerber
Download or read book Insights in RNA Networks and Biology written by André P. Gerber and published by Frontiers Media SA. This book was released on 2023-04-13 with total page 121 pages. Available in PDF, EPUB and Kindle. Book excerpt: We are now entering the third decade of the 21st Century, and recent, major achievements by scientists have led to major advancements in the fast-growing field of RNA Networks and Biology. This Research Topic aims to highlight the latest advancements in RNA research, and also reflect on the future of the field – what are the next expected breakthroughs and advancements? The Research Topic will collect articles from the members of our accomplished Editorial Board and is led by our Chief Editors, André Gerber and Gian Tartaglia. We are excited to receive brief, forward-looking contributions that describe the state of the art, outlining recent developments and major accomplishments that have been achieved and that need to occur to move the field forward. Authors are encouraged to identify the greatest challenges in the sub-disciplines, and how to address those challenges.
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 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 The Blossoming of RNA Biology by : Pennsylvania State University
Download or read book The Blossoming of RNA Biology written by Pennsylvania State University and published by . This book was released on 2006 with total page 12 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 0 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 Analyzing Network Data in Biology and Medicine by : Nataša Pržulj
Download or read book Analyzing Network Data in Biology and Medicine written by Nataša Pržulj and published by Cambridge University Press. This book was released on 2019-03-28 with total page 647 pages. Available in PDF, EPUB and Kindle. Book excerpt: The increased and widespread availability of large network data resources in recent years has resulted in a growing need for effective methods for their analysis. The challenge is to detect patterns that provide a better understanding of the data. However, this is not a straightforward task because of the size of the data sets and the computer power required for the analysis. The solution is to devise methods for approximately answering the questions posed, and these methods will vary depending on the data sets under scrutiny. This cutting-edge text introduces biological concepts and biotechnologies producing the data, graph and network theory, cluster analysis and machine learning, before discussing the thought processes and creativity involved in the analysis of large-scale biological and medical data sets, using a wide range of real-life examples. Bringing together leading experts, this text provides an ideal introduction to and insight into the interdisciplinary field of network data analysis in biomedicine.
Book Synopsis RNA Binding Landscapes in Germ Cells by : Aman Prasad
Download or read book RNA Binding Landscapes in Germ Cells written by Aman Prasad and published by . This book was released on 2016 with total page 153 pages. Available in PDF, EPUB and Kindle. Book excerpt: PUF (Pumilio/FBF) proteins are RNA-binding proteins and conserved stem cell regulators. The Caenorhabditis elegans PUF proteins FBF-1 and FBF-2 (collectively FBF) regulate mRNAs in germ cells. Without FBF, adult germlines lose all stem cells. Major gaps in our understanding of PUF proteins is a global view of their binding sites in their native context (i.e., their "binding landscape") and their in vivo binding specificity, which forms the logic of their network of regulated RNAs. In order to understand the interactions underlying FBF function in vivo, we used high resolution methods to precisely determine the targets and binding sites of FBF-1 and FBF-2 in two different contexts: 1) the germline tissue of intact animals and 2) germline tissue of different gamete fates (i.e., spermatogenic versus oogenic germlines). My findings provide insights into the nature of sequences bound by these nearly identical PUF paralogs and the locations of their binding sites within their targets. It also defines a robust FBF-RNA regulatory network, biological functions of FBF targets, and conserved aspects of the network. We discovered that in all contexts, the RNA targets and binding sites of FBF-1 and FBF-2 are strikingly similar and directly relevant to stem cell regulation. We also discovered that non-canonical motifs are recognized in vivo. These common binding landscapes reveal the molecular basis of the biological redundancy of these two PUF paralogs. The cell cycle emerged as the major biological process among FBF target mRNAs. Moreover, cell cycle regulators are enriched as conserved targets for both nematode and human PUFs. Besides its expansive control over the cell cycle, FBF regulates a spectrum of previously unknown targets, including lncRNAs, the RNA degradation machinery, and components of miRNA biogenesis. The landscapes defined here are the first in vivo CLIP-based PUF-RNA networks in a metazoan in vivo. Our analysis also identifies optimal background data to be used to call iCLIP peaks, and we present an optimized computational strategy for peak calling which will be of general utility to others in the field.
Download or read book RNA written by Henrik Nielsen and published by Humana Press. This book was released on 2010-12-10 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent insight into the transcripts generated from the mammalian genome (i.e. the transcriptome) has revealed that transcription is a far more complex phenomenon than previously thought. In RNA: Methods and Protocols, expert researchers provide the procedures and methods used to describe the structure of messenger RNAs and non-coding RNAs that are transcribed by RNA polymerase II as the immediate gene products in mammalian cells. Focused on the structure of the RNA products of “gene X” and the mapping of proteins associated with these RNAs, the volume presents appropriate information for non-specialists in RNA biology. Written in the highly successful Methods in Molecular BiologyTM series format, many chapters contain 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 practical, RNA: Methods and Protocols views the transcriptional landscape with an appreciation for the role that proteins play in the processing and interpretation of genetic information in an attempt to further our crucial knowledge of the many products and sophisticated regulatory networks that result from it.
Book Synopsis Long Noncoding RNAs by : Riki Kurokawa
Download or read book Long Noncoding RNAs written by Riki Kurokawa and published by Springer. This book was released on 2016-10-18 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a common principle of actions of long noncoding RNAs (lncRNAs) from points of view at the atomic, molecular and cellular levels. At the atomic level, chemical studies of ribonucleic acids explain the chemical behavior of lncRNAs. Structural biological analysis of lncRNAs and its binding proteins also reveal the precise mechanisms of their actions. Molecular biological approaches lead to insights into molecular mechanisms of these lncRNA actions. At the cellular or individual level of analysis, we grasp the biology and medicine of lncRNAs. These three layers of approaches are thoroughly new and produce novel insights into functions of lncRNAs in living cells. The book consists of five parts: 1) Bioinformatics and other methodologies for lncRNAs, 2) Atomic and molecular structures of lncRNAs, 3) Molecular functions of lncRNAs, 4) Biological actions of lncRNAs, and 5) Potential outcomes for clinical medicine. These sections connect well and work synergistically. The book is for researchers whose specialty is RNA biology and chemistry and also for advanced students at the graduate and undergraduate levels. Readers can grasp the leading edge of lncRNA studies in a comprehensive manner and are inspired to pursue their own particular interests.
Book Synopsis Biological Sequence Analysis by : Richard Durbin
Download or read book Biological Sequence Analysis written by Richard Durbin and published by Cambridge University Press. This book was released on 1998-04-23 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Probabilistic models are becoming increasingly important in analysing the huge amount of data being produced by large-scale DNA-sequencing efforts such as the Human Genome Project. For example, hidden Markov models are used for analysing biological sequences, linguistic-grammar-based probabilistic models for identifying RNA secondary structure, and probabilistic evolutionary models for inferring phylogenies of sequences from different organisms. This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis. Written by an interdisciplinary team of authors, it aims to be accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time present the state-of-the-art in this new and highly important field.
Download or read book Molecular Biology of the Cell written by and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Mining Biological Data with Machine Learning to Obtain New Insights by : Chengyu Liu
Download or read book Mining Biological Data with Machine Learning to Obtain New Insights written by Chengyu Liu and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular biology is a highly complicated subject due to the complexity of cells and organisms as systems. To decode them, recent efforts are dedicated to generating data at an increasingly large scale. Luckily, the emergence of two major methods in bioinformatics, network analysis and machine learning, have provided us with tools to digest these data into biological insights. During my PhD, I have improved and developed methods in network analysis and machine learning to make them more efficient and generate human understandable insights. In chapter I, colleague and I developed a new version of information flow analysis algorithm with time complexity of O(n2m) instead of O(n4). We also developed a GPU version of this algorithm that can achieve a 17.4x speed up over the original implementation on a Hi-C network of a relatively small chromosome. This would allow us to apply information flow analysis on much larger biological networks. In chapter II, I developed contextual regression, a deep neural network framework that can achieve state of the art prediction accuracy while generating human interpretable outputs. We tested this method on a simulated biological signal dataset and found our method not only has good prediction performance, but also is able to uncover the ground truth model even under a noise level of 80%. To test this method on real world data, we also applied this method to analyze the effect of histone marks on open chromatin. The model not only outperforms previous models in terms of prediction, but also uncover histone mark patterns that are associated with open chromatin formation. In chapter III, colleague and I applied the contextual regression framework on circular RNA data. Combining this new method and the circNet database, we uncovered 7 types of circular RNA genesis mechanisms. This discovery supports the hypothesis that multiple biogenesis mechanisms co-exist for different subsets of human circRNAs. In chapter IV, I developed a new contextual regression architecture and applied it to the task of predicting RNA expression level from gene sequences. The new architecture not only achieved state of the art accuracy, but also learned important motifs that can affect gene expression. I then developed a selection process and generated a linear formula of 300 sequence motifs that can predict expression level as accurately as deep neural network models. The most influential motifs among these motifs are deeply involved in development, regulation and stimulus response. When we applied this linear formula to different cell lines, we found the parameters of this formula are associated with biological properties such as epigenetic influence through development, cell lineages and difference of expression patterns among cell lines. We anticipate that these studies have created tools towards the challenge of mining biological insights from increasing amounts of biological data.
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
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 Biological Network Analysis by : Pietro Hiram Guzzi
Download or read book Biological Network Analysis written by Pietro Hiram Guzzi and published by Elsevier. This book was released on 2020-05-11 with total page 212 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biological Network Analysis: Trends, Approaches, Graph Theory, and Algorithms considers three major biological networks, including Gene Regulatory Networks (GRN), Protein-Protein Interaction Networks (PPIN), and Human Brain Connectomes. The book's authors discuss various graph theoretic and data analytics approaches used to analyze these networks with respect to available tools, technologies, standards, algorithms and databases for generating, representing and analyzing graphical data. As a wide variety of algorithms have been developed to analyze and compare networks, this book is a timely resource. Presents recent advances in biological network analysis, combining Graph Theory, Graph Analysis, and various network models Discusses three major biological networks, including Gene Regulatory Networks (GRN), Protein-Protein Interaction Networks (PPIN) and Human Brain Connectomes Includes a discussion of various graph theoretic and data analytics approaches
Book Synopsis Handbook of Systems Biology by : Marian Walhout
Download or read book Handbook of Systems Biology written by Marian Walhout and published by Academic Press. This book was released on 2012-12-31 with total page 553 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides an entry point into Systems Biology for researchers in genetics, molecular biology, cell biology, microbiology and biomedical science to understand the key concepts to expanding their work. Chapters organized around broader themes of Organelles and Organisms, Systems Properties of Biological Processes, Cellular Networks, and Systems Biology and Disease discuss the development of concepts, the current applications, and the future prospects. Emphasis is placed on concepts and insights into the multi-disciplinary nature of the field as well as the importance of systems biology in human biological research. Technology, being an extremely important aspect of scientific progress overall, and in the creation of new fields in particular, is discussed in 'boxes' within each chapter to relate to appropriate topics. 2013 Honorable Mention for Single Volume Reference in Science from the Association of American Publishers' PROSE Awards Emphasizes the interdisciplinary nature of systems biology with contributions from leaders in a variety of disciplines Includes the latest research developments in human and animal models to assist with translational research Presents biological and computational aspects of the science side-by-side to facilitate collaboration between computational and biological researchers
Book Synopsis Network Medicine by : Joseph Loscalzo
Download or read book Network Medicine written by Joseph Loscalzo and published by Harvard University Press. This book was released on 2017-02-01 with total page 449 pages. Available in PDF, EPUB and Kindle. Book excerpt: Big data, genomics, and quantitative approaches to network-based analysis are combining to advance the frontiers of medicine as never before. With contributions from leading experts, Network Medicine introduces this rapidly evolving field of research, which promises to revolutionize the diagnosis and treatment of human diseases.
