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.
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.
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.
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:
Download or read book Fungal RNA Biology written by Ane Sesma and published by Springer Science & Business Media. This book was released on 2014-04-15 with total page 396 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an overview of the RNA networks controlling gene expression in fungi highlighting the remaining questions and future challenges in this area. It covers several aspects of the RNA-mediated mechanisms that regulate gene expression in model yeasts and filamentous fungi, organisms of great importance for industry, medicine and agriculture. It is estimated that there are more than one million fungal species on the Earth. Despite their diversity (saprophytic, parasitic and mutualistic), fungi share common features distinctive from plants and animals and have been grouped taxonomically as an independent eukaryotic kingdom. In this book, 15 chapters written by experts in their fields cover the RNA-dependent processes that take place in a fungal cell ranging from formation of coding and non-coding RNAs to mRNA translation, ribosomal RNA biogenesis, gene silencing, RNA editing and epigenetic regulation.
Download or read book Molecular Biology of Long Non coding RNAs written by Ahmad M. Khalil and published by Springer. This book was released on 2019-06-06 with total page 187 pages. Available in PDF, EPUB and Kindle. Book excerpt: This second edition shows how long non-coding RNAs (lnc)RNAs have emerged as a new paradigm in epigenetic regulation of the genome. Thousands of lncRNAs have been identified and observed in a wide range of organisms. Unlike mRNA, lncRNA have no protein-coding capacity. So, while their function is not entirely clear, they may serve as key organizers of protein complexes that allow for higher order regulatory events. Advances in the field also include better characterization of human long non-coding RNAs, novel insights into their roles in human development and disease, their diverse mechanisms of action and novel technologies to study them.
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.
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.
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 Synthetic Receptors for Biomolecules written by Bradley D. Smith and published by Royal Society of Chemistry. This book was released on 2015-07-10 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt: Synthetic receptor molecules, molecules that mimic antibody recognition, are widely used for developing drug leads; drug delivery vehicles; imaging agents; sensing agents; capture agents and separation systems. Synthetic Receptors for Biomolecules covers the most effective synthetic receptors for each major class of biomolecules within the context of specific applications. The book starts with an introduction to the applications of synthetic receptors for biomolecules and their design and synthesis for biomolecule recognition. Dedicated chapters then cover synthetic receptors for the key biomolecules including inorganic cations; small organic and inorganic anions; carbohydrates; nucleosides/nucleotides; oligonucleotides; amino acids and peptides; protein surfaces as well as non-polar and polar lipids; Each chapter follows the same systematic format of (a) chemical structures and physical properties of the biomolecule, (b) biological recognition of the biomolecule, (c) synthetic receptors for the biomolecule, (d) future directions and challenges. Edited by a leader in the field, the book is written in an accessible style for readers new to supramolecular chemistry or for those looking for synthetic receptors.
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.
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.
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.
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 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.
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:
Download or read book Complex Systems Science in Biomedicine written by Thomas Deisboeck and published by Springer Science & Business Media. This book was released on 2007-06-13 with total page 857 pages. Available in PDF, EPUB and Kindle. Book excerpt: Complex Systems Science in Biomedicine Thomas S. Deisboeck and J. Yasha Kresh Complex Systems Science in Biomedicine covers the emerging field of systems science involving the application of physics, mathematics, engineering and computational methods and techniques to the study of biomedicine including nonlinear dynamics at the molecular, cellular, multi-cellular tissue, and organismic level. With all chapters helmed by leading scientists in the field, Complex Systems Science in Biomedicine's goal is to offer its audience a timely compendium of the ongoing research directed to the understanding of biological processes as whole systems instead of as isolated component parts. In Parts I & II, Complex Systems Science in Biomedicine provides a general systems thinking perspective and presents some of the fundamental theoretical underpinnings of this rapidly emerging field. Part III then follows with a multi-scaled approach, spanning from the molecular to macroscopic level, exemplified by studying such diverse areas as molecular networks and developmental processes, the immune and nervous systems, the heart, cancer and multi-organ failure. The volume concludes with Part IV that addresses methods and techniques driven in design and development by this new understanding of biomedical science. Key Topics Include: • Historic Perspectives of General Systems Thinking • Fundamental Methods and Techniques for Studying Complex Dynamical Systems • Applications from Molecular Networks to Disease Processes • Enabling Technologies for Exploration of Systems in the Life Sciences Complex Systems Science in Biomedicine is essential reading for experimental, theoretical, and interdisciplinary scientists working in the biomedical research field interested in a comprehensive overview of this rapidly emerging field. About the Editors: Thomas S. Deisboeck is currently Assistant Professor of Radiology at Massachusetts General Hospital and Harvard Medical School in Boston. An expert in interdisciplinary cancer modeling, Dr. Deisboeck is Director of the Complex Biosystems Modeling Laboratory which is part of the Harvard-MIT Martinos Center for Biomedical Imaging. J. Yasha Kresh is currently Professor of Cardiothoracic Surgery and Research Director, Professor of Medicine and Director of Cardiovascular Biophysics at the Drexel University College of Medicine. An expert in dynamical systems, he holds appointments in the School of Biomedical Engineering and Health Systems, Dept. of Mechanical Engineering and Molecular Pathobiology Program. Prof. Kresh is Fellow of the American College of Cardiology, American Heart Association, Biomedical Engineering Society, American Institute for Medical and Biological Engineering.
