Computational Non coding RNA Biology Book

Computational Non coding RNA Biology

  • Author : Yun Zheng
  • Publisher : Academic Press
  • Release Date : 2018-09-14
  • Genre: Science
  • Pages : 320
  • ISBN 10 : 9780128143667
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Computational Non coding RNA Biology Excerpt :

Computational Non-coding RNA Biology is a resource for the computation of non-coding RNAs. The book covers computational methods for the identification and quantification of non-coding RNAs, including miRNAs, tasiRNAs, phasiRNAs, lariat originated circRNAs and back-spliced circRNAs, the identification of miRNA/siRNA targets, and the identification of mutations and editing sites in miRNAs. The book introduces basic ideas of computational methods, along with their detailed computational steps, a critical component in the development of high throughput sequencing technologies for identifying different classes of non-coding RNAs and predicting the possible functions of these molecules. Finding, quantifying, and visualizing non-coding RNAs from high throughput sequencing datasets at high volume is complex. Therefore, it is usually possible for biologists to complete all of the necessary steps for analysis. Presents a comprehensive resource of computational methods for the identification and quantification of non-coding RNAs Introduces 23 practical computational pipelines for various topics of non-coding RNAs Provides a guide to assist biologists and other researchers dealing with complex datasets Introduces basic computational methods and provides guidelines for their replication by researchers Offers a solution to researchers approaching large and complex sequencing datasets

Computational Biology of Non Coding RNA Book

Computational Biology of Non Coding RNA

  • Author : Xin Lai
  • Publisher : Humana Press
  • Release Date : 2019-02-04
  • Genre: Science
  • Pages : 390
  • ISBN 10 : 1493989812
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Computational Biology of Non Coding RNA Excerpt :

This volume details a collection of state-of-art methods including identification of novel ncRNAs and their targets, functional annotation and disease association in different biological contexts. Chapters guide readers through an overview of disease-specific ncRNAs, computational methods and workflows for ncRNA discovery, annotation based on high-throughput sequencing data, bioinformatics tools and databases for ncRNA analyses, network-based methods, and kinetic modelling of ncRNA-mediated gene regulation. 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 tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Biology of Non-Coding RNA: Methods and Protocols aims to provide a state-of-the-art collection of computational methods and approaches that will be of value to researchers interested in ncRNA field.

Long Noncoding RNAs in Plants Book

Long Noncoding RNAs in Plants

  • Author : Santosh Kumar Upadhyay
  • Publisher : Academic Press
  • Release Date : 2020-11-13
  • Genre: Science
  • Pages : 390
  • ISBN 10 : 9780128214633
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Long Noncoding RNAs in Plants Excerpt :

The growth of human population has increased the demand for improved yield and quality of crops and horticultural plants. However, plant productivity continues to be threatened by stresses such as heat, cold, drought, heavy metals, UV radiations, bacterial and fungal pathogens, and insect pests. Long noncoding RNAs are associated with various developmental pathways, regulatory systems, abiotic and biotic stress responses and signaling, and can provide an alternative strategy for stress management in plants. Long Noncoding RNAs in Plants: Roles in development and stress provides the most recent advances in LncRNAs, including identification, characterization, and their potential applications and uses. Introductory chapters include the basic features and brief history of development of lncRNAs studies in plants. The book then provides the knowledge about the lncRNAs in various important agricultural and horticultural crops such as cereals, legumes, fruits, vegetables, and fiber crop cotton, and their roles and applications in abiotic and biotic stress management. Includes the latest advances and research in long noncoding RNAs in plants Provides alternative strategies for abiotic and biotic stress management in horticultural plants and agricultural crops Focuses on the application and uses of long noncoding RNAs

Long Non Coding RNA Biology Book

Long Non Coding RNA Biology

  • Author : M.R.S. Rao
  • Publisher : Springer
  • Release Date : 2017-08-16
  • Genre: Medical
  • Pages : 323
  • ISBN 10 : 9789811052033
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Long Non Coding RNA Biology Excerpt :

This contributed volume offers a comprehensive and detailed overview of the various aspects of long non-coding RNAs and discusses their emerging significance. Written by leading experts in the field, it motivates young researchers around the globe, and offers graduate and postgraduate students fascinating insights into genes and their regulation in eukaryotes and higher organisms.

Applications of RNA Seq and Omics Strategies Book

Applications of RNA Seq and Omics Strategies

  • Author : Fabio Marchi
  • Publisher : BoD – Books on Demand
  • Release Date : 2017-09-13
  • Genre: Medical
  • Pages : 328
  • ISBN 10 : 9789535135036
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Applications of RNA Seq and Omics Strategies Excerpt :

The large potential of RNA sequencing and other "omics" techniques has contributed to the production of a huge amount of data pursuing to answer many different questions that surround the science's great unknowns. This book presents an overview about powerful and cost-efficient methods for a comprehensive analysis of RNA-Seq data, introducing and revising advanced concepts in data analysis using the most current algorithms. A holistic view about the entire context where transcriptome is inserted is also discussed here encompassing biological areas with remarkable technological advances in the study of systems biology, from microorganisms to precision medicine.

Non coding RNAs in Cardiovascular Diseases Book

Non coding RNAs in Cardiovascular Diseases

  • Author : Junjie Xiao
  • Publisher : Springer Nature
  • Release Date : 2020-04-13
  • Genre: Science
  • Pages : 426
  • ISBN 10 : 9789811516719
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Non coding RNAs in Cardiovascular Diseases Excerpt :

This book presents the latest research on non-coding RNAs in cardiovascular disease, a major cause of death worldwide. Non-coding RNAs play a significant role in development, proliferation, differentiation and apoptosis. Since altered non-coding RNA expression is often associated with various diseases, their potential use in diagnostics, prognostics and therapeutics is an important current area of study. The book consists of six parts: 1) An overview of non-coding RNAs and cardiovascular system, 2) Bioinformatics and interactions, 3) Non-coding RNA regulation in cardiovascular system, 4) Non-coding RNAs and cardiovascular diseases, 5) Potential biomarkers and therapeutic implications, 6) Future prospects. It is particularly useful for researchers and students in the field of non-coding RNA and cardiovascular biology, as well as for cardiologists, pharmacologists and physiologists.

Gene Expression Profiling in Cancer Book

Gene Expression Profiling in Cancer

  • Author : Dimitrios Vlachakis
  • Publisher : BoD – Books on Demand
  • Release Date : 2019-06-19
  • Genre: Medical
  • Pages : 78
  • ISBN 10 : 9781838801755
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Gene Expression Profiling in Cancer Excerpt :

The contribution of modern-day genetics in designing efficient gene expression profiles for cancer is immense. The progress of technology and science in recent years provides the opportunity for discovery and application of new techniques for treating various diseases that affect humanity. Methods for finding and analyzing the profile of gene expression of infected cells give scientists the ability to develop more targeted and effective treatments, especially for diseases such as cancer. The development of gene expression profiling is one of the most important achievements in cancer genetics in our time. It is essentially the driving force behind personalized and precision medicine. This book highlights recent developments, applications, and breakthroughs in the field of gene expression profiling in cancer.

Cancer and Noncoding RNAs Book
Score: 5
From 1 Ratings

Cancer and Noncoding RNAs

  • Author : Jayprokas Chakrabarti
  • Publisher : Academic Press
  • Release Date : 2017-10-13
  • Genre: Medical
  • Pages : 576
  • ISBN 10 : 9780128134375
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Cancer and Noncoding RNAs Excerpt :

Cancer and Noncoding RNAs offers an in-depth exploration of noncoding RNAs and their role in epigenetic regulation of complex human disease, most notably cancer. In addition to examining microRNAs, this volume provides a unique evaluation of more recently profiled noncoding RNAs now implicated in carcinogenesis, including lncRNAs, piRNAs, circRNAs, and tRNAs, identifying differences in function between these noncoding RNAs and how they interact with the rest of the epigenome. A broad range of chapters from experts in the field detail epigenetic regulation of various cancer types, along with recent next generation sequencing technologies, genome-wide association studies (GWAS) and bioinformatics approaches. This book will help researchers in genomic medicine and cancer biology better understand the role of noncoding RNAs in epigenetics, aiding in the development of useful biomarkers for diagnosis, prognosis and new RNA-based disease therapies. Provides a comprehensive analysis of noncoding RNAs implicated in epigenetic regulation of gene expression and chromatin dynamics Educates researchers and graduate students by highlighting, in addition to miRNAs, a range of noncoding RNAs newly associated with carcinogenesis Applies current knowledge of noncoding RNAs and epigenomics towards developing cancer and RNA-based disease therapies Features contributions by leading experts in the field

Kernel Methods in Computational Biology Book
Score: 3
From 1 Ratings

Kernel Methods in Computational Biology

  • Author : Managing Director of the Max Planck Institute for Biological Cybernetics in Tubingen Germany Profe Bernhard Scholkopf
  • Publisher : MIT Press
  • Release Date : 2004
  • Genre: Computers
  • Pages : 400
  • ISBN 10 : 0262195097
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Kernel Methods in Computational Biology Excerpt :

A Primer on Molecular Biology. A Primer on Kernel Methods. Support Vector Machine Applications in Computational Biology. Inexact Matching String Kernels for Protein Classification. Fast Kernels for String and Tree Matching. Local Alignment Kernels for Biological Sequences. Kernels for Graphs. Diffusion Kernels. A Kernel for Protein Secondary Structure Prediction. Heterogeneous Data Comparsion and Gene Selection with Kernel Canonical Correlation Analysis. Kernel-Based Integration of Genomic Data Using Semdefinite Programming. Protein Classification via Kernel Matrix Completion. Accurate Splice Site Detection for Caenorhabditid elegans. Gene Espression Analysis: Joint Feature Selection and Classifier Design. Gene Selection for Microarray Data.

Long Non Coding Rnas Methods and Protocols Book

Long Non Coding Rnas Methods and Protocols

  • Author : Yi Feng
  • Publisher : Methods in Molecular Biology
  • Release Date : 2018-04-15
  • Genre: Medical
  • Pages : 312
  • ISBN 10 : 1493980351
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Long Non Coding Rnas Methods and Protocols Excerpt :

This volume assembles a broad spectrum of methods used in long non-coding RNAs (lncRNA) research, ranging from computational annotation of lncRNA genes to molecular and cellular analyses of the function of individual lncRNA. Long Non-Coding RNAs: Methods and Protocols also discusses methods used to study circular RNAs and RNA splicing, as well as influential findings on lncRNA in human diseases. 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 tips on troubleshooting and avoiding known pitfalls. Thorough and cutting-edge, Long Non-Coding RNAs: Methods and Protocols is a must-have for molecular biologists, cell and developmental biologists, specialists who conduct disease-oriented research, and bioinformatics experts who seek a better understanding on lncRNA expression and function by computational analysis of the massive sequencing data that are rapidly accumulating in recent years.

RNA Bioinformatics Book

RNA Bioinformatics

  • Author : Ernesto Picardi
  • Publisher : Humana Press
  • Release Date : 2015-01-11
  • Genre: Science
  • Pages : 415
  • ISBN 10 : 1493922904
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RNA Bioinformatics Excerpt :

This volume provides an overview of RNA bioinformatics methodologies, including basic strategies to predict secondary and tertiary structures, and novel algorithms based on massive RNA sequencing. Interest in RNA bioinformatics has rapidly increased thanks to the recent high-throughput sequencing technologies allowing scientists to investigate complete transcriptomes at single nucleotide resolution. Adopting advanced computational technics, scientists are now able to conduct more in-depth studies and present them to you in this book. Written in the highly successful Methods of Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and equipment, step-by-step, readily reproducible bioinformatics protocols, and key tips to avoid known pitfalls. Authoritative and practical, RNA Bioinformatics seeks to aid scientists in the further study of bioinformatics and computational biology of RNA.

Non Coding RNAs in Plants Book

Non Coding RNAs in Plants

  • Author : Volker A. Erdmann
  • Publisher : Springer Science & Business Media
  • Release Date : 2011-07-20
  • Genre: Science
  • Pages : 510
  • ISBN 10 : 3642194540
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Non Coding RNAs in Plants Excerpt :

In the most recent years, each of the RNA silencing pathways of plants have appeared to generate ncRNAs with dedicated functions, specialized biological activities and specific functional scopes. RNA silencing plays a crucial role in coordinating the expression, stability, protection and inheritance of eukaryotic genomes. It compromises several mechanisms, that invariably depend on core small non coding RNAs and that achieve dedicated sequence-specific functions. RNA silencing has been recognized to carry critical developmental, stress-response and bodyguard functions be coordinating the expression, protection, stability and inheritance of virtually all eukaryotic genomes. Thus, the ncRNAs encompass a wide set of mechanisms that achieve specialized functions.

RNA Based Regulation in Human Health and Disease Book

RNA Based Regulation in Human Health and Disease

  • Author : Anonim
  • Publisher : Academic Press
  • Release Date : 2020-08-19
  • Genre: Medical
  • Pages : 444
  • ISBN 10 : 9780128171943
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RNA Based Regulation in Human Health and Disease Excerpt :

RNA-based Regulation in Human Health and Disease offers an in-depth exploration of RNA mediated genome regulation at different hierarchies. Beginning with multitude of canonical and non-canonical RNA populations, especially noncoding RNA in human physiology and evolution, further sections examine the various classes of RNAs (from small to large noncoding and extracellular RNAs), functional categories of RNA regulation (RNA-binding proteins, alternative splicing, RNA editing, antisense transcripts and RNA G-quadruplexes), dynamic aspects of RNA regulation modulating physiological homeostasis (aging), role of RNA beyond humans, tools and technologies for RNA research (wet lab and computational) and future prospects for RNA-based diagnostics and therapeutics. One of the core strengths of the book includes spectrum of disease-specific chapters from experts in the field highlighting RNA-based regulation in metabolic & neurodegenerative disorders, cancer, inflammatory disease, viral and bacterial infections. We hope the book helps researchers, students and clinicians appreciate the role of RNA-based regulation in genome regulation, aiding the development of useful biomarkers for prognosis, diagnosis, and novel RNA-based therapeutics. Comprehensive information of non-canonical RNA-based genome regulation modulating human health and disease Defines RNA classes with special emphasis on unexplored world of noncoding RNA at different hierarchies Disease specific role of RNA - causal, prognostic, diagnostic and therapeutic Features contributions from leading experts in the field

Computational Methods for Genome wide Non coding RNA Discovery and Analysis Book

Computational Methods for Genome wide Non coding RNA Discovery and Analysis

  • Author : Shaojie Zhang
  • Publisher : Unknown
  • Release Date : 2007
  • Genre: Uncategoriezed
  • Pages : 108
  • ISBN 10 : OCLC:180189876
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Computational Methods for Genome wide Non coding RNA Discovery and Analysis Excerpt :

The discovery of novel non-coding RNAs has been among the most exciting recent developments in Biology, yet, many more remain undiscovered. It has been hypothesized that there is in fact an abundance of functional non-coding RNAs (ncRNAs) with various catalytic and regulatory functions. Computational methods tailored specifically for ncRNA discovery are being actively developed. As the inherent signal for ncRNA is weaker than that for protein coding genes, comparative methods offer the most promising approach. In this dissertation, we address several open issues and problems on computational methods for genome wide non-coding RNA discovery and analysis: (1) We first consider the following problem: Given an RNA sequence with a known secondary structure, efficiently detect all structural homologs in a genomic database by computing the sequence and structure similarity to the query. Our approach, based on structural filters that eliminate a large portion of the database, while retaining the true homologs, allows us to search a typical bacterial genome in minutes on a standard PC. This results is two orders of magnitude better than currently available software for the problem. (2) We formalize the concept of a filter and provide figures of merit that allow comparison between filters. We design efficient sequence based filters that dominate the current state-of-the-art HMM filters. We provide a new formulation of the covariance model that allows speeding up RNA alignment. We demonstrate the power of our approach on both synthetic data and real bacterial genomes. We then apply our algorithm to the detection of novel riboswitch elements from the whole bacterial and archaeal genomes and environmental sequence data. Our results point to a number of novel riboswitch candidates, and include genomes that were not previously known to contain riboswitches. (3) We propose a novel framework to predict the common secondary structure for unaligned RNA sequences. By matching putative

Plant Long Non Coding RNAs Book

Plant Long Non Coding RNAs

  • Author : Julia A. Chekanova
  • Publisher : Humana Press
  • Release Date : 2019-04-20
  • Genre: Science
  • Pages : 480
  • ISBN 10 : 1493990446
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Plant Long Non Coding RNAs Excerpt :

This volume focuses on various approaches to studying long non-coding RNAs (lncRNAs), including techniques for finding lncRNAs, localization, and observing their functions. The chapters in this book cover how to catalog lncRNAs in various plant species; determining subcellular localization; protein interactions; structures; and RNA modifications. 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 tips on troubleshooting and avoiding known pitfalls. Cutting-edge and innovative, Plant Long Non-Coding RNAs: Methods and Protocols is a valuable resource that aids researchers in understanding the functions of lncRNAs in different plant species, and helps them explore currently uncharted facets of plant biology.