RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods

RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods

Author: Jan Gorodkin

Publisher: Humana

Published: 2014-03-18

Total Pages: 0

ISBN-13: 9781627037082

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The existence of genes for RNA molecules not coding for proteins (ncRNAs) has been recognized since the 1950's, but until recently, aside from the critically important ribosomal and transfer RNA genes, most focus has been on protein coding genes. However, a long series of striking discoveries, from RNA's ability to carry out catalytic function, to discovery of riboswitches, microRNAs and other ribo-regulators performing critical tasks in essentially all living organisms, has created a burgeoning interest in this primordial component of the biosphere. However, the structural characteristics and evolutionary constraints on RNA molecules are very different from those of proteins, necessitating development of a completely new suite of informatic tools to address these challenges. In RNA Sequence, Structure, Function: Computational and Bioinformatic Methods, expert researchers in the field describe a substantial and relevant fraction of these methodologies from both practical and computational/algorithmic perspectives. Focusing on both of these directions addresses both the biologist interested in knowing more about RNA bioinformatics as well as the bioinformaticist interested in more detailed aspects of the algorithms. Written in the highly successful Methods in Molecular Biology series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results. Thorough and intuitive, RNA Sequence, Structure, Function: Computational and Bioinformatic Methods aids scientists in continuing to study key methods and principles of RNA bioinformatics.


Book Synopsis RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods by : Jan Gorodkin

Download or read book RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods written by Jan Gorodkin and published by Humana. This book was released on 2014-03-18 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The existence of genes for RNA molecules not coding for proteins (ncRNAs) has been recognized since the 1950's, but until recently, aside from the critically important ribosomal and transfer RNA genes, most focus has been on protein coding genes. However, a long series of striking discoveries, from RNA's ability to carry out catalytic function, to discovery of riboswitches, microRNAs and other ribo-regulators performing critical tasks in essentially all living organisms, has created a burgeoning interest in this primordial component of the biosphere. However, the structural characteristics and evolutionary constraints on RNA molecules are very different from those of proteins, necessitating development of a completely new suite of informatic tools to address these challenges. In RNA Sequence, Structure, Function: Computational and Bioinformatic Methods, expert researchers in the field describe a substantial and relevant fraction of these methodologies from both practical and computational/algorithmic perspectives. Focusing on both of these directions addresses both the biologist interested in knowing more about RNA bioinformatics as well as the bioinformaticist interested in more detailed aspects of the algorithms. Written in the highly successful Methods in Molecular Biology series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results. Thorough and intuitive, RNA Sequence, Structure, Function: Computational and Bioinformatic Methods aids scientists in continuing to study key methods and principles of RNA bioinformatics.

Biological Sequence Analysis

Biological Sequence Analysis

Author: Richard Durbin

Publisher: Cambridge University Press

Published: 1998-04-23

Total Pages: 372

ISBN-13: 113945739X

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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.


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.

Bioinformatics and RNA

Bioinformatics and RNA

Author: Dolly Sharma

Publisher: CRC Press

Published: 2021-08-17

Total Pages: 149

ISBN-13: 1000428338

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This book offers a unique balance between a basic introductory knowledge of bioinformatics and a detailed study of algorithmic techniques. Bioinformatics and RNA: A Practice-Based Approach is a complete guide on the fundamental concepts, applications, algorithms, protocols, new trends, challenges, and research results in the area of bioinformatics and RNA. The book offers a broad introduction to the explosively growing new discipline of bioinformatics. It covers theoretical topics along with computational algorithms. It explores RNA bioinformatics, which contribute to therapeutics and drug discovery. Implementation of algorithms in a DotNet Framework with code and complete insight on the state-of-the-art and recent advancements are presented in detail. The book targets both novice readers as well as practitioners in the field. FEATURES Offers a broad introduction to the explosively growing new discipline of bioinformatics Covers theoretical topics and computational algorithms Explores RNA bioinformatics to unleash the potential from therapeutics to drug discovery Discusses implementation of algorithms in DotNet Frameworks with code Presents insights into the state of the art and recent advancements in bioinformatics The book is useful to undergraduate students with engineering, science, mathematics, or biology backgrounds. Researchers will be equally interested.


Book Synopsis Bioinformatics and RNA by : Dolly Sharma

Download or read book Bioinformatics and RNA written by Dolly Sharma and published by CRC Press. This book was released on 2021-08-17 with total page 149 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book offers a unique balance between a basic introductory knowledge of bioinformatics and a detailed study of algorithmic techniques. Bioinformatics and RNA: A Practice-Based Approach is a complete guide on the fundamental concepts, applications, algorithms, protocols, new trends, challenges, and research results in the area of bioinformatics and RNA. The book offers a broad introduction to the explosively growing new discipline of bioinformatics. It covers theoretical topics along with computational algorithms. It explores RNA bioinformatics, which contribute to therapeutics and drug discovery. Implementation of algorithms in a DotNet Framework with code and complete insight on the state-of-the-art and recent advancements are presented in detail. The book targets both novice readers as well as practitioners in the field. FEATURES Offers a broad introduction to the explosively growing new discipline of bioinformatics Covers theoretical topics and computational algorithms Explores RNA bioinformatics to unleash the potential from therapeutics to drug discovery Discusses implementation of algorithms in DotNet Frameworks with code Presents insights into the state of the art and recent advancements in bioinformatics The book is useful to undergraduate students with engineering, science, mathematics, or biology backgrounds. Researchers will be equally interested.

RNA Bioinformatics

RNA Bioinformatics

Author: Ernesto Picardi

Publisher: Humana

Published: 2016-09-24

Total Pages: 0

ISBN-13: 9781493946440

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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.


Book Synopsis RNA Bioinformatics by : Ernesto Picardi

Download or read book RNA Bioinformatics written by Ernesto Picardi and published by Humana. This book was released on 2016-09-24 with total page 0 pages. Available in PDF, EPUB and Kindle. Book 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.

Virus Bioinformatics

Virus Bioinformatics

Author: Manja Marz

Publisher: MDPI

Published: 2020-02-21

Total Pages: 330

ISBN-13: 3039218824

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Virus bioinformatics is evolving and succeeding as an area of research in its own right, representing the interface of virology and computer science. Bioinformatic approaches to investigate viral infections and outbreaks have become central to virology research, and have been successfully used to detect, control, and treat infections of humans and animals. As part of the Third Annual Meeting of the European Virus Bioinformatics Center (EVBC), we have published this Special Issue on Virus Bioinformatics.


Book Synopsis Virus Bioinformatics by : Manja Marz

Download or read book Virus Bioinformatics written by Manja Marz and published by MDPI. This book was released on 2020-02-21 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: Virus bioinformatics is evolving and succeeding as an area of research in its own right, representing the interface of virology and computer science. Bioinformatic approaches to investigate viral infections and outbreaks have become central to virology research, and have been successfully used to detect, control, and treat infections of humans and animals. As part of the Third Annual Meeting of the European Virus Bioinformatics Center (EVBC), we have published this Special Issue on Virus Bioinformatics.

RNA-seq Data Analysis

RNA-seq Data Analysis

Author: Eija Korpelainen

Publisher: CRC Press

Published: 2014-09-19

Total Pages: 322

ISBN-13: 1466595019

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The State of the Art in Transcriptome AnalysisRNA sequencing (RNA-seq) data offers unprecedented information about the transcriptome, but harnessing this information with bioinformatics tools is typically a bottleneck. RNA-seq Data Analysis: A Practical Approach enables researchers to examine differential expression at gene, exon, and transcript le


Book Synopsis RNA-seq Data Analysis by : Eija Korpelainen

Download or read book RNA-seq Data Analysis written by Eija Korpelainen and published by CRC Press. This book was released on 2014-09-19 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: The State of the Art in Transcriptome AnalysisRNA sequencing (RNA-seq) data offers unprecedented information about the transcriptome, but harnessing this information with bioinformatics tools is typically a bottleneck. RNA-seq Data Analysis: A Practical Approach enables researchers to examine differential expression at gene, exon, and transcript le

Bioinformatics

Bioinformatics

Author: Andrzej Polanski

Publisher: Springer Science & Business Media

Published: 2007-04-19

Total Pages: 386

ISBN-13: 3540241663

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This textbook presents mathematical models in bioinformatics and describes biological problems that inspire the computer science tools used to manage the enormous data sets involved. The first part of the book covers mathematical and computational methods, with practical applications presented in the second part. The mathematical presentation avoids unnecessary formalism, while remaining clear and precise. The book closes with a thorough bibliography, reaching from classic research results to very recent findings. This volume is suited for a senior undergraduate or graduate course on bioinformatics, with a strong focus on mathematical and computer science background.


Book Synopsis Bioinformatics by : Andrzej Polanski

Download or read book Bioinformatics written by Andrzej Polanski and published by Springer Science & Business Media. This book was released on 2007-04-19 with total page 386 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook presents mathematical models in bioinformatics and describes biological problems that inspire the computer science tools used to manage the enormous data sets involved. The first part of the book covers mathematical and computational methods, with practical applications presented in the second part. The mathematical presentation avoids unnecessary formalism, while remaining clear and precise. The book closes with a thorough bibliography, reaching from classic research results to very recent findings. This volume is suited for a senior undergraduate or graduate course on bioinformatics, with a strong focus on mathematical and computer science background.

R Bioinformatics Cookbook

R Bioinformatics Cookbook

Author: Dan MacLean

Publisher: Packt Publishing Ltd

Published: 2019-10-11

Total Pages: 307

ISBN-13: 1789955599

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Over 60 recipes to model and handle real-life biological data using modern libraries from the R ecosystem Key FeaturesApply modern R packages to handle biological data using real-world examplesRepresent biological data with advanced visualizations suitable for research and publicationsHandle real-world problems in bioinformatics such as next-generation sequencing, metagenomics, and automating analysesBook Description Handling biological data effectively requires an in-depth knowledge of machine learning techniques and computational skills, along with an understanding of how to use tools such as edgeR and DESeq. With the R Bioinformatics Cookbook, you’ll explore all this and more, tackling common and not-so-common challenges in the bioinformatics domain using real-world examples. This book will use a recipe-based approach to show you how to perform practical research and analysis in computational biology with R. You will learn how to effectively analyze your data with the latest tools in Bioconductor, ggplot, and tidyverse. The book will guide you through the essential tools in Bioconductor to help you understand and carry out protocols in RNAseq, phylogenetics, genomics, and sequence analysis. As you progress, you will get up to speed with how machine learning techniques can be used in the bioinformatics domain. You will gradually develop key computational skills such as creating reusable workflows in R Markdown and packages for code reuse. By the end of this book, you’ll have gained a solid understanding of the most important and widely used techniques in bioinformatic analysis and the tools you need to work with real biological data. What you will learnEmploy Bioconductor to determine differential expressions in RNAseq dataRun SAMtools and develop pipelines to find single nucleotide polymorphisms (SNPs) and IndelsUse ggplot to create and annotate a range of visualizationsQuery external databases with Ensembl to find functional genomics informationExecute large-scale multiple sequence alignment with DECIPHER to perform comparative genomicsUse d3.js and Plotly to create dynamic and interactive web graphicsUse k-nearest neighbors, support vector machines and random forests to find groups and classify dataWho this book is for This book is for bioinformaticians, data analysts, researchers, and R developers who want to address intermediate-to-advanced biological and bioinformatics problems by learning through a recipe-based approach. Working knowledge of R programming language and basic knowledge of bioinformatics are prerequisites.


Book Synopsis R Bioinformatics Cookbook by : Dan MacLean

Download or read book R Bioinformatics Cookbook written by Dan MacLean and published by Packt Publishing Ltd. This book was released on 2019-10-11 with total page 307 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over 60 recipes to model and handle real-life biological data using modern libraries from the R ecosystem Key FeaturesApply modern R packages to handle biological data using real-world examplesRepresent biological data with advanced visualizations suitable for research and publicationsHandle real-world problems in bioinformatics such as next-generation sequencing, metagenomics, and automating analysesBook Description Handling biological data effectively requires an in-depth knowledge of machine learning techniques and computational skills, along with an understanding of how to use tools such as edgeR and DESeq. With the R Bioinformatics Cookbook, you’ll explore all this and more, tackling common and not-so-common challenges in the bioinformatics domain using real-world examples. This book will use a recipe-based approach to show you how to perform practical research and analysis in computational biology with R. You will learn how to effectively analyze your data with the latest tools in Bioconductor, ggplot, and tidyverse. The book will guide you through the essential tools in Bioconductor to help you understand and carry out protocols in RNAseq, phylogenetics, genomics, and sequence analysis. As you progress, you will get up to speed with how machine learning techniques can be used in the bioinformatics domain. You will gradually develop key computational skills such as creating reusable workflows in R Markdown and packages for code reuse. By the end of this book, you’ll have gained a solid understanding of the most important and widely used techniques in bioinformatic analysis and the tools you need to work with real biological data. What you will learnEmploy Bioconductor to determine differential expressions in RNAseq dataRun SAMtools and develop pipelines to find single nucleotide polymorphisms (SNPs) and IndelsUse ggplot to create and annotate a range of visualizationsQuery external databases with Ensembl to find functional genomics informationExecute large-scale multiple sequence alignment with DECIPHER to perform comparative genomicsUse d3.js and Plotly to create dynamic and interactive web graphicsUse k-nearest neighbors, support vector machines and random forests to find groups and classify dataWho this book is for This book is for bioinformaticians, data analysts, researchers, and R developers who want to address intermediate-to-advanced biological and bioinformatics problems by learning through a recipe-based approach. Working knowledge of R programming language and basic knowledge of bioinformatics are prerequisites.

Molecular Biology - Not Only for Bioinformaticians

Molecular Biology - Not Only for Bioinformaticians

Author: Wiesława Widłak

Publisher: Springer

Published: 2013-12-05

Total Pages: 159

ISBN-13: 3642453619

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Bioinformatics, which can be defined as the application of computer science and information technology to the field of biology and medicine, has been rapidly developing over the past few decades. It generates new knowledge as well as the computational tools to create that knowledge. Understanding the basic processes in living organisms is therefore indispensable for bioinformaticians. This book addresses beginners in molecular biology, especially computer scientists who would like to work as bioinformaticians. It presents basic processes in living organisms in a condensed manner. Additionally, principles of several high-throughput technologies in molecular biology, which need the assistance of bioinformaticians, are explained from a biological point of view. It is structured in the following 9 chapters: cells and viruses; protein structure and function; nucleic acids; DNA replication, mutations, and repair; transcription and posttranscriptional processes; synthesis and posttranslational modifications of proteins; cell division; cell signaling pathways; and high-throughput technologies in molecular biology.


Book Synopsis Molecular Biology - Not Only for Bioinformaticians by : Wiesława Widłak

Download or read book Molecular Biology - Not Only for Bioinformaticians written by Wiesława Widłak and published by Springer. This book was released on 2013-12-05 with total page 159 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioinformatics, which can be defined as the application of computer science and information technology to the field of biology and medicine, has been rapidly developing over the past few decades. It generates new knowledge as well as the computational tools to create that knowledge. Understanding the basic processes in living organisms is therefore indispensable for bioinformaticians. This book addresses beginners in molecular biology, especially computer scientists who would like to work as bioinformaticians. It presents basic processes in living organisms in a condensed manner. Additionally, principles of several high-throughput technologies in molecular biology, which need the assistance of bioinformaticians, are explained from a biological point of view. It is structured in the following 9 chapters: cells and viruses; protein structure and function; nucleic acids; DNA replication, mutations, and repair; transcription and posttranscriptional processes; synthesis and posttranslational modifications of proteins; cell division; cell signaling pathways; and high-throughput technologies in molecular biology.

Bioinformatics for High Throughput Sequencing

Bioinformatics for High Throughput Sequencing

Author: Naiara Rodríguez-Ezpeleta

Publisher: Springer Science & Business Media

Published: 2011-10-26

Total Pages: 258

ISBN-13: 1461407826

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Next generation sequencing is revolutionizing molecular biology. Owing to this new technology it is now possible to carry out a panoply of experiments at an unprecedented low cost and high speed. These go from sequencing whole genomes, transcriptomes and small non-coding RNAs to description of methylated regions, identification protein – DNA interaction sites and detection of structural variation. The generation of gigabases of sequence information for each of this huge bandwidth of applications in just a few days makes the development of bioinformatics applications for next generation sequencing data analysis as urgent as challenging.


Book Synopsis Bioinformatics for High Throughput Sequencing by : Naiara Rodríguez-Ezpeleta

Download or read book Bioinformatics for High Throughput Sequencing written by Naiara Rodríguez-Ezpeleta and published by Springer Science & Business Media. This book was released on 2011-10-26 with total page 258 pages. Available in PDF, EPUB and Kindle. Book excerpt: Next generation sequencing is revolutionizing molecular biology. Owing to this new technology it is now possible to carry out a panoply of experiments at an unprecedented low cost and high speed. These go from sequencing whole genomes, transcriptomes and small non-coding RNAs to description of methylated regions, identification protein – DNA interaction sites and detection of structural variation. The generation of gigabases of sequence information for each of this huge bandwidth of applications in just a few days makes the development of bioinformatics applications for next generation sequencing data analysis as urgent as challenging.