Computational Methods For Next Generation Sequencing Data Analysis
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Computational Methods For Next Generation Sequencing Data Analysis
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Author : Ion Mandoiu
language : en
Publisher: John Wiley & Sons
Release Date : 2016-10-03
Computational Methods For Next Generation Sequencing Data Analysis written by Ion Mandoiu and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-10-03 with Computers categories.
Introduces readers to core algorithmic techniques for next-generation sequencing (NGS) data analysis and discusses a wide range of computational techniques and applications This book provides an in-depth survey of some of the recent developments in NGS and discusses mathematical and computational challenges in various application areas of NGS technologies. The 18 chapters featured in this book have been authored by bioinformatics experts and represent the latest work in leading labs actively contributing to the fast-growing field of NGS. The book is divided into four parts: Part I focuses on computing and experimental infrastructure for NGS analysis, including chapters on cloud computing, modular pipelines for metabolic pathway reconstruction, pooling strategies for massive viral sequencing, and high-fidelity sequencing protocols. Part II concentrates on analysis of DNA sequencing data, covering the classic scaffolding problem, detection of genomic variants, including insertions and deletions, and analysis of DNA methylation sequencing data. Part III is devoted to analysis of RNA-seq data. This part discusses algorithms and compares software tools for transcriptome assembly along with methods for detection of alternative splicing and tools for transcriptome quantification and differential expression analysis. Part IV explores computational tools for NGS applications in microbiomics, including a discussion on error correction of NGS reads from viral populations, methods for viral quasispecies reconstruction, and a survey of state-of-the-art methods and future trends in microbiome analysis. Computational Methods for Next Generation Sequencing Data Analysis: Reviews computational techniques such as new combinatorial optimization methods, data structures, high performance computing, machine learning, and inference algorithms Discusses the mathematical and computational challenges in NGS technologies Covers NGS error correction, de novo genome transcriptome assembly, variant detection from NGS reads, and more This text is a reference for biomedical professionals interested in expanding their knowledge of computational techniques for NGS data analysis. The book is also useful for graduate and post-graduate students in bioinformatics.
Next Generation Sequencing Data Analysis
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Author : Xinkun Wang
language : en
Publisher: CRC Press
Release Date : 2016-04-06
Next Generation Sequencing Data Analysis written by Xinkun Wang and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-04-06 with Mathematics categories.
A Practical Guide to the Highly Dynamic Area of Massively Parallel SequencingThe development of genome and transcriptome sequencing technologies has led to a paradigm shift in life science research and disease diagnosis and prevention. Scientists are now able to see how human diseases and phenotypic changes are connected to DNA mutation, polymorphi
Genome Analysis Current Procedures And Applications
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Author : Maria S. Poptsova
language : en
Publisher: Caister Academic Press
Release Date : 2019-04-28
Genome Analysis Current Procedures And Applications written by Maria S. Poptsova and has been published by Caister Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-04-28 with Computers categories.
In recent years there have been tremendous achievements made in DNA sequencing technologies and corresponding innovations in data analysis and bioinformatics that have revolutionized the field of genome analysis.In this book, an impressive array of expert authors highlight and review current advances in genome analysis. This volume provides an invaluable, up-to-date and comprehensive overview of the methods currently employed for next-generation sequencing (NGS) data analysis, highlights their problems and limitations, demonstrates the applications and indicates the developing trends in various fields of genome research. The first part of the book is devoted to the methods and applications that arose from, or were significantly advanced by, NGS technologies: the identification of structural variation from DNA-seq data; whole-transcriptome analysis and discovery of small interfering RNAs (siRNAs) from RNA-seq data; motif finding in promoter regions, enhancer prediction and nucleosome sequence code discovery from ChiP-Seq data; identification of methylation patterns in cancer from MeDIP-seq data; transposon identification in NGS data; metagenomics and metatranscriptomics; NGS of viral communities; and causes and consequences of genome instabilities. The second part is devoted to the field of RNA biology with the last three chapters devoted to computational methods of RNA structure prediction including context-free grammar applications.An essential book for everyone involved in sequence data analysis, next-generation sequencing, high-throughput sequencing, RNA structure prediction, bioinformatics and genome analysis.
Bioinformatics
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Author : Hamid D. Ismail
language : en
Publisher: CRC Press
Release Date : 2023-06-29
Bioinformatics written by Hamid D. Ismail and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-06-29 with Computers categories.
This book contains the latest material in the subject, covering next generation sequencing (NGS) applications and meeting the requirements of a complete semester course. This book digs deep into analysis, providing both concept and practice to satisfy the exact need of researchers seeking to understand and use NGS data reprocessing, genome assembly, variant discovery, gene profiling, epigenetics, and metagenomics. The book does not introduce the analysis pipelines in a black box, but with detailed analysis steps to provide readers with the scientific and technical backgrounds required to enable them to conduct analysis with confidence and understanding. The book is primarily designed as a companion for researchers and graduate students using sequencing data analysis but will also serve as a textbook for teachers and students in biology and bioscience.
Genome Analysis
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Author : Maria S. Poptsova
language : en
Publisher: Caister Academic Press Limited
Release Date : 2014
Genome Analysis written by Maria S. Poptsova and has been published by Caister Academic Press Limited this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014 with Science categories.
In recent years there have been tremendous achievements made in DNA sequencing technologies and corresponding innovations in data analysis and bioinformatics that have revolutionized the field of genome analysis. In this book, an impressive array of expert authors highlight and review current advances in genome analysis. This volume provides an invaluable, up-to-date and comprehensive overview of the methods currently employed for next-generation sequencing (NGS) data analysis, highlights their problems and limitations, demonstrates the applications and indicates the developing trends in various fields of genome research. The first part of the book is devoted to the methods and applications that arose from, or were significantly advanced by, NGS technologies: the identification of structural variation from DNA-seq data; whole-transcriptome analysis and discovery of small interfering RNAs (siRNAs) from RNA-seq data; motif finding in promoter regions, enhancer prediction and nucleosome sequence code discovery from ChiP-Seq data; identification of methylation patterns in cancer from MeDIP-seq data; transposon identification in NGS data; metagenomics and metatranscriptomics; NGS of viral communities; and causes and consequences of genome instabilities. The second part is devoted to the field of RNA biology with the last three chapters devoted to computational methods of RNA structure prediction including context-free grammar applications. An essential book for everyone involved in sequence data analysis, next-generation sequencing, high-throughput sequencing, RNA structure prediction, bioinformatics and genome analysis.
Algorithms For Next Generation Sequencing Data
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Author : Mourad Elloumi
language : en
Publisher: Springer
Release Date : 2017-09-18
Algorithms For Next Generation Sequencing Data written by Mourad Elloumi and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-09-18 with Computers categories.
The 14 contributed chapters in this book survey the most recent developments in high-performance algorithms for NGS data, offering fundamental insights and technical information specifically on indexing, compression and storage; error correction; alignment; and assembly. The book will be of value to researchers, practitioners and students engaged with bioinformatics, computer science, mathematics, statistics and life sciences.
Computational Methods For Multi Omics Data Analysis In Cancer Precision Medicine
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Author : Ehsan Nazemalhosseini-Mojarad
language : en
Publisher: Frontiers Media SA
Release Date : 2023-08-02
Computational Methods For Multi Omics Data Analysis In Cancer Precision Medicine written by Ehsan Nazemalhosseini-Mojarad and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-08-02 with Science categories.
Cancer is a complex and heterogeneous disease often caused by different alterations. The development of human cancer is due to the accumulation of genetic and epigenetic modifications that could affect the structure and function of the genome. High-throughput methods (e.g., microarray and next-generation sequencing) can investigate a tumor at multiple levels: i) DNA with genome-wide association studies (GWAS), ii) epigenetic modifications such as DNA methylation, histone changes and microRNAs (miRNAs) iii) mRNA. The availability of public datasets from different multi-omics data has been growing rapidly and could facilitate better knowledge of the biological processes of cancer. Computational approaches are essential for the analysis of big data and the identification of potential biomarkers for early and differential diagnosis, and prognosis.
Next Generation Sequencing
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Author : Jerzy Kulski
language : en
Publisher: BoD – Books on Demand
Release Date : 2016-01-14
Next Generation Sequencing written by Jerzy Kulski and has been published by BoD – Books on Demand this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-01-14 with Medical categories.
Next generation sequencing (NGS) has surpassed the traditional Sanger sequencing method to become the main choice for large-scale, genome-wide sequencing studies with ultra-high-throughput production and a huge reduction in costs. The NGS technologies have had enormous impact on the studies of structural and functional genomics in all the life sciences. In this book, Next Generation Sequencing Advances, Applications and Challenges, the sixteen chapters written by experts cover various aspects of NGS including genomics, transcriptomics and methylomics, the sequencing platforms, and the bioinformatics challenges in processing and analysing huge amounts of sequencing data. Following an overview of the evolution of NGS in the brave new world of omics, the book examines the advances and challenges of NGS applications in basic and applied research on microorganisms, agricultural plants and humans. This book is of value to all who are interested in DNA sequencing and bioinformatics across all fields of the life sciences.
High Performance Computational Methods For Biological Sequence Analysis
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Author : Tieng K. Yap
language : en
Publisher: Springer Science & Business Media
Release Date : 2012-12-06
High Performance Computational Methods For Biological Sequence Analysis written by Tieng K. Yap and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-12-06 with Computers categories.
High Performance Computational Methods for Biological Sequence Analysis presents biological sequence analysis using an interdisciplinary approach that integrates biological, mathematical and computational concepts. These concepts are presented so that computer scientists and biomedical scientists can obtain the necessary background for developing better algorithms and applying parallel computational methods. This book will enable both groups to develop the depth of knowledge needed to work in this interdisciplinary field. This work focuses on high performance computational approaches that are used to perform computationally intensive biological sequence analysis tasks: pairwise sequence comparison, multiple sequence alignment, and sequence similarity searching in large databases. These computational methods are becoming increasingly important to the molecular biology community allowing researchers to explore the increasingly large amounts of sequence data generated by the Human Genome Project and other related biological projects. The approaches presented by the authors are state-of-the-art and show how to reduce analysis times significantly, sometimes from days to minutes. High Performance Computational Methods for Biological Sequence Analysis is tremendously important to biomedical science students and researchers who are interested in applying sequence analyses to their studies, and to computational science students and researchers who are interested in applying new computational approaches to biological sequence analyses.
Statistical Analysis Of Next Generation Sequencing Data
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Author : Somnath Datta
language : en
Publisher: Springer
Release Date : 2014-07-03
Statistical Analysis Of Next Generation Sequencing Data written by Somnath Datta and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-07-03 with Medical categories.
Next Generation Sequencing (NGS) is the latest high throughput technology to revolutionize genomic research. NGS generates massive genomic datasets that play a key role in the big data phenomenon that surrounds us today. To extract signals from high-dimensional NGS data and make valid statistical inferences and predictions, novel data analytic and statistical techniques are needed. This book contains 20 chapters written by prominent statisticians working with NGS data. The topics range from basic preprocessing and analysis with NGS data to more complex genomic applications such as copy number variation and isoform expression detection. Research statisticians who want to learn about this growing and exciting area will find this book useful. In addition, many chapters from this book could be included in graduate-level classes in statistical bioinformatics for training future biostatisticians who will be expected to deal with genomic data in basic biomedical research, genomic clinical trials and personalized medicine. About the editors: Somnath Datta is Professor and Vice Chair of Bioinformatics and Biostatistics at the University of Louisville. He is Fellow of the American Statistical Association, Fellow of the Institute of Mathematical Statistics and Elected Member of the International Statistical Institute. He has contributed to numerous research areas in Statistics, Biostatistics and Bioinformatics. Dan Nettleton is Professor and Laurence H. Baker Endowed Chair of Biological Statistics in the Department of Statistics at Iowa State University. He is Fellow of the American Statistical Association and has published research on a variety of topics in statistics, biology and bioinformatics.