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Author : 鐘緯駿
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (11 download)
Download or read book Algorithms for Correcting Next-generation Sequencing Errors Based on Mapreduce Big Data Framework written by 鐘緯駿 and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Mourad Elloumi
Publisher : Springer
ISBN 13 : 3319598260
Total Pages : 356 pages
Book Rating : 4.3/5 (195 download)
Download or read book Algorithms for Next-Generation Sequencing Data written by Mourad Elloumi and published by Springer. This book was released on 2017-09-18 with total page 356 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Author : Ion Mandoiu
Publisher : John Wiley & Sons
ISBN 13 : 1118169484
Total Pages : 460 pages
Book Rating : 4.1/5 (181 download)
Download or read book Computational Methods for Next Generation Sequencing Data Analysis written by Ion Mandoiu and published by John Wiley & Sons. This book was released on 2016-10-03 with total page 460 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Author : Wing-Kin Sung
Publisher : CRC Press
ISBN 13 : 1498752985
Total Pages : 233 pages
Book Rating : 4.4/5 (987 download)
Download or read book Algorithms for Next-Generation Sequencing written by Wing-Kin Sung and published by CRC Press. This book was released on 2017-05-18 with total page 233 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in sequencing technology have allowed scientists to study the human genome in greater depth and on a larger scale than ever before – as many as hundreds of millions of short reads in the course of a few days. But what are the best ways to deal with this flood of data? Algorithms for Next-Generation Sequencing is an invaluable tool for students and researchers in bioinformatics and computational biology, biologists seeking to process and manage the data generated by next-generation sequencing, and as a textbook or a self-study resource. In addition to offering an in-depth description of the algorithms for processing sequencing data, it also presents useful case studies describing the applications of this technology.
Author :
Publisher : Elsevier
ISBN 13 : 0128114320
Total Pages : 3421 pages
Book Rating : 4.1/5 (281 download)
Download or read book Encyclopedia of Bioinformatics and Computational Biology written by and published by Elsevier. This book was released on 2018-08-21 with total page 3421 pages. Available in PDF, EPUB and Kindle. Book excerpt: Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Three Volume Set combines elements of computer science, information technology, mathematics, statistics and biotechnology, providing the methodology and in silico solutions to mine biological data and processes. The book covers Theory, Topics and Applications, with a special focus on Integrative –omics and Systems Biology. The theoretical, methodological underpinnings of BCB, including phylogeny are covered, as are more current areas of focus, such as translational bioinformatics, cheminformatics, and environmental informatics. Finally, Applications provide guidance for commonly asked questions. This major reference work spans basic and cutting-edge methodologies authored by leaders in the field, providing an invaluable resource for students, scientists, professionals in research institutes, and a broad swath of researchers in biotechnology and the biomedical and pharmaceutical industries. Brings together information from computer science, information technology, mathematics, statistics and biotechnology Written and reviewed by leading experts in the field, providing a unique and authoritative resource Focuses on the main theoretical and methodological concepts before expanding on specific topics and applications Includes interactive images, multimedia tools and crosslinking to further resources and databases
Author : Farideh Fazayeli
Publisher :
ISBN 13 :
Total Pages : 110 pages
Book Rating : 4.:/5 (16 download)
Download or read book Algorithms for Correcting Next Generation Sequencing Errors written by Farideh Fazayeli and published by . This book was released on 2011 with total page 110 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Valeria V. Krzhizhanovskaya
Publisher : Springer Nature
ISBN 13 : 3030503712
Total Pages : 726 pages
Book Rating : 4.0/5 (35 download)
Download or read book Computational Science – ICCS 2020 written by Valeria V. Krzhizhanovskaya and published by Springer Nature. This book was released on 2020-06-18 with total page 726 pages. Available in PDF, EPUB and Kindle. Book excerpt: The seven-volume set LNCS 12137, 12138, 12139, 12140, 12141, 12142, and 12143 constitutes the proceedings of the 20th International Conference on Computational Science, ICCS 2020, held in Amsterdam, The Netherlands, in June 2020.* The total of 101 papers and 248 workshop papers presented in this book set were carefully reviewed and selected from 719 submissions (230 submissions to the main track and 489 submissions to the workshops). The papers were organized in topical sections named: Part I: ICCS Main Track Part II: ICCS Main Track Part III: Advances in High-Performance Computational Earth Sciences: Applications and Frameworks; Agent-Based Simulations, Adaptive Algorithms and Solvers; Applications of Computational Methods in Artificial Intelligence and Machine Learning; Biomedical and Bioinformatics Challenges for Computer Science Part IV: Classifier Learning from Difficult Data; Complex Social Systems through the Lens of Computational Science; Computational Health; Computational Methods for Emerging Problems in (Dis-)Information Analysis Part V: Computational Optimization, Modelling and Simulation; Computational Science in IoT and Smart Systems; Computer Graphics, Image Processing and Artificial Intelligence Part VI: Data Driven Computational Sciences; Machine Learning and Data Assimilation for Dynamical Systems; Meshfree Methods in Computational Sciences; Multiscale Modelling and Simulation; Quantum Computing Workshop Part VII: Simulations of Flow and Transport: Modeling, Algorithms and Computation; Smart Systems: Bringing Together Computer Vision, Sensor Networks and Machine Learning; Software Engineering for Computational Science; Solving Problems with Uncertainties; Teaching Computational Science; UNcErtainty QUantIficatiOn for ComputationAl modeLs *The conference was canceled due to the COVID-19 pandemic.
Author : Wei-Chun Kao
Publisher :
ISBN 13 :
Total Pages : 94 pages
Book Rating : 4.:/5 (827 download)
Download or read book Algorithms for Next-generation High-throughput Sequencing Technologies written by Wei-Chun Kao and published by . This book was released on 2011 with total page 94 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Lizhen Shi
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (134 download)
Download or read book Leveraging Big Data and Machine Learning Technologies for Accurate and Scalable Genomic Analysis written by Lizhen Shi and published by . This book was released on 2020 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The revolution in next-generation DNA sequencing technologies is leading to explosive data growth in genomics, posing a significant challenge to the computing infrastructure and software algorithms for genomics analysis. Various big data and machine learning technologies have been explored to mine the complex large-scale genomics data. In this dissertation, we first survey some of the existing scalable approaches for genomic analysis and identify the limitations of these solutions. We then investigate the still-unsolved challenges faced by computational biologists in large-scale genomic analysis. Specifically, in terms of using MapReduce-based bioinformatics analysis tools, Hadoop has a large number of parameters to control the behavior of a MapReduce job. The unique characteristics of MapReduce-based bioinformatics tools makes all the existing guidelines inapplicable; In Metagenomics, the intrinsic complexity and massive quantity of metagenomic data create tremendous challenges for microbial genomes recovery; When we applying NLP technologies to genome analysis, the enormous k-mer size and the low-frequency k-mers caused by the sequencing errors post significant challenges for k-mer embedding. To overcome the aforementioned problems, this dissertation introduces three countermeasures. First, we extract the key parameters from the large space of MapReduce parameters and present an exemplary case for tuning MapReduce-based bioinformatics analysis tools based on their unique characteristics. Second, we design and implement SpaRC, a scalable sequence clustering tool built on Apache Spark, to partition reads based on their molecules of origin to enable downstream assembly optimization in Metagenomics. SpaRC achieves high clustering accuracy, with the capability of scaling near linearly with the data size and the number of computing nodes. Lastly, we leverage Locality Sensitive Hashing (LSH) to overcome the two challenges faced by $k$-mer embedding and design LSHvec. With LSHvec, a DNA sequence can be represented as a dense low-dimensional vector. The trained sequence vectors are capable of capturing the rich characteristics of DNA sequences and can be fed to machine learning models for a wide variety of applications in genomics analysis. We compare our approaches with existing solutions. The experiments demonstrate our approaches achieve the state-of-the-art results. We open source our implementation of SpaRC and LSHvec to facilitate comparison of future work and inspire future research in genomic analysis.
Author : Michael Molnar
Publisher :
ISBN 13 :
Total Pages : 72 pages
Book Rating : 4.:/5 (16 download)
Download or read book Error Correction in Next Generation DNA Sequencing Data written by Michael Molnar and published by . This book was released on 2012 with total page 72 pages. Available in PDF, EPUB and Kindle. Book excerpt: Motivation: High throughput Next Generation Sequencing (NGS) technologies can sequence the genome of a species quickly and cheaply. Errors that are introduced by NGS technologies limit the full potential of the applications that rely on their data. Current techniques used to correct these errors are not su cient due to issues with time, space, or accuracy. A more e cient and accurate program is needed to correct errors from NGS technologies. Results: We have designed and implemented RACER (Rapid Accurate Correction of Errors in Reads), an error correction program that targets the Illumina genome sequencer, which is currently the dominant NGS technology. RACER combines advanced data structures with an intricate analysis of data to achieve high performance. It has been implemented in C++ and OpenMP for parallelization. We have performed extensive testing on a variety of real data sets to compare RACER with the current leading programs. RACER performs better than all the current technologies in time, space, and accuracy. RACER corrects up to twice as many errors as other parallel programs, while being one order of magnitude faster. We hope RACER will become a very useful tool for many applications that use NGS data.
Author : Isaac Akogwu
Publisher :
ISBN 13 :
Total Pages : 11 pages
Book Rating : 4.:/5 (958 download)
Download or read book A Comparative Study of K-spectrum-based Error Correction Methods for Next-generation Sequencing Data Analysis written by Isaac Akogwu and published by . This book was released on 2016 with total page 11 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Jimmy Lin
Publisher : Springer Nature
ISBN 13 : 3031021363
Total Pages : 171 pages
Book Rating : 4.0/5 (31 download)
Download or read book Data-Intensive Text Processing with MapReduce written by Jimmy Lin and published by Springer Nature. This book was released on 2022-05-31 with total page 171 pages. Available in PDF, EPUB and Kindle. Book excerpt: Our world is being revolutionized by data-driven methods: access to large amounts of data has generated new insights and opened exciting new opportunities in commerce, science, and computing applications. Processing the enormous quantities of data necessary for these advances requires large clusters, making distributed computing paradigms more crucial than ever. MapReduce is a programming model for expressing distributed computations on massive datasets and an execution framework for large-scale data processing on clusters of commodity servers. The programming model provides an easy-to-understand abstraction for designing scalable algorithms, while the execution framework transparently handles many system-level details, ranging from scheduling to synchronization to fault tolerance. This book focuses on MapReduce algorithm design, with an emphasis on text processing algorithms common in natural language processing, information retrieval, and machine learning. We introduce the notion of MapReduce design patterns, which represent general reusable solutions to commonly occurring problems across a variety of problem domains. This book not only intends to help the reader "think in MapReduce", but also discusses limitations of the programming model as well. Table of Contents: Introduction / MapReduce Basics / MapReduce Algorithm Design / Inverted Indexing for Text Retrieval / Graph Algorithms / EM Algorithms for Text Processing / Closing Remarks
Author : Jens Dörpinghaus
Publisher : Springer Nature
ISBN 13 : 303108411X
Total Pages : 593 pages
Book Rating : 4.0/5 (31 download)
Download or read book Computational Life Sciences written by Jens Dörpinghaus and published by Springer Nature. This book was released on 2023-03-04 with total page 593 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book broadly covers the given spectrum of disciplines in Computational Life Sciences, transforming it into a strong helping hand for teachers, students, practitioners and researchers. In Life Sciences, problem-solving and data analysis often depend on biological expertise combined with technical skills in order to generate, manage and efficiently analyse big data. These technical skills can easily be enhanced by good theoretical foundations, developed from well-chosen practical examples and inspiring new strategies. This is the innovative approach of Computational Life Sciences-Data Engineering and Data Mining for Life Sciences: We present basic concepts, advanced topics and emerging technologies, introduce algorithm design and programming principles, address data mining and knowledge discovery as well as applications arising from real projects. Chapters are largely independent and often flanked by illustrative examples and practical advise.
Author : Management Association, Information Resources
Publisher : IGI Global
ISBN 13 : 152258904X
Total Pages : 2183 pages
Book Rating : 4.5/5 (225 download)
Download or read book Biotechnology: Concepts, Methodologies, Tools, and Applications written by Management Association, Information Resources and published by IGI Global. This book was released on 2019-06-07 with total page 2183 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biotechnology can be defined as the manipulation of biological process, systems, and organisms in the production of various products. With applications in a number of fields such as biomedical, chemical, mechanical, and civil engineering, research on the development of biologically inspired materials is essential to further advancement. Biotechnology: Concepts, Methodologies, Tools, and Applications is a vital reference source for the latest research findings on the application of biotechnology in medicine, engineering, agriculture, food production, and other areas. It also examines the economic impacts of biotechnology use. Highlighting a range of topics such as pharmacogenomics, biomedical engineering, and bioinformatics, this multi-volume book is ideally designed for engineers, pharmacists, medical professionals, practitioners, academicians, and researchers interested in the applications of biotechnology.
Author : Neil C. Jones
Publisher : MIT Press
ISBN 13 : 9780262101066
Total Pages : 460 pages
Book Rating : 4.1/5 (1 download)
Download or read book An Introduction to Bioinformatics Algorithms written by Neil C. Jones and published by MIT Press. This book was released on 2004-08-06 with total page 460 pages. Available in PDF, EPUB and Kindle. Book excerpt: An introductory text that emphasizes the underlying algorithmic ideas that are driving advances in bioinformatics. This introductory text offers a clear exposition of the algorithmic principles driving advances in bioinformatics. Accessible to students in both biology and computer science, it strikes a unique balance between rigorous mathematics and practical techniques, emphasizing the ideas underlying algorithms rather than offering a collection of apparently unrelated problems. The book introduces biological and algorithmic ideas together, linking issues in computer science to biology and thus capturing the interest of students in both subjects. It demonstrates that relatively few design techniques can be used to solve a large number of practical problems in biology, and presents this material intuitively. An Introduction to Bioinformatics Algorithms is one of the first books on bioinformatics that can be used by students at an undergraduate level. It includes a dual table of contents, organized by algorithmic idea and biological idea; discussions of biologically relevant problems, including a detailed problem formulation and one or more solutions for each; and brief biographical sketches of leading figures in the field. These interesting vignettes offer students a glimpse of the inspirations and motivations for real work in bioinformatics, making the concepts presented in the text more concrete and the techniques more approachable.PowerPoint presentations, practical bioinformatics problems, sample code, diagrams, demonstrations, and other materials can be found at the Author's website.
Author : Panwen Wang
Publisher : Frontiers Media SA
ISBN 13 : 2832529658
Total Pages : 126 pages
Book Rating : 4.8/5 (325 download)
Download or read book Enhanced biological mechanism study, drug discovery and individualized medicine with single-cell multiomics data and integrative analysis written by Panwen Wang and published by Frontiers Media SA. This book was released on 2023-07-20 with total page 126 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Rashid Mehmood
Publisher : Springer
ISBN 13 : 3030137058
Total Pages : 665 pages
Book Rating : 4.0/5 (31 download)
Download or read book Smart Infrastructure and Applications written by Rashid Mehmood and published by Springer. This book was released on 2019-06-20 with total page 665 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a multidisciplinary view of smart infrastructure through a range of diverse introductory and advanced topics. The book features an array of subjects that include: smart cities and infrastructure, e-healthcare, emergency and disaster management, Internet of Vehicles, supply chain management, eGovernance, and high performance computing. The book is divided into five parts: Smart Transportation, Smart Healthcare, Miscellaneous Applications, Big Data and High Performance Computing, and Internet of Things (IoT). Contributions are from academics, researchers, and industry professionals around the world. Features a broad mix of topics related to smart infrastructure and smart applications, particularly high performance computing, big data, and artificial intelligence; Includes a strong emphasis on methodological aspects of infrastructure, technology and application development; Presents a substantial overview of research and development on key economic sectors including healthcare and transportation.
