Introduction To Computational Metagenomics

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Introduction To Computational Metagenomics

Zhong Wang
Introduction To Computational Metagenomics Book PDF

Author : Zhong Wang
Publisher : World Scientific
Page : 210 pages
File Size : 49,8 Mb
Release : 2022-04-11
Category : Science
ISBN : 9789811242489

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Introduction To Computational Metagenomics by Zhong Wang Pdf

Breakthroughs in high-throughput genome sequencing and high-performance computing technologies have empowered scientists to decode many genomes including our own. Now they have a bigger ambition: to fully understand the vast diversity of microbial communities within us and around us, and to exploit their potential for the improvement of our health and environment. In this new field called metagenomics, microbial genomes are sequenced directly from the habitats without lab cultivation. Computational metagenomics, however, faces both a data challenge that deals with tens of tera-bases of sequences and an algorithmic one that deals with the complexity of thousands of species and their interactions.This interdisciplinary book is essential reading for those who are interested in beginning their own journey in computational metagenomics. It is a prism to look through various intricate computational metagenomics problems and unravel their three distinctive aspects: metagenomics, data engineering, and algorithms. Graduate students and advanced undergraduates from genomics science or computer science fields will find that the concepts explained in this book can serve as stepping stones for more advanced topics, while metagenomics practitioners and researchers from similar disciplines may use it to broaden their knowledge or identify new research targets.

Introduction to Computational Biology

Michael S. Waterman
Introduction to Computational Biology Book PDF

Author : Michael S. Waterman
Publisher : CRC Press
Page : 248 pages
File Size : 43,6 Mb
Release : 2018-05-02
Category : Mathematics
ISBN : 9781351437080

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Introduction to Computational Biology by Michael S. Waterman Pdf

Biology is in the midst of a era yielding many significant discoveries and promising many more. Unique to this era is the exponential growth in the size of information-packed databases. Inspired by a pressing need to analyze that data, Introduction to Computational Biology explores a new area of expertise that emerged from this fertile field- the combination of biological and information sciences. This introduction describes the mathematical structure of biological data, especially from sequences and chromosomes. After a brief survey of molecular biology, it studies restriction maps of DNA, rough landmark maps of the underlying sequences, and clones and clone maps. It examines problems associated with reading DNA sequences and comparing sequences to finding common patterns. The author then considers that statistics of pattern counts in sequences, RNA secondary structure, and the inference of evolutionary history of related sequences. Introduction to Computational Biology exposes the reader to the fascinating structure of biological data and explains how to treat related combinatorial and statistical problems. Written to describe mathematical formulation and development, this book helps set the stage for even more, truly interdisciplinary work in biology.

Computational Genomics with R

Altuna Akalin
Computational Genomics with R Book PDF

Author : Altuna Akalin
Publisher : CRC Press
Page : 462 pages
File Size : 41,6 Mb
Release : 2020-12-16
Category : Mathematics
ISBN : 9781498781862

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Computational Genomics with R by Altuna Akalin Pdf

Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.

Computational Genome Analysis

Richard C. Deonier,Simon Tavaré,Michael S. Waterman
Computational Genome Analysis Book PDF

Author : Richard C. Deonier,Simon Tavaré,Michael S. Waterman
Publisher : Springer Science & Business Media
Page : 542 pages
File Size : 49,6 Mb
Release : 2005-12-27
Category : Computers
ISBN : 9780387288079

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Computational Genome Analysis by Richard C. Deonier,Simon Tavaré,Michael S. Waterman Pdf

This book presents the foundations of key problems in computational molecular biology and bioinformatics. It focuses on computational and statistical principles applied to genomes, and introduces the mathematics and statistics that are crucial for understanding these applications. The book features a free download of the R software statistics package and the text provides great crossover material that is interesting and accessible to students in biology, mathematics, statistics and computer science. More than 100 illustrations and diagrams reinforce concepts and present key results from the primary literature. Exercises are given at the end of chapters.

Introduction to Computational Proteomics

Golan Yona
Introduction to Computational Proteomics Book PDF

Author : Golan Yona
Publisher : CRC Press
Page : 545 pages
File Size : 41,6 Mb
Release : 2010-12-09
Category : Mathematics
ISBN : 9781000738278

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Introduction to Computational Proteomics by Golan Yona Pdf

Introduction to Computational Proteomics introduces the field of computational biology through a focused approach that tackles the different steps and problems involved with protein analysis, classification, and meta-organization. The book starts with the analysis of individual entities and works its way through the analysis of more complex entitie

Metagenomics

Muniyandi Nagarajan
Metagenomics Book PDF

Author : Muniyandi Nagarajan
Publisher : Academic Press
Page : 398 pages
File Size : 48,9 Mb
Release : 2017-11-06
Category : Medical
ISBN : 9780128134030

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Metagenomics by Muniyandi Nagarajan Pdf

Metagenomics: Perspectives, Methods, and Applications provides thorough coverage of the growing field of metagenomics. A diverse range of chapters from international experts offer an introduction to the field and examine methods for metagenomic analysis of microbiota, metagenomic computational tools, and recent metagenomic studies in various environments. The emphasis on application makes this text particularly useful for applied researchers, practitioners, clinicians and students seeking to employ metagenomic approaches to advance knowledge in the biomedical and life sciences. Case-study based application chapters examine topics ranging from viral metagenome profiling, metagenomics in oral disease and health, metagenomic insights into the human gut microbiome and metabolic syndromes, and more. Additionally, perspectives on future potential at the end of each chapter provoke new thought and motivations for continued study in this exciting and fruitful research area. Provides thorough coverage of the rapidly growing field of metagenomics, with an emphasis on applications of relevance to translational researchers, practitioners, clinicians and students Features a diverse range of chapters from international experts that offer an introduction to the field and examine methods for metagenomic analysis of microbiota, metagenomic computational tools and research pipelines Highlights perspectives on future potential at the end of each chapter to provoke new thought and motivations for continued study in this exciting and fruitful research area

Guide To The Umbral Calculus, A Different Mathematical Language

Silvia Licciardi,Giuseppe Dattoli
Guide To The Umbral Calculus A Different Mathematical Language Book PDF

Author : Silvia Licciardi,Giuseppe Dattoli
Publisher : World Scientific
Page : 295 pages
File Size : 48,5 Mb
Release : 2022-06-14
Category : Science
ISBN : 9789811255342

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Guide To The Umbral Calculus, A Different Mathematical Language by Silvia Licciardi,Giuseppe Dattoli Pdf

This book covers different aspects of umbral calculus and of its more recent developments. It discusses the technical details in depth, including its relevant applications. The book has therefore manyfold scopes to introduce a mathematical tool, not widespread known as it should be; to present a complete account of the relevant capabilities through the use of different examples of applications; to provide a formal bridge between different fields of research in pure and applied.

Introduction to Computational Genomics

Nello Cristianini
Introduction to Computational Genomics Book PDF

Author : Nello Cristianini
Publisher : Unknown
Page : 182 pages
File Size : 55,8 Mb
Release : 2007
Category : Computational biology
ISBN : 1107166284

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Introduction to Computational Genomics by Nello Cristianini Pdf

Are we related to Neanderthals? Where did SARS come from? Which part of our genome is evolving the fastest? These are some of the questions that can be answered by statistical and computational analysis of genetic data. This text presents an introduction to computational genomics.

Introduction to Computational Genomics

Nello Cristianini,Matthew W. Hahn
Introduction to Computational Genomics Book PDF

Author : Nello Cristianini,Matthew W. Hahn
Publisher : Cambridge University Press
Page : 7 pages
File Size : 49,7 Mb
Release : 2006-12-14
Category : Computers
ISBN : 9781139460156

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Introduction to Computational Genomics by Nello Cristianini,Matthew W. Hahn Pdf

Where did SARS come from? Have we inherited genes from Neanderthals? How do plants use their internal clock? The genomic revolution in biology enables us to answer such questions. But the revolution would have been impossible without the support of powerful computational and statistical methods that enable us to exploit genomic data. Many universities are introducing courses to train the next generation of bioinformaticians: biologists fluent in mathematics and computer science, and data analysts familiar with biology. This readable and entertaining book, based on successful taught courses, provides a roadmap to navigate entry to this field. It guides the reader through key achievements of bioinformatics, using a hands-on approach. Statistical sequence analysis, sequence alignment, hidden Markov models, gene and motif finding and more, are introduced in a rigorous yet accessible way. A companion website provides the reader with Matlab-related software tools for reproducing the steps demonstrated in the book.

Metagenomics: Techniques, Applications, Challenges and Opportunities

Reena Singh Chopra,Chirag Chopra,Neeta Raj Sharma
Metagenomics Techniques Applications Challenges and Opportunities Book PDF

Author : Reena Singh Chopra,Chirag Chopra,Neeta Raj Sharma
Publisher : Springer Nature
Page : 225 pages
File Size : 42,9 Mb
Release : 2020-09-08
Category : Science
ISBN : 9789811565298

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Metagenomics: Techniques, Applications, Challenges and Opportunities by Reena Singh Chopra,Chirag Chopra,Neeta Raj Sharma Pdf

This book summarizes the various areas of research in metagenomics and their potential applications in medicine, the environment and biotechnology. The book presents the recent advances in theoretical, methodological and applied aspects of metagenomics and highlights their applications in the fields of environmental microbial forensics, bioremediation, drug-discovery and agriculture. In addition, the book discusses various metagenomics approaches used for understanding the microbial physiology and biochemistry. Lastly the book describes a range of bioinformatics tools and computational methods for metagenomics analysis as well as the functional diversity and dynamics of microbial communities colonizing the human skin.

Metagenomic Data Analysis

Suparna Mitra
Metagenomic Data Analysis Book PDF

Author : Suparna Mitra
Publisher : Springer Nature
Page : 443 pages
File Size : 43,7 Mb
Release : 2023-05-31
Category : Science
ISBN : 9781071630723

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Metagenomic Data Analysis by Suparna Mitra Pdf

This volume describes different sequencing methods, pipelines and tools for metagenome data analyses. Chapters guide readers through quality control of raw sequence data, metagenomics databases for bacterial annotations such Greengenes, SILVA, RDP and GTDB, guide to 16S rRNA microbiome analysis and pipelines such as mothur, DADA2, QIIME2 , whole genome shotgun metagenomics data analyses pipeline using MEGAN and DIAMOND, web service such as PATRIC, RDP, mothur, Kaiju, PhyloPythiaS, MG-RAST, WebMGA, MicrobiomeAnalyst, WHAM!, METAGENassist and MGnify: EBI-Metagenomics, MG-RAST Metagenomics Analysis. Then the chapters inform the readers regarding Third-generation sequencing (TGS) approaches as MinION sequencing and teaches use of Ubuntu Linux Virtual Machine configuration, clinical and environmental resistomes, use of FISH techniques and designing FISH probes, protocols for viral metagenomics, and comprehensive guideline for microbiome analysis using most used R packages. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Metagenomic Data Analysis: Methods and Protocols aims to be comprehensive guide for researchers to specialize in the metagenomics field.

Computational Methods for Understanding Bacterial and Archaeal Genomes

Ying Xu,J. Peter Gogarten
Computational Methods for Understanding Bacterial and Archaeal Genomes Book PDF

Author : Ying Xu,J. Peter Gogarten
Publisher : World Scientific
Page : 494 pages
File Size : 46,8 Mb
Release : 2008
Category : Medical
ISBN : 9781860949821

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Computational Methods for Understanding Bacterial and Archaeal Genomes by Ying Xu,J. Peter Gogarten Pdf

Over 500 prokaryotic genomes have been sequenced to date, and thousands more have been planned for the next few years. While these genomic sequence data provide unprecedented opportunities for biologists to study the world of prokaryotes, they also raise extremely challenging issues such as how to decode the rich information encoded in these genomes. This comprehensive volume includes a collection of cohesively written chapters on prokaryotic genomes, their organization and evolution, the information they encode, and the computational approaches needed to derive such information. A comparative view of bacterial and archaeal genomes, and how information is encoded differently in them, is also presented. Combining theoretical discussions and computational techniques, the book serves as a valuable introductory textbook for graduate-level microbial genomics and informatics courses.

Distributed, High-Performance and Grid Computing in Computational Biology

Werner Dubitzky,Assaf Schuster,Peter Sloot,Michael Schroeder,Mathilde Romberg
Distributed High Performance and Grid Computing in Computational Biology Book PDF

Author : Werner Dubitzky,Assaf Schuster,Peter Sloot,Michael Schroeder,Mathilde Romberg
Publisher : Springer Science & Business Media
Page : 202 pages
File Size : 52,6 Mb
Release : 2007-01-03
Category : Science
ISBN : 9783540698418

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Distributed, High-Performance and Grid Computing in Computational Biology by Werner Dubitzky,Assaf Schuster,Peter Sloot,Michael Schroeder,Mathilde Romberg Pdf

The book constitutes the refereed proceedings of the International Workshop on Distributed, High-Performance and Grid Computing in Computational Biology, GCCB 2006, held in Eilat, Israel in January 2007 in conjunction with the 5th European Conference on Computational Biology, ECCB 2006. The 13 revised full papers presented were carefully reviewed and selected from many high quality submissions.

Computational Methods for Understanding Bacterial and Archaeal Genomes

Ying Xu
Computational Methods for Understanding Bacterial and Archaeal Genomes Book PDF

Author : Ying Xu
Publisher : Imperial College Press
Page : 494 pages
File Size : 41,6 Mb
Release : 2008
Category : Science
ISBN : 9781860949838

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Computational Methods for Understanding Bacterial and Archaeal Genomes by Ying Xu Pdf

Over 500 prokaryotic genomes have been sequenced to date, and thousands more have been planned for the next few years. While these genomic sequence data provide unprecedented opportunities for biologists to study the world of prokaryotes, they also raise extremely challenging issues such as how to decode the rich information encoded in these genomes. This comprehensive volume includes a collection of cohesively written chapters on prokaryotic genomes, their organization and evolution, the information they encode, and the computational approaches needed to derive such information. A comparative view of bacterial and archaeal genomes, and how information is encoded differently in them, is also presented. Combining theoretical discussions and computational techniques, the book serves as a valuable introductory textbook for graduate-level microbial genomics and informatics courses.

Introduction to Computational Biology

Bernhard Haubold,Thomas Wiehe
Introduction to Computational Biology Book PDF

Author : Bernhard Haubold,Thomas Wiehe
Publisher : Birkhäuser
Page : 328 pages
File Size : 49,7 Mb
Release : 2009-09-03
Category : Science
ISBN : 3764390174

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Introduction to Computational Biology by Bernhard Haubold,Thomas Wiehe Pdf

Written with the advanced undergraduate in mind, this book introduces into the field of Bioinformatics. The authors explain the computational and conceptional background to the analysis of large-scale sequence data. Many of the corresponding analysis methods are rooted in evolutionary thinking, which serves as a common thread throughout the book. The focus is on methods of comparative genomics and subjects covered include: alignments, gene finding, phylogeny, and the analysis of single nucleotide polymorphisms (SNPs). The volume contains exercises, questions & answers to selected problems.