Read Books Online and Download eBooks, EPub, PDF, Mobi, Kindle, Text Full Free.
Genomic And Transcriptomic Reference Assemblies And Analyses With Sequencing Datasets From Multiple Non Traditional Model Species
Download Genomic And Transcriptomic Reference Assemblies And Analyses With Sequencing Datasets From Multiple Non Traditional Model Species full books in PDF, epub, and Kindle. Read online Genomic And Transcriptomic Reference Assemblies And Analyses With Sequencing Datasets From Multiple Non Traditional Model Species ebook anywhere anytime directly on your device. Fast Download speed and no annoying ads. We cannot guarantee that every ebooks is available!
Book Synopsis Genomic and Transcriptomic Reference Assemblies and Analyses with Sequencing Datasets from Multiple Non-traditional Model Species by : Lisa Kristine Johnson
Download or read book Genomic and Transcriptomic Reference Assemblies and Analyses with Sequencing Datasets from Multiple Non-traditional Model Species written by Lisa Kristine Johnson and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: High-throughput nucleic acid "Next-Generation" sequencing (NGS) methods have revolutionized the biological sciences over the past decade by facilitating research and discoveries at the whole-genome level. However, generating high-quality genome and transcriptome references and navigating downstream analyses still remain challenging and computationally-intensive endeavors, especially for non-model species. This dissertation focused on automating bioinformatics methods for two different projects with multiple non-model species: the Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP) and differential expression analysis of gill epithelium from Fundulus North American killifish following salinity challenge. With these two projects, I sought to generate high quality de novo transcriptomes and genomes in a uniform and automated way. Three aims were addressed: how the re-analysis of old data with new tools affects the outcome of the reference assemblies, how to generate data and draft de novo assemblies for several high-quality reference genomes from non-model species in a cost-efficient manner, and how to generate high quality species-specific de novo transcriptomes and annotations using annotations from a closely-related model species reference. Furthermore, I used these de novo transcriptomes and annotations to examine gene expression responses of multiple species of Fundulus killifish to a common salinity challenge experiment.
Book Synopsis Computational Methods for Next Generation Sequencing Data Analysis by : Ion Mandoiu
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 2016-09-12 with total page 518 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.
Book Synopsis Assembly and Alignment Free Methods for Phylogenetic Reconstruction and Genome-wide Association Studies by : Huan Fan
Download or read book Assembly and Alignment Free Methods for Phylogenetic Reconstruction and Genome-wide Association Studies written by Huan Fan and published by . This book was released on 2017 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in sequencing technology have the potential to change almost every field in biology. For the first time, ecologists and evolutionary biologists can sequence any species of interest. However, the many types of sequencing techniques are bewildering, and the analysis of the sequences is hampered if no reference genome is available. Therefore, despite the sequencing effort devoted to many understudied species, the actual insights we have drawn from the sequences are limited. To bridge the gap between model and non-model organisms, and to provide more options for genomes of model organisms, this thesis is devoted to developing tools based on the k-mer (short strands of DNA) composition of genomes. These tools give a simple but informative way to compare genomes that does not require reference genomes. k-mers can be directly extracted from short read sequences, making k-mer-based analyses assembly and alignment-free (AAF). I developed three AAF methods for different genomic analyses using different types of sequencing data. The first, AAF, reconstructs phylogenies directly from unassembled genome sequence data (available at https://github.com/fanhuan/AAF). The second, phyloRAD, also reconstructs phylogeny without assembly or alignment but from Restriction-Associated DNA (RAD) sequences, a type of reduced representation genome sequencing that is especially popular in studying non-model organisms (available at https://github.com/fanhuan/phyloRAD). The third, AAF-GWAS, scores association between the presence or absence of a k-mer and the trait of interest; the highly associated ones are likely to be related to the underlying genetic mechanism (available at https://github.com/fanhuan/AAF-GWAS). I verified the accuracy and demonstrated the application of these three assembly and alignment-free tools using sequence simulation and real genome datasets. They were all effective for analysis without reference genomes and useful alternatives even if there are reference genomes. These k-mer based methods should aid the ecological and evolutionary study of non-model organisms. They are also effective and computationally efficient alternatives to alignment-based methods and will therefore remain useful even as sequencing technologies advance and reference genomes become more widely available.
Book Synopsis Genomic and Transcriptomic Studies on Non-Model Organisms by : Shuhua Fu
Download or read book Genomic and Transcriptomic Studies on Non-Model Organisms written by Shuhua Fu and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: As the advance in high-throughput sequencing enables the generation of large volumes of genomic information, it provides researchers the opportunity to study non-model organisms even in the absence of a fully sequenced genome. The hugely advantageous progress calls for powerful sequencing assembly algorithms as these technologies also raise challenging assembly problems: (1) Some RNA products are highly expressed but others may have much lower expression level. (2) Data cannot easily be represented as linear structure, due to post-transcriptional modification like alternative splicing. (3) Conserved sequences in domains in gene families can result in assembly errors, (4) Sequencing errors due to technique limitations. Useful assembly algorithms are required to overcome the difficulties above. In these studies, there is often a need to identify similar transcripts in non-model organisms to transcripts found in related organisms. The traditional approach to address this problem is to perform de novo transcriptome assemblies to obtain predicted transcripts for these organisms and then employ similarity comparison algorithms to identify them. I observe it is possible to obtain a more complete set of similar transcripts from transcriptome assembly by making use of evolutionary information. I apply new algorithms to study non-model organisms which play an important role in applied biology. Moreover, improvement of sequencing technologies and application of current algorithms also help to study interkingdom signals between blow flies and bacteria community. With current computational tools, I annotate genomes of Proteus mirabilis and Providencia stuartii, which play an important role in bacteria-insect interaction. The study shows significant features of these strains isolated, which provides useful information to develop and test hypothesis in related interactions in insects and bacteria. The electronic version of this dissertation is accessible from http://hdl.handle.net/1969.1/155184
Book Synopsis Paleogenomics by : Charlotte Lindqvist
Download or read book Paleogenomics written by Charlotte Lindqvist and published by Springer. This book was released on 2019-01-07 with total page 427 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in genome-scale DNA sequencing technologies have revolutionized genetic research on ancient organisms, extinct species, and past environments. When it is recoverable after hundreds or thousands of years of unintended preservation, “ancient DNA” (or aDNA) is often highly degraded, necessitating specialized handling and analytical approaches. Paleogenomics defines the field of reconstructing and analyzing the genomes of historic or long-dead organisms, most often through comparison with modern representatives of the same or similar species. The opportunity to isolate and study paleogenomes has radically transformed many fields, spanning biology, anthropology, agriculture, and medicine. Examples include understanding evolutionary relationships of extinct species known only from fossils, the domestication of plants and animals, and the evolution and geographical spread of certain pathogens. This pioneering book presents a snapshot view of the history, current status, and future prospects of paleogenomics, taking a broad viewpoint that covers a range of topics and organisms to provide an up-to-date status of the applications, challenges, and promise of the field. This book is intended for a variety of readerships, including upper-level undergraduate and graduate students, professionals and experts in the field, as well as anyone excited by the extraordinary insights that paleogenomics offers.
Book Synopsis Next-Generation Sequencing and Sequence Data Analysis by : Kuo Ping Chiu
Download or read book Next-Generation Sequencing and Sequence Data Analysis written by Kuo Ping Chiu and published by Bentham Science Publishers. This book was released on 2015-11-04 with total page 160 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nucleic acid sequencing techniques have enabled researchers to determine the exact order of base pairs - and by extension, the information present - in the genome of living organisms. Consequently, our understanding of this information and its link to genetic expression at molecular and cellular levels has lead to rapid advances in biology, genetics, biotechnology and medicine. Next-Generation Sequencing and Sequence Data Analysis is a brief primer on DNA sequencing techniques and methods used to analyze sequence data. Readers will learn about recent concepts and methods in genomics such as sequence library preparation, cluster generation for PCR technologies, PED sequencing, genome assembly, exome sequencing, transcriptomics and more. This book serves as a textbook for students undertaking courses in bioinformatics and laboratory methods in applied biology. General readers interested in learning about DNA sequencing techniques may also benefit from the simple format of information presented in the book.
Book Synopsis Applications of RNA-Seq and Omics Strategies by : Fabio Marchi
Download or read book Applications of RNA-Seq and Omics Strategies written by Fabio Marchi and published by BoD – Books on Demand. This book was released on 2017-09-13 with total page 330 pages. Available in PDF, EPUB and Kindle. Book 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.
Book Synopsis Contemporary High Performance Computing by : Jeffrey S. Vetter
Download or read book Contemporary High Performance Computing written by Jeffrey S. Vetter and published by CRC Press. This book was released on 2019-04-30 with total page 434 pages. Available in PDF, EPUB and Kindle. Book excerpt: Contemporary High Performance Computing: From Petascale toward Exascale, Volume 3 focuses on the ecosystems surrounding the world’s leading centers for high performance computing (HPC). It covers many of the important factors involved in each ecosystem: computer architectures, software, applications, facilities, and sponsors. This third volume will be a continuation of the two previous volumes, and will include other HPC ecosystems using the same chapter outline: description of a flagship system, major application workloads, facilities, and sponsors. Features: Describes many prominent, international systems in HPC from 2015 through 2017 including each system’s hardware and software architecture Covers facilities for each system including power and cooling Presents application workloads for each site Discusses historic and projected trends in technology and applications Includes contributions from leading experts Designed for researchers and students in high performance computing, computational science, and related areas, this book provides a valuable guide to the state-of-the art research, trends, and resources in the world of HPC.
Book Synopsis Marsupial Genetics and Genomics by : Paul D. Waters
Download or read book Marsupial Genetics and Genomics written by Paul D. Waters and published by Springer Science & Business Media. This book was released on 2010-08-05 with total page 518 pages. Available in PDF, EPUB and Kindle. Book excerpt: Marsupials belong to the Class Mammalia, sharing some features with other mammals, yet they also possess many unique features. It is their differences from the more traditionally studied mammals, such as mice and humans, that is of greatest value to comparative studies. Sequencing of genomes from two distantly related marsupials, the short grey-tailed opossum from South America and the Australian tammar wallaby, has launched marsupials into the genomics era and accelerated the rate of progress in marsupial research. With the current worldwide concern for the plight of the endangered Tasmanian devil, marsupial genetics and genomics research is even more important than ever if this species is to be saved from extinction. This volume recounts some of the history of research in this field and highlights the most recent advances in the many different areas of marsupial genetics and genomics research.
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.
Download or read book The Barley Genome written by Nils Stein and published by Springer. This book was released on 2018-08-18 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an overview of the state-of-the-art in barley genome analysis, covering all aspects of sequencing the genome and translating this important information into new knowledge in basic and applied crop plant biology and new tools for research and crop improvement. Unlimited access to a high-quality reference sequence is removing one of the major constraints in basic and applied research. This book summarizes the advanced knowledge of the composition of the barley genome, its genes and the much larger non-coding part of the genome, and how this information facilitates studying the specific characteristics of barley. One of the oldest domesticated crops, barley is the small grain cereal species that is best adapted to the highest altitudes and latitudes, and it exhibits the greatest tolerance to most abiotic stresses. With comprehensive access to the genome sequence, barley’s importance as a genetic model in comparative studies on crop species like wheat, rye, oats and even rice is likely to increase.
Book Synopsis Advances in crop biomass production based on multi-omics approach by : Yin Li
Download or read book Advances in crop biomass production based on multi-omics approach written by Yin Li and published by Frontiers Media SA. This book was released on 2023-05-12 with total page 145 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis New Trends on Genome and Transcriptome Characterizations by : Rosalba Giugno
Download or read book New Trends on Genome and Transcriptome Characterizations written by Rosalba Giugno and published by Frontiers Media SA. This book was released on 2018-10-11 with total page 157 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Quantitative Genetics, Genomics and Plant Breeding, 2nd Edition by : Manjit S. Kang
Download or read book Quantitative Genetics, Genomics and Plant Breeding, 2nd Edition written by Manjit S. Kang and published by CABI. This book was released on 2020-04-01 with total page 433 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents state-of-the-art, authoritative chapters on contemporary issues in the broad areas of quantitative genetics, genomics and plant breeding. Section 1 (Chapters 2 to 12) emphasizes the application of genomics, and genome and epigenome editing techniques, in plant breeding; bioinformatics; quantitative trait loci mapping; and the latest approaches of examining and exploiting genotype-environment interactions. Section 2 (Chapters 13 to 20) represents the intersection of breeding, genetics and genomics. This section describes the use of cutting-edge molecular breeding and quantitative genetics techniques in wheat, rice, maize, root and tuber crops and pearl millet. Overall, the book focuses on using genomic information to help evaluate traits that can combat biotic/abiotic stresses, genome-wide association mapping, high-throughput genotyping/phenotyping, biofortification, use of big data, orphan crops, and gene editing techniques. The examples featured are taken from across crop science research and cover a wide geographical base.
Download or read book Plant Omics written by Hajime Ohyanagi and published by CABI. This book was released on 2022-12-14 with total page 311 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a comprehensive overview of plant omics and big data in the fields of plant and crop biology. It discusses each omics layer individually, including genomics, transcriptomics, proteomics, and covers model and non-model species. In a section on advanced topics, it considers developments in each specialized domain, including genome editing and enhanced breeding strategies (such as genomic selection and high-throughput phenotyping), with the aim of providing tools to help tackle global food security issues. The importance of online resources in big data biology are highlighted in a section summarizing both wet- and dry-biological portals. This section introduces biological resources, datasets, online bioinformatics tools and approaches that are in the public domain. This book is for students, engineers, researchers and academics in plant biology, genetics, biotechnology and bioinformatics.
Book Synopsis Evolution of Translational Omics by : Institute of Medicine
Download or read book Evolution of Translational Omics written by Institute of Medicine and published by National Academies Press. This book was released on 2012-09-13 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt: Technologies collectively called omics enable simultaneous measurement of an enormous number of biomolecules; for example, genomics investigates thousands of DNA sequences, and proteomics examines large numbers of proteins. Scientists are using these technologies to develop innovative tests to detect disease and to predict a patient's likelihood of responding to specific drugs. Following a recent case involving premature use of omics-based tests in cancer clinical trials at Duke University, the NCI requested that the IOM establish a committee to recommend ways to strengthen omics-based test development and evaluation. This report identifies best practices to enhance development, evaluation, and translation of omics-based tests while simultaneously reinforcing steps to ensure that these tests are appropriately assessed for scientific validity before they are used to guide patient treatment in clinical trials.
Book Synopsis Bioinformatics in the Era of Post Genomics and Big Data by : Ibrokhim Y. Abdurakhmonov
Download or read book Bioinformatics in the Era of Post Genomics and Big Data written by Ibrokhim Y. Abdurakhmonov and published by BoD – Books on Demand. This book was released on 2018-06-20 with total page 190 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioinformatics has evolved significantly in the era of post genomics and big data. Huge advancements were made toward storing, handling, mining, comparing, extracting, clustering and analysis as well as visualization of big macromolecular data using novel computational approaches, machine and deep learning methods, and web-based server tools. There are extensively ongoing world-wide efforts to build the resources for regional hosting, organized and structured access and improving the pre-existing bioinformatics tools to efficiently and meaningfully analyze day-to-day increasing big data. This book intends to provide the reader with updates and progress on genomic data analysis, data modeling and network-based system tools.
