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Transcriptome De Novo Assembly Clustering And Annotation Of Novel Transcripts
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Book Synopsis Transcriptome De Novo Assembly, Clustering, and Annotation of Novel Transcripts by : Fatemeh Shaadi Pooyaei Mehr
Download or read book Transcriptome De Novo Assembly, Clustering, and Annotation of Novel Transcripts written by Fatemeh Shaadi Pooyaei Mehr and published by . This book was released on 2013 with total page 342 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent advances in Next Generation Sequencing (NGS) have allowed for unparalleled access to genetic information for organisms in both the functional and phylogenetic realms of biology. Analysis of the RNA transcripts of cells of organisms using Next Generation Sequencing (called RNA-seq) has opened doors for unique insights into the genomic complexity of organisms and has provided researchers with invaluable tools for analysis of function of gene products and phylogenetic relatedness. Application of this method has moved beyond model organisms. It has provided a lot of potentials, in ecological research and comparative transcriptomics, in non-model organisms. This thesis presents an overview on existing applications of RNA-seq in non-model organisms. Furthermore, it presents a new clustering design on handling the data, which led to identification of twelve new fluorescent protein isoforms in corals. In addition, de novo assembly and annotation of the data from polychaete Hermodice carunculata made possible the identification of one new phylogenetic marker and eight bioluminescent protein isoforms. Also, twelve new bilirubin-induced fluorescent proteins were identified from false moray eel Kaupichthys hyproroides. This approach can be applied on any other data.
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.
Book Synopsis Transcriptome Analysis by : Miroslav Blumenberg
Download or read book Transcriptome Analysis written by Miroslav Blumenberg and published by BoD – Books on Demand. This book was released on 2019-11-20 with total page 110 pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcriptome analysis is the study of the transcriptome, of the complete set of RNA transcripts that are produced under specific circumstances, using high-throughput methods. Transcription profiling, which follows total changes in the behavior of a cell, is used throughout diverse areas of biomedical research, including diagnosis of disease, biomarker discovery, risk assessment of new drugs or environmental chemicals, etc. Transcriptome analysis is most commonly used to compare specific pairs of samples, for example, tumor tissue versus its healthy counterpart. In this volume, Dr. Pyo Hong discusses the role of long RNA sequences in transcriptome analysis, Dr. Shinichi describes the next-generation single-cell sequencing technology developed by his team, Dr. Prasanta presents transcriptome analysis applied to rice under various environmental factors, Dr. Xiangyuan addresses the reproductive systems of flowering plants and Dr. Sadovsky compares codon usage in conifers.
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.
Book Synopsis Next Generation Sequencing by : Jerzy Kulski
Download or read book Next Generation Sequencing written by Jerzy Kulski and published by BoD – Books on Demand. This book was released on 2016-01-14 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
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 Transcriptomics and Gene Regulation by : Jiaqian Wu
Download or read book Transcriptomics and Gene Regulation written by Jiaqian Wu and published by Springer. This book was released on 2015-11-17 with total page 190 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume focuses on modern computational and statistical tools for translational gene expression and regulation research to improve prognosis, diagnostics, prediction of severity, and therapies for human diseases. It introduces some of state of the art technologies as well as computational and statistical tools for translational bioinformatics in the areas of gene transcription and regulation, including the tools for next generation sequencing analyses, alternative spicing, the modeling of signaling pathways, network analyses in predicting disease genes, as well as protein and gene expression data integration in complex human diseases etc. The book is particularly useful for researchers and students in the field of molecular biology, clinical biology and bioinformatics, as well as physicians etc. Dr. Jiaqian Wu is assistant professor in the Vivian L. Smith Department of Neurosurgery and Center for Stem Cell and Regenerative Medicine, University of Texas Health Science Centre, Houston, TX, USA.
Book Synopsis Plant Long Non-Coding RNAs by : Julia A. Chekanova
Download or read book Plant Long Non-Coding RNAs written by Julia A. Chekanova and published by Humana Press. This book was released on 2019-04-20 with total page 480 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume focuses on various approaches to studying long non-coding RNAs (lncRNAs), including techniques for finding lncRNAs, localization, and observing their functions. The chapters in this book cover how to catalog lncRNAs in various plant species; determining subcellular localization; protein interactions; structures; and RNA modifications. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and innovative, Plant Long Non-Coding RNAs: Methods and Protocols is a valuable resource that aids researchers in understanding the functions of lncRNAs in different plant species, and helps them explore currently uncharted facets of plant biology.
Book Synopsis The Amaranth Genome by : Dinesh Adhikary
Download or read book The Amaranth Genome written by Dinesh Adhikary and published by Springer Nature. This book was released on 2021-06-01 with total page 181 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the development of genetic resources in amaranths, with a major focus on genomics, reverse, and forward genetics tools and strategies that have been developed for crop improvement. Amaranth is an ancient crop native to the New World. Interest in amaranths is being renewed, due to their adaptability, stress tolerance, and nutritional value. There are about 65 species in the genus, including Amaranthus caudatus L., A. cruentus L., and A. hypochondriacus L., which are primarily grown as protein-rich grains or pseudocereals. The genus also includes major noxious weeds (e.g., A. palmeri). The amaranths are within the Caryophyllales order and thus many species (e.g., A. tricolor) produce red (betacyanin) or yellow (betaxanthin) betalain pigments, which are chemically distinct from the anthocyanins responsible for red pigmentation in other plants. A. hypochondriacus, which shows disomic inheritance (2n = 32; n= 466 Mb), has been sequenced and annotated with 23,059 protein-coding genes. Additional members of the genus are now also been sequenced including weedy amaranths, other grain amaranths, and their putative progenitors.
Book Synopsis Research in Computational Molecular Biology by : Lenore J. Cowen
Download or read book Research in Computational Molecular Biology written by Lenore J. Cowen and published by Springer. This book was released on 2019-04-15 with total page 337 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the proceedings of the 23rd Annual Conference on Research in Computational Molecular Biology, RECOMB 2019, held in Washington, DC, USA, in April 2019. The 17 extended and 20 short abstracts presented were carefully reviewed and selected from 175 submissions. The short abstracts are included in the back matter of the volume. The papers report on original research in all areas of computational molecular biology and bioinformatics.
Book Synopsis The Kiwifruit Genome by : Raffaele Testolin
Download or read book The Kiwifruit Genome written by Raffaele Testolin and published by Springer. This book was released on 2016-05-02 with total page 275 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the basic botanical features of kiwifruit and its wild relatives, reports on the steps that led to its genome sequencing, and discusses the results obtained with the assembly and annotation. The core chapters provide essential insights into the main gene families that characterize this species as a crop, including the genes controlling sugar and starch metabolism, pigment biosynthesis and degradation, the ascorbic-acid pathway, fruit softening and postharvest metabolism, allergens, and resistance to pests and diseases. The book offers a valuable reference guide for taxonomists, geneticists and horticulturists. Further, since information gained from the genome sequence is extraordinarily useful in assessing the breeding value of individuals based on whole-genome scans, it will especially benefit plant breeders. Accordingly, chapters are included that focus on gene introgression from wild relatives and genome-based breeding.
Book Synopsis Bioinformatics Algorithms by : Phillip Compeau
Download or read book Bioinformatics Algorithms written by Phillip Compeau and published by . This book was released on 1986-06 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioinformatics Algorithms: an Active Learning Approach is one of the first textbooks to emerge from the recent Massive Online Open Course (MOOC) revolution. A light-hearted and analogy-filled companion to the authors' acclaimed online course (http://coursera.org/course/bioinformatics), this book presents students with a dynamic approach to learning bioinformatics. It strikes a unique balance between practical challenges in modern biology and fundamental algorithmic ideas, thus capturing the interest of students of biology and computer science students alike.Each chapter begins with a central biological question, such as "Are There Fragile Regions in the Human Genome?" or "Which DNA Patterns Play the Role of Molecular Clocks?" and then steadily develops the algorithmic sophistication required to answer this question. Hundreds of exercises are incorporated directly into the text as soon as they are needed; readers can test their knowledge through automated coding challenges on Rosalind (http://rosalind.info), an online platform for learning bioinformatics.The textbook website (http://bioinformaticsalgorithms.org) directs readers toward additional educational materials, including video lectures and PowerPoint slides.
Book Synopsis De Novo Assembly of Bacterial Transcriptomes from RNA-Seq Data by : Maidstone Maidstone Press
Download or read book De Novo Assembly of Bacterial Transcriptomes from RNA-Seq Data written by Maidstone Maidstone Press and published by . This book was released on 2016-01-26 with total page 38 pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcriptome assays are increasingly being performed by high-throughput RNA sequencing (RNA-seq). For organisms whose genomes have not been sequenced and annotated, transcriptomes must be assembled de novo from the RNA-seq data. Here, we present novel algorithms, specific to bacterial gene structures and transcriptomes, for analysis of bacterial RNA-seq data and de novo transcriptome assembly. The algorithms are implemented in an open source software system called Rockhopper 2. We find that Rockhopper 2 outperforms other de novo transcriptome assemblers and offers accurate and efficient analysis of bacterial RNA-seq data. Rockhopper 2 is available at http://cs.wellesley.edu/~btjaden/Rockhopper.
Book Synopsis Lipids and Essential Oils as Antimicrobial Agents by : Halldor Thormar
Download or read book Lipids and Essential Oils as Antimicrobial Agents written by Halldor Thormar and published by John Wiley & Sons. This book was released on 2010-12-28 with total page 341 pages. Available in PDF, EPUB and Kindle. Book excerpt: Lipids and essential oils have strong antimicrobial properties — they kill or inhibit the growth of microbes such as bacteria, fungi, or viruses. They are being studied for use in the prevention and treatment of infections, as potential disinfectants, and for their preservative and antimicrobial properties when formulated as pharmaceuticals, in food products, and in cosmetics. Lipids and Essential Oils as Antimicrobial Agents is a comprehensive review of the scientific knowledge in this field. International experts provide summaries on: the chemical and biological properties of lipids and essential oils use of lipids and essential oils in pharmaceuticals, cosmetics and health foods antimicrobial effects of lipids in vivo and in vitro antimicrobial lipids in milk antimicrobial lipids of the skin antibacterial lipids as sanitizers and disinfectants antibacterial, antifungal, and antiviral activities of essential oils antimicrobial lipids in milk antimicrobial lipids of the skin antibacterial lipids as sanitizers and disinfectants antibacterial, antifungal, and antiviral activities of essential oils Lipids and Essential Oils as Antimicrobial Agents is an essential guide to this important topic for researchers and advanced students in academia and research working in pharmaceutical, cosmetic and food sciences, biochemistry and natural products chemistry, microbiology; and for health care scientists and professionals working in the fields of public health and infectious diseases. It will also be of interest to anyone concerned about health issues and particularly to those who are conscious of the benefits of health food and natural products.
Book Synopsis RNA-Seq Analysis: Methods, Applications and Challenges by : Filippo Geraci
Download or read book RNA-Seq Analysis: Methods, Applications and Challenges written by Filippo Geraci and published by Frontiers Media SA. This book was released on 2020-06-08 with total page 169 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Encyclopedia of Modern Coral Reefs by : David Hopley
Download or read book Encyclopedia of Modern Coral Reefs written by David Hopley and published by Springer Science & Business Media. This book was released on 2010-11-26 with total page 1226 pages. Available in PDF, EPUB and Kindle. Book excerpt: Coral reefs are the largest landforms built by plants and animals. Their study therefore incorporates a wide range of disciplines. This encyclopedia approaches coral reefs from an earth science perspective, concentrating especially on modern reefs. Currently coral reefs are under high stress, most prominently from climate change with changes to water temperature, sea level and ocean acidification particularly damaging. Modern reefs have evolved through the massive environmental changes of the Quaternary with long periods of exposure during glacially lowered sea level periods and short periods of interglacial growth. The entries in this encyclopedia condense the large amount of work carried out since Charles Darwin first attempted to understand reef evolution. Leading authorities from many countries have contributed to the entries covering areas of geology, geography and ecology, providing comprehensive access to the most up-to-date research on the structure, form and processes operating on Quaternary coral reefs.
Book Synopsis Phylogeny and Evolution of the Mollusca by : Winston Ponder
Download or read book Phylogeny and Evolution of the Mollusca written by Winston Ponder and published by Univ of California Press. This book was released on 2008-03-25 with total page 496 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Ponder and Lindberg provides a breathtaking overview of the evolutionary history of the Mollusca, effectively melding information from anatomy, ecology, genomics, and paleobiology to explore the depths of molluscan phylogeny. Its outstanding success is due to thoughtful planning, focused complementary contributions from 36 expert authors, and careful editing. This volume is a must for malacologists."—Bruce Runnegar, Department of Earth and Space Sciences, University of California, Los Angeles "Our understanding of the phylogeny and evolutionary history of the mollusca has been revolutionized over the past two decades through new molecular data and analysis, and reinvestigation of morphological characters. In this volume Ponder, Lindberg, and their colleagues do a wonderful job of integrating this work to provide new perspectives on the relationships of the major molluscan clades, their evolutionary dynamics, and their history. Particularly timely is the coverage of molluscan evo-devo and genomics."—Douglas H. Erwin, Curator of Paleozoic Invertebrates, National Museum of Natural History
