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Rsem Accurate Transcript Quantification From Rna Seq Data With Or Without A Reference Genome
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Book Synopsis RSEM: Accurate Transcript Quantification from RNA-Seq Data with Or Without a Reference Genome by : Applied Research Applied Research Press
Download or read book RSEM: Accurate Transcript Quantification from RNA-Seq Data with Or Without a Reference Genome written by Applied Research Applied Research Press and published by . This book was released on 2015-09-16 with total page 44 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms. This issue is particularly important for quantification with de novo transcriptome assemblies in the absence of sequenced genomes, as it is difficult to determine which transcripts are isoforms of the same gene. A second significant issue is the design of RNA-Seq experiments, in terms of the number of reads, read length, and whether reads come from one or both ends of cDNA fragments. RSEM is an accurate and user-friendly software tool for quantifying transcript abundances from RNA-Seq data. As it does not rely on the existence of a reference genome, it is particularly useful for quantification with de novo transcriptome assemblies. In addition, RSEM has enabled valuable guidance for cost-efficient design of quantification experiments with RNA-Seq, which is currently relatively expensive.
Download or read book Bioinformatics written by Yu Liu and published by CRC Press. This book was released on 2014-02-24 with total page 412 pages. Available in PDF, EPUB and Kindle. Book excerpt: This title includes a number of Open Access chapters. The book introduces bioinformatic and statistical methodology and shows approaches to bias correction and error estimation. It also presents quantitative methods for genome and proteome analysis.
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 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 464 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 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 Fungal Biotechnology for Biofuel Production by : Roberto Nascimento Silva
Download or read book Fungal Biotechnology for Biofuel Production written by Roberto Nascimento Silva and published by Bentham Science Publishers. This book was released on 2016-01-25 with total page 440 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mycology: Current and Future Developments is a book series that brings together the latest contributions to research on the biology, genetics, and industrial use of fungi. Each book chapter is written by academic / professional experts from around the world. The book series is of interest to mycologists and allied researchers seeking to gain new knowledge perspectives about fungi. This volume of the book series focuses chiefly on advances biofuel production. Topics covered in this volume include an overview of biofuel production, the use of lignocelluloses in fungal biofuel production, fungal metabolic engineering, biomass pretreatment for biofuel refineries, and more. The volume also contains chapters about research on other fungi such as S. Cerevisiae. The reviews presented in this volume serve as a useful reference for researchers and readers interested in learning about new developments in biofuel production at a time when the need for alternative energy sources is ever increasing.
Book Synopsis Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing by : Ana M. Aransay
Download or read book Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing written by Ana M. Aransay and published by Springer. This book was released on 2016-06-02 with total page 399 pages. Available in PDF, EPUB and Kindle. Book excerpt: High throughput sequencing (HTS) technologies have conquered the genomics and epigenomics worlds. The applications of HTS methods are wide, and can be used to sequence everything from whole or partial genomes, transcriptomes, non-coding RNAs, ribosome profiling, to single-cell sequencing. Having such diversity of alternatives, there is a demand for information by research scientists without experience in HTS that need to choose the most suitable methodology or combination of platforms and to define their experimental designs to achieve their specific objectives. Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing aims to collect in a single volume all aspects that should be taken into account when HTS technologies are being incorporated into a research project and the reasons behind them. Moreover, examples of several successful strategies will be analyzed to make the point of the crucial features. This book will be of use to all scientist that are unfamiliar with HTS and want to incorporate such technologies to their research.
Book Synopsis Next-Generation Sequencing Data Analysis by : Xinkun Wang
Download or read book Next-Generation Sequencing Data Analysis written by Xinkun Wang and published by CRC Press. This book was released on 2023-07-06 with total page 435 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA-seq: both bulk and single-cell (separate chapters) Genotyping and variant discovery through whole genome/exome sequencing Clinical sequencing and detection of actionable variants De novo genome assembly ChIP-seq to map protein-DNA interactions Epigenomics through DNA methylation sequencing Metagenome sequencing for microbiome analysis
Book Synopsis Data Analysis for Omic Sciences: Methods and Applications by :
Download or read book Data Analysis for Omic Sciences: Methods and Applications written by and published by Elsevier. This book was released on 2018-09-22 with total page 730 pages. Available in PDF, EPUB and Kindle. Book excerpt: Data Analysis for Omic Sciences: Methods and Applications, Volume 82, shows how these types of challenging datasets can be analyzed. Examples of applications in real environmental, clinical and food analysis cases help readers disseminate these approaches. Chapters of note include an Introduction to Data Analysis Relevance in the Omics Era, Omics Experimental Design and Data Acquisition, Microarrays Data, Analysis of High-Throughput RNA Sequencing Data, Analysis of High-Throughput DNA Bisulfite Sequencing Data, Data Quality Assessment in Untargeted LC-MS Metabolomic, Data Normalization and Scaling, Metabolomics Data Preprocessing, and more. Presents the best reference book for omics data analysis Provides a review of the latest trends in transcriptomics and metabolomics data analysis tools Includes examples of applications in research fields, such as environmental, biomedical and food analysis
Book Synopsis Statistical Analysis of Next Generation Sequencing Data by : Somnath Datta
Download or read book Statistical Analysis of Next Generation Sequencing Data written by Somnath Datta and published by Springer. This book was released on 2014-07-03 with total page 438 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Applications of RNA-Seq in Biology and Medicine by : Irina Vlasova-St. Louis
Download or read book Applications of RNA-Seq in Biology and Medicine written by Irina Vlasova-St. Louis and published by BoD – Books on Demand. This book was released on 2021-10-13 with total page 144 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book evaluates and comprehensively summarizes the scientific findings that have been achieved through RNA-sequencing (RNA-Seq) technology. RNA-Seq transcriptome profiling of healthy and diseased tissues allows FOR understanding the alterations in cellular phenotypes through the expression of differentially spliced RNA isoforms. Assessment of gene expression by RNA-Seq provides new insight into host response to pathogens, drugs, allergens, and other environmental triggers. RNA-Seq allows us to accurately capture all subtypes of RNA molecules, in any sequenced organism or single-cell type, under different experimental conditions. Merging genomics and transcriptomic profiling provides novel information underlying causative DNA mutations. Combining RNA-Seq with immunoprecipitation and cross-linking techniques is a clever multi-omics strategy assessing transcriptional, post-transcriptional and post-translational levels of gene expression regulation.
Book Synopsis Genetics and Genomics of Eye Disease by : Xiaoyi Raymond Gao
Download or read book Genetics and Genomics of Eye Disease written by Xiaoyi Raymond Gao and published by Academic Press. This book was released on 2019-09-12 with total page 383 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genetics and Genomics of Eye Disease: Advancing to Precision Medicine thoroughly examines the latest genomics methods for studying eye disease, including complex eye disorders associated with multiple genes. GWAS, WES, WGS, RNA-sequencing, and transcriptome analysis as employed in ocular genomics are discussed in-depth, as are genomics findings tied to early-onset glaucoma, strabismus, age-related macular degeneration, adult-onset glaucoma, diabetic retinopathy, keratoconus, and leber congenital amaurosis, among other diseases. Research and clinical specialists offer guidance on conducting preventative screenings and counseling patients, as well as the promise of machine learning, computational statistics and artificial intelligence in advancing ocular genomics research. Offers thorough guidance on conducting genetic and genomic studies of eye disease Examines the genetic basis of a wide range of complex eye diseases and single-gene and Mendelian disorders Discusses the application of genetic testing and genetic risk prediction in eye disease diagnosis and patient counseling
Book Synopsis Bioinformatics Research and Applications by : Mitra Basu
Download or read book Bioinformatics Research and Applications written by Mitra Basu and published by Springer. This book was released on 2014-06-23 with total page 424 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 10th International Symposium on Bioinformatics Research and Applications, ISBRA 2014, held in Zhangjiajie, China, in June 2014. The 33 revised full papers and 31 one-page abstracts included in this volume were carefully reviewed and selected from 119 submissions. The papers cover a wide range of topics in bioinformatics and computational biology and their applications including the development of experimental or commercial systems.
Book Synopsis Sustainable Agriculture by : Javid Ahmad Parray
Download or read book Sustainable Agriculture written by Javid Ahmad Parray and published by Academic Press. This book was released on 2019-11-21 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt: Sustainable Agriculture: Advances in Plant Metabolome and Microbiome focuses on the advancement of basic and applied research related to plant-microbe interaction and their implementation in progressive agricultural sustainability. The book also highlights the developing area of bioinformatics tools for the interpretation of metabolome, the integration of statistical and bioinformatics tools to manage huge generating data, metabolite profiling, and key signaling-driven substances, along with a section on the role of key biosynthetic pathways. Focused on selecting positive and effective interactive core-microbiome which will be adaptive and sustainable, this book will help researchers further improve the quality and productivity of crops through sustainable agriculture. Details the two-way interactive approach to both plants and microbes Describes setting up core and functional microbiomes Presents the relationship of metabolomics and biocontrol
Book Synopsis Enhanced biological mechanism study, drug discovery and individualized medicine with single-cell multiomics data and integrative analysis by : Panwen Wang
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:
Book Synopsis Pan-Genome Level Genotype and Phenotype Prediction: Advances in Precision Agriculture by : Penghao Wang
Download or read book Pan-Genome Level Genotype and Phenotype Prediction: Advances in Precision Agriculture written by Penghao Wang and published by Frontiers Media SA. This book was released on 2021-11-26 with total page 187 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Mycoviruses written by Ioly Kotta-Loizou and published by MDPI. This book was released on 2019-06-21 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt: A virus (from the Latin word ‘vīrus’ meaning ‘venom’ or ‘poison’) is a microorganism invisible to the naked eye. Viruses can multiply exclusively by entering a cell and using the cell’s resources to create copies of themselves. As the origin of their name suggests, viruses are generally considered dangerous, harmful and often deadly. Some of the most well-studied and widely known viruses, such as HIV and influenza, infect humans. However, viruses can also infect animals, plants and microorganisms, including fungi. Many fungi are medically, ecologically and economically significant, for example, causing diseases to humans, plants and insects or being used in industry to produce bread, cheese, beer and wine. Viruses that infect fungi are called mycoviruses (from the Greek work ‘myco’, meaning ‘fungus’). Mycoviruses do not cause harm to or kill the infected fungus; in contrast, they are ‘friendly’ viruses and we can utilize them to control the growth, pathogenicity and toxin production of fungi. This book describes a range of different mycoviruses and their geographical distribution, transmission and evolution, together with their effects on the fungal hosts and how these are brought about.]
