RSEM: Accurate Transcript Quantification from RNA-Seq Data with Or Without a Reference Genome PDF Download
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Author: Applied Research Applied Research Press
Publisher:
ISBN: 9781517392185
Category :
Languages : en
Pages : 44
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Book Description
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.
Author: Applied Research Applied Research Press
Publisher:
ISBN: 9781517392185
Category :
Languages : en
Pages : 44
Get Book Here
Book Description
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.
Author: Fabio Marchi
Publisher: BoD – Books on Demand
ISBN: 9535135031
Category : Medical
Languages : en
Pages : 330
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Book Description
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.
Author: Ion Mandoiu
Publisher: John Wiley & Sons
ISBN: 1118169484
Category : Computers
Languages : en
Pages : 460
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Book Description
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: Mourad Elloumi
Publisher: John Wiley & Sons
ISBN: 1118853725
Category : Computers
Languages : en
Pages : 1126
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Book Description
The first comprehensive overview of preprocessing, mining, and postprocessing of biological data Molecular biology is undergoing exponential growth in both the volume and complexity of biological data and knowledge discovery offers the capacity to automate complex search and data analysis tasks. This book presents a vast overview of the most recent developments on techniques and approaches in the field of biological knowledge discovery and data mining (KDD) providing in-depth fundamental and technical field information on the most important topics encountered. Written by top experts, Biological Knowledge Discovery Handbook: Preprocessing, Mining, and Postprocessing of Biological Data covers the three main phases of knowledge discovery (data preprocessing, data processing also known as data mining and data postprocessing) and analyzes both verification systems and discovery systems. BIOLOGICAL DATA PREPROCESSING Part A: Biological Data Management Part B: Biological Data Modeling Part C: Biological Feature Extraction Part D Biological Feature Selection BIOLOGICAL DATA MINING Part E: Regression Analysis of Biological Data Part F Biological Data Clustering Part G: Biological Data Classification Part H: Association Rules Learning from Biological Data Part I: Text Mining and Application to Biological Data Part J: High-Performance Computing for Biological Data Mining Combining sound theory with practical applications in molecular biology, Biological Knowledge Discovery Handbook is ideal for courses in bioinformatics and biological KDD as well as for practitioners and professional researchers in computer science, life science, and mathematics.
Author: Pawan Raghav
Publisher: Elsevier
ISBN: 0443132216
Category : Science
Languages : en
Pages : 568
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Book Description
Computational Biology for Stem Cell Research is an invaluable guide for researchers as they explore HSCs and MSCs in computational biology. With the growing advancement of technology in the field of biomedical sciences, computational approaches have reduced the financial and experimental burden of the experimental process. In the shortest span, it has established itself as an integral component of any biological research activity. HSC informatics (in silico) techniques such as machine learning, genome network analysis, data mining, complex genome structures, docking, system biology, mathematical modeling, programming (R, Python, Perl, etc.) help to analyze, visualize, network constructions, and protein-ligand or protein-protein interactions. This book is aimed at beginners with an exact correlation between the biomedical sciences and in silico computational methods for HSCs transplantation and translational research and provides insights into methods targeting HSCs properties like proliferation, self-renewal, differentiation, and apoptosis. - Modeling Stem Cell Behavior: Explore stem cell behavior through animal models, bridging laboratory studies to real-world clinical allogeneic HSC transplantation (HSCT) scenarios. - Bioinformatics-Driven Translational Research: Navigate a path from bench to bedside with cutting-edge bioinformatics approaches, translating computational insights into tangible advancements in stem cell research and medical applications. - Interdisciplinary Resource: Discover a single comprehensive resource catering to biomedical sciences, life sciences, and chemistry fields, offering essential insights into computational tools vital for modern research.
Author: Ibrokhim Y. Abdurakhmonov
Publisher: BoD – Books on Demand
ISBN: 1789232686
Category : Medical
Languages : en
Pages : 190
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Book Description
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.
Author: Fumiaki Uchiumi
Publisher: BoD – Books on Demand
ISBN: 1803556218
Category : Medical
Languages : en
Pages : 214
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Book Description
Gene expression is dependent on multiple steps, including transcription, RNA processing, and translation. Importantly, recent studies revealed that gene expression is regulated by chromatin structures and non-coding RNA profiles. Elucidating the molecular mechanisms may contribute to the development of novel therapeutics for aging-related diseases, including cancer and neurodegenerative diseases. This book provides a comprehensive overview of gene expression and its role in human disease. It consists of nine chapters organized into two sections on molecular mechanisms in controlling gene expression and the relationships between transcriptional control and human disease.
Author: Sajal Ray
Publisher: BoD – Books on Demand
ISBN: 9535133055
Category : Science
Languages : en
Pages : 244
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Book Description
The book with two sections represents the current trend of research in basic and applied malacology. In the section "Organismal Malacology", high-impact articles were contributed in the frontier areas of taxonomy, ecology and aquaculture of molluscs. Importance of mussel in water quality monitoring was highlighted. Biology and conservation of keystone molluscs were discussed from organismal point of view. "Cellular and Molecular Biology" section contains informative chapters on toxin-induced differential gene expression, spatiotemporal neural activity in olfactory processing in slug and immunity of hydrothermal vent molluscs. Biochemistry of cellulose degradation, lipid profile and C-reactive protein were elucidated in detail in separate chapters. This book represents a rich source of malacological information for the scientists, teachers and students.
Author: Joong Hyoun Chin
Publisher: MDPI
ISBN: 3036509763
Category : Medical
Languages : en
Pages : 314
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Book Description
To meet the global food demand of an increasing population, food production has to be increased by 60% by 2050. The main production constraints, such as climate change, biotic stresses, abiotic stresses, soil nutrition deficiency problems, problematic soils, etc., have to be addressed on an urgent basis. More than 50% of human calories are from three major cereals: rice, wheat, and maize. The harnessing of genetic diversity by novel allele mining assisted by recent advances in biotechnological and bioinformatics tools will enhance the utilization of the hidden treasures in the gene bank. Technological advances in plant breeding will provide some solutions for the biofortification, stress resistance, yield potential, and quality improvement in staple crops. The elucidation of the genetic, physiological, and molecular basis of useful traits and the improvement of the improved donors containing multiple traits are key activities for variety development. High-throughput genotyping systems assisted by bioinformatics and data science provide efficient and easy tools for geneticists and breeders. Recently, new breeding techniques applied in some food crops have become game-changers in the global food crop market. With this background, we invited 18 eminent researchers working on food crops from across the world to contribute their high-quality original research manuscripts. The research studies covered modern food crop genetics and breeding: plant molecular systems focusing to food crops; plant genetic diversity—QTL and gene identification utilizing high-throughput genotyping systems and their validation; new breeding techniques in food crops—targeted mutagenesis, genome editing, etc.; abiotic and biotic stresses—QTL/gene identification and their molecular physiology; plant nutrition, grain quality improvement, and yield enhancement.
Author: Zhanjiang (John) Liu
Publisher: John Wiley & Sons
ISBN: 1118782356
Category : Science
Languages : en
Pages : 605
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Book Description
Bioinformatics derives knowledge from computer analysis of biological data. In particular, genomic and transcriptomic datasets are processed, analysed and, whenever possible, associated with experimental results from various sources, to draw structural, organizational, and functional information relevant to biology. Research in bioinformatics includes method development for storage, retrieval, and analysis of the data. Bioinformatics in Aquaculture provides the most up to date reviews of next generation sequencing technologies, their applications in aquaculture, and principles and methodologies for the analysis of genomic and transcriptomic large datasets using bioinformatic methods, algorithm, and databases. The book is unique in providing guidance for the best software packages suitable for various analysis, providing detailed examples of using bioinformatic software and command lines in the context of real world experiments. This book is a vital tool for all those working in genomics, molecular biology, biochemistry and genetics related to aquaculture, and computational and biological sciences.
