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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.
Book Synopsis Computational Analysis of RNA-Seq Data in the Absence of a Known Genome by :
Download or read book Computational Analysis of RNA-Seq Data in the Absence of a Known Genome written by and published by . This book was released on 2013 with total page 108 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA0́3Seq technology has revolutionized the way we study transcriptomes. In particular, it has enabled us to investigate the transcriptomes of species that have not yet had their genomes sequenced. This thesis focuses on two computational tasks that are crucial to analyzing RNA0́3Seq data in the absence of a sequenced genome: transcript quantification and de novo transcriptome assembly evaluation. For transcript quantification, RNA0́3Seq is considered a more accurate replacement for microarrays. However, to allow for the highest accuracy, methods for analyzing RNA0́3Seq data must address the challenge of handling reads that map to multiple genes or isoforms. We present RSEM, a generative statistical model of the sequencing process and associated inference methods, which tackles this challenge in a principled manner. Our results on both simulated and real data sets suggest that RSEM has superior or comparable performance to other quantification methods developed at the same time. To facilitate the usage of our method, we implement RSEM as a robust and user0́3friendly software package for quantifying gene and isoform abundances from single0́3end or paired0́3end RNA0́3Seq data. RSEM outputs abundance estimates, 95% credibility intervals, and visualization files and can also simulate RNA0́3Seq data. In contrast to other existing tools, the software does not require a reference genome. Thus, in combination with a de novo transcriptome assembler, RSEM enables accurate transcript quantification for species without sequenced genomes. Building off of RSEM, we have developed a novel probabilistic model based method, RSEM0́3EVAL, for evaluating de novo transcriptome assemblies from RNA0́3Seq data without the ground truth. Our RSEM0́3EVAL score has a broad range of potential applications, such as selecting assemblers, optimizing parameters for an assembler and guiding new assembler design. Results on both simulated and real data sets show that the RSEM0́3EVAL score correctly reflects the accuracies of the assemblies. To demonstrate its usage, we assembled the transcriptome of the regenerating axolotl limb by selecting among over 100 candidate assemblies based on their RSEM0́3EVAL scores.
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 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 Genomics and Bioinformatics by : Tore Samuelsson
Download or read book Genomics and Bioinformatics written by Tore Samuelsson and published by Cambridge University Press. This book was released on 2012-06-07 with total page 357 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the arrival of genomics and genome sequencing projects, biology has been transformed into an incredibly data-rich science. The vast amount of information generated has made computational analysis critical and has increased demand for skilled bioinformaticians. Designed for biologists without previous programming experience, this textbook provides a hands-on introduction to Unix, Perl and other tools used in sequence bioinformatics. Relevant biological topics are used throughout the book and are combined with practical bioinformatics examples, leading students through the process from biological problem to computational solution. All of the Perl scripts, sequence and database files used in the book are available for download at the accompanying website, allowing the reader to easily follow each example using their own computer. Programming examples are kept at an introductory level, avoiding complex mathematics that students often find daunting. The book demonstrates that even simple programs can provide powerful solutions to many complex bioinformatics problems.
Book Synopsis RNA-seq Data Analysis by : Eija Korpelainen
Download or read book RNA-seq Data Analysis written by Eija Korpelainen and published by CRC Press. This book was released on 2014-09-19 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: The State of the Art in Transcriptome AnalysisRNA sequencing (RNA-seq) data offers unprecedented information about the transcriptome, but harnessing this information with bioinformatics tools is typically a bottleneck. RNA-seq Data Analysis: A Practical Approach enables researchers to examine differential expression at gene, exon, and transcript le
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 2016-10-03 with total page 460 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 Insect Olfactory Proteins (From Gene Identification to Functional Characterization), Volume II by : Peng He
Download or read book Insect Olfactory Proteins (From Gene Identification to Functional Characterization), Volume II written by Peng He and published by Frontiers Media SA. This book was released on 2022-03-21 with total page 233 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Omics Technologies for Sustainable Agriculture and Global Food Security Volume 1 by : Anirudh Kumar
Download or read book Omics Technologies for Sustainable Agriculture and Global Food Security Volume 1 written by Anirudh Kumar and published by Springer Nature. This book was released on 2021-05-13 with total page 297 pages. Available in PDF, EPUB and Kindle. Book excerpt: Increasing world population, unpredictable climate and various kind of biotic and abiotic stresses necessitate the sustainable increase in crop production through developing improved cultivars possessing enhanced genetic resilience against all odds. An exploration of these challenges and near possible solution to improve yield is addressed in this book. It comprehensively and coherently reviews the application of various aspect of rapidly growing omics technology including genomics, proteomics, transcriptomics and metabolomics for crop development. It provides detailed examination of how omics can help crop science and introduces the benefits of using these technologies to enhance crop production, resistance and other values. It also provides platform to ponder upon the integrative approach of omics to deal with complex biological problems. The book highlights crop improvement such as yield enhancement, biotic and abiotic resistance, genetic modification, bioremediation, food security etc. It explores how the different omics technology independently and collectively would be used to improve the quantitative and qualitative traits of crop plants. The book is useful for graduate and post-graduate students of life science including researchers who are keen to know about the application of omics technologies in the different area of plant science. This book is also an asset to the modern plant breeders, and agriculture biotechnologist.
Book Synopsis Computational Mathematics Modeling in Cancer Analysis by : Wenjian Qin
Download or read book Computational Mathematics Modeling in Cancer Analysis written by Wenjian Qin and published by Springer Nature. This book was released on 2022-09-22 with total page 171 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the proceedings of the First Workshop on Computational Mathematics Modeling in Cancer Analysis (CMMCA2022), held in conjunction with MICCAI 2022, in Singapore in September 2022. Due to the COVID-19 pandemic restrictions, the CMMCA2022 was held virtually. DALI 2022 accepted 15 papers from the 16 submissions that were reviewed. A major focus of CMMCA2022 is to identify new cutting-edge techniques and their applications in cancer data analysis in response to trends and challenges in theoretical, computational and applied aspects of mathematics in cancer data analysis.
Book Synopsis Transcriptome Profiling by : Mohammad Ajmal Ali
Download or read book Transcriptome Profiling written by Mohammad Ajmal Ali and published by Elsevier. This book was released on 2022-10-07 with total page 530 pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcriptome Profiling: Progress and Prospects assists readers in assessing and interpreting a large number of genes, up to and including an entire genome. It provides key insights into the latest tools and techniques used in transcriptomics and its relevant topics which can reveal a global snapshot of the complete RNA component of a cell at a given time. This snapshot, in turn, enables the distinction between different cell types, different disease states, and different time points during development. Transcriptome analysis has been a key area of biological inquiry for decades. The next-generation sequencing technologies have revolutionized transcriptomics by providing opportunities for multidimensional examinations of cellular transcriptomes in which high-throughput expression data are obtained at a single-base resolution. Transcriptome analysis has evolved from the detection of single RNA molecules to large-scale gene expression profiling and genome annotation initiatives. Written by a team of global experts, key topics in Transcriptome Profiling include transcriptome characterization, expression analysis of transcripts, transcriptome and gene regulation, transcriptome profiling and human health, medicinal plants transcriptomics, transcriptomics and genetic engineering, transcriptomics in agriculture, and phylotranscriptomics. Presents recent development in the tools and techniques in transcriptomic characterization Integrates expression analysis of transcripts and gene regulation Includes the application of transcriptomics in human health, genetic engineering and agriculture
Book Synopsis Integrative Omics by : Manish Kumar Gupta
Download or read book Integrative Omics written by Manish Kumar Gupta and published by Elsevier. This book was released on 2024-05-10 with total page 434 pages. Available in PDF, EPUB and Kindle. Book excerpt: Integrative Omics: Concepts, Methodology and Applications provides a holistic and integrated view of defining and applying network approaches, integrative tools, and methods to solve problems for the rationalization of genotype to phenotype relationships. The reference includes a range of chapters in a systemic ‘step by step’ manner, which begins with the basic concepts from Omic to Multi Integrative Omics approaches, followed by their full range of approaches, applications, emerging trends, and future trends. All key areas of Omics are covered including biological databases, sequence alignment, pharmacogenomics, nutrigenomics and microbial omics, integrated omics for Food Science and Identification of genes associated with disease, clinical data integration and data warehousing, translational omics as well as omics technology policy and society research. Integrative Omics: Concepts, Methodology and Applications highlights the recent concepts, methodologies, advancements in technologies and is also well-suited for researchers from both academic and industry background, undergraduate and graduate students who are mainly working in the area of computational systems biology, integrative omics and translational science. The book bridges the gap between biological sciences, physical sciences, computer science, statistics, data science, information technology and mathematics by presenting content specifically dedicated to mathematical models of biological systems. Provides a holistic, integrated view of a defining and applying network approach, integrative tools, and methods to solve problems for rationalization of genotype to phenotype relationships Offers an interdisciplinary approach to Databases, data analytics techniques, biological tools, network construction, analysis, modeling, prediction and simulation of biological systems leading to ‘translational research’, i.e., drug discovery, drug target prediction, and precision medicine Covers worldwide methods, concepts, databases, and tools used in the construction of integrated pathways
Book Synopsis Applying Big Data Analytics in Bioinformatics and Medicine by : Lytras, Miltiadis D.
Download or read book Applying Big Data Analytics in Bioinformatics and Medicine written by Lytras, Miltiadis D. and published by IGI Global. This book was released on 2017-06-16 with total page 492 pages. Available in PDF, EPUB and Kindle. Book excerpt: Many aspects of modern life have become personalized, yet healthcare practices have been lagging behind in this trend. It is now becoming more common to use big data analysis to improve current healthcare and medicinal systems, and offer better health services to all citizens. Applying Big Data Analytics in Bioinformatics and Medicine is a comprehensive reference source that overviews the current state of medical treatments and systems and offers emerging solutions for a more personalized approach to the healthcare field. Featuring coverage on relevant topics that include smart data, proteomics, medical data storage, and drug design, this publication is an ideal resource for medical professionals, healthcare practitioners, academicians, and researchers interested in the latest trends and techniques in personalized medicine.
Book Synopsis Gene Expression by : Fumiaki Uchiumi
Download or read book Gene Expression written by Fumiaki Uchiumi and published by BoD – Books on Demand. This book was released on 2022-10-05 with total page 214 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Bioinformatics in Aquaculture by : Zhanjiang (John) Liu
Download or read book Bioinformatics in Aquaculture written by Zhanjiang (John) Liu and published by John Wiley & Sons. This book was released on 2017-01-24 with total page 587 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Introduction to Single Cell Omics by : Xinghua Pan
Download or read book Introduction to Single Cell Omics written by Xinghua Pan and published by Frontiers Media SA. This book was released on 2019-09-19 with total page 129 pages. Available in PDF, EPUB and Kindle. Book excerpt: Single-cell omics is a progressing frontier that stems from the sequencing of the human genome and the development of omics technologies, particularly genomics, transcriptomics, epigenomics and proteomics, but the sensitivity is now improved to single-cell level. The new generation of methodologies, especially the next generation sequencing (NGS) technology, plays a leading role in genomics related fields; however, the conventional techniques of omics require number of cells to be large, usually on the order of millions of cells, which is hardly accessible in some cases. More importantly, harnessing the power of omics technologies and applying those at the single-cell level are crucial since every cell is specific and unique, and almost every cell population in every systems, derived in either vivo or in vitro, is heterogeneous. Deciphering the heterogeneity of the cell population hence becomes critical for recognizing the mechanism and significance of the system. However, without an extensive examination of individual cells, a massive analysis of cell population would only give an average output of the cells, but neglect the differences among cells. Single-cell omics seeks to study a number of individual cells in parallel for their different dimensions of molecular profile on genome-wide scale, providing unprecedented resolution for the interpretation of both the structure and function of an organ, tissue or other system, as well as the interaction (and communication) and dynamics of single cells or subpopulations of cells and their lineages. Importantly single-cell omics enables the identification of a minor subpopulation of cells that may play a critical role in biological process over a dominant subpolulation such as a cancer and a developing organ. It provides an ultra-sensitive tool for us to clarify specific molecular mechanisms and pathways and reveal the nature of cell heterogeneity. Besides, it also empowers the clinical investigation of patients when facing a very low quantity of cell available for analysis, such as noninvasive cancer screening with circulating tumor cells (CTC), noninvasive prenatal diagnostics (NIPD) and preimplantation genetic test (PGT) for in vitro fertilization. Single-cell omics greatly promotes the understanding of life at a more fundamental level, bring vast applications in medicine. Accordingly, single-cell omics is also called as single-cell analysis or single-cell biology. Within only a couple of years, single-cell omics, especially transcriptomic sequencing (scRNA-seq), whole genome and exome sequencing (scWGS, scWES), has become robust and broadly accessible. Besides the existing technologies, recently, multiplexing barcode design and combinatorial indexing technology, in combination with microfluidic platform exampled by Drop-seq, or even being independent of microfluidic platform but using a regular PCR-plate, enable us a greater capacity of single cell analysis, switching from one single cell to thousands of single cells in a single test. The unique molecular identifiers (UMIs) allow the amplification bias among the original molecules to be corrected faithfully, resulting in a reliable quantitative measurement of omics in single cells. Of late, a variety of single-cell epigenomics analyses are becoming sophisticated, particularly single cell chromatin accessibility (scATAC-seq) and CpG methylation profiling (scBS-seq, scRRBS-seq). High resolution single molecular Fluorescence in situ hybridization (smFISH) and its revolutionary versions (ex. seqFISH, MERFISH, and so on), in addition to the spatial transcriptome sequencing, make the native relationship of the individual cells of a tissue to be in 3D or 4D format visually and quantitatively clarified. On the other hand, CRISPR/cas9 editing-based In vivo lineage tracing methods enable dynamic profile of a whole developmental process to be accurately displayed. Multi-omics analysis facilitates the study of multi-dimensional regulation and relationship of different elements of the central dogma in a single cell, as well as permitting a clear dissection of the complicated omics heterogeneity of a system. Last but not the least, the technology, biological noise, sequence dropout, and batch effect bring a huge challenge to the bioinformatics of single cell omics. While significant progress in the data analysis has been made since then, revolutionary theory and algorithm logics for single cell omics are expected. Indeed, single-cell analysis exert considerable impacts on the fields of biological studies, particularly cancers, neuron and neural system, stem cells, embryo development and immune system; other than that, it also tremendously motivates pharmaceutic RD, clinical diagnosis and monitoring, as well as precision medicine. This book hereby summarizes the recent developments and general considerations of single-cell analysis, with a detailed presentation on selected technologies and applications. Starting with the experimental design on single-cell omics, the book then emphasizes the consideration on heterogeneity of cancer and other systems. It also gives an introduction of the basic methods and key facts for bioinformatics analysis. Secondary, this book provides a summary of two types of popular technologies, the fundamental tools on single-cell isolation, and the developments of single cell multi-omics, followed by descriptions of FISH technologies, though other popular technologies are not covered here due to the fact that they are intensively described here and there recently. Finally, the book illustrates an elastomer-based integrated fluidic circuit that allows a connection between single cell functional studies combining stimulation, response, imaging and measurement, and corresponding single cell sequencing. This is a model system for single cell functional genomics. In addition, it reports a pipeline for single-cell proteomics with an analysis of the early development of Xenopus embryo, a single-cell qRT-PCR application that defined the subpopulations related to cell cycling, and a new method for synergistic assembly of single cell genome with sequencing of amplification product by phi29 DNA polymerase. Due to the tremendous progresses of single-cell omics in recent years, the topics covered here are incomplete, but each individual topic is excellently addressed, significantly interesting and beneficial to scientists working in or affiliated with this field.
Book Synopsis Dinophysis Toxins: Distribution, Fate in Shellfish and Impacts by : Beatriz Reguera
Download or read book Dinophysis Toxins: Distribution, Fate in Shellfish and Impacts written by Beatriz Reguera and published by MDPI. This book was released on 2019-10-01 with total page 374 pages. Available in PDF, EPUB and Kindle. Book excerpt: Several species of Dinophysis produce one or two groups of lipophilic toxins: okadaic acid (OA) and its derivatives; or the dinophysistoxins (DTXs) (also known as diarrhetic shellfish poisons or DSP toxins) and pectenotoxins (PTXs). DSP toxins are potent inhibitors of protein phosphatases, causing gastrointestinal intoxication in consumers of contaminated seafood. Forty years after the identification of Dinophysis as the causative agent of DSP in Japan, contamination of filter feeding shellfish exposed to Dinophysis blooms is recognized as a problem worldwide. DSP events affect public health and cause considerable losses to the shellfish industry. Costly monitoring programs are implemented in regions with relevant shellfish production to prevent these socioeconomic impacts. Harvest closures are enforced whenever toxin levels exceed regulatory limits (RLs). Dinophysis species are kleptoplastidic dinoflagellates; they feed on ciliates (Mesodinium genus) that have previously acquired plastids from cryptophycean (genera Teleaulax, Plagioselmis, and Geminigera) nanoflagellates. The interactions of Dinophysis with different prey regulate their growth and toxin production. When Dinophysis cells are ingested by shellfish, their toxins are partially biotransformed and bioaccumulated, rendering the shellfish unsuitable for human consumption. DSP toxins may also affect shellfish metabolism. This book covers diverse aspects of the abovementioned topics—from the laboratory culture of Dinophysis and the kinetics of uptake, transformation, and depuration of DSP toxins in shellfish to Dinophysis population dynamics, the monitoring and regulation of DSP toxins, and their impact on the shellfish industry in some of the aquaculture regions that are traditionally most affected, namely, northeastern Japan, western Europe, southern Chile, and New Zealand.
