Rsem Accurate Transcript Quantification From Rna Seq Data With Or Without A Reference Genome
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| Author | : Applied Research Applied Research Press |
| Publisher | : |
| Total Pages | : 44 |
| Release | : 2015-09-16 |
| Genre | : |
| ISBN | : 9781517392185 |
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 |
| Total Pages | : 330 |
| Release | : 2017-09-13 |
| Genre | : Medical |
| ISBN | : 9535135031 |
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 | : Tore Samuelsson |
| Publisher | : Cambridge University Press |
| Total Pages | : 357 |
| Release | : 2012-06-07 |
| Genre | : Science |
| ISBN | : 1107378338 |
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.
| Author | : Ibrokhim Y. Abdurakhmonov |
| Publisher | : BoD – Books on Demand |
| Total Pages | : 190 |
| Release | : 2018-06-20 |
| Genre | : Medical |
| ISBN | : 1789232686 |
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 | : Ion Mandoiu |
| Publisher | : John Wiley & Sons |
| Total Pages | : 460 |
| Release | : 2016-10-03 |
| Genre | : Computers |
| ISBN | : 1118169484 |
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 | : Wenjian Qin |
| Publisher | : Springer Nature |
| Total Pages | : 171 |
| Release | : 2022-09-22 |
| Genre | : Computers |
| ISBN | : 3031172663 |
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.
| Author | : Mohammad Ajmal Ali |
| Publisher | : Elsevier |
| Total Pages | : 530 |
| Release | : 2022-10-07 |
| Genre | : Science |
| ISBN | : 0323972314 |
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
| Author | : Gyun Min Lee |
| Publisher | : John Wiley & Sons |
| Total Pages | : 436 |
| Release | : 2020-01-13 |
| Genre | : Science |
| ISBN | : 3527343342 |
Offers a comprehensive overview of cell culture engineering, providing insight into cell engineering, systems biology approaches and processing technology In Cell Culture Engineering: Recombinant Protein Production, editors Gyun Min Lee and Helene Faustrup Kildegaard assemble top class authors to present expert coverage of topics such as: cell line development for therapeutic protein production; development of a transient gene expression upstream platform; and CHO synthetic biology. They provide readers with everything they need to know about enhancing product and bioprocess attributes using genome-scale models of CHO metabolism; omics data and mammalian systems biotechnology; perfusion culture; and much more. This all-new, up-to-date reference covers all of the important aspects of cell culture engineering, including cell engineering, system biology approaches, and processing technology. It describes the challenges in cell line development and cell engineering, e.g. via gene editing tools like CRISPR/Cas9 and with the aim to engineer glycosylation patterns. Furthermore, it gives an overview about synthetic biology approaches applied to cell culture engineering and elaborates the use of CHO cells as common cell line for protein production. In addition, the book discusses the most important aspects of production processes, including cell culture media, batch, fed-batch, and perfusion processes as well as process analytical technology, quality by design, and scale down models. -Covers key elements of cell culture engineering applied to the production of recombinant proteins for therapeutic use -Focuses on mammalian and animal cells to help highlight synthetic and systems biology approaches to cell culture engineering, exemplified by the widely used CHO cell line -Part of the renowned "Advanced Biotechnology" book series Cell Culture Engineering: Recombinant Protein Production will appeal to biotechnologists, bioengineers, life scientists, chemical engineers, and PhD students in the life sciences.
| Author | : Manish Kumar Gupta |
| Publisher | : Elsevier |
| Total Pages | : 434 |
| Release | : 2024-05-03 |
| Genre | : Science |
| ISBN | : 0443160937 |
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
| Author | : Lytras, Miltiadis D. |
| Publisher | : IGI Global |
| Total Pages | : 492 |
| Release | : 2017-06-16 |
| Genre | : Computers |
| ISBN | : 1522526080 |
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.
