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Stitching And Sketching Large Scale Single Cell Transcriptomic Data
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Book Synopsis Stitching and Sketching Large-scale Single-cell Transcriptomic Data by : Brian Hie
Download or read book Stitching and Sketching Large-scale Single-cell Transcriptomic Data written by Brian Hie and published by . This book was released on 2019 with total page 111 pages. Available in PDF, EPUB and Kindle. Book excerpt: Researchers are generating single-cell RNA sequencing (scRNA-seq) profiles of diverse biological systems [1]-[7] and every cell type in the human body [8] at an unprecedented scale, with scRNA-seq experiments regularly profiling gene expression in hundreds of thousands or even millions of cells [9]. Leveraging this data to gain unprecedented insight into biology and disease requires algorithms that can scale to the tremendous amount of data being generated and can integrate information across multiple experiments, laboratories, and technologies. Here, we present two algorithms that aim to aid researchers in gaining better insight from scRNA-seq data sets. The first, Scanorama, inspired by algorithms for panorama stitching, achieves accurate integration of heterogeneous scRNA-seq data sets, which we use to integrate a number of large and complex collections of data sets. The second algorithm, geometric sketching, is a sampling approach that aims to evenly cover the low-dimensional manifold spanned by the cells to capture more of the rare transcriptional structure than would uniform subsampling with equal probability for each cell, obtaining sketches that better capture the transcriptional heterogeneity of the original data. Moreover, geometric sketching can be used to improve the computational efficiency of algorithms for single-cell integration, including Scanorama. We anticipate that both algorithms will play an important role in the analysis and interpretation of large-scale single-cell transcriptomic data sets.
Book Synopsis The Mouse Nervous System by : Charles Watson
Download or read book The Mouse Nervous System written by Charles Watson and published by Academic Press. This book was released on 2011-11-28 with total page 815 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Mouse Nervous System provides a comprehensive account of the central nervous system of the mouse. The book is aimed at molecular biologists who need a book that introduces them to the anatomy of the mouse brain and spinal cord, but also takes them into the relevant details of development and organization of the area they have chosen to study. The Mouse Nervous System offers a wealth of new information for experienced anatomists who work on mice. The book serves as a valuable resource for researchers and graduate students in neuroscience. Systematic consideration of the anatomy and connections of all regions of the brain and spinal cord by the authors of the most cited rodent brain atlases A major section (12 chapters) on functional systems related to motor control, sensation, and behavioral and emotional states A detailed analysis of gene expression during development of the forebrain by Luis Puelles, the leading researcher in this area Full coverage of the role of gene expression during development and the new field of genetic neuroanatomy using site-specific recombinases Examples of the use of mouse models in the study of neurological illness
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 Computational Optimal Transport by : Gabriel Peyre
Download or read book Computational Optimal Transport written by Gabriel Peyre and published by Foundations and Trends(r) in M. This book was released on 2019-02-12 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt: The goal of Optimal Transport (OT) is to define geometric tools that are useful to compare probability distributions. Their use dates back to 1781. Recent years have witnessed a new revolution in the spread of OT, thanks to the emergence of approximate solvers that can scale to sizes and dimensions that are relevant to data sciences. Thanks to this newfound scalability, OT is being increasingly used to unlock various problems in imaging sciences (such as color or texture processing), computer vision and graphics (for shape manipulation) or machine learning (for regression, classification and density fitting). This monograph reviews OT with a bias toward numerical methods and their applications in data sciences, and sheds lights on the theoretical properties of OT that make it particularly useful for some of these applications. Computational Optimal Transport presents an overview of the main theoretical insights that support the practical effectiveness of OT before explaining how to turn these insights into fast computational schemes. Written for readers at all levels, the authors provide descriptions of foundational theory at two-levels. Generally accessible to all readers, more advanced readers can read the specially identified more general mathematical expositions of optimal transport tailored for discrete measures. Furthermore, several chapters deal with the interplay between continuous and discrete measures, and are thus targeting a more mathematically-inclined audience. This monograph will be a valuable reference for researchers and students wishing to get a thorough understanding of Computational Optimal Transport, a mathematical gem at the interface of probability, analysis and optimization.
Book Synopsis Molecular Epidemiology by : Paul A. Schulte
Download or read book Molecular Epidemiology written by Paul A. Schulte and published by Academic Press. This book was released on 2012-12-02 with total page 609 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book will serve as a primer for both laboratory and field scientists who are shaping the emerging field of molecular epidemiology. Molecular epidemiology utilizes the same paradigm as traditional epidemiology but uses biological markers to identify exposure, disease or susceptibility. Schulte and Perera present the epidemiologic methods pertinent to biological markers. The book is also designed to enumerate the considerations necessary for valid field research and provide a resource on the salient and subtle features of biological indicators.
Book Synopsis The Craft and Science of Coffee by : Britta Folmer
Download or read book The Craft and Science of Coffee written by Britta Folmer and published by Academic Press. This book was released on 2016-12-16 with total page 558 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Craft and Science of Coffee follows the coffee plant from its origins in East Africa to its current role as a global product that influences millions of lives though sustainable development, economics, and consumer desire. For most, coffee is a beloved beverage. However, for some it is also an object of scientifically study, and for others it is approached as a craft, both building on skills and experience. By combining the research and insights of the scientific community and expertise of the crafts people, this unique book brings readers into a sustained and inclusive conversation, one where academic and industrial thought leaders, coffee farmers, and baristas are quoted, each informing and enriching each other. This unusual approach guides the reader on a journey from coffee farmer to roaster, market analyst to barista, in a style that is both rigorous and experience based, universally relevant and personally engaging. From on-farming processes to consumer benefits, the reader is given a deeper appreciation and understanding of coffee's complexity and is invited to form their own educated opinions on the ever changing situation, including potential routes to further shape the coffee future in a responsible manner. Presents a novel synthesis of coffee research and real-world experience that aids understanding, appreciation, and potential action Includes contributions from a multitude of experts who address complex subjects with a conversational approach Provides expert discourse on the coffee calue chain, from agricultural and production practices, sustainability, post-harvest processing, and quality aspects to the economic analysis of the consumer value proposition Engages with the key challenges of future coffee production and potential solutions
Book Synopsis Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment by : National Research Council
Download or read book Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment written by National Research Council and published by National Academies Press. This book was released on 2007-12-19 with total page 300 pages. Available in PDF, EPUB and Kindle. Book excerpt: The new field of toxicogenomics presents a potentially powerful set of tools to better understand the health effects of exposures to toxicants in the environment. At the request of the National Institute of Environmental Health Sciences, the National Research Council assembled a committee to identify the benefits of toxicogenomics, the challenges to achieving them, and potential approaches to overcoming such challenges. The report concludes that realizing the potential of toxicogenomics to improve public health decisions will require a concerted effort to generate data, make use of existing data, and study data in new waysâ€"an effort requiring funding, interagency coordination, and data management strategies.
Book Synopsis Precision Public Health by : Tarun Weeramanthri
Download or read book Precision Public Health written by Tarun Weeramanthri and published by Frontiers Media SA. This book was released on 2018-06-25 with total page 149 pages. Available in PDF, EPUB and Kindle. Book excerpt: Precision Public Health is a new and rapidly evolving field, that examines the application of new technologies to public health policy and practice. It draws on a broad range of disciplines including genomics, spatial data, data linkage, epidemiology, health informatics, big data, predictive analytics and communications. The hope is that these new technologies will strengthen preventive health, improve access to health care, and reach disadvantaged populations in all areas of the world. But what are the downsides and what are the risks, and how can we ensure the benefits flow to those population groups most in need, rather than simply to those individuals who can afford to pay? This is the first collection of theoretical frameworks, analyses of empirical data, and case studies to be assembled on this topic, published to stimulate debate and promote collaborative work.
Book Synopsis Network Medicine by : Joseph Loscalzo
Download or read book Network Medicine written by Joseph Loscalzo and published by Harvard University Press. This book was released on 2017-02-01 with total page 449 pages. Available in PDF, EPUB and Kindle. Book excerpt: Big data, genomics, and quantitative approaches to network-based analysis are combining to advance the frontiers of medicine as never before. With contributions from leading experts, Network Medicine introduces this rapidly evolving field of research, which promises to revolutionize the diagnosis and treatment of human diseases.
Book Synopsis Prognosis Research in Healthcare by : Richard D. Riley
Download or read book Prognosis Research in Healthcare written by Richard D. Riley and published by Oxford University Press. This book was released on 2019-01-17 with total page 384 pages. Available in PDF, EPUB and Kindle. Book excerpt: "What is going to happen to me?" Most patients ask this question during a clinical encounter with a health professional. As well as learning what problem they have (diagnosis) and what needs to be done about it (treatment), patients want to know about their future health and wellbeing (prognosis). Prognosis research can provide answers to this question and satisfy the need for individuals to understand the possible outcomes of their condition, with and without treatment. Central to modern medical practise, the topic of prognosis is the basis of decision making in healthcare and policy development. It translates basic and clinical science into practical care for patients and populations. Prognosis Research in Healthcare: Concepts, Methods and Impact provides a comprehensive overview of the field of prognosis and prognosis research and gives a global perspective on how prognosis research and prognostic information can improve the outcomes of healthcare. It details how to design, carry out, analyse and report prognosis studies, and how prognostic information can be the basis for tailored, personalised healthcare. In particular, the book discusses how information about the characteristics of people, their health, and environment can be used to predict an individual's future health. Prognosis Research in Healthcare: Concepts, Methods and Impact, addresses all types of prognosis research and provides a practical step-by-step guide to undertaking and interpreting prognosis research studies, ideal for medical students, health researchers, healthcare professionals and methodologists, as well as for guideline and policy makers in healthcare wishing to learn more about the field of prognosis.
Book Synopsis Cancer Immune Therapy by : Gernot Stuhler
Download or read book Cancer Immune Therapy written by Gernot Stuhler and published by John Wiley & Sons. This book was released on 2002-12-03 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cure or life with cancer? What can be achieved by cancer immune therapy? The past decade has seen substantial advancements in tumor immunology. Much of the new knowledge has been translated into new strategies for cancer treatment and into clinical trials. Some of these trials herald future breakthroughs, others have been disappointing and have prompted intensive search for alternatives.Major contributors to the field summarize the knowledge on the molecular and cellular mechanisms of tumorigenesis, critically review the instruments of the immune system that might be exploited for therapy, and discuss the clinical experiences with the different immune therapy concepts. Researchers in the fields of immunology, tumor biology and medicine will highly appreciate this up-to-date volume for evaluating future research activities.
Book Synopsis Deep Learning in Biology and Medicine by : Davide Bacciu
Download or read book Deep Learning in Biology and Medicine written by Davide Bacciu and published by World Scientific Publishing Europe Limited. This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biology, medicine and biochemistry have become data-centric fields for which Deep Learning methods are delivering groundbreaking results. Addressing high impact challenges, Deep Learning in Biology and Medicine provides an accessible and organic collection of Deep Learning essays on bioinformatics and medicine. It caters for a wide readership, ranging from machine learning practitioners and data scientists seeking methodological knowledge to address biomedical applications, to life science specialists in search of a gentle reference for advanced data analytics.With contributions from internationally renowned experts, the book covers foundational methodologies in a wide spectrum of life sciences applications, including electronic health record processing, diagnostic imaging, text processing, as well as omics-data processing. This survey of consolidated problems is complemented by a selection of advanced applications, including cheminformatics and biomedical interaction network analysis. A modern and mindful approach to the use of data-driven methodologies in the life sciences also requires careful consideration of the associated societal, ethical, legal and transparency challenges, which are covered in the concluding chapters of this book.
Book Synopsis Systems Biomedicine by : Edison T. Liu
Download or read book Systems Biomedicine written by Edison T. Liu and published by Academic Press. This book was released on 2009-09-17 with total page 450 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems biology is a critical emerging field that quantifies and annotates the complexity of biological systems in order to construct algorithmic models to predict outcomes from component input. Applications in medicine are revolutionizing our understanding of biological processes and systems. Systems Biomedicine is organized around foundations, computational modeling, network biology, and integrative biology, with the extension of examples from human biology and pharmacology, to focus on the applications of systems approaches to medical problems. An integrative approach to the underlying genomic, proteomic, and computational biology principles provides researchers with guidance in the use of qualitative systems and hypothesis generators. To reflect the highly interdisciplinary nature of the field, careful detail has been extended to ensure explanations of complex mathematical and biological principles are clear with minimum technical jargon. Organized to reflect the important distinguishing characteristics of systems strategies in experimental biology and medicine Provides precise and comprehensive measurement tools for constructing a model of the system and tools for defining complexity as an experimental dependent variable Includes a thorough discussion of the applications of quantitative principles to biomedical problems
Book Synopsis Genetics Meets Metabolomics by : Karsten Suhre
Download or read book Genetics Meets Metabolomics written by Karsten Suhre and published by Springer Science & Business Media. This book was released on 2012-06-15 with total page 328 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is written by leading researchers in the fields about the intersection of genetics and metabolomics which can lead to more comprehensive studies of inborn variation of metabolism.
Book Synopsis The Immunoglobulin FactsBook by : Marie-Paule Lefranc
Download or read book The Immunoglobulin FactsBook written by Marie-Paule Lefranc and published by Academic Press. This book was released on 2001-05-23 with total page 472 pages. Available in PDF, EPUB and Kindle. Book excerpt: The FactsBook series has established itself as the best source of easily accessible and accurate facts about protein groups. Books in the series use an easy-to-follow format and are meticulously researched and compiled by experts in the field.The Immunoglobulin FactsBook is the first published reference for all 203 human functional and ORF immunoglobulin genes. It is complete and standardized and employs nomenclature approved by the HUGO Nomenclature Committee.
Book Synopsis Single Cell Analysis by : Tuhin Subhra Santra
Download or read book Single Cell Analysis written by Tuhin Subhra Santra and published by MDPI. This book was released on 2021-06-02 with total page 254 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cells are the most fundamental building block of all living organisms. The investigation of any type of disease mechanism and its progression still remains challenging due to cellular heterogeneity characteristics and physiological state of cells in a given population. The bulk measurement of millions of cells together can provide some general information on cells, but it cannot evolve the cellular heterogeneity and molecular dynamics in a certain cell population. Compared to this bulk or the average measurement of a large number of cells together, single-cell analysis can provide detailed information on each cell, which could assist in developing an understanding of the specific biological context of cells, such as tumor progression or issues around stem cells. Single-cell omics can provide valuable information about functional mutation and a copy number of variations of cells. Information from single-cell investigations can help to produce a better understanding of intracellular interactions and environmental responses of cellular organelles, which can be beneficial for therapeutics development and diagnostics purposes. This Special Issue is inviting articles related to single-cell analysis and its advantages, limitations, and future prospects regarding health benefits.
Book Synopsis Systems Biology by : Bernhard Palsson
Download or read book Systems Biology written by Bernhard Palsson and published by Cambridge University Press. This book was released on 2015-01-26 with total page 551 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first comprehensive single-authored textbook on genome-scale models and the bottom-up approach to systems biology.
