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Benchmarking And Development Of Computational Methods For Single Cell Data Analysis Challenges And Opportunities
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Book Synopsis Computational Methods for Single-Cell Data Analysis by : Guo-Cheng Yuan
Download or read book Computational Methods for Single-Cell Data Analysis written by Guo-Cheng Yuan and published by Humana Press. This book was released on 2019-02-14 with total page 271 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed book provides state-of-art computational approaches to further explore the exciting opportunities presented by single-cell technologies. Chapters each detail a computational toolbox aimed to overcome a specific challenge in single-cell analysis, such as data normalization, rare cell-type identification, and spatial transcriptomics analysis, all with a focus on hands-on implementation of computational methods for analyzing experimental data. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Methods for Single-Cell Data Analysis aims to cover a wide range of tasks and serves as a vital handbook for single-cell data analysis.
Book Synopsis Computational Stem Cell Biology by : Patrick Cahan
Download or read book Computational Stem Cell Biology written by Patrick Cahan and published by Humana. This book was released on 2019-05-07 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume details methods and protocols to further the study of stem cells within the computational stem cell biology (CSCB) field. Chapters are divided into four sections covering the theory and practice of modeling of stem cell behavior, analyzing single cell genome-scale measurements, reconstructing gene regulatory networks, and metabolomics. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Stem Cell Biology: Methods and Protocols will be an invaluable guide to researchers as they explore stem cells from the perspective of computational biology.
Book Synopsis RNA-Seq Analysis: Methods, Applications and Challenges by : Filippo Geraci
Download or read book RNA-Seq Analysis: Methods, Applications and Challenges written by Filippo Geraci and published by Frontiers Media SA. This book was released on 2020-06-08 with total page 169 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Hi-C Data Analysis by : Silvio Bicciato
Download or read book Hi-C Data Analysis written by Silvio Bicciato and published by Humana. This book was released on 2022-09-04 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume details a comprehensive set of methods and tools for Hi-C data processing, analysis, and interpretation. Chapters cover applications of Hi-C to address a variety of biological problems, with a specific focus on state-of-the-art computational procedures adopted for the data analysis. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Hi-C Data Analysis: Methods and Protocols aims to help computational and molecular biologists working in the field of chromatin 3D architecture and transcription regulation.
Book Synopsis Frontiers in Massive Data Analysis by : National Research Council
Download or read book Frontiers in Massive Data Analysis written by National Research Council and published by National Academies Press. This book was released on 2013-09-03 with total page 191 pages. Available in PDF, EPUB and Kindle. Book excerpt: Data mining of massive data sets is transforming the way we think about crisis response, marketing, entertainment, cybersecurity and national intelligence. Collections of documents, images, videos, and networks are being thought of not merely as bit strings to be stored, indexed, and retrieved, but as potential sources of discovery and knowledge, requiring sophisticated analysis techniques that go far beyond classical indexing and keyword counting, aiming to find relational and semantic interpretations of the phenomena underlying the data. Frontiers in Massive Data Analysis examines the frontier of analyzing massive amounts of data, whether in a static database or streaming through a system. Data at that scale-terabytes and petabytes-is increasingly common in science (e.g., particle physics, remote sensing, genomics), Internet commerce, business analytics, national security, communications, and elsewhere. The tools that work to infer knowledge from data at smaller scales do not necessarily work, or work well, at such massive scale. New tools, skills, and approaches are necessary, and this report identifies many of them, plus promising research directions to explore. Frontiers in Massive Data Analysis discusses pitfalls in trying to infer knowledge from massive data, and it characterizes seven major classes of computation that are common in the analysis of massive data. Overall, this report illustrates the cross-disciplinary knowledge-from computer science, statistics, machine learning, and application disciplines-that must be brought to bear to make useful inferences from massive data.
Book Synopsis Computational Molecular Evolution by : Ziheng Yang
Download or read book Computational Molecular Evolution written by Ziheng Yang and published by Oxford University Press, USA. This book was released on 2006-10-05 with total page 374 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the models, methods and algorithms that are most useful for analysing the ever-increasing supply of molecular sequence data, with a view to furthering our understanding of the evolution of genes and genomes.
Book Synopsis Tumor Immunology and Immunotherapy - Cellular Methods Part B by :
Download or read book Tumor Immunology and Immunotherapy - Cellular Methods Part B written by and published by Academic Press. This book was released on 2020-01-28 with total page 586 pages. Available in PDF, EPUB and Kindle. Book excerpt: Tumor Immunology and Immunotherapy - Cellular Methods Part B, Volume 632, the latest release in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. Topics covered include Quantitation of calreticulin exposure associated with immunogenic cell death, Side-by-side comparisons of flow cytometry and immunohistochemistry for detection of calreticulin exposure in the course of immunogenic cell death, Quantitative determination of phagocytosis by bone marrow-derived dendritic cells via imaging flow cytometry, Cytofluorometric assessment of dendritic cell-mediated uptake of cancer cell apoptotic bodies, Methods to assess DC-dependent priming of T cell responses by dying cells, and more.
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 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 Artificial Intelligence and Computational Dynamics for Biomedical Research by : Ankur Saxena
Download or read book Artificial Intelligence and Computational Dynamics for Biomedical Research written by Ankur Saxena and published by Walter de Gruyter GmbH & Co KG. This book was released on 2022-11-07 with total page 298 pages. Available in PDF, EPUB and Kindle. Book excerpt: This work presents the latest development in the field of computational intelligence to advance Big Data and Cloud Computing concerning applications in medical diagnosis. As forum for academia and professionals it covers state-of-the-art research challenges and issues in the digital information & knowledge management and the concerns along with the solutions adopted in these fields.
Book Synopsis Systems Genetics by : Florian Markowetz
Download or read book Systems Genetics written by Florian Markowetz and published by Cambridge University Press. This book was released on 2015-07-02 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: Whereas genetic studies have traditionally focused on explaining heritance of single traits and their phenotypes, recent technological advances have made it possible to comprehensively dissect the genetic architecture of complex traits and quantify how genes interact to shape phenotypes. This exciting new area has been termed systems genetics and is born out of a synthesis of multiple fields, integrating a range of approaches and exploiting our increased ability to obtain quantitative and detailed measurements on a broad spectrum of phenotypes. Gathering the contributions of leading scientists, both computational and experimental, this book shows how experimental perturbations can help us to understand the link between genotype and phenotype. A snapshot of current research activity and state-of-the-art approaches to systems genetics are provided, including work from model organisms such as Saccharomyces cerevisiae and Drosophila melanogaster, as well as from human studies.
Book Synopsis Relative Distribution Methods in the Social Sciences by : Mark S. Handcock
Download or read book Relative Distribution Methods in the Social Sciences written by Mark S. Handcock and published by Springer Science & Business Media. This book was released on 2006-05-10 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt: This monograph presents methods for full comparative distributional analysis based on the relative distribution. This provides a general integrated framework for analysis, a graphical component that simplifies exploratory data analysis and display, a statistically valid basis for the development of hypothesis-driven summary measures, and the potential for decomposition - enabling the examination of complex hypotheses regarding the origins of distributional changes within and between groups. Written for data analysts and those interested in measurement, the text can also serve as a textbook for a course on distributional methods.
Book Synopsis Handbook of Cell Signaling, Three-Volume Set by : Ralph A. Bradshaw
Download or read book Handbook of Cell Signaling, Three-Volume Set written by Ralph A. Bradshaw and published by Academic Press. This book was released on 2003-12-02 with total page 2560 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Handbook of Cell Signaling is a comprehensive work covering all aspects of intracellular signal processing, including extra/intracellular membrane receptors, signal transduction, gene expression/translation, and cellular/organotypic signal responses. The subject matter has been divided into five main parts (each of which is headed by a recognized expert in the field):* Initiation: Extracellular and Membrane Events* Transmission: Effectors and Cytosolic Events * Nuclear Responses: Gene Expression and Translation* Events in Intracellular Compartments* Cell-Cell and Cell-Matrix Interactions Covered in extensive detail, these areas will appeal to a broad, cross-disciplinary audience interested in the structure, biochemistry, molecular biology and pathology of cellular effectors. Tabular and well-illustrated, the Handbook will serve as an in-depth reference for this complex and evolving field.Tabular and well illustrated, the Handbook will serve as an in-depth reference for this complex and evolving field!* Contains approximately 470 articles* Provides well-organized sections on each essential area in signaling* Includes discussion on everything from ligand/receptor interactions to organ/organism responses* Extremely user-friendly
Book Synopsis Single-cell analysis on the pathophysiology of autoimmune diseases by : Shiang-Jong Tzeng
Download or read book Single-cell analysis on the pathophysiology of autoimmune diseases written by Shiang-Jong Tzeng and published by Frontiers Media SA. This book was released on 2024-07-11 with total page 213 pages. Available in PDF, EPUB and Kindle. Book excerpt: Despite increasing research to facilitate the understanding of the pathophysiology of autoimmune disorders, the exact cause of the incident of autoimmunity is unknown. Current concepts on the occurrence of autoimmune diseases are thought to involve autoantigens, genetic predisposition, disease triggers, and the breakdown of immune tolerance. In addition to the breakdown of immunological tolerance, one key characteristic of autoimmune disease is that within a single disease there is considerable variability in the clinical manifestation and severity in patients. Single-cell omics have emerged as an effective means of unraveling the complexity and heterogeneity of chronic disease development and therapeutic responses. Recently, advances in cutting-edge spatial profiling of diverse cell types have increased our understanding of how distinct cells interact and orchestrate at specific locations across a tissue landscape in both physiological and pathological contexts at the single-cell level.
Book Synopsis Machine Learning in Single-Cell RNA-seq Data Analysis by : Khalid Raza
Download or read book Machine Learning in Single-Cell RNA-seq Data Analysis written by Khalid Raza and published by Springer Nature. This book was released on with total page 104 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Interactive Web-Based Data Visualization with R, plotly, and shiny by : Carson Sievert
Download or read book Interactive Web-Based Data Visualization with R, plotly, and shiny written by Carson Sievert and published by CRC Press. This book was released on 2020-01-30 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt: The richly illustrated Interactive Web-Based Data Visualization with R, plotly, and shiny focuses on the process of programming interactive web graphics for multidimensional data analysis. It is written for the data analyst who wants to leverage the capabilities of interactive web graphics without having to learn web programming. Through many R code examples, you will learn how to tap the extensive functionality of these tools to enhance the presentation and exploration of data. By mastering these concepts and tools, you will impress your colleagues with your ability to quickly generate more informative, engaging, and reproducible interactive graphics using free and open source software that you can share over email, export to pdf, and more. Key Features: Convert static ggplot2 graphics to an interactive web-based form Link, animate, and arrange multiple plots in standalone HTML from R Embed, modify, and respond to plotly graphics in a shiny app Learn best practices for visualizing continuous, discrete, and multivariate data Learn numerous ways to visualize geo-spatial data This book makes heavy use of plotly for graphical rendering, but you will also learn about other R packages that support different phases of a data science workflow, such as tidyr, dplyr, and tidyverse. Along the way, you will gain insight into best practices for visualization of high-dimensional data, statistical graphics, and graphical perception. The printed book is complemented by an interactive website where readers can view movies demonstrating the examples and interact with graphics.
Book Synopsis Gene Network Inference by : Alberto Fuente
Download or read book Gene Network Inference written by Alberto Fuente and published by Springer Science & Business Media. This book was released on 2014-01-03 with total page 135 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents recent methods for Systems Genetics (SG) data analysis, applying them to a suite of simulated SG benchmark datasets. Each of the chapter authors received the same datasets to evaluate the performance of their method to better understand which algorithms are most useful for obtaining reliable models from SG datasets. The knowledge gained from this benchmarking study will ultimately allow these algorithms to be used with confidence for SG studies e.g. of complex human diseases or food crop improvement. The book is primarily intended for researchers with a background in the life sciences, not for computer scientists or statisticians.
