Single Cell Transcriptomics
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Single Cell Transcriptomics
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Author : Raffaele A. Calogero
language : en
Publisher: Springer Nature
Release Date : 2022-12-10
Single Cell Transcriptomics written by Raffaele A. Calogero and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-12-10 with Science categories.
This volume provides up-to-date methods on single cell wet and bioinformatics protocols based on the researcher experiment requirements. Chapters detail basic analytical procedures, single-cell data QC, dimensionality reduction, clustering, cluster-specific features selection, RNA velocity, multi-modal data integration, and single cell RNA editing. 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. Cutting-edge and comprehensive, Single Cell Transcriptomics: Methods and Protocols aims to be a valuable resource for all researchers interested in learning more about this important and developing field.
Computational Methods For Single Cell Data Analysis
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Author : Guo-Cheng Yuan
language : en
Publisher: Humana Press
Release Date : 2019-02-14
Computational Methods For Single Cell Data Analysis written by Guo-Cheng Yuan and has been published by Humana Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-02-14 with Science categories.
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.
Introduction To Single Cell Omics
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Author : Xinghua Pan
language : en
Publisher: Frontiers Media SA
Release Date : 2019-09-19
Introduction To Single Cell Omics written by Xinghua Pan and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-09-19 with categories.
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.
Hepatocellular Carcinoma
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Author : Yujin Hoshida
language : en
Publisher: Springer
Release Date : 2019-08-05
Hepatocellular Carcinoma written by Yujin Hoshida and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-08-05 with Medical categories.
This book provides a comprehensive overview of the current limitations and unmet needs in Hepatocellular Carcinoma (HCC) diagnosis, treatment, and prevention. It also provides newly emerging concepts, approaches, and technologies to address challenges. Topics covered include changing landscape of HCC etiologies in association with health disparities, framework of clinical management algorithm, new and experimental modalities of HCC diagnosis and prognostication, multidisciplinary treatment options including rapidly evolving molecular targeted therapies and immune therapies, multi-omics molecular characterization, and clinically relevant experimental models. The book is intended to assist collaboration between the diverse disciplines and facilitate forward and reverse translation between basic and clinical research by providing a comprehensive overview of relevant areas, covering epidemiological trend and population-level patient management strategies, new diagnostic and prognostic tools, recent advances in the standard care and novel therapeutic approaches, and new concepts in pathogenesis and experimental approaches and tools, by experts and opinion leaders in their respective fields. By thoroughly and concisely covering whole aspects of HCC care, Hepatocellular Carcinoma serves as a valuable reference for multidisciplinary readers, and promotes the development of personalized precision care strategies that lead to substantial improvement of disease burden and patient prognosis in HCC.
Omics In Plant Breeding
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Author : Aluízio Borém
language : en
Publisher: John Wiley & Sons
Release Date : 2014-06-03
Omics In Plant Breeding written by Aluízio Borém and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-06-03 with Science categories.
Computational and high-throughput methods, such as genomics, proteomics, and transcriptomics, known collectively as “-omics,” have been used to study plant biology for well over a decade now. As these technologies mature, plant and crop scientists have started using these methods to improve crop varieties. Omics in Plant Breeding provides a timely introduction to key omicsbased methods and their application in plant breeding. Omics in Plant Breeding is a practical and accessible overview of specific omics-based methods ranging from metabolomics to phenomics. Covering a single methodology within each chapter, this book provides thorough coverage that ensures a strong understanding of each methodology both in its application to, and improvement of, plant breeding. Accessible to advanced students, researchers, and professionals, Omics in Plant Breeding will be an essential entry point into this innovative and exciting field. • A valuable overview of high-throughput, genomics-based technologies and their applications to plant breeding • Each chapter explores a single methodology, allowing for detailed and thorough coverage • Coverage ranges from well-established methodologies, such as genomics and proteomics, to emerging technologies, including phenomics and physionomics Aluízio Borém is a Professor of Plant Breeding at the University of Viçosa in Brazil. Roberto Fritsche-Neto is a Professor of Genetics and Plant Breeding at the University of São Paulo in Brazil.
Leukemia Stem Cells
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Author : César Cobaleda
language : en
Publisher:
Release Date : 2021
Leukemia Stem Cells written by César Cobaleda and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021 with Leukemia categories.
Machine Learning In Single Cell Rna Seq Data Analysis
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Author : Khalid Raza
language : en
Publisher: Springer Nature
Release Date : 2024-09-02
Machine Learning In Single Cell Rna Seq Data Analysis written by Khalid Raza and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-09-02 with Computers categories.
This book provides a concise guide tailored for researchers, bioinformaticians, and enthusiasts eager to unravel the mysteries hidden within single-cell RNA sequencing (scRNA-seq) data using cutting-edge machine learning techniques. The advent of scRNA-seq technology has revolutionized our understanding of cellular diversity and function, offering unprecedented insights into the intricate tapestry of gene expression at the single-cell level. However, the deluge of data generated by these experiments presents a formidable challenge, demanding advanced analytical tools, methodologies, and skills for meaningful interpretation. This book bridges the gap between traditional bioinformatics and the evolving landscape of machine learning. Authored by seasoned experts at the intersection of genomics and artificial intelligence, this book serves as a roadmap for leveraging machine learning algorithms to extract meaningful patterns and uncover hidden biological insights within scRNA-seq datasets.
Single Cell Omics
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Author : Debmalya Barh
language : en
Publisher: Academic Press
Release Date : 2019-06-06
Single Cell Omics written by Debmalya Barh and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-06-06 with Medical categories.
Single-Cell Omics: Volume 1: Technological Advances and Applications provides the latest technological developments and applications of single-cell technologies in the field of biomedicine. In the current era of precision medicine, the single-cell omics technology is highly promising due to its potential in diagnosis, prognosis and therapeutics. Sections in the book cover single-cell omics research and applications, diverse technologies applied in the topic, such as pangenomics, metabolomics, and multi-omics of single cells, data analysis, and several applications of single-cell omics within the biomedical field, for example in cancer, metabolic and neuro diseases, immunology, pharmacogenomics, personalized medicine and reproductive health. This book is a valuable source for bioinformaticians, molecular diagnostic researchers, clinicians and members of the biomedical field who are interested in understanding more about single-cell omics and its potential for research and diagnosis. - Covers not only the technological aspects, but also the diverse applications of single cell omics in the biomedical field - Summarizes the latest progress in single cell omics and discusses potential future developments for research and diagnosis - Written by experts across the world, bringing different points-of-view and case studies to give a comprehensive overview on the topic
Machine Learning And Mathematical Models For Single Cell Data Analysis
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Author : Le Ou-Yang
language : en
Publisher: Frontiers Media SA
Release Date : 2022-11-29
Machine Learning And Mathematical Models For Single Cell Data Analysis written by Le Ou-Yang and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-11-29 with Science categories.
The Individual Microbe Single Cell Analysis And Agent Based Modelling
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Author : Johan H. J. Leveau
language : en
Publisher: Frontiers Media SA
Release Date : 2019-02-19
The Individual Microbe Single Cell Analysis And Agent Based Modelling written by Johan H. J. Leveau and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-02-19 with categories.
Recent technological advances in single-cell microbiology, using flow cytometry, microfluidics, x-ray fluorescence microprobes, and single-cell -omics, allow for the observation of individuals within populations. Simultaneously, individual-based models (or more generally agent-based models) allow for individual microbes to be simulated. Bridging these techniques forms the foundation of individual-based ecology of microbes (µIBE). µIBE has elucidated genetic and phenotypic heterogeneity that has important consequences for a number of human interests, including antibiotic or biocide resistance, the productivity and stability of industrial fermentations, the efficacy of food preservatives, and the potential of pathogens to cause disease. Individual-based models can help us to understand how these sets of traits of individual microbes influence the above. This eBook compiles all publications from a recent Research Topic in Frontiers in Microbiology. It features recent research where individual observational and/or modelling techniques are applied to gain unique insights into the ecology of microorganisms. The Research Topic “The Individual Microbe: Single-Cell Analysis and Agent-Based Modelling” arose from the 2016 @ASM conference of the same name hosted by the American Society for Microbiology at its headquarters in Washington, D.C. We are grateful to ASM for funding and hosting this conference.