Single Cell Sequencing And Systems Immunology

Author : Xiangdong Wang
Publisher : Springer
ISBN 13 : 9401797536
Total Pages : 184 pages
Book Rating : 4.35/5 ( download)

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Download or read book Single Cell Sequencing and Systems Immunology written by Xiangdong Wang and published by Springer. This book was released on 2015-03-27 with total page 184 pages. Available in PDF, EPUB and Kindle. Book excerpt: The volume focuses on the genomics, proteomics, metabolomics, and bioinformatics of a single cell, especially lymphocytes and on understanding the molecular mechanisms of systems immunology. Based on the author’s personal experience, it provides revealing insights into the potential applications, significance, workflow, comparison, future perspectives and challenges of single-cell sequencing for identifying and developing disease-specific biomarkers in order to understand the biological function, activation and dysfunction of single cells and lymphocytes and to explore their functional roles and responses to therapies. It also provides detailed information on individual subgroups of lymphocytes, including cell characters, function, surface markers, receptor function, intracellular signals and pathways, production of inflammatory mediators, nuclear receptors and factors, omics, sequencing, disease-specific biomarkers, bioinformatics, networks and dynamic networks, their role in disease and future prospects. Dr. Xiangdong Wang is a Professor of Medicine, Director of Shanghai Institute of Clinical Bioinformatics, Director of Fudan University Center for Clinical Bioinformatics, Director of the Biomedical Research Center of Zhongshan Hospital, Deputy Director of Shanghai Respiratory Research Institute, Shanghai, China.

Author : Buwei Yu
Publisher : Springer Nature
ISBN 13 : 9811544948
Total Pages : 247 pages
Book Rating : 4.41/5 ( download)

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Download or read book Single-cell Sequencing and Methylation written by Buwei Yu and published by Springer Nature. This book was released on 2020-09-19 with total page 247 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the rapid development of biotechnologies, single-cell sequencing has become an important tool for understanding the molecular mechanisms of diseases, defining cellular heterogeneities and characteristics, and identifying intercellular communications and single-cell-based biomarkers. Providing a clear overview of the clinical applications, the book presents state-of-the-art information on immune cell function, cancer progression, infection, and inflammation gained from single-cell DNA or RNA sequencing. Furthermore, it explores the role of target gene methylation in the pathogenesis of diseases, with a focus on respiratory cancer, infection and chronic diseases. As such it is a valuable resource for clinical researchers and physicians, allowing them to refresh their knowledge and improve early diagnosis and therapy for patients.

Author : Yutaka Suzuki
Publisher : Springer
ISBN 13 : 9811360375
Total Pages : 150 pages
Book Rating : 4.74/5 ( download)

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Download or read book Single Molecule and Single Cell Sequencing written by Yutaka Suzuki and published by Springer. This book was released on 2019-04-09 with total page 150 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an overview of the recent technologies in single molecule and single cell sequencing. These sequencing technologies are revolutionizing the way of the genomic studies and the understanding of complex biological systems. The PacBio sequencer has enabled extremely long-read sequencing and the MinION sequencer has made the sequencing possible in developing countries. New developments and technologies are constantly emerging, which will further expand sequencing applications. In parallel, single cell sequencing technologies are rapidly becoming a popular platform. This volume presents not only an updated overview of these technologies, but also of the related developments in bioinformatics. Without powerful bioinformatics software, where rapid progress is taking place, these new technologies will not realize their full potential. All the contributors to this volume have been involved in the development of these technologies and software and have also made significant progress on their applications. This book is intended to be of interest to a wide audience ranging from genome researchers to basic molecular biologists and clinicians.

Author : Kumar Selvarajoo
Publisher : Springer Science & Business Media
ISBN 13 : 1461476909
Total Pages : 153 pages
Book Rating : 4.00/5 ( download)

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Download or read book Immuno Systems Biology written by Kumar Selvarajoo and published by Springer Science & Business Media. This book was released on 2013-10-01 with total page 153 pages. Available in PDF, EPUB and Kindle. Book excerpt: Immuno Systems Biology aims to study the immune system in the more integrated manner on how cells and molecules participate at different system levels to the immune function. Through this book Kumar Selvarajoo introduces to physicists, chemists, computer scientists, biologists and immunologists the idea of an integrated approach to the understanding of mammalian immune system. Geared towards a researcher with limited immunological and computational analytical experience, the book provides a broad overview to the subject and some instruction in basic computational, theoretical and experimental approaches. The book links complex immunological processes with computational analysis and emphasizes the importance of immunology to the mammalian system.

Author : Ramit Mehr
Publisher : Frontiers Media SA
ISBN 13 : 2889195015
Total Pages : 402 pages
Book Rating : 4.15/5 ( download)

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Download or read book Immune system modeling and analysis written by Ramit Mehr and published by Frontiers Media SA. This book was released on 2015-04-22 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: The rapid development of new methods for immunological data collection – from multicolor flow cytometry, through single-cell imaging, to deep sequencing – presents us now, for the first time, with the ability to analyze and compare large amounts of immunological data in health, aging and disease. The exponential growth of these datasets, however, challenges the theoretical immunology community to develop methods for data organization and analysis. Furthermore, the need to test hypotheses regarding immune function, and generate predictions regarding the outcomes of medical interventions, necessitates the development of mathematical and computational models covering processes on multiple scales, from the genetic and molecular to the cellular and system scales. The last few decades have seen the development of methods for presentation and analysis of clonal repertoires (those of T and B lymphocytes) and phenotypic (surface-marker based) repertoires of all lymphocyte types, and for modeling the intricate network of molecular and cellular interactions within the immune systems. This e-Book, which has first appeared as a ‘Frontiers in Immunology’ research topic, provides a comprehensive, online, open access snapshot of the current state of the art on immune system modeling and analysis.

Author : Institute of Medicine
Publisher : National Academies Press
ISBN 13 : 0309219396
Total Pages : 570 pages
Book Rating : 4.96/5 ( download)

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Download or read book The Science and Applications of Synthetic and Systems Biology written by Institute of Medicine and published by National Academies Press. This book was released on 2011-12-30 with total page 570 pages. Available in PDF, EPUB and Kindle. Book excerpt: Many potential applications of synthetic and systems biology are relevant to the challenges associated with the detection, surveillance, and responses to emerging and re-emerging infectious diseases. On March 14 and 15, 2011, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to explore the current state of the science of synthetic biology, including its dependency on systems biology; discussed the different approaches that scientists are taking to engineer, or reengineer, biological systems; and discussed how the tools and approaches of synthetic and systems biology were being applied to mitigate the risks associated with emerging infectious diseases. The Science and Applications of Synthetic and Systems Biology is organized into sections as a topic-by-topic distillation of the presentations and discussions that took place at the workshop. Its purpose is to present information from relevant experience, to delineate a range of pivotal issues and their respective challenges, and to offer differing perspectives on the topic as discussed and described by the workshop participants. This report also includes a collection of individually authored papers and commentary.

Author : Shuo Jia
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.82/5 ( download)

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Download or read book A Novel Computational Algorithm for Predicting Immune Cell Types Using Single-cell RNA Sequencing Data written by Shuo Jia and published by . This book was released on 2020 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Background: Cells from our immune system detect and kill pathogens to protect our body against many diseases. However, current methods for determining cell types have some major limitations, such as being time-consuming and with low throughput rate, etc. These problems stack up and hinder the deep exploration of cellular heterogeneity. Immune cells that are associated with cancer tissues play a critical role in revealing the stages of tumor development. Identifying the immune composition within tumor microenvironments in a timely manner will be helpful to improve clinical prognosis and therapeutic management for cancer. Single-cell RNA sequencing (scRNA-seq), an RNA sequencing (RNA-seq) technique that focuses on a single cell level, has provided us with the ability to conduct cell type classification. Although unsupervised clustering approaches are the major methods for analyzing scRNA-seq datasets, their results vary among studies with different input parameters and sizes. However, in supervised machine learning methods, information loss and low prediction accuracy are the key limitations. Methods and Results: Genes in the human genome align to chromosomes in a particular order. Hence, we hypothesize incorporating this information into our model will potentially improve the cell type classification performance. In order to utilize gene positional information, we introduce chromosome-based neural network, namely ChrNet, a novel chromosome-specific re-trainable supervised learning method based on a one-dimensional convolutional neural network (1D-CNN). The model's performance was evaluated and compared with other supervised learning architectures. Overall, the ChrNet showed highest performance among the 3 models we benchmarked. In addition, we demonstrated the advantages of our new model over unsupervised clustering approaches using gene expression profiles from healthy, and tumor infiltrating immune cells. The codes for our model are packed into a Python package publicly available online on Github. Conclusions: We established an innovative chromosome-based 1D-CNN architecture to extract scRNA-seq expression information for immune cell type classification. It is expected that this model can become a reference architecture for future cell type classification methods.

Author : David Richard Glass
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.19/5 ( download)

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Download or read book Applied Single-cell Methods for Basic and Translational Immunology written by David Richard Glass and published by . This book was released on 2021 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The immune system is a complex network of specialized cells that coordinate to eliminate immune challenges while minimally damaging self. Understanding the role of each cell in that network requires accurate quantification of informative biological features of single cells. Here, we innovated and applied single-cell methods and purpose- driven computational analyses to problems in basic and translational immunology. We developed a highly-multiplexed screen to quantify the co-expression of 351 surface molecules on millions of human B cells. We identified differentially expressed molecules and aligned their variance with isotype usage, VDJ sequence, metabolic profile, biosynthesis activity, and signaling response. Based on these analyses, we proposed a classification scheme to segregate B cells from four lymphoid tissues into twelve unique subsets, providing a framework for further investigations of human B cell identity and function. Additionally, we introduced morphometry, a high-throughput, quantitative, single-cell mass-cytometry-based assay that measures cell morphological features by their underlying molecular components. We applied multiplexed morphometric profiling and surface molecule immunophenotyping to 71 diverse clinical hematopathology samples and demonstrated that our approach was superior to flow cytometry and comparable to expert microscopy for tumor cell identification and enumeration. We introduced linear discriminant analysis (LDA) to generate morphometric maps that facilitate visualization and quantification of tumor cells. This contextualization of traditional surface markers on independent morphometric frameworks permits more sensitive and automated diagnosis of complex hematopoietic diseases.

Author :
Publisher : Academic Press
ISBN 13 : 0128186763
Total Pages : 588 pages
Book Rating : 4.63/5 ( download)

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Download or read book Tumor Immunology and Immunotherapy - Cellular Methods Part B written by and published by Academic Press. This book was released on 2020-01-29 with total page 588 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. Contains content written by authorities in the field Provides a comprehensive view on the topics covered Includes a high level of detail

Author : Bruce Alberts
Publisher :
ISBN 13 : 9780815332183
Total Pages : 0 pages
Book Rating : 4.81/5 ( download)

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Download or read book Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: