Download or read book High Dimensional Single Cell Analysis written by Harris G. Fienberg and published by Springer. This book was released on 2014-04-22 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume highlights the most interesting biomedical and clinical applications of high-dimensional flow and mass cytometry. It reviews current practical approaches used to perform high-dimensional experiments and addresses key bioinformatic techniques for the analysis of data sets involving dozens of parameters in millions of single cells. Topics include single cell cancer biology; studies of the human immunome; exploration of immunological cell types such as CD8+ T cells; decipherment of signaling processes of cancer; mass-tag cellular barcoding; analysis of protein interactions by proximity ligation assays; Cytobank, a platform for the analysis of cytometry data; computational analysis of high-dimensional flow cytometric data; computational deconvolution approaches for the description of intracellular signaling dynamics and hyperspectral cytometry. All 10 chapters of this book have been written by respected experts in their fields. It is an invaluable reference book for both basic and clinical researchers.
Download or read book Learning Cell States from High dimensional Single cell Data written by and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent developments in single-cell measurement technologies have yielded dramatic increases in throughput (measured cells per experiment) and dimensionality (measured features per cell). In particular, the introduction of mass cytometry has made possible the simultaneous quantification of dozens of protein species in millions of individual cells in a single experiment. The raw data produced by such high-dimensional single-cell measurements provide unprecedented potential to reveal the phenotypic heterogeneity of cellular systems. In order to realize this potential, novel computational techniques are required to extract knowledge from these complex data. Analysis of single-cell data is a new challenge for computational biology, as early development in the field was tailored to technologies that sacrifice single-cell resolution, such as DNA microarrays. The challenges for single-cell data are quite distinct and require multidimensional modeling of complex population structure. Particular challenges include nonlinear relationships between measured features and non-convex subpopulations.
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.
Download or read book Immunophenotyping written by J Philip McCoy Jr and published by Humana. This book was released on 2019-09-29 with total page 375 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents the latest collection of immunophenotypic techniques and applications used in research and clinical settings. Chapters in this book cover topics such as constructions of high dimensions fluorescence and mass cytometry panels; fluorescence barcoding; using dried or lyophilized reagents; and immunophenotypic examples of specific cell types. The book concludes with a discussion on the critical roles of quality control and immunophenotyping in the clinical environment. 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, Immunophenotyping: Methods and Protocols is a valuable resource for any researchers, clinician, or scientist interested in learning more about this evolving field.
Download or read book Analysis and Control of Cellular Ensembles Exploiting dimensionality reduction in single cell data and models written by Karsten Kuritz and published by Logos Verlag Berlin GmbH. This book was released on 2020-11-20 with total page 150 pages. Available in PDF, EPUB and Kindle. Book excerpt: An ensemble system is a collection of nearly identical dynamical systems which admit a certain degree of heterogeneity, and which are subject to the restriction that they may only be manipulated or observed as a whole. This thesis presents analysis and control methods for cellular ensembles by considering reduced 1-dimensional dynamics of biological processes in high-dimensional single-cell data and models. To be more specific, we address the quest for real-time analysis of biological processes within single-cell data by introducing the measure-preserving map of pseudotime into real-time, in short MAPiT. MAPiT enables the reconstruction of temporal and spatial dynamics from single-cell snapshot experiments. In addition, we propose a PDE-constrained learning algorithm which allows for efficient inference of changes in cell cycle progression from time series single-cell snapshot data. The second part of this thesis, is devoted to controlling a heterogeneous cell population, in the sense, that we aim at achieving a desired distribution of cellular oscillators on their periodic orbit. A systems theoretic approach to the ensemble control problem provides novel necessary and sufficient conditions for the control of phase distributions in terms of the Fourier coefficients of the phase response curve. This thesis establishes a connection between the previously separate areas of single cell analysis and ensemble control. Our holistic view opens new perspectives for theoretic concepts in basic research and therapeutic strategies in precision medicine.
Download or read book Kernel Methods for Pattern Analysis written by John Shawe-Taylor and published by Cambridge University Press. This book was released on 2004-06-28 with total page 520 pages. Available in PDF, EPUB and Kindle. Book excerpt: Publisher Description
Download or read book Inflammation written by Björn E. Clausen and published by Humana. This book was released on 2017-01-07 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents a broad selection of cutting-edge methods and tools that will enable the reader to investigate the multi-faceted manifestations of inflammation. Inflammation: Methods and Protocols is divided into four sections: the first three sections describe protocols investigating immune-mediated inflammatory disease models affecting barrier organs to the environment; the skin, the lung, and the intestinal and oral mucosa. The fourth section illustrates inflammatory disease models of the brain, joints, and vasculature. 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 notes on troubleshooting and avoiding known pitfalls. Authoritative and practical, Inflammation: Methods and Protocols aims to inspire the experienced investigator and the young experimenter alike to disentangle the fascinating process of inflammation.
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:
Download or read book Introduction to High Dimensional Statistics written by Christophe Giraud and published by CRC Press. This book was released on 2021-08-25 with total page 410 pages. Available in PDF, EPUB and Kindle. Book excerpt: Praise for the first edition: "[This book] succeeds singularly at providing a structured introduction to this active field of research. ... it is arguably the most accessible overview yet published of the mathematical ideas and principles that one needs to master to enter the field of high-dimensional statistics. ... recommended to anyone interested in the main results of current research in high-dimensional statistics as well as anyone interested in acquiring the core mathematical skills to enter this area of research." —Journal of the American Statistical Association Introduction to High-Dimensional Statistics, Second Edition preserves the philosophy of the first edition: to be a concise guide for students and researchers discovering the area and interested in the mathematics involved. The main concepts and ideas are presented in simple settings, avoiding thereby unessential technicalities. High-dimensional statistics is a fast-evolving field, and much progress has been made on a large variety of topics, providing new insights and methods. Offering a succinct presentation of the mathematical foundations of high-dimensional statistics, this new edition: Offers revised chapters from the previous edition, with the inclusion of many additional materials on some important topics, including compress sensing, estimation with convex constraints, the slope estimator, simultaneously low-rank and row-sparse linear regression, or aggregation of a continuous set of estimators. Introduces three new chapters on iterative algorithms, clustering, and minimax lower bounds. Provides enhanced appendices, minimax lower-bounds mainly with the addition of the Davis-Kahan perturbation bound and of two simple versions of the Hanson-Wright concentration inequality. Covers cutting-edge statistical methods including model selection, sparsity and the Lasso, iterative hard thresholding, aggregation, support vector machines, and learning theory. Provides detailed exercises at the end of every chapter with collaborative solutions on a wiki site. Illustrates concepts with simple but clear practical examples.
Download or read book Statistical and Computational Method Development and Benchmarking for Analysis of High dimensional Single cell Cytometry Data written by Lukas Martin Weber and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book NK Cell Subsets in Health and Disease New Developments written by and published by . This book was released on 2017 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Natural Killer (NK) cells were discovered ca 1975, as the first group of lymphoid cells that were neither T cells nor B cells. Since then, the dissection of the biology of NK cells has been growing exponentially with many seminal discoveries from the identification of MHC class I-specific inhibitory receptors to the discovery of receptor-ligand pairs involved in NK cell activation and to the manipulation of NK cells in cancer. In this research topic, we asked a group of thought leaders in NK cell biology to review recent advances in their origins and biology, and their roles in cancer, infection and inflammation. Together, these 25 articles provide a timely survey of NK cells as critical immunologic components of health and disease. They will hopefully prompt further dialogue and developments in basic and translational immunology.
Download or read book Next Generation Sequencing Data Analysis written by Xinkun Wang and published by CRC Press. This book was released on 2023-07-06 with total page 435 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA-seq: both bulk and single-cell (separate chapters) Genotyping and variant discovery through whole genome/exome sequencing Clinical sequencing and detection of actionable variants De novo genome assembly ChIP-seq to map protein-DNA interactions Epigenomics through DNA methylation sequencing Metagenome sequencing for microbiome analysis
Download or read book Genes Signals written by Mark Ptashne and published by CSHL Press. This book was released on 2002 with total page 212 pages. Available in PDF, EPUB and Kindle. Book excerpt: P. 103.
Download or read book Essentials of Single Cell Analysis written by Fan-Gang Tseng and published by Springer. This book was released on 2016-01-21 with total page 415 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides an overview of single-cell isolation, separation, injection, lysis and dynamics analysis as well as a study of their heterogeneity using different miniaturized devices. As an important part of single-cell analysis, different techniques including electroporation, microinjection, optical trapping, optoporation, rapid electrokinetic patterning and optoelectronic tweezers are described in detail. It presents different fluidic systems (e.g. continuous micro/nano-fluidic devices, microfluidic cytometry) and their integration with sensor technology, optical and hydrodynamic stretchers etc., and demonstrates the applications of single-cell analysis in systems biology, proteomics, genomics, epigenomics, cancer transcriptomics, metabolomics, biomedicine and drug delivery systems. It also discusses the future challenges for single-cell analysis, including the advantages and limitations. This book is enjoyable reading material while at the same time providing essential information to scientists in academia and professionals in industry working on different aspects of single-cell analysis. Dr. Fan-Gang Tseng is a Distinguished Professor of Engineering and System Science at the National Tsing Hua University, Taiwan. Dr. Tuhin Subhra Santra is a Research Associate at the California Nano Systems Institute, University of California at Los Angeles, USA.
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.
Download or read book Regulatory T Cells written by Masahiro Ono and published by Springer Nature. This book was released on 2022-09-30 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides methods and models for investigating the immunosuppressive subset of CD4+ T-cells, regulatory T-cells (Treg). Chapters guide readers through, basic protocols for analyzing Treg in mice and humans, single-cell analysis for analyzing Treg, and methods for the analysis of Treg in clinical application. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Regulatory T-Cells: Methods and Protocols aims to be a useful and practical guide to new researchers and experts looking to expand their knowledge.
Download or read book Histochemistry of Single Molecules written by Carlo Pellicciari and published by Springer Nature. This book was released on 2022-09-24 with total page 351 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume details histochemical techniques for the detection of specific molecules or metabolic processes, both at light and electron microscopy. Chapters are divided into seven sections covering Vital histochemistry, Carbohydrate histochemistry, Protein histochemistry, Lipid histochemistry, Nuclear histochemistry, Plant histochemistry and Histochemistry for Nanoscience. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. The volume also contains three discursive chapters on Histochemistry in advanced cytometry, Lectins and Detection of molecules in plant cell walls by fluorescence microscopy. Authoritative and cutting-edge, Histochemistry of Single Molecules: Methods and Protocols, Second Edition aims to be a useful practical guide for researchers to help further their study in this field.
