Multimodal and Integrative Analysis of Single-Cell or Bulk Sequencing Data PDF Download
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Author: Geng Chen
Publisher: Frontiers Media SA
ISBN: 2889666689
Category : Science
Languages : en
Pages : 116
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Book Description
Author: Geng Chen
Publisher: Frontiers Media SA
ISBN: 2889666689
Category : Science
Languages : en
Pages : 116
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Book Description
Author: Guo-Cheng Yuan
Publisher: Humana Press
ISBN: 9781493990566
Category : Science
Languages : en
Pages : 271
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Book Description
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.
Author: Geng Chen
Publisher: Frontiers Media SA
ISBN: 2832513328
Category : Science
Languages : en
Pages : 189
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Book Description
Author: Mark S. Handcock
Publisher: Springer Science & Business Media
ISBN: 0387226583
Category : Social Science
Languages : en
Pages : 272
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Book Description
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.
Author: Florian Markowetz
Publisher: Cambridge University Press
ISBN: 1107013844
Category : Science
Languages : en
Pages : 287
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Book Description
The first book to comprehensively cover the field of systems genetics, gathering contributions from leading scientists.
Author: Qun Xue
Publisher: Frontiers Media SA
ISBN: 2832544290
Category : Medical
Languages : en
Pages : 321
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Book Description
Author: Xinghua Pan
Publisher: Frontiers Media SA
ISBN: 2889459209
Category :
Languages : en
Pages : 129
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Book Description
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.
Author: Chiara Romualdi
Publisher: Frontiers Media SA
ISBN: 2889661512
Category : Medical
Languages : en
Pages : 187
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Book Description
This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.
Author: John Riches
Publisher: Frontiers Media SA
ISBN: 2832519709
Category : Medical
Languages : en
Pages : 160
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Book Description
Author: Ewy Mathé
Publisher: Humana
ISBN: 9781493935765
Category : Medical
Languages : en
Pages : 0
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Book Description
This volume expands on statistical analysis of genomic data by discussing cross-cutting groundwork material, public data repositories, common applications, and representative tools for operating on genomic data. Statistical Genomics: Methods and Protocols is divided into four sections. The first section discusses overview material and resources that can be applied across topics mentioned throughout the book. The second section covers prominent public repositories for genomic data. The third section presents several different biological applications of statistical genomics, and the fourth section highlights software tools that can be used to facilitate ad-hoc analysis and data integration. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible analysis protocols, and tips on troubleshooting and avoiding known pitfalls. Through and practical, Statistical Genomics: Methods and Protocols, explores a range of both applications and tools and is ideal for anyone interested in the statistical analysis of genomic data.
