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Integrative Approaches To Single Cell Rna Sequencing Analysis
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Book Synopsis Integrative Approaches to Single Cell RNA Sequencing Analysis by : Travis S. Johnson
Download or read book Integrative Approaches to Single Cell RNA Sequencing Analysis written by Travis S. Johnson and published by . This book was released on 2020 with total page 193 pages. Available in PDF, EPUB and Kindle. Book excerpt: There are trillions of cells, which make up hundreds of different cell types, found in the human body. These cells make up not only tissues but dictate the functions of those tissues. In diseased tissues, cell types can have a profound impact on the outcome of a patient. For these reasons, having a comprehensive understanding of cell types is important. In the past 10 years, single cell RNA sequencing has profoundly impacted our understanding of known and previously unknown cell types. Along with the numerous single cell datasets, a multitude of bulk expression datasets, multi-omic datasets, and curated information also exist. All of these data sources must be leveraged together to most improve our understanding of human tissues and diseases at the single cell level. We developed methodologies, frameworks, and algorithms that leverage multiple diverse datasets simultaneously to better understand single cell RNA sequencing data and as a result tissue heterogeneity as a whole.
Book Synopsis Integrative Analysis of Genome-Wide Association Studies and Single-Cell Sequencing Studies by : Sheng Yang
Download or read book Integrative Analysis of Genome-Wide Association Studies and Single-Cell Sequencing Studies written by Sheng Yang and published by Frontiers Media SA. This book was released on 2021-09-09 with total page 113 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Methods and Applications of Integrating Single Nucleus and Bulk Tissue RNA Sequencing by : Marcus Fernando Alvarez
Download or read book Methods and Applications of Integrating Single Nucleus and Bulk Tissue RNA Sequencing written by Marcus Fernando Alvarez and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Obesity typically precedes and accompanies the development of cardiometabolic diseases (CMD) that lead to increased morbidity and mortality. One of these disorders is non-alcoholic fatty liver disease (NAFLD), which encompasses a spectrum of varying degrees of fat accumulation and inflammation in the liver. More severe forms of NAFLD, such as non-alcoholic steatohepatitis (NASH), lead to a higher risk of developing hepatocellular carcinoma (HCC), the most prevalent form of liver cancer. Adipose tissue dysfunction in obesity can lead to increased circulating free fatty acids, and thus to ectopic lipid deposition in the liver. Left unchecked, lipotoxicity in the liver can result in inflammation, cell death, fibrosis, and ultimately the development of HCC. In both adipose and liver tissues, non-parenchymal cells, such as vascular and immune cell-types, play important roles in the normal function of these tissues and the pathophysiology of obesity, NAFLD, and HCC. A holistic approach to studying cell-types in a global manner would therefore greatly enhance our understanding of these common obesity-related diseases. Single-cell technologies, such as single-cell RNA-sequencing (scRNA-seq), assay individual cells and provide an excellent tool to study cell-type changes. While these approaches provide high resolution, they are currently costly and low-throughput. Traditional methods that measure molecular phenotypes at the tissue level are therefore still more practical. These assess a composite sum of cells present in the sample or biopsy, leading to inherent uncertainty in whether observed results are due to changes at the compositional level, cellular level, or both. Given these limitations, I aimed to integrate bulk-tissue RNA-sequencing (RNA-seq) and scRNA-seq data to leverage larger sample sizes in bulk RNA-seq and higher resolution in scRNA-seq. The application of single-cell technologies is especially promising for biobanks, as they can contain multiple levels of data on participants to uncover novel associations. Tissues are typically stored frozen, however, and this usually requires nuclei suspensions for single-nucleus RNA-seq (snRNA-seq), whereas whole cells would typically be used for scRNA-seq. This presents challenges for current droplet-based technologies. RNA from the ambient pool of lysed cells and nuclei can encapsulate into droplets, confounding results. In Chapter 2, I present a computational method to remove empty droplets from gene expression data (Alvarez et al. 2020). This allows for cleaner downstream data analysis by ensuring that only droplets with nuclei or cells are used. As current scRNA-seq technologies are low-throughput, their application to population-based studies and cohorts are limited. Present scRNA-seq technologies have lower throughput compared to bulk-tissue RNA-seq, which are typically available in higher sample sizes. In Chapter 3, I developed a method to help address this methodological gap. This approach, called Bisque (Jew et al. 2020), estimates cell-type composition in bulk RNA-seq data sets using single cell level reference data from the same tissue. The estimated cell-type proportions can be associated with sample-level data to uncover relevant cell-types, or they can be included as covariates in a model to reduce confounding caused by cell-type heterogeneity. One advantage of our method is that it requires only a minimum amount of information in the form of cell-type markers. This makes it attractive for existing data sets, which may not have accompanying single-cell level RNA-seq data. In the fourth chapter of this dissertation, I present our application of snRNA-seq to HCC. Carcinomas, such as HCC, are typically characterized by high amounts of tissue heterogeneity. Larger scale cancer cohorts usually lack single-cell level data, making interpretation of bulk-tissue results challenging. Here, I integrated HCC single-cell level experiments with relatively large HCC case-control bulk RNA-seq cohorts. The results from these analyses highlighted the role that proliferating cells play in HCC (Alvarez et al. 2022). These cycling cells were highly enriched in cancer tissue, as expected, and were prognostic of poor survival outcomes consistently in two independent cohorts. Furthermore, we observed that individuals with TP53 mutations have higher levels of these proliferating cells. Thus, our integration helped to interpret tumor gene expression changes as cell-type composition changes. In the fifth chapter, I present our human adipose tissue snRNA-seq results, showing changes in obesity and insulin resistance (Alvarez et al. manuscript in preparation). We applied multiplexing to increase our snRNA-seq sample size to roughly 100 subcutaneous adipose samples and over 100,000 nuclei, providing unprecedented resolution of human adipose tissue. This allowed us to identify finer resolution subcell-types, or cell states, which are more challenging to study as they are lower in frequency and exhibit more subtle differences. In addition to substantiating previous findings, we identified subcell-types associated with CMD. Then, we apply integrative approaches to corroborate these cell state changes in adipose bulk RNA-seq. Overall, our results show that both main cell-type and subcell-type variations are associated with metabolic traits. In summary, this dissertation presents my work on the integration of snRNA-seq and bulk- tissue RNA-seq to leverage distinct advantages provided by each. This has allowed us to gain a better understanding of the origin of gene expression changes in CMD.
Book Synopsis Multimodal and Integrative Analysis of Single-Cell or Bulk Sequencing Data by : Geng Chen
Download or read book Multimodal and Integrative Analysis of Single-Cell or Bulk Sequencing Data written by Geng Chen and published by Frontiers Media SA. This book was released on 2021-04-07 with total page 116 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 Integrative Approaches to Biotechnology by : Atul Bhargava
Download or read book Integrative Approaches to Biotechnology written by Atul Bhargava and published by CRC Press. This book was released on 2023-09-29 with total page 292 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biotechnology is one of the fastest emerging fields that has attracted attention of conventional biologists, biochemists, microbiologists, medical and agricultural scientists. The coming decades are likely to witness a boom in biotechnology, which is expected to surpass information technology as the new engine of the global economy. Biotechnology is experiencing a revolution that will affect every facet of our lives, from crop improvement to commerce, drugs and sustainable development. New approaches and a plethora of information available at a frantic pace demands its dissemination to the scientific community. The current book has been written with the specific objective of providing information on the recent developments in biotechnology to the readers. The proposed book presents a multidisciplinary approach to the latest information and developments in biotechnology in an easy-to-read, succinct format. The book has been divided into 6 sections and 15 chapters giving an in-depth analysis of the latest research and developments in the biotechnological realm. The topics have been presented in a lucid, easy-to-read methodical way with illustrations and suitable case studies to provide additional help and clarity. The authors have tried to present state-of-the-art and integrative information in a manner that familiarizes the reader with the important concepts and tools of recent biotechnological studies. Apart from biotechnological personnel, the book would also be useful for readers of diverse disciplines such as bioinformatics, agriculture, environmental science, pharmaceutical sciences, biochemistry and general biology. Features A systematic overview of the recent state-of-the-art technologies. Novel contents with maximum coherence. Extensive use of examples and case studies to illustrate how each technique has been used in practice. Incorporation of the latest information on these topics from recent research papers. This book serves as a reference book and presents information in an accessible way for students, researchers and scientific investigators in biotechnology. It may also be used as a textbook for postgraduate-level courses in biological sciences.
Book Synopsis Bioinformatics Analysis of Single Cell Sequencing Data and Applications in Precision Medicine by : Jialiang Yang
Download or read book Bioinformatics Analysis of Single Cell Sequencing Data and Applications in Precision Medicine written by Jialiang Yang and published by Frontiers Media SA. This book was released on 2020-02-27 with total page 136 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Single Cell Transcriptomics by : Raffaele A. Calogero
Download or read book Single Cell Transcriptomics written by Raffaele A. Calogero and published by Springer Nature. This book was released on 2022-12-10 with total page 394 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
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 2020-01-29 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
Book Synopsis Computational Systems Biology by : Andres Kriete
Download or read book Computational Systems Biology written by Andres Kriete and published by Academic Press. This book was released on 2013-11-26 with total page 549 pages. Available in PDF, EPUB and Kindle. Book excerpt: This comprehensively revised second edition of Computational Systems Biology discusses the experimental and theoretical foundations of the function of biological systems at the molecular, cellular or organismal level over temporal and spatial scales, as systems biology advances to provide clinical solutions to complex medical problems. In particular the work focuses on the engineering of biological systems and network modeling. Logical information flow aids understanding of basic building blocks of life through disease phenotypes Evolved principles gives insight into underlying organizational principles of biological organizations, and systems processes, governing functions such as adaptation or response patterns Coverage of technical tools and systems helps researchers to understand and resolve specific systems biology problems using advanced computation Multi-scale modeling on disparate scales aids researchers understanding of dependencies and constraints of spatio-temporal relationships fundamental to biological organization and function.
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 Integrative Omics by : Manish Kumar Gupta
Download or read book Integrative Omics written by Manish Kumar Gupta and published by Elsevier. This book was released on 2024-05-10 with total page 434 pages. Available in PDF, EPUB and Kindle. Book excerpt: Integrative Omics: Concepts, Methodology and Applications provides a holistic and integrated view of defining and applying network approaches, integrative tools, and methods to solve problems for the rationalization of genotype to phenotype relationships. The reference includes a range of chapters in a systemic ‘step by step’ manner, which begins with the basic concepts from Omic to Multi Integrative Omics approaches, followed by their full range of approaches, applications, emerging trends, and future trends. All key areas of Omics are covered including biological databases, sequence alignment, pharmacogenomics, nutrigenomics and microbial omics, integrated omics for Food Science and Identification of genes associated with disease, clinical data integration and data warehousing, translational omics as well as omics technology policy and society research. Integrative Omics: Concepts, Methodology and Applications highlights the recent concepts, methodologies, advancements in technologies and is also well-suited for researchers from both academic and industry background, undergraduate and graduate students who are mainly working in the area of computational systems biology, integrative omics and translational science. The book bridges the gap between biological sciences, physical sciences, computer science, statistics, data science, information technology and mathematics by presenting content specifically dedicated to mathematical models of biological systems. Provides a holistic, integrated view of a defining and applying network approach, integrative tools, and methods to solve problems for rationalization of genotype to phenotype relationships Offers an interdisciplinary approach to Databases, data analytics techniques, biological tools, network construction, analysis, modeling, prediction and simulation of biological systems leading to ‘translational research’, i.e., drug discovery, drug target prediction, and precision medicine Covers worldwide methods, concepts, databases, and tools used in the construction of integrated pathways
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 Single-cell Sequencing and Methylation by : Buwei Yu
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.
Book Synopsis Integrative analysis of single-cell and/or bulk multi-omics sequencing data by : Geng Chen
Download or read book Integrative analysis of single-cell and/or bulk multi-omics sequencing data written by Geng Chen and published by Frontiers Media SA. This book was released on 2023-03-13 with total page 189 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Development of Highly Sensitive Single-cell RNA-SEQ Technologies and Their Applications by : Kuanwei Sheng
Download or read book Development of Highly Sensitive Single-cell RNA-SEQ Technologies and Their Applications written by Kuanwei Sheng and published by . This book was released on 2019 with total page 40 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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
