Download or read book Orchestrating the Single cell Transcriptome written by Boyan Li and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Single-cell RNA-sequencing (scRNA-seq) is a technique that measures the transcriptional profile of the samples at single-cell resolution. Such a breakthrough technique brings the genomic study to an entirely new level, providing potential to understand some of the fundamental problems in biology, including gene expression, cell differentiation, cancer progression, and many more. With the help from statisticians, bioinformaticians and computer scientists, pipelines have been developed to process and analyze the huge amount of information from scRNA-seq experiments. However, challenges remain as customization is still needed depending on specific input dataset. In this study, we applied scRNA-seq to mouse embryos at early organogenesis to understand the cell type dynamics and gene regulations during development, using a variety of data analysis tools with experimental validation. In Chapter 1, we introduced our data analysis pipeline for analyzing large-scale high-heterogeneity dataset obtained from mouse whole embryos at E11.5, and presented a complete catalog of cell types using an integrated annotation approach. In Chapter 2, we extended such a pipeline to time-series datasets from mouse embryos at different stages, by successful removal of batch effects and integration of multiple datasets we provided insights into how cell types emerge and disappear during embryogenesis. In Chapter 3, we focused on the gene expression pattern revealed by scRNA-seq datasets, and presented a novel approach to identify housekeeping genes from these datasets. In Chapter 4, we have investigated the scRNA-seq datasets from a completely different perspective, treating genes as samples and clustered genes into groups with similar biological functions named 'metagene', and successfully using metagene as a novel approach to understand genes with unknown functions. Our results showed the possibility of using scRNA-seq as a powerful tool to understand mouse embryonic development from different perspectives, and provided valuable data that could be used for more detailed studies on specific cell types or genes.
Download or read book Single Cell Transcriptomics Reveal Regulators of Progenitor Cell Fate and Postmitotic Maturation During Brain Development written by Daniel Pensold and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: In this thesis the NanoString nCounter technology was applied to validate an improved PCR-based strategy for quantitative and qualitative global single cell transcriptome analysis. RNA isolates from whole tissue were quantitatively compared with cDNA amplificates prepared from single cell equivalent dilutions of the same RNA. A significant correlation was obtained between the values measured for RNA and cDNA amplificates for transcript copy numbers from 10 to several thousand. This method was then used to investigate two distinct neurodevelopmental issues. The first neuroscientific question dealt with the generation of cortical projection neurons, whose fate is specified at the progenitor level and depends on the mode of division. With the help of the high resolution of the single cell amplification method, it was possible to provide evidence for an extra-cortical fine-tuning of cortical progenitor output via the Eph-receptor/ephrin-ligand system. The method was further applied to investigate cortical interneuron development, especially to their post-mitotic phase of tangential migration. To identify factors orchestrating the migration, we analyzed single cell transcriptomes of cells derived from distinct proliferative niches of interneurons in the basal telencephalon. Interestingly, we observed DNA methyltransferase 1 (Dnmt1) expression in a fraction of post-mitotic POA-derived cortical interneurons. Deletion of Dnmt1 in this interneurons caused defective migration, resulting in drastically reduced numbers of cortical interneurons in adults. Next generation sequencing analysis of FAC-sorted Dnmt1 wildtype and knockout mice revealed DNMT1-dependent repression of genes involved in late maturational processes like neurite outgrowth. In this context, further experiments provide evidence that DNMT1 preserves the migratory shape of postmitotic GABAergic interneurons in part through negative regulation of Pak6, which stimulates neuritogenesis at post-migratory stages.
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 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.
Download or read book Advances in Computational Biology written by Hamid R. Arabnia and published by Springer Science & Business Media. This book was released on 2010-09-24 with total page 732 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proceedings of The 2009 International Conference on Bioinformatics and Computational Biology in Las Vegas, NV, July 13-16, 2009. Recent advances in Computational Biology are covered through a variety of topics. Both inward research (core areas of computational biology and computer science) and outward research (multi-disciplinary, Inter-disciplinary, and applications) will be covered during the conferences. These include: Gene regulation, Gene expression databases, Gene pattern discovery and identification, Genetic network modeling and inference, Gene expression analysis, RNA and DNA structure and sequencing, Biomedical engineering, Microarrays, Molecular sequence and structure databases, Molecular dynamics and simulation, Molecular sequence classification, alignment and assembly, Image processing In medicine and biological sciences, Sequence analysis and alignment, Informatics and Statistics in Biopharmaceutical Research, Software tools for computational biology and bioinformatics, Comparative genomics; and more.
Download or read book Interactive Web Based Data Visualization with R plotly and shiny written by Carson Sievert and published by CRC Press. This book was released on 2020-01-30 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt: The richly illustrated Interactive Web-Based Data Visualization with R, plotly, and shiny focuses on the process of programming interactive web graphics for multidimensional data analysis. It is written for the data analyst who wants to leverage the capabilities of interactive web graphics without having to learn web programming. Through many R code examples, you will learn how to tap the extensive functionality of these tools to enhance the presentation and exploration of data. By mastering these concepts and tools, you will impress your colleagues with your ability to quickly generate more informative, engaging, and reproducible interactive graphics using free and open source software that you can share over email, export to pdf, and more. Key Features: Convert static ggplot2 graphics to an interactive web-based form Link, animate, and arrange multiple plots in standalone HTML from R Embed, modify, and respond to plotly graphics in a shiny app Learn best practices for visualizing continuous, discrete, and multivariate data Learn numerous ways to visualize geo-spatial data This book makes heavy use of plotly for graphical rendering, but you will also learn about other R packages that support different phases of a data science workflow, such as tidyr, dplyr, and tidyverse. Along the way, you will gain insight into best practices for visualization of high-dimensional data, statistical graphics, and graphical perception. The printed book is complemented by an interactive website where readers can view movies demonstrating the examples and interact with graphics.
Download or read book Transcriptome Data Analysis written by Yejun Wang and published by Humana. This book was released on 2019-03-20 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed volume provides comprehensive practical guidance on transcriptome data analysis for a variety of scientific purposes. Beginning with general protocols, the collection moves on to explore protocols for gene characterization analysis with RNA-seq data as well as protocols on several new applications of transcriptome studies. Written for the highly successful Methods in Molecular Biology series, 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 useful, Transcriptome Data Analysis: Methods and Protocols serves as an ideal guide to the expanding purposes of this field of study.
Download or read book Heritable Human Genome Editing written by The Royal Society and published by National Academies Press. This book was released on 2021-01-16 with total page 239 pages. Available in PDF, EPUB and Kindle. Book excerpt: Heritable human genome editing - making changes to the genetic material of eggs, sperm, or any cells that lead to their development, including the cells of early embryos, and establishing a pregnancy - raises not only scientific and medical considerations but also a host of ethical, moral, and societal issues. Human embryos whose genomes have been edited should not be used to create a pregnancy until it is established that precise genomic changes can be made reliably and without introducing undesired changes - criteria that have not yet been met, says Heritable Human Genome Editing. From an international commission of the U.S. National Academy of Medicine, U.S. National Academy of Sciences, and the U.K.'s Royal Society, the report considers potential benefits, harms, and uncertainties associated with genome editing technologies and defines a translational pathway from rigorous preclinical research to initial clinical uses, should a country decide to permit such uses. The report specifies stringent preclinical and clinical requirements for establishing safety and efficacy, and for undertaking long-term monitoring of outcomes. Extensive national and international dialogue is needed before any country decides whether to permit clinical use of this technology, according to the report, which identifies essential elements of national and international scientific governance and oversight.
Download or read book Transcription Regulation Brain Development and Homeostasis A Finely Tuned and Orchestrated Scenario in Physiology and Pathology written by Estela Maris Muñoz and published by Frontiers Media SA. This book was released on 2022-02-21 with total page 194 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Deciphering Cellular Heterogeneity by Single cell Transcriptome Analysis written by Lam-Ha Ly and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Precision Medicine in Cancer Therapy written by Daniel D. Von Hoff and published by Springer. This book was released on 2019-06-17 with total page 283 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents the latest advances in precision medicine in some of the most common cancer types, including hematological, lung and breast malignancies. It also discusses emerging technologies that are making a significant impact on precision medicine in cancer therapy. In addition to describing specific approaches that have already entered clinical practice, the book explores new concepts and tools that are being developed. Precision medicine aims to deliver personalized healthcare tailored to a patient’s genetics, lifestyle and environment, and cancer therapy is one of the areas in which it has flourished in recent years. Documenting the latest advances, this book is of interest to physicians and clinical fellows in the front line of the war on cancer, as well as to basic scientists working in the fields of cancer biology, drug development, biomarker discovery, and biomedical engineering. The contributing authors include translational physicians with first-hand experience in precision patient care.
Download or read book Machine Learning and Mathematical Models for Single Cell Data Analysis written by Le Ou-Yang and published by Frontiers Media SA. This book was released on 2022-11-29 with total page 118 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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:
Download or read book Green Systems Biology written by Wolfram Weckwerth and published by Walter de Gruyter. This book was released on 2016-03-05 with total page 350 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems biology is an approach to combine molecular data, genetic evolution, environmental cues and species-interaction with the understanding, modeling and prediction of active biochemical networks. This book provides a thorough introduction to the field and treats applications of systems biology in ecology, nutrition, biofuel and drug discovery. With increasing problems in feeding the world population, changes in the global climate and limited energy resources from fossil fuels, researchers and industry are turning to plants as a resource of raw materials for solving the human dilemma on earth. At the brink of the third "Green Revolution", systems biology isidentifying key issues for the investigation of plant model systems up to whole ecosystems.
Download or read book Transcription Regulation Brain Development and Homeostasis A Finely Tuned and Orchestrated Scenario in Physiology and Pathology Volume II written by Estela Maris Muñoz and published by Frontiers Media SA. This book was released on 2023-10-03 with total page 169 pages. Available in PDF, EPUB and Kindle. Book excerpt: A finely tuned regulation of gene expression is essential for shaping the nervous system and for maintaining its homeostasis throughout life. Disruptions in gene regulation can impact brain development and physiology in ways that contribute to diverse pathologies. The master orchestrators of gene activity in the nucleus are transcription factors, proteins that recognize and bind to specific DNA motifs in regulatory regions and drive changes in gene expression. Transcription factors act with the help of other co-factor proteins, including components of the Mediator complex, histone modifying enzymes, chromatin modelers, and DNA methylases. In addition, transcription factor activity in the nervous system can be modulated by extracellular signals, including growth factors, hormones, neuropeptides and neurotransmitters that activate specific receptors and intracellular transduction pathways. An in-depth understanding of the mechanisms of transcription regulation is needed in order to better describe how each element, from genes to cells, defines and maintains identities and functionalities in the healthy and diseased brain. This Research Topic is oriented to developing an integrative view about transcription regulation within the nervous system, focusing on developmental and homeostatic processes, dysregulation in functionality and expression levels and consequent associated pathologies such as neurodevelopmental disorders, brain tumors, and neurodegenerative diseases. Transcription regulation investigations will specifically focus on transcription factors that belong to the bHLH (e.g. NeuroD), homeobox (e.g. Islet, Pax, Rax, and Lhx) and CREB families, and on their roles over defined nervous system areas: cerebral cortex, thalamic and hypothalamic areas, interacting with the developing brain.
Download or read book Mobile DNA Finding Treasure in Junk written by Haig H. Kazazian and published by FT Press. This book was released on 2011 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: Annotation What we now know about mobile DNA--and the substantial roles it plays in humans, animals, and plants. & bull; & bull;Mobile DNA accounts for more than half of our genome: This book explains the important role it plays in shaping evolutionary change. & bull;A rich, thorough, and accessible introduction for all serious students, practitioners, and researchers in human and medical genetics, molecular biology, or evolutionary biology. & bull;By one of the field's leading researchers, Dr. Haig Kazazian. This book thoroughly reviews our current scientific understanding of the significant role that mobile genetic elements play in the evolution and function of genomes and organisms--from plants and animals to humans. Highly regarded geneticist Haig Kazazian offers an accessible intellectual history of the field's research strategies and concerns, explaining how advances opened up new questions, and how new tools and capabilities have encouraged progress in the field. Kazazian introduces the key strategies and approaches taken in leading laboratories (including his own) to gain greater insight into the large proportion of our genome that derives from mobile genetic elements, including viruses, plasmids, and transposons. He also presents intriguing insights into long-term research strategies that may lead to an even deeper understanding.
Download or read book Handbook of Maize Its Biology written by Jeff L. Bennetzen and published by Springer Science & Business Media. This book was released on 2008-12-25 with total page 593 pages. Available in PDF, EPUB and Kindle. Book excerpt: Handbook of Maize: Its Biology centers on the past, present and future of maize as a model for plant science research and crop improvement. The book includes brief, focused chapters from the foremost maize experts and features a succinct collection of informative images representing the maize germplasm collection.
