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Author : Himel Mallick
Publisher : Frontiers Media SA
ISBN 13 : 2889762807
Total Pages : 129 pages
Book Rating : 4.04/5 ( download)
Download or read book Methods for Single-Cell and Microbiome Sequencing Data written by Himel Mallick and published by Frontiers Media SA. This book was released on 2022-05-31 with total page 129 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Ruochen Jiang
Publisher :
ISBN 13 :
Total Pages : 175 pages
Book Rating : 4.05/5 ( download)
Download or read book Development and Benchmarking of Imputation Methods for Micriobome and Single-cell Sequencing Data written by Ruochen Jiang and published by . This book was released on 2021 with total page 175 pages. Available in PDF, EPUB and Kindle. Book excerpt: Next generation sequencing (NGS) has revolutionized biomedical research and has a broad impact and applications. Since its advent around 15 years ago, this high scalable DNA sequencing technology has generated numerous biological data with new features and brought new challenges to data analysis. For example, researchers utilize RNA sequencing (RNA-seq) technology to more accurately quantify the gene expression levels. However, the NGS technology involves many processing steps and technical variations when measuring the expression values in the biological samples. In other words, the NGS data researchers observed could be biased due to the randomness and constraints in the NGS technology. This dissertation will mainly focus on microbiome sequencing data and single-cell RNA-seq (scRNA-seq) data. Both of them are highly sparse matrix-form count data. The zeros could either be biological or non-biological, and the high sparsity in the data have brought challenges to data analysis. Missing data imputation problem has been studied in statistics and social science as the survey data often experience non-response to some of the survey questions and those unresponded questions will be marked as "NA" or missing values in the data. Imputation methods are used to provide a sophisticated guess for the missing values, and the purpose is to avoid discarding the collected samples and for the ease of using the state-of-the-art statistical methods. In machine learning, the famous Netflix data challenge regarding film recommendation system also falls into the missing data imputation problem category. Netflix wants to find a way to predict users' fondness of the movies they have not watched. The potential scores these users would give to the unwatched films are regarded as missing values in the data. NGS data imputation problem is different from the previous two cases in that the missing values in the NGS data are not so well-defined. The zeros in the NGS data could either come from the biological origin (should not be regarded as missing values) or non-biological origin (due to the limitation of the sequencing technology and should be regarded as missing values). The size (number of samples and features) of the NGS matrix data is usually larger than the size of survey data but smaller than the size of the recommendation system data. In addition, in most cases, the percentage of missing values in the survey data is less than the percentage of zeros in the NGS data, and the missing values in the film recommendation system data have the highest percentage (> 99.9%). As a result, the commonly used missing data imputation methods in statistics and machine learning are not directly applicable to NGS data. In recent years, numerous imputation methods have been proposed to deal with the highly sparse scRNA-seq data. In light of this, this dissertation aims to address two questions. First, the microbiome sequencing data, having additional information comparing to the scRNA-seq data, lacks an imputation method. Secondly, whether to use imputation or not in scRNA-seq data analysis is still a controversial problem. The first part of this dissertation focuses on the first imputation method developed for the microbiome sequencing data: mbImpute. Microbiome studies have gained increased attention since many discoveries revealed connections between human microbiome compositions and diseases. A critical challenge in microbiome data analysis is the existence of many non-biological zeros, which distort taxon abundance distributions, complicate data analysis, and jeopardize the reliability of scientific discoveries. To address this issue, we propose the first imputation method for microbiome data---mbImpute---to identify and recover likely non-biological zeros by borrowing information jointly from similar samples, similar taxa, and optional metadata including sample covariates and taxon phylogeny. Comprehensive simulations verify that mbImpute achieves better imputation accuracy under multiple metrics, compared with five state-of-the-art imputation methods designed for non-microbiome data. In real data applications, we demonstrate that mbImpute improves the power of identifying disease-related taxa from microbiome data of type 2 diabetes and colorectal cancer, and mbImpute preserves non-zero distributions of taxa abundances. The second part of this dissertation focuses on how to deal with high sparsity in the scRNA-seq data. ScRNA-seq technologies have revolutionized biomedical sciences by enabling genome-wide profiling of gene expression levels at an unprecedented single-cell resolution. A distinct characteristic of scRNA-seq data is the vast proportion of zeros unseen in bulk RNA-seq data. Researchers view these zeros differently: some regard zeros as biological signals representing no or low gene expression, while others regard zeros as false signals or missing data to be corrected. As a result, the scRNA-seq field faces much controversy regarding how to handle zeros in data analysis. We first discuss the sources of biological and non-biological zeros in scRNA-seq data. Second, we evaluate the impacts of non-biological zeros on cell clustering and differential gene expression analysis. Third, we summarize the advantages, disadvantages, and suitable users of three input data types: observed counts, imputed counts, and binarized counts and evaluate the performance of downstream analysis on these three input data types. Finally, we discuss the open questions regarding non-biological zeros, the need for benchmarking, and the importance of transparent analysis.
Author : Robert G. Beiko
Publisher :
ISBN 13 : 9781493987283
Total Pages : 324 pages
Book Rating : 4.83/5 ( download)
Download or read book Microbiome Analysis written by Robert G. Beiko and published by . This book was released on 2018 with total page 324 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : National Academies of Sciences, Engineering, and Medicine
Publisher : National Academies Press
ISBN 13 : 0309468698
Total Pages : 123 pages
Book Rating : 4.95/5 ( download)
Download or read book Environmental Chemicals, the Human Microbiome, and Health Risk written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2018-03-01 with total page 123 pages. Available in PDF, EPUB and Kindle. Book excerpt: A great number of diverse microorganisms inhabit the human body and are collectively referred to as the human microbiome. Until recently, the role of the human microbiome in maintaining human health was not fully appreciated. Today, however, research is beginning to elucidate associations between perturbations in the human microbiome and human disease and the factors that might be responsible for the perturbations. Studies have indicated that the human microbiome could be affected by environmental chemicals or could modulate exposure to environmental chemicals. Environmental Chemicals, the Human Microbiome, and Health Risk presents a research strategy to improve our understanding of the interactions between environmental chemicals and the human microbiome and the implications of those interactions for human health risk. This report identifies barriers to such research and opportunities for collaboration, highlights key aspects of the human microbiome and its relation to health, describes potential interactions between environmental chemicals and the human microbiome, reviews the risk-assessment framework and reasons for incorporating chemicalâ€"microbiome interactions.
Author : Pallaval Veera Bramhachari
Publisher : Springer Nature
ISBN 13 : 9811631565
Total Pages : 306 pages
Book Rating : 4.66/5 ( download)
Download or read book Microbiome in Human Health and Disease written by Pallaval Veera Bramhachari and published by Springer Nature. This book was released on 2021-10-18 with total page 306 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book provides an overview on how the microbiome contributes to human health and disease. The microbiome has also become a burgeoning field of research in medicine, agriculture & environment. The readers will obtain profound knowledge on the connection between intestinal microbiota and immune defense systems, medicine, agriculture & environment. The book may address several researchers, clinicians and scholars working in biomedicine, microbiology and immunology. The application of new technologies has no doubt revolutionized the research initiatives providing new insights into the dynamics of these complex microbial communities and their role in medicine, agriculture & environment shall be more emphasized. Drawing on broad range concepts of disciplines and model systems, this book primarily provides a conceptual framework for understanding these human-microbe, animal-microbe & plant-microbe, interactions while shedding critical light on the scientific challenges that lie ahead. Furthermore this book explains why microbiome research demands a creative and interdisciplinary thinking—the capacity to combine microbiology with human, animal and plant physiology, ecological theory with immunology, and evolutionary perspectives with metabolic science.This book provides an accessible and authoritative guide to the fundamental principles of microbiome science, an exciting and fast-emerging new discipline that is reshaping many aspects of the life sciences. These microbial partners can also drive ecologically important traits, from thermal tolerance to diet in a typical immune system, and have contributed to animal and plant diversification over long evolutionary timescales. Also this book explains why microbiome research presents a more complete picture of the biology of humans and other animals, and how it can deliver novel therapies for human health and new strategies.
Author : Vera Pawlowsky-Glahn
Publisher : John Wiley & Sons
ISBN 13 : 0470711353
Total Pages : 405 pages
Book Rating : 4.54/5 ( download)
Download or read book Compositional Data Analysis written by Vera Pawlowsky-Glahn and published by John Wiley & Sons. This book was released on 2011-09-19 with total page 405 pages. Available in PDF, EPUB and Kindle. Book excerpt: It is difficult to imagine that the statistical analysis of compositional data has been a major issue of concern for more than 100 years. It is even more difficult to realize that so many statisticians and users of statistics are unaware of the particular problems affecting compositional data, as well as their solutions. The issue of ``spurious correlation'', as the situation was phrased by Karl Pearson back in 1897, affects all data that measures parts of some whole, such as percentages, proportions, ppm and ppb. Such measurements are present in all fields of science, ranging from geology, biology, environmental sciences, forensic sciences, medicine and hydrology. This book presents the history and development of compositional data analysis along with Aitchison's log-ratio approach. Compositional Data Analysis describes the state of the art both in theoretical fields as well as applications in the different fields of science. Key Features: Reflects the state-of-the-art in compositional data analysis. Gives an overview of the historical development of compositional data analysis, as well as basic concepts and procedures. Looks at advances in algebra and calculus on the simplex. Presents applications in different fields of science, including, genomics, ecology, biology, geochemistry, planetology, chemistry and economics. Explores connections to correspondence analysis and the Dirichlet distribution. Presents a summary of three available software packages for compositional data analysis. Supported by an accompanying website featuring R code. Applied scientists working on compositional data analysis in any field of science, both in academia and professionals will benefit from this book, along with graduate students in any field of science working with compositional data.
Author : Jialiang Yang
Publisher : Frontiers Media SA
ISBN 13 : 2889635287
Total Pages : 136 pages
Book Rating : 4.83/5 ( download)
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:
Author : Xinghua Pan
Publisher : Frontiers Media SA
ISBN 13 : 2889459209
Total Pages : 129 pages
Book Rating : 4.09/5 ( download)
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.
Author : National Research Council
Publisher : National Academies Press
ISBN 13 : 0309106761
Total Pages : 170 pages
Book Rating : 4.64/5 ( download)
Download or read book The New Science of Metagenomics written by National Research Council and published by National Academies Press. This book was released on 2007-06-24 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt: Although we can't usually see them, microbes are essential for every part of human life-indeed all life on Earth. The emerging field of metagenomics offers a new way of exploring the microbial world that will transform modern microbiology and lead to practical applications in medicine, agriculture, alternative energy, environmental remediation, and many others areas. Metagenomics allows researchers to look at the genomes of all of the microbes in an environment at once, providing a "meta" view of the whole microbial community and the complex interactions within it. It's a quantum leap beyond traditional research techniques that rely on studying-one at a time-the few microbes that can be grown in the laboratory. At the request of the National Science Foundation, five Institutes of the National Institutes of Health, and the Department of Energy, the National Research Council organized a committee to address the current state of metagenomics and identify obstacles current researchers are facing in order to determine how to best support the field and encourage its success. The New Science of Metagenomics recommends the establishment of a "Global Metagenomics Initiative" comprising a small number of large-scale metagenomics projects as well as many medium- and small-scale projects to advance the technology and develop the standard practices needed to advance the field. The report also addresses database needs, methodological challenges, and the importance of interdisciplinary collaboration in supporting this new field.
Author : S. Rosenthal
Publisher : Elsevier
ISBN 13 : 1483188515
Total Pages : 565 pages
Book Rating : 4.15/5 ( download)
Download or read book Gene Function written by S. Rosenthal and published by Elsevier. This book was released on 2014-05-09 with total page 565 pages. Available in PDF, EPUB and Kindle. Book excerpt: Gene Function, contains the proceedings of the 12th Meeting of the Federation of European Biochemical Societies held in Dresden, Germany in 1978. The meeting provided a forum for discussing progress in the understanding of gene function and covered topics ranging from the functional organization of chromatin to principles of interactions and recognition models. The role of DNA sequence in the recognition of restriction endonucleases and modification enzymes is also examined, along with gene expression, RNA processing and modification, and isolation and synthesis of genes. Comprised of 49 chapters, this volume begins with an overview of what can be learned from the genetic analysis of the lac repressor, followed by a discussion on the topography of the interaction the lac repressor, RNA polymerase, and histones with DNA. The reader is then introduced to complementarity and recognition code between regulatory proteins and DNA; chromatin replication in vitro; and the cytoplasmic "petite" mutation in Saccharomyces cerevisiae. Subsequent chapters explore arc-like and helical arrangements of nucleosome cores; changes in gene expression during cellular differentiation; polyadenylation and processing of pre-messenger RNA; and the molecular biology of bacteriophages T3 and T7. This book will be of interest to geneticists, biochemists, and molecular biologists.
