Methods For Single Cell And Microbiome Sequencing Data

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Methods For Single Cell And Microbiome Sequencing Data

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Author : Himel Mallick
language : en
Publisher: Frontiers Media SA
Release Date : 2022-05-31

Methods For Single Cell And Microbiome Sequencing Data written by Himel Mallick and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-05-31 with Science categories.

Microbiome Analysis

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Author : Robert G. Beiko
language : en
Publisher:
Release Date : 2018

Microbiome Analysis written by Robert G. Beiko and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018 with Microbiology categories.

Methodologies Of Multi Omics Data Integration And Data Mining

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Author : Kang Ning
language : en
Publisher: Springer Nature
Release Date : 2023-01-15

Methodologies Of Multi Omics Data Integration And Data Mining written by Kang Ning and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-01-15 with Medical categories.

This book features multi-omics big-data integration and data-mining techniques. In the omics age, paramount of multi-omics data from various sources is the new challenge we are facing, but it also provides clues for several biomedical or clinical applications. This book focuses on data integration and data mining methods for multi-omics research, which explains in detail and with supportive examples the “What”, “Why” and “How” of the topic. The contents are organized into eight chapters, out of which one is for the introduction, followed by four chapters dedicated for omics integration techniques focusing on several omics data resources and data-mining methods, and three chapters dedicated for applications of multi-omics analyses with application being demonstrated by several data mining methods. This book is an attempt to bridge the gap between the biomedical multi-omics big data and the data-mining techniques for the best practice of contemporary bioinformatics and the in-depth insights for the biomedical questions. It would be of interests for the researchers and practitioners who want to conduct the multi-omics studies in cancer, inflammation disease, and microbiome researches.

Introduction To Single Cell Omics

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Author : Xinghua Pan
language : en
Publisher: Frontiers Media SA
Release Date : 2019-09-19

Introduction To Single Cell Omics written by Xinghua Pan and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-09-19 with categories.

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.

Computational Methods For Microbiome Analysis Volume 2

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Author : Setubal
language : en
Publisher: Frontiers Media SA
Release Date : 2023-01-04

Computational Methods For Microbiome Analysis Volume 2 written by Setubal and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-01-04 with Science categories.

Computational And Systems Biology Methods For Elucidating Associations Between Cancer And Microbes

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Author : Lihong Peng
language : en
Publisher: Frontiers Media SA
Release Date : 2024-02-01

Computational And Systems Biology Methods For Elucidating Associations Between Cancer And Microbes written by Lihong Peng and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-02-01 with Science categories.

Bioinformatics Analysis Of Single Cell Sequencing Data And Applications In Precision Medicine

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Author : Jialiang Yang
language : en
Publisher: Frontiers Media SA
Release Date : 2020-02-27

Bioinformatics Analysis Of Single Cell Sequencing Data And Applications In Precision Medicine written by Jialiang Yang and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-02-27 with categories.

Advances In Host Genetics And Microbiome In Colorectal Cancer Related Phenotypes

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Author :
language : en
Publisher: Elsevier
Release Date : 2024-10-11

Advances In Host Genetics And Microbiome In Colorectal Cancer Related Phenotypes written by and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-10-11 with Science categories.

Advances in Host Genetics and Microbiome in Colorectal Cancer-Related Phenotypes, Volume 112 in the Advances in Genetics series, highlights new advances in the field with this new volume presenting interesting chapters on topics such as What we need in colorectal cancer research, and why?, Host Genetics and Microbiota procedures in colorectal cancer research, Host Genetics-associated mechanisms in colorectal cancer, Microbiota-associated mechanisms in colorectal cancer, Inflammation regulation in colorectal cancer, Microbiota and detrimental protein metabolites in colorectal cancer, Microbiota and other detrimental metabolites in colorectal cancer, Microbiota and beneficial metabolites in colorectal cancer, and much more. - Provides the authority and expertise of leading contributors from an international board of authors - Presents the latest release in the Advances in Genetics series - Includes the latest information on new advancements in the study of genetics

Compositional Data Analysis

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Author : Vera Pawlowsky-Glahn
language : en
Publisher: John Wiley & Sons
Release Date : 2011-09-19

Compositional Data Analysis written by Vera Pawlowsky-Glahn and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-09-19 with Mathematics categories.

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.

Marine Microbiomes Towards Standard Methods And Best Practices

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Author : Stéphane Pesant
language : en
Publisher: Frontiers Media SA
Release Date : 2023-12-14

Marine Microbiomes Towards Standard Methods And Best Practices written by Stéphane Pesant and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-12-14 with Science categories.

A decade of technological advances and research on the human microbiome has re-defined our understanding of biological systems, and now offers diagnostic tools and new approaches to human health. Likewise, marine ecosystems are driven by their microbiome, the ensemble of microscopic organisms that inhabit the water column, sediments and aquatic organisms, and regulate most fluxes of energy and matter. While the human microbiome is composed principally of bacteria, the marine microbiome has a much broader ensemble of microscopic organisms with sizes spanning from viruses of a few tens of nanometres to metazoans of several centimetres. Advances in high throughput imaging and sequencing are emerging in aquatic science, providing important insights into ecosystem structure and functions, and contributing to develop new indicators of ecosystem health and potential hazards to living resources and humans. A number of research exploration and monitoring programs such as the Tara Oceans global expedition and the Marine Biological Observing Network (MBON), and the rising popularity of environmental DNA (eDNA) already led to a wealth of data. However, the wide range of methodologies used in this early exploration phase poses a challenge to integrative studies, prompting community responses such as the Genomic Standards Consortium. This Research Topic will foster cross-community exchange of standards and best practices. It is an opportunity for the different communities working on marine microbiomes to discuss the advantages and the limitations of their sampling and analysis methods. The collection of papers will constitute a knowledge base aimed at (1) addressing the integration of existing observations from heterogenous methods and data types, and (2) working towards cross-communities standards and best practices for future observations and experiments. This Research Topic will publish comprehensive methodological papers that review a sufficiently large body of field or experimental work. Supporting (meta)data, such as environmental context, sampling materials, sample treatments, extraction and imaging yields, must be provided and should preferably be uploaded to an online sample registry such as BioSamples. Protocols and analytical methods should preferably be uploaded to an online repository such as Protocols.io. We welcome contributions from communities working in different environments: · focus on marine systems, but also interested in estuarine and freshwater systems · coastal, open ocean and deep-sea regions · benthic, pelagic and aerosol environments We strongly encourage contributions from communities involved in: · networks of local observatories and long-term monitoring programs · regional & basin-scale surveys, and global expeditions · biodiscovery linked to economic sectors such as pharmaceutics and bioengineering · environmental and health assessments linked to economic sectors such as aquaculture, fisheries, seabed mining, wind-farms, and oil and gas