Benchmarking And Development Of Computational Methods For Single Cell Data Analysis Challenges And Opportunities

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Benchmarking And Development Of Computational Methods For Single Cell Data Analysis Challenges And Opportunities

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Author : Almut Lütge
language : en
Publisher:
Release Date : 2023

Benchmarking And Development Of Computational Methods For Single Cell Data Analysis Challenges And Opportunities written by Almut Lütge and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023 with categories.

Computational Methods For Single Cell Data Analysis

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Author : Guo-Cheng Yuan
language : en
Publisher: Humana Press
Release Date : 2019-02-14

Computational Methods For Single Cell Data Analysis written by Guo-Cheng Yuan and has been published by Humana Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-02-14 with Science categories.

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.

Biocomputing 2019 Proceedings Of The Pacific Symposium

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Author : Russ B Altman
language : en
Publisher: World Scientific
Release Date : 2018-11-28

Biocomputing 2019 Proceedings Of The Pacific Symposium written by Russ B Altman and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-11-28 with Computers categories.

The Pacific Symposium on Biocomputing (PSB) 2019 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2019 will be held on January 3 - 7, 2019 in Kohala Coast, Hawaii. Tutorials and workshops will be offered prior to the start of the conference.PSB 2019 will bring together top researchers from the US, the Asian Pacific nations, and around the world to exchange research results and address open issues in all aspects of computational biology. It is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling, and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology.The PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are organized by leaders of research in biocomputing's 'hot topics.' In this way, the meeting provides an early forum for serious examination of emerging methods and approaches in this rapidly changing field.

Rna Seq Analysis Methods Applications And Challenges

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Author : Filippo Geraci
language : en
Publisher: Frontiers Media SA
Release Date : 2020-06-08

Rna Seq Analysis Methods Applications And Challenges written by Filippo Geraci 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 2020-06-08 with categories.

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 Intelligence For Genomics Data

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Author : Babita Pandey
language : en
Publisher: Elsevier
Release Date : 2025-01-21

Computational Intelligence For Genomics Data written by Babita Pandey and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2025-01-21 with Computers categories.

Computational Intelligence for Genomics Data presents an overview of machine learning and deep learning techniques being developed for the analysis of genomic data and the development of disease prediction models. The book focuses on machine and deep learning techniques applied to dimensionality reduction, feature extraction, and expressive gene selection. It includes designs, algorithms, and simulations on MATLAB and Python for larger prediction models and explores the possibilities of software and hardware-based applications and devices for genomic disease prediction. With the inclusion of important case studies and examples, this book will be a helpful resource for researchers, graduate students, and professional engineers. - Provides comparative analysis of machine learning and deep learning methods in the analysis of genomic data, discussing major design challenges, best practices, pitfalls, and research potential - Explores machine and deep learning techniques applied to dimensionality reduction, feature extraction, data selection, and their application in genomics - Presents case studies of various diseases based on gene microarray expression data, including cancer, liver disorders, neuromuscular disorders, and neurodegenerative disorders

Artificial Intelligence And Computational Dynamics For Biomedical Research

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Author : Ankur Saxena
language : en
Publisher: Walter de Gruyter GmbH & Co KG
Release Date : 2022-11-07

Artificial Intelligence And Computational Dynamics For Biomedical Research written by Ankur Saxena and has been published by Walter de Gruyter GmbH & Co KG this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-11-07 with Computers categories.

This work presents the latest development in the field of computational intelligence to advance Big Data and Cloud Computing concerning applications in medical diagnosis. As forum for academia and professionals it covers state-of-the-art research challenges and issues in the digital information & knowledge management and the concerns along with the solutions adopted in these fields.

Bioinformatics Sequences Structures Phylogeny

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Author : Asheesh Shanker
language : en
Publisher: Springer
Release Date : 2018-10-13

Bioinformatics Sequences Structures Phylogeny written by Asheesh Shanker and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-10-13 with Science categories.

This book provides a comprehensive overview of the concepts and approaches used for sequence, structure, and phylogenetic analysis. Starting with an introduction to the subject and intellectual property protection for bioinformatics, it guides readers through the latest sequencing technologies, sequence analysis, genomic variations, metagenomics, epigenomics, molecular evolution and phylogenetics, structural bioinformatics, protein folding, structure analysis and validation, drug discovery, reverse vaccinology, machine learning, application of R programming in biological data analysis, and the use of Linux in handling large data files.

Single Cell Analysis On The Pathophysiology Of Autoimmune Diseases

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Author : Shiang-Jong Tzeng
language : en
Publisher: Frontiers Media SA
Release Date : 2024-07-11

Single Cell Analysis On The Pathophysiology Of Autoimmune Diseases written by Shiang-Jong Tzeng 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 2024-07-11 with Medical categories.

Despite increasing research to facilitate the understanding of the pathophysiology of autoimmune disorders, the exact cause of the incident of autoimmunity is unknown. Current concepts on the occurrence of autoimmune diseases are thought to involve autoantigens, genetic predisposition, disease triggers, and the breakdown of immune tolerance. In addition to the breakdown of immunological tolerance, one key characteristic of autoimmune disease is that within a single disease there is considerable variability in the clinical manifestation and severity in patients. Single-cell omics have emerged as an effective means of unraveling the complexity and heterogeneity of chronic disease development and therapeutic responses. Recently, advances in cutting-edge spatial profiling of diverse cell types have increased our understanding of how distinct cells interact and orchestrate at specific locations across a tissue landscape in both physiological and pathological contexts at the single-cell level.

Guide To Plant Single Cell Technology

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Author : Jen-Tsung Chen
language : en
Publisher: Elsevier
Release Date : 2024-11-25

Guide To Plant Single Cell Technology written by Jen-Tsung Chen and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-11-25 with Technology & Engineering categories.

Guide to Plant Single-Cell Technology: Functional Genomics and Crop Improvement summarizes the current status of single-cell technology in plants involving food and energy crops. Presenting methods and applications of emerging high-throughput technologies performed using the single-cell platform it includes an emphasis on single-cell RNA sequencing and eventually towards single-cell omics, which are highly complementary and effective for profiling the plant cell subject to either environmental factors or pathogenic threats. These technologies can advance the exploration of plant physiology as well as precision crop breeding for future anti-stress and high-yield plants and achieve sustainable agriculture.The book covers crop improvement and breeding strategies involving single-cell technology to produce future stress-tolerant and high-yield plants, which have better performances on growth, and development to achieve enhanced production of foods and biomass.Guide to Plant Single-Cell Technology: Functional Genomics and Crop Improvement will be a valuable reference resource for academics and researchers in plant and crop sciences. - Focuses on plant molecular profiling using single-cell technology and the integration with functional genomics - Discusses the current methods and challenges of single-cell RNA sequencing in plants - Summarizes the emerging findings of plant single-cell technology - Presents advanced high-throughput technologies for plant omics