Introduction To Single Cell Omics

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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.

Single Cell Omics

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Author : Debmalya Barh
language : en
Publisher: Academic Press
Release Date : 2019-07-30

Single Cell Omics written by Debmalya Barh and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-07-30 with Medical categories.

Single-cell Omics, Volume 2: Advances in Applications provides the latest single-cell omics applications in the field of biomedicine. The advent of omics technologies have enabled us to identify the differences between cell types and subpopulations at the level of the genome, proteome, transcriptome, epigenome, and in several other fields of omics. The book is divided into two sections: the first is dedicated to biomedical applications, such as cell diagnostics, non-invasive prenatal testing (NIPT), circulating tumor cells, breast cancer, gliomas, nervous systems and autoimmune disorders, and more. The second focuses on cell omics in plants, discussing micro algal and single cell omics, and more. This book is a valuable source for bioinformaticians, molecular diagnostic researchers, clinicians and several members of biomedical field interested in understanding more about single-cell omics and its potential for research and diagnosis. - Covers the diverse single cell omics applications in the biomedical field - Summarizes the latest progress in single cell omics and discusses potential future developments for research and diagnosis - Written by experts across the world, it brings different points-of-view and study cases to fully give a comprehensive overview of the topic

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

Single Cell Transcriptomics

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Author : Raffaele A. Calogero
language : en
Publisher: Springer Nature
Release Date : 2022-12-10

Single Cell Transcriptomics written by Raffaele A. Calogero and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-12-10 with Science categories.

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.

Single Cell Omics Of Neuronal Cells

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Author : Jonathan V. Sweedler
language : en
Publisher: Springer Nature
Release Date : 2022-08-10

Single Cell Omics Of Neuronal Cells written by Jonathan V. Sweedler and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-08-10 with Medical categories.

This volume discusses the latest techniques used in the diverse fields of single cell ‘omics and covers topics such as quantifying the single cell transcriptome; isolation of cells in nanoliter volumes for single cell proteomics measurements by nano-LC-MS/MS; and single cell protein characterization by immunoblotting. A wide range of methodologies are highlighted, ranging from high-yield chemical amplification to mass spectrometry and nanotechnology for the analysis of the chemical constituents of cells. In the Neuromethods series style, chapters include both in-depth overviews, as well as detailed protocols that provide the key advice from specialists you need to get successful results in your laboratory. Cutting-edge and comprehensive, Single Cell ‘Omics of Neuronal Cells is a valuable resource for experienced and novice researchers interested in learning more about this field and its future developments.

Mass Spectrometry Based Single Cell Proteomics

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Author : Akos Vegvari
language : en
Publisher: Springer Nature
Release Date : 2024-06-21

Mass Spectrometry Based Single Cell Proteomics written by Akos Vegvari and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-06-21 with Science categories.

This volume explores the latest advancements made in the field of mass spectrometry (MS) based single cell proteomics. The chapters in this book focus on technologies, methods, and biological applications and together cover the entire single cell proteomics analysis workflow, from sample collection and preparation through liquid chromatographic separation and mass spectrometric data acquisition to data analysis and interpretation. 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 authoritative, Mass Spectrometry Based Single Cell Proteomics: Methods and Protocols is a valuable resource for all researchers interested in using these technologies and methods in their laboratories to continue making biological discoveries in this important field.

Deep Learning In Genetics And Genomics

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Author : Khalid Raza
language : en
Publisher: Elsevier
Release Date : 2024-11-28

Deep Learning In Genetics And Genomics written by Khalid Raza and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-11-28 with Science categories.

Deep Learning in Genetics and Genomics: Vol. 2 (Advanced Applications) delves into the Deep Learning methods and their applications in various fields of studies, including genetics and genomics, bioinformatics, health informatics and medical informatics generating the momentum of today's developments in the field. In 25 chapters this title covers advanced applications in the field which includes deep learning in predictive medicines), analysis of genetic and clinical features, transcriptomics and gene expression patterns analysis, clinical decision support in genetic diagnostics, deep learning in personalised genomics and gene editing, and understanding genetic discoveries through Explainable AI. Further, it also covers various deep learning-based case studies, making this book a unique resource for wider, deeper, and in-depth coverage of recent advancement in deep learning based approaches. This volume is not only a valuable resource for health educators, clinicians, and healthcare professionals but also to graduate students of genetics, genomics, biology, biostatistics, biomedical sciences, bioinformatics, and interdisciplinary sciences. - Embraces the potential that deep learning holds for understanding genome biology - Encourages further advances in this area, extending to all aspects of genomics research - Provides Deep Learning algorithms in genetic and genomic research

Epigenetics For Climate Smart And Sustainable Agriculture

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Author : Jen-Tsung Chen
language : en
Publisher: CABI
Release Date : 2025-07-29

Epigenetics For Climate Smart And Sustainable Agriculture written by Jen-Tsung Chen and has been published by CABI this book supported file pdf, txt, epub, kindle and other format this book has been release on 2025-07-29 with Science categories.

This book provides a state-of-the-art overview of current achievements and future possibilities for the application of epigenetic and epigenomic techniques to the improvement of crops. Creating crops more resilient to the stresses caused by climate change will be an important part of a climate-smart and sustainable agriculture strategy for the future. All critical environmental stressors are explored: temperature, salt, drought, pollutants, pests, fungi, bacteria, and viruses. The exciting possibilities for the integration of epigenetic resources and technologies with plant functional genomics and the new field of precision molecular breeding in crops are discussed. Examples are shown of crops showing better growth performance, enhanced yields, more efficient nutrient utilization, and higher quality food production. This book is an ideal complete guide for students, researchers, experts, and professionals to overview this critical topic.

Omics Technologies For Clinical Diagnosis And Gene Therapy Medical Applications In Human Genetics

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Author : Syeda Marriam Bakhtiar
language : en
Publisher: Bentham Science Publishers
Release Date : 2022-10-03

Omics Technologies For Clinical Diagnosis And Gene Therapy Medical Applications In Human Genetics written by Syeda Marriam Bakhtiar and has been published by Bentham Science Publishers this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-10-03 with Medical categories.

Genetic disorders have been the focus of scientists for a long time. The emergence of next-generation sequencing techniques has ushered a new era in genetics and several developments have occurred in human genetics. The scientific perspective has also been widened with omics technologies that allow researchers to analyze genetic sequences and their expression products. An integrated approach is being used not only for diagnosis but also for disease management and therapeutic purposes. This book highlights emerging areas of omics technology and its application in the diagnosis and management of human genetic disorders. The book covers three areas of research and implementation: 1) Diagnosis (covering conventional strategies to next-generation platforms). This section focuses on the role of in silico analysis, databases and multi-omics of single-cell which will help in designing better management strategies. 2) Disease Management and therapeutic interventions. This section starts with genetic counselling and progresses to more specific techniques such as pharmacogenomics and personalized medicine, gene editing techniques and their applications in gene therapies and regenerative medicine. 3) Case studies. This section discusses the applications and success of all the above-mentioned strategies on selected human disorders. This book serves as a handy reference for students and academics studying advanced omics techniques in biochemistry and molecular genetics as part of courses in life sciences, pharmacology and medicine.

Research In Computational Molecular Biology

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Author : Jian Ma
language : en
Publisher: Springer Nature
Release Date : 2024-05-16

Research In Computational Molecular Biology written by Jian Ma and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-05-16 with Computers categories.

This book constitutes the proceedings of the 28th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2024, held in Cambridge, MA, USA, during April 29–May 2, 2024. The 57 full papers included in this book were carefully reviewed and selected from 352 submissions. They were organized in topical sections as follows: theoretical and foundational algorithm contributions and more applied directions that engage with new technologies and intriguing biological questions.