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:
Download or read book Tumor Immunology and Immunotherapy Cellular Methods Part B written by and published by Academic Press. This book was released on 2020-01-29 with total page 588 pages. Available in PDF, EPUB and Kindle. Book excerpt: Tumor Immunology and Immunotherapy – Cellular Methods Part B, Volume 632, the latest release in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. Topics covered include Quantitation of calreticulin exposure associated with immunogenic cell death, Side-by-side comparisons of flow cytometry and immunohistochemistry for detection of calreticulin exposure in the course of immunogenic cell death, Quantitative determination of phagocytosis by bone marrow-derived dendritic cells via imaging flow cytometry, Cytofluorometric assessment of dendritic cell-mediated uptake of cancer cell apoptotic bodies, Methods to assess DC-dependent priming of T cell responses by dying cells, and more. - Contains content written by authorities in the field - Provides a comprehensive view on the topics covered - Includes a high level of detail
Download or read book Clinical Bioinformatics written by Ronald Trent and published by Humana. This book was released on 2016-08-23 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: In Clinical Bioinformatics, Second Edition, leading experts in the field provide a series of articles focusing on software applications used to translate information into outcomes of clinical relevance. Recent developments in omics, such as increasingly sophisticated analytic platforms allowing changes in diagnostic strategies from the traditional focus on single or small number of analytes to what might be possible when large numbers or all analytes are measured, are now impacting patient care. Covering such topics as gene discovery, gene function (microarrays), DNA sequencing, online approaches and resources, and informatics in clinical practice, this volume concisely yet thoroughly explores this cutting-edge subject. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Clinical Bioinformatics, Second Edition serves as an ideal guide for scientists and health professionals working in genetics and genomics.
Download or read book Gene Quantification written by Francois Ferre and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 379 pages. Available in PDF, EPUB and Kindle. Book excerpt: Geneticists and molecular biologists have been interested in quantifying genes and their products for many years and for various reasons (Bishop, 1974). Early molecular methods were based on molecular hybridization, and were devised shortly after Marmur and Doty (1961) first showed that denaturation of the double helix could be reversed - that the process of molecular reassociation was exquisitely sequence dependent. Gillespie and Spiegelman (1965) developed a way of using the method to titrate the number of copies of a probe within a target sequence in which the target sequence was fixed to a membrane support prior to hybridization with the probe - typically a RNA. Thus, this was a precursor to many of the methods still in use, and indeed under development, today. Early examples of the application of these methods included the measurement of the copy numbers in gene families such as the ribosomal genes and the immunoglo bulin family. Amplification of genes in tumors and in response to drug treatment was discovered by this method. In the same period, methods were invented for estimating gene num bers based on the kinetics of the reassociation process - the so-called Cot analysis. This method, which exploits the dependence of the rate of reassociation on the concentration of the two strands, revealed the presence of repeated sequences in the DNA of higher eukaryotes (Britten and Kohne, 1968). An adaptation to RNA, Rot analysis (Melli and Bishop, 1969), was used to measure the abundance of RNAs in a mixed population.
Download or read book Me Medicine Vs We Medicine written by Donna Dickenson and published by . This book was released on 2016-02-23 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Personalized healthcare--or what the award-winning author Donna Dickenson calls "Me Medicine"--is radically transforming our longstanding "one-size-fits-all" model. Technologies such as direct-to-consumer genetic testing, pharmacogenetically developed therapies in cancer care, private umbilical cord blood banking, and neurocognitive enhancement claim to cater to an individual's specific biological character, and, in some cases, these technologies have shown powerful potential. Yet in others they have produced negligible or even negative results. Whatever is behind the rise of Me Medicine, it isn't just science. So why is Me Medicine rapidly edging out We Medicine, and how has our commitment to our collective health suffered as a result? In her cogent, provocative analysis, Dickenson examines the economic and political factors fueling the Me Medicine phenomenon and explores how, over time, this paradigm shift in how we approach our health might damage our individual and collective well-being. Historically, the measures of "We Medicine," such as vaccination and investment in public-health infrastructure, have radically extended our life spans, and Dickenson argues we've lost sight of that truth in our enthusiasm for "Me Medicine." Dickenson explores how personalized medicine illustrates capitalism's protean capacity for creating new products and markets where none existed before--and how this, rather than scientific plausibility, goes a long way toward explaining private umbilical cord blood banks and retail genetics. Drawing on the latest findings from leading scientists, social scientists, and political analysts, she critically examines four possible hypotheses driving our Me Medicine moment: a growing sense of threat; a wave of patient narcissism; corporate interests driving new niche markets; and the dominance of personal choice as a cultural value. She concludes with insights from political theory that emphasize a conception of the commons and the steps we can take to restore its value to modern biotechnology.
Download or read book Application of Bioinformatics in Cancers written by Chad Brenner and published by MDPI. This book was released on 2019-11-20 with total page 418 pages. Available in PDF, EPUB and Kindle. Book excerpt: This collection of 25 research papers comprised of 22 original articles and 3 reviews is brought together from international leaders in bioinformatics and biostatistics. The collection highlights recent computational advances that improve the ability to analyze highly complex data sets to identify factors critical to cancer biology. Novel deep learning algorithms represent an emerging and highly valuable approach for collecting, characterizing and predicting clinical outcomes data. The collection highlights several of these approaches that are likely to become the foundation of research and clinical practice in the future. In fact, many of these technologies reveal new insights about basic cancer mechanisms by integrating data sets and structures that were previously immiscible. Accordingly, the series presented here bring forward a wide range of artificial intelligence approaches and statistical methods that can be applied to imaging and genomics data sets to identify previously unrecognized features that are critical for cancer. Our hope is that these articles will serve as a foundation for future research as the field of cancer biology transitions to integrating electronic health record, imaging, genomics and other complex datasets in order to develop new strategies that improve the overall health of individual patients.
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 Biological Sequence Analysis written by Richard Durbin and published by Cambridge University Press. This book was released on 1998-04-23 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Probabilistic models are becoming increasingly important in analysing the huge amount of data being produced by large-scale DNA-sequencing efforts such as the Human Genome Project. For example, hidden Markov models are used for analysing biological sequences, linguistic-grammar-based probabilistic models for identifying RNA secondary structure, and probabilistic evolutionary models for inferring phylogenies of sequences from different organisms. This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis. Written by an interdisciplinary team of authors, it aims to be accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time present the state-of-the-art in this new and highly important field.
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.
Download or read book Omics for Personalized Medicine written by Debmalya Barh and published by Springer Science & Business Media. This book was released on 2013-10-14 with total page 825 pages. Available in PDF, EPUB and Kindle. Book excerpt: “Omics for Personalized Medicine” will give to its prospective readers the insight of both the current developments and the future potential of personalized medicine. The book brings into light how the pharmacogenomics and omics technologies are bringing a revolution in transforming the medicine and the health care sector for the better. Students of biomedical research and medicine along with medical professionals will benefit tremendously from the book by gaining from the diverse fields of knowledge of new age personalized medicine presented in the highly detailed chapters of the book. The book chapters are divided into two sections for convenient reading with the first section covering the general aspects of pharmaocogenomic technology that includes latest research and development in omics technologies. The first section also highlights the role of omics in modern clinical trials and even discusses the ethical consideration in pharmocogenomics. The second section is focusing on the development of personalized medicine in several areas of human health. The topics covered range from metabolic and neurological disorders to non-communicable as well as infectious diseases, and even explores the role of pharmacogenomics in cell therapy and transplantation technology. Thirty-four chapters of the book cover several aspects of pharmacogenomics and personalized medicine and have taken into consideration the varied interest of the readers from different fields of biomedical research and medicine. Advent of pharmacogenomics is the future of modern medicine, which has resulted from culmination of decades of research and now is showing the way forward. The book is an honest endeavour of researchers from all over the world to disseminate the latest knowledge and knowhow in personalized medicine to the community health researchers in particular and the educated public in general.
Download or read book Molecular Pathology in Cancer Research written by Sunil R. Lakhani and published by Springer. This book was released on 2017-01-20 with total page 369 pages. Available in PDF, EPUB and Kindle. Book excerpt: The aim of the book is to discuss the application of molecular pathology in cancer research, and its contribution in the classification of different tumors and identification of potential molecular targets, as well as how this knowledge may be translated into clinical practice, and the huge impact this field is likely to have in the next 5 to 10 years.
Download or read book Single Cell OMICs Analyses in Cardiovascular Diseases written by and published by Frontiers Media SA. This book was released on 2024-05-14 with total page 150 pages. Available in PDF, EPUB and Kindle. Book excerpt: Single-cell OMICs analyses have recently become one of the most promising tools to probe biology at the cellular level, in large part due to its ability to address issues beyond the bulk analysis – a window into cellular heterogeneity. The ability to profile transcriptomic, epigenomic, proteomics, and metabolomics at the single cell level including more recently the spatial information has enhanced our ability to understand interactions between biomolecules in different contexts leading to the discovery of specific cellular subpopulations as well as biological mechanisms underlying pathologies which may be amenable to therapeutic interventions. The scale and availability of a variety of technologies to measure intricate molecular details have provided an impetus to research in many disease areas, including cardiovascular medicine.
Download or read book Toward Precision Medicine written by National Research Council and published by National Academies Press. This book was released on 2012-01-16 with total page 142 pages. Available in PDF, EPUB and Kindle. Book excerpt: Motivated by the explosion of molecular data on humans-particularly data associated with individual patients-and the sense that there are large, as-yet-untapped opportunities to use this data to improve health outcomes, Toward Precision Medicine explores the feasibility and need for "a new taxonomy of human disease based on molecular biology" and develops a potential framework for creating one. The book says that a new data network that integrates emerging research on the molecular makeup of diseases with clinical data on individual patients could drive the development of a more accurate classification of diseases and ultimately enhance diagnosis and treatment. The "new taxonomy" that emerges would define diseases by their underlying molecular causes and other factors in addition to their traditional physical signs and symptoms. The book adds that the new data network could also improve biomedical research by enabling scientists to access patients' information during treatment while still protecting their rights. This would allow the marriage of molecular research and clinical data at the point of care, as opposed to research information continuing to reside primarily in academia. Toward Precision Medicine notes that moving toward individualized medicine requires that researchers and health care providers have access to very large sets of health- and disease-related data linked to individual patients. These data are also critical for developing the information commons, the knowledge network of disease, and ultimately the new taxonomy.
Download or read book Applications of RNA Seq and Omics Strategies written by Fabio Marchi and published by BoD – Books on Demand. This book was released on 2017-09-13 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: The large potential of RNA sequencing and other "omics" techniques has contributed to the production of a huge amount of data pursuing to answer many different questions that surround the science's great unknowns. This book presents an overview about powerful and cost-efficient methods for a comprehensive analysis of RNA-Seq data, introducing and revising advanced concepts in data analysis using the most current algorithms. A holistic view about the entire context where transcriptome is inserted is also discussed here encompassing biological areas with remarkable technological advances in the study of systems biology, from microorganisms to precision medicine.
Download or read book Computational Exome and Genome Analysis written by Peter N. Robinson and published by CRC Press. This book was released on 2017-09-13 with total page 575 pages. Available in PDF, EPUB and Kindle. Book excerpt: Exome and genome sequencing are revolutionizing medical research and diagnostics, but the computational analysis of the data has become an extremely heterogeneous and often challenging area of bioinformatics. Computational Exome and Genome Analysis provides a practical introduction to all of the major areas in the field, enabling readers to develop a comprehensive understanding of the sequencing process and the entire computational analysis pipeline.
Download or read book Microarray Bioinformatics written by Dov Stekel and published by Cambridge University Press. This book was released on 2003-09-08 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is a comprehensive guide to all of the mathematics, statistics and computing you will need to successfully operate DNA microarray experiments. It is written for researchers, clinicians, laboratory heads and managers, from both biology and bioinformatics backgrounds, who work with, or who intend to work with microarrays. The book covers all aspects of microarray bioinformatics, giving you the tools to design arrays and experiments, to analyze your data, and to share your results with your organisation or with the international community. There are chapters covering sequence databases, oligonucleotide design, experimental design, image processing, normalisation, identifying differentially expressed genes, clustering, classification and data standards. The book is based on the highly successful Microarray Bioinformatics course at Oxford University, and therefore is ideally suited for teaching the subject at postgraduate or professional level.
Download or read book Seurat written by Hajo Düchting and published by Taschen. This book was released on 2000 with total page 106 pages. Available in PDF, EPUB and Kindle. Book excerpt: Georges Seurat died in 1891, aged only 32, and yet in a career that lasted little more than a decade he revolutionized technique in painting, spearheaded a new movement, Neoimpressionism, and bought a degree of scientific rigour to his investigations of colour that would prove profoundly influential well into the 20th century. As a student at the Ecole des Beaux-Arts, Seurat read Chevreul's 1839 book on the theory of colour and this, along with his own analysis of Delacroix' paintings and the aesthetic observations of scientist Charles Henry, led him to formulate the concept of Divisionism. This was a method of painting around colour contrasts in which shade and tone are built up through dots of paint (pointillism) that emphasise the complex inter-relation of light and shadow.
