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Development And Application Of Multi Omics Integration Tools To Understand Metabolic Contributions To Alzheimers Disease
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Book Synopsis Development and Application of Multi-omics Integration Tools to Understand Metabolic Contributions to Alzheimer's Disease by : Jessica Ding
Download or read book Development and Application of Multi-omics Integration Tools to Understand Metabolic Contributions to Alzheimer's Disease written by Jessica Ding and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Physiological functioning of an organ system such as healthy brain functioning is enabled by orchestrated information flow between molecular entities within cells, between cells, and across tissues and its understanding requires a systems approach. In complex disease such as Alzheimer's disease, there are numerous subtle, moderate, and strong perturbations across biological networks which result in disease onset and progression. High-throughput multi-omics profiling of genetic variants, the epigenome, transcriptome, proteome, metabolome, and microbiome is a first step in probing the complexity of biological systems and disease etiologies. There remains the problems of multi-omics integration, modeling and interpretation, and accessibility of computational analyses. To address these issues, in the methods development section of my dissertation research, I developed the complete overhaul of the web server for Mergeomics, a method for pathway- and network-level understanding of complex disease using multi-omics integration, which significantly improved the usability and functionality of the tool. To facilitate omics-driven drug discovery, I implemented the PharmOmics web server and the direct pipeline from Mergeomics, allowing users to gain immediate therapeutic insight from disease-associated pathways, key drivers, and key driver subnetworks. The second focus of my dissertation was the application of systems biology analytical tools to understand metabolic contributions to Alzheimer's disease. I determined hippocampal and hypothalamic cell type specific alterations in response to amyloid-beta accumulation in the 5XFAD mouse model and investigated the effect of metabolically challenging 5XFAD mice with fructose overconsumption and supplementation with docosahexaenoic acid and nicotinamide riboside. I identified cell type- and tissue-resolved pathway and network mechanisms of disease exacerbation by metabolic challenge and disease alleviation by docosahexaenoic acid and nicotinamide. My efforts in developing the web server implementations of Mergeomics and PharmOmics have promoted greater accessibility of deriving mechanistic insight from big biological data for the broader scientific community, and use of these tools have allowed unbiased examination into the connection between metabolic syndrome and Alzheimer's disease and uncovered potential therapeutic targets and strategies via dietary modulation.
Book Synopsis Multi-Omics Approaches to Study Signaling Pathways by : Jyoti Sharma
Download or read book Multi-Omics Approaches to Study Signaling Pathways written by Jyoti Sharma and published by Frontiers Media SA. This book was released on 2020-11-18 with total page 154 pages. Available in PDF, EPUB and Kindle. Book excerpt: This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.
Book Synopsis Learning to Classify Text Using Support Vector Machines by : Thorsten Joachims
Download or read book Learning to Classify Text Using Support Vector Machines written by Thorsten Joachims and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 218 pages. Available in PDF, EPUB and Kindle. Book excerpt: Based on ideas from Support Vector Machines (SVMs), Learning To Classify Text Using Support Vector Machines presents a new approach to generating text classifiers from examples. The approach combines high performance and efficiency with theoretical understanding and improved robustness. In particular, it is highly effective without greedy heuristic components. The SVM approach is computationally efficient in training and classification, and it comes with a learning theory that can guide real-world applications. Learning To Classify Text Using Support Vector Machines gives a complete and detailed description of the SVM approach to learning text classifiers, including training algorithms, transductive text classification, efficient performance estimation, and a statistical learning model of text classification. In addition, it includes an overview of the field of text classification, making it self-contained even for newcomers to the field. This book gives a concise introduction to SVMs for pattern recognition, and it includes a detailed description of how to formulate text-classification tasks for machine learning.
Book Synopsis Heterogeneity of Alzheimer’s Disease by : Francois Boller
Download or read book Heterogeneity of Alzheimer’s Disease written by Francois Boller and published by Springer Science & Business Media. This book was released on 2013-03-08 with total page 205 pages. Available in PDF, EPUB and Kindle. Book excerpt: The term "Alzheimer's disease" is currently used to refer to senile and also presenile dementia, but the heterogeneity of this disorder is demonstrated in many of its aspects. This is of great theoretical interest, and with the appearance of new therapeutic interventions, it may well also start to have very significant practical importance. To shed some light on the debate, the Fondation Ipsen organized an international symposium which took place on April 6, 1992. This volume contains the proceedings of this meeting, which was attended by researchers in epidemiology, clinical neurology and geriatrics, neuropsychology, neuropathology, molecular biology, and genetics.
Book Synopsis Rare Diseases Epidemiology: Update and Overview by : Manuel Posada de la Paz
Download or read book Rare Diseases Epidemiology: Update and Overview written by Manuel Posada de la Paz and published by Springer. This book was released on 2017-12-06 with total page 675 pages. Available in PDF, EPUB and Kindle. Book excerpt: The fields of rare diseases research and orphan products development continue to expand with more products in research and development status. In recent years, the role of the patient advocacy groups has evolved into a research partner with the academic research community and the bio-pharmaceutical industry. Unique approaches to research and development require epidemiological data not previously available to assist in protocol study design and patient recruitment for clinical trials required by regulatory agencies prior to approval for access by patents and practicing physicians.
Book Synopsis Computational Systems Biology by : Andres Kriete
Download or read book Computational Systems Biology written by Andres Kriete and published by Academic Press. This book was released on 2013-11-26 with total page 549 pages. Available in PDF, EPUB and Kindle. Book excerpt: This comprehensively revised second edition of Computational Systems Biology discusses the experimental and theoretical foundations of the function of biological systems at the molecular, cellular or organismal level over temporal and spatial scales, as systems biology advances to provide clinical solutions to complex medical problems. In particular the work focuses on the engineering of biological systems and network modeling. Logical information flow aids understanding of basic building blocks of life through disease phenotypes Evolved principles gives insight into underlying organizational principles of biological organizations, and systems processes, governing functions such as adaptation or response patterns Coverage of technical tools and systems helps researchers to understand and resolve specific systems biology problems using advanced computation Multi-scale modeling on disparate scales aids researchers understanding of dependencies and constraints of spatio-temporal relationships fundamental to biological organization and function.
Book Synopsis Genetics Meets Metabolomics by : Karsten Suhre
Download or read book Genetics Meets Metabolomics written by Karsten Suhre and published by Springer Science & Business Media. This book was released on 2012-06-15 with total page 328 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is written by leading researchers in the fields about the intersection of genetics and metabolomics which can lead to more comprehensive studies of inborn variation of metabolism.
Book Synopsis Introduction to Single Cell Omics by : Xinghua Pan
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.
Book Synopsis Lipidomics in Health & Disease by : Xiangdong Wang
Download or read book Lipidomics in Health & Disease written by Xiangdong Wang and published by Springer. This book was released on 2018-08-30 with total page 204 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume covers the emerging area of science, Clinical Lipidomics, which is the application of lipidology to the understanding of physiological and pathophysiological changes of lipidomes, with a special focus on lipidomic profiles in human diseases. Lipidomics is widely used to map lipid molecular species in a biological system. Clinical lipidomic analysis has demonstrated the comprehensive characterization of molecular lipids in various severities, durations, and therapies as a critical tool in identification and validation of disease-specific biomarkers. This volume on Clinical Lipidomics will add to the literature and help advance the knowledge of the pathogenesis, diagnosis, prevention and treatment of diseases.
Book Synopsis Omics Technologies and Bio-engineering by : Debmalya Barh
Download or read book Omics Technologies and Bio-engineering written by Debmalya Barh and published by Academic Press. This book was released on 2017-12-01 with total page 645 pages. Available in PDF, EPUB and Kindle. Book excerpt: Omics Technologies and Bio-Engineering: Towards Improving Quality of Life, Volume 1 is a unique reference that brings together multiple perspectives on omics research, providing in-depth analysis and insights from an international team of authors. The book delivers pivotal information that will inform and improve medical and biological research by helping readers gain more direct access to analytic data, an increased understanding on data evaluation, and a comprehensive picture on how to use omics data in molecular biology, biotechnology and human health care. Covers various aspects of biotechnology and bio-engineering using omics technologies Focuses on the latest developments in the field, including biofuel technologies Provides key insights into omics approaches in personalized and precision medicine Provides a complete picture on how one can utilize omics data in molecular biology, biotechnology and human health care
Book Synopsis Probabilistic Boolean Networks by : Ilya Shmulevich
Download or read book Probabilistic Boolean Networks written by Ilya Shmulevich and published by SIAM. This book was released on 2010-01-21 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first comprehensive treatment of probabilistic Boolean networks, unifying different strands of current research and addressing emerging issues.
Book Synopsis Systems Analytics and Integration of Big Omics Data by : Gary Hardiman
Download or read book Systems Analytics and Integration of Big Omics Data written by Gary Hardiman and published by . This book was released on 2020 with total page 202 pages. Available in PDF, EPUB and Kindle. Book excerpt: A “genotype"" is essentially an organism's full hereditary information which is obtained from its parents. A ""phenotype"" is an organism's actual observed physical and behavioral properties. These may include traits such as morphology, size, height, eye color, metabolism, etc. One of the pressing challenges in computational and systems biology is genotype-to-phenotype prediction. This is challenging given the amount of data generated by modern Omics technologies. This “Big Data” is so large and complex that traditional data processing applications are not up to the task. Challenges arise in collection, analysis, mining, sharing, transfer, visualization, archiving, and integration of these data. In this Special Issue, there is a focus on the systems-level analysis of Omics data, recent developments in gene ontology annotation, and advances in biological pathways and network biology. The integration of Omics data with clinical and biomedical data using machine learning is explored. This Special Issue covers new methodologies in the context of gene-environment interactions, tissue-specific gene expression, and how external factors or host genetics impact the microbiome.
Book Synopsis Frontotemporal Dementias by : Bernardino Ghetti
Download or read book Frontotemporal Dementias written by Bernardino Ghetti and published by Springer Nature. This book was released on 2021-01-12 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt: Under the name of Frontotemporal Dementias (FTD) numerous hereditary and sporadic disorders are listed. FTD may take away speech and language, social skills and ethical judgement, wishes and will, empathy and emotions; it may also impair motor functions. FTD may affect men and women in midlife or during old age leading to the demolition of the uniqueness of the human mind. In the last decade of the 20th century and in the first two decades of the 21st century, progress in the understanding of clinical, neuropathological, biochemical, and genetic aspects of FTD has accelerated. The novel awareness about FTD has directed young generations of researchers toward the study of this complex group of disorders. This Volume has been formulated with the participation of some of the leading scientists who have contributed to the development of knowledge in the clinical and basic science arenas. It captures the current central elements that are relevant to an up-to-date understanding of causes and pathogenesis of multiple forms of FTD. The volume is an opus that represents a distillation of the work of many scientists and addresses the current directions in the study of one of the most complex groups of diseases. In view of its structure, the book could also be used as a textbook, that offers both a broad and deep analysis of major areas in FTD. This book, planned by the International Society for Frontotemporal Dementias, is distinctive as it opens a window to a wide landscape about the biology of FTD. Thus, the book represents a moment of reflection on the present state of our knowledge of FTD and a collective vision toward scientific progress. The authors of each chapter share their knowledge and vision aimed at reducing the suffering which is caused by FTD.
Book Synopsis Integrating Omics Data by : George Tseng
Download or read book Integrating Omics Data written by George Tseng and published by Cambridge University Press. This book was released on 2015-09-23 with total page 497 pages. Available in PDF, EPUB and Kindle. Book excerpt: Tutorial chapters by leaders in the field introduce state-of-the-art methods to handle information integration problems of omics data.
Author :National Academies of Sciences Engineering and Medicine Publisher : ISBN 13 :9780309684736 Total Pages : pages Book Rating :4.6/5 (847 download)
Book Synopsis High and Rising Mortality Rates Among Working-Age Adults by : National Academies of Sciences Engineering and Medicine
Download or read book High and Rising Mortality Rates Among Working-Age Adults written by National Academies of Sciences Engineering and Medicine and published by . This book was released on 2021-12-02 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Systems Biology and the Challenge of Deciphering the Metabolic Mechanisms Underlying Cancer by : Osbaldo Resendis-Antonio
Download or read book Systems Biology and the Challenge of Deciphering the Metabolic Mechanisms Underlying Cancer written by Osbaldo Resendis-Antonio and published by Frontiers Media SA. This book was released on 2017-11-23 with total page 144 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the discovery of the Warburg effect in the 1920s cancer has been tightly associated with the genetic and metabolic state of the cell. One of the hallmarks of cancer is the alteration of the cellular metabolism in order to promote proliferation and undermine cellular defense mechanisms such as apoptosis or detection by the immune system. However, the strategies by which this is achieved in different cancers and sometimes even in different patients of the same cancer is very heterogeneous, which hinders the design of general treatment options. Recently, there has been an ongoing effort to study this phenomenon on a genomic scale in order to understand the causality underlying the disease. Hence, current “omics” technologies have contributed to identify and monitor different biological pieces at different biological levels, such as genes, proteins or metabolites. These technological capacities have provided us with vast amounts of clinical data where a single patient may often give rise to various tissue samples, each of them being characterized in detail by genomescale data on the sequence, expression, proteome and metabolome level. Data with such detail poses the imminent problem of extracting meaningful interpretations and translating them into specific treatment options. To this purpose, Systems Biology provides a set of promising computational tools in order to decipher the mechanisms driving a healthy cell’s metabolism into a cancerous one. However, this enterprise requires bridging the gap between large data resources, mathematical analysis and modeling specifically designed to work with the available data. This is by no means trivial and requires high levels of communication and adaptation between the experimental and theoretical side of research.
Download or read book OMICS written by Debmalya Barh and published by CRC Press. This book was released on 2013-03-26 with total page 721 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the advent of new technologies and acquired knowledge, the number of fields in omics and their applications in diverse areas are rapidly increasing in the postgenomics era. Such emerging fields—including pharmacogenomics, toxicogenomics, regulomics, spliceomics, metagenomics, and environomics—present budding solutions to combat global challenges in biomedicine, agriculture, and the environment. OMICS: Applications in Biomedical, Agricultural, and Environmental Sciences provides valuable insights into the applications of modern omics technologies to real-world problems in the life sciences. Filling a gap in the literature, it offers a broad, multidisciplinary view of current and emerging applications of omics in a single volume. Written by highly experienced active researchers, each chapter describes a particular area of omics and the associated technologies and applications. Topics covered include: Proteomics, epigenomics, and pharmacogenomics Toxicogenomics and the assessment of environmental pollutants Applications of plant metabolomics Nutrigenomics and its therapeutic applications Microalgal omics and omics approaches in biofuel production Next-generation sequencing and omics technology for transgenic plant analysis Omics approaches in crop improvement Engineering dark-operative chlorophyll synthesis Computational regulomics Omics techniques for the analysis of RNA splicing New fields, including metagenomics, glycomics, and miRNA Breast cancer biomarkers for early detection Environomics strategies for environmental sustainability This timely book explores a wide range of omics application areas in the biomedical, agricultural, and environmental sciences. Throughout, it highlights working solutions as well as open problems and future challenges. Demonstrating the diversity of omics, it introduces readers to state-of-the-art developments and trends in omics-driven research.
