A Bayesian Modeling For Paired Data In Genome Wide Association Studies With Application To Breast Cancer

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A Bayesian Modeling For Paired Data In Genome Wide Association Studies With Application To Breast Cancer

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Author : Yashi Bu
language : en
Publisher:
Release Date : 2020

A Bayesian Modeling For Paired Data In Genome Wide Association Studies With Application To Breast Cancer written by Yashi Bu and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020 with Antibody diversity categories.

Many complex human diseases are associated with genetic factors. Identifying genetic markers is the key step to account for disease heritability, and develop disease diagnosis, risk prediction, prevention and therapeutic strategies. Genome-wide association study (GWAS) has emerged as a powerful tool to identify genetic variants that are associated with various cancers. The common statistical methodologies in GWAS focus on case-control data where cases and controls are sampled independently from the populations. Despite the success of GWAS in finding a number of genetic variants that are associated with cancers, the power of conventional GWAS is limited. Extensive research has shown that many tumors develop as a consequence of the progressive accumulation of somatic mutations over time. We focus on GWAS data from tumor and paired normal tissues to unravel the genetic association of somatic mutations. To address the limitation that conventional GWAS methods are not applicable to matched-paired data, we propose in this dissertation a framework that incorporates allelic relative risk, frequency and mutation rate to accommodate the structure of paired data. We first apply the penalized maximum likelihood estimation (MLE) to perform single marker analysis based on the framework. Simulation studies are carried out to assess the performance of penalized MLE. To further improve the estimation accuracy and power of single marker analysis, we develop a Bayesian hierarchical model that takes advantage of applying Bayesian shrinkage and making inferences based on the posterior distributions. The hierarchical Bayesian model has the flexibility to take into account the prior knowledge and extend to multiple marker analysis. We find that the single-marker Bayesian model has improved the estimation and power performance in most simulation scenarios. To identify DNA segments and SNP sets, rather than single genetic variants that are associated with the disease, we develop a multiple-SNP Bayesian model which considers SNP sets that are grouped together in a biologically meaningful way, such as genes or pathways. The multiple SNP analysis considers the joint effects of the SNP set, which improves the power to identify SNPs that have moderate marginal effects by themselves. Simulation studies show that the multi-marker Bayesian model has higher power to identify associated SNPs and lower type I error rates. Next, we apply the proposed methods to a breast cancer data set from The Cancer Genome Atlas (TCGA).We compare the most significant genes identified by single marker analysis and multiple marker analysis to external resources on somatic mutations of breast cancer. We find that both methods identify genes associated with breast cancer, and multiple marker analysis provides more consistent results with external resources.

Data Mining Foundations And Intelligent Paradigms

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Author : Dawn E. Holmes
language : en
Publisher: Springer Science & Business Media
Release Date : 2012-01-12

Data Mining Foundations And Intelligent Paradigms written by Dawn E. Holmes and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-01-12 with Technology & Engineering categories.

There are many invaluable books available on data mining theory and applications. However, in compiling a volume titled “DATA MINING: Foundations and Intelligent Paradigms: Volume 3: Medical, Health, Social, Biological and other Applications” we wish to introduce some of the latest developments to a broad audience of both specialists and non-specialists in this field.

Cancer Genomics

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Author : Graham Dellaire
language : en
Publisher: Academic Press
Release Date : 2013-11-21

Cancer Genomics written by Graham Dellaire and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-11-21 with Science categories.

Cancer Genomics addresses how recent technological advances in genomics are shaping how we diagnose and treat cancer. Built on the historical context of cancer genetics over the past 30 years, the book provides a snapshot of the current issues and state-of-the-art technologies used in cancer genomics. Subsequent chapters highlight how these approaches have informed our understanding of hereditary cancer syndromes and the diagnosis, treatment and outcome in a variety of adult and pediatric solid tumors and hematologic malignancies. The dramatic increase in cancer genomics research and ever-increasing availability of genomic testing are not without significant ethical issues, which are addressed in the context of the return of research results and the legal considerations underlying the commercialization of genomic discoveries. Finally, the book concludes with "Future Directions", examining the next great challenges to face the field of cancer genomics, namely the contribution of non-coding RNAs to disease pathogenesis and the interaction of the human genome with the environment. - Tools such as sidebars, key concept summaries, a glossary, and acronym and abbreviation definitions make this book highly accessible to researchers from several fields associated with cancer genomics. - Contributions from thought leaders provide valuable historical perspective to relate the advances in the field to current technologies and literature.

Integrating Omics Data

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Author : George Tseng
language : en
Publisher: Cambridge University Press
Release Date : 2015-09-23

Integrating Omics Data written by George Tseng and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-09-23 with Mathematics categories.

Tutorial chapters by leaders in the field introduce state-of-the-art methods to handle information integration problems of omics data.

Journal Of The American Statistical Association

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Author :
language : en
Publisher:
Release Date : 2008

Journal Of The American Statistical Association written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008 with Electronic journals categories.

Artificial Intelligence Bioinformatics Development And Application Of Tools For Omics And Inter Omics Studies

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Author : Angelo Facchiano
language : en
Publisher: Frontiers Media SA
Release Date : 2020-06-18

Artificial Intelligence Bioinformatics Development And Application Of Tools For Omics And Inter Omics Studies written by Angelo Facchiano 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 2020-06-18 with categories.

Goldman Cecil Medicine E Book

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Author : Lee Goldman
language : en
Publisher: Elsevier Health Sciences
Release Date : 2015-04-21

Goldman Cecil Medicine E Book written by Lee Goldman and has been published by Elsevier Health Sciences this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-04-21 with Medical categories.

Since 1927, Goldman-Cecil Medicine has been the world’s most influential internal medicine resource. In the ground-breaking 25th edition, your original purchase ensures you will be up-to-date without the need for a subscription. Through the new, more powerful Expert Consult eBook platform, this "living text" provides continuous updates that will integrate the latest research, guidelines, and treatments into each chapter, ensuring that the content is as current as the day this edition was first published. Goldman-Cecil Medicine offers definitive, unbiased guidance on the evaluation and management of every medical condition, presented by a veritable "Who's Who" of modern medicine. A practical, straightforward style; templated organization; evidence-based references; and robust interactive content combine to make this dynamic resource quite simply the fastest and best place to find all of the authoritative, state-of-the-art clinical answers you need. Expert Consult eBook version included with print purchase: Access continuous updates from Editor Lee Goldman, MD, who thoroughly reviews internal medicine and specialty journals, updating online content to reflect the latest guidelines and translating that evidence into treatment. Interactive Q&A section features over 1,500 board-style questions and answers to aid in preparing for certification or recertification exams. Outstanding supplementary tools include figures, tables, videos, heart and lung sounds, treatment and management algorithms, fully integrated references, and thousands of illustrations and full-color photos. Search all of the text, figures, supplementary material, and references from the book on a variety of devices and at no additional cost — Expert Consult access is included with this title! Practical, bulleted, highly templated text with easy-to-use features including flow charts and treatment boxes. New chapters on global health, cancer biology and genetics, and the human microbiome in health and disease keep you on the cutting edge of medicine. Today's most current evidence-based medicine guidelines help you form a definitive diagnosis and create the best treatment plans possible. Focused coverage of the latest developments in biology includes the specifics of current diagnosis, therapy, and medication doses. The reference of choice for every stage of your career! Goldman-Cecil Medicine is an ideal learning tool for residents, physicians, and students as well as a valuable go-to resource for experienced healthcare professionals.

Microbial Genomics Clinical Pharmaceutical And Industrial Applications

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Author : Huseyin Tombuloglu
language : en
Publisher: Elsevier
Release Date : 2024-07-27

Microbial Genomics Clinical Pharmaceutical And Industrial Applications written by Huseyin Tombuloglu and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-07-27 with Science categories.

As the field of genomics has progressed, our understanding of microbiology has also developed. With the advent of next-generation sequencing methods and advancements in instrumental resolution, complex transcriptome, proteome, and metabolome data could be analyzed, as well as detailed annotation of microbial genomes. Microbial Genomics: Clinical, Pharmaceutical and Industrial Applications focuses on the various applications of microbial genomics in clinical, pharmaceutical and industrial fields. It consists of four parts devoted to bacterial, viral, and fungal genomics, as well as their applications in clinical, pharmaceutical, and industrial fields. Chapters are written by experts in their respective disciplines and are tightly organized with an introduction to detailed descriptions, available software implementation, applications, advanced topics, summaries, analytic questions, exercises, and suggested readings. Throughout this book, the latest genomics and biotechnological developments and discoveries as well as open problems and future challenges on microbial genomics will be highlighted. Readers will be introduced to state-of-the-art developments and trends of microbial genomics, its clinical, pharmaceutical, and industrial applications. The book will be beneficial for researchers who study microbial genomics in universities, post-graduate and graduate programs (biology, biotechnology, medicine, genetics, microbiology, industrial and environmental microbiology, etc.), as well as the pharmaceutical and industrial sector. - Presents the recent genomic developments in the industrial applications of microorganisms - Summarizes recent developments in microbial genomics, emphasizing the role of next-generation sequencing in functional genomics - Focus on how transcriptomics can help better understand host responses to pathogen infection - Describes applications of genomics in clinical microbiology

Index Medicus

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Author :
language : en
Publisher:
Release Date : 2004

Index Medicus written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2004 with Medicine categories.

Vols. for 1963- include as pt. 2 of the Jan. issue: Medical subject headings.

Cumulated Index Medicus

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Author :
language : en
Publisher:
Release Date : 1999

Cumulated Index Medicus written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1999 with Medicine categories.