Meta Analysis And Combining Information In Genetics And Genomics

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Meta Analysis And Combining Information In Genetics And Genomics

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Author : Rudy Guerra
language : en
Publisher: CRC Press
Release Date : 2016-04-19

Meta Analysis And Combining Information In Genetics And Genomics written by Rudy Guerra and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-04-19 with Mathematics categories.

Novel Techniques for Analyzing and Combining Data from Modern Biological StudiesBroadens the Traditional Definition of Meta-AnalysisWith the diversity of data and meta-data now available, there is increased interest in analyzing multiple studies beyond statistical approaches of formal meta-analysis. Covering an extensive range of quantitative infor

Meta Analysis And Combining Information In Genetics And Genomics

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Author : Rudy Guerra
language : en
Publisher: CRC Press
Release Date : 2016-04-19

Meta Analysis And Combining Information In Genetics And Genomics written by Rudy Guerra and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-04-19 with Mathematics categories.

Novel Techniques for Analyzing and Combining Data from Modern Biological StudiesBroadens the Traditional Definition of Meta-AnalysisWith the diversity of data and meta-data now available, there is increased interest in analyzing multiple studies beyond statistical approaches of formal meta-analysis. Covering an extensive range of quantitative infor

Assessing Rare Variation In Complex Traits

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Author : Eleftheria Zeggini
language : en
Publisher: Springer
Release Date : 2015-08-13

Assessing Rare Variation In Complex Traits written by Eleftheria Zeggini and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-08-13 with Medical categories.

This book is unique in covering a wide range of design and analysis issues in genetic studies of rare variants, taking advantage of collaboration of the editors with many experts in the field through large-scale international consortia including the UK10K Project, GO-T2D and T2D-GENES. Chapters provide details of state-of-the-art methodology for rare variant detection and calling, imputation and analysis in samples of unrelated individuals and families. The book also covers analytical issues associated with the study of rare variants, such as the impact of fine-scale population structure, and with combining information on rare variants across studies in a meta-analysis framework. Genetic association studies have in the last few years substantially enhanced our understanding of factors underlying traits of high medical importance, such as body mass index, lipid levels, blood pressure and many others. There is growing empirical evidence that low-frequency and rare variants play an important role in complex human phenotypes. This book covers multiple aspects of study design, analysis and interpretation for complex trait studies focusing on rare sequence variation. In many areas of genomic research, including complex trait association studies, technology is in danger of outstripping our capacity to analyse and interpret the vast amounts of data generated. The field of statistical genetics in the whole-genome sequencing era is still in its infancy, but powerful methods to analyse the aggregation of low-frequency and rare variants are now starting to emerge. The chapter Functional Annotation of Rare Genetic Variants is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

Rigor And Reproducibility In Genetics And Genomics

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Author :
language : en
Publisher: Academic Press
Release Date : 2023-11-24

Rigor And Reproducibility In Genetics And Genomics written by and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-11-24 with Medical categories.

Rigor and Reproducibility in Genetics and Genomics: Peer-reviewed, Published, Cited provides a full methodological and statistical overview for researchers, clinicians, students, and post-doctoral fellows conducting genetic and genomic research. Here, active geneticists, clinicians, and bioinformaticists offer practical solutions for a variety of challenges associated with several modern approaches in genetics and genomics, including genotyping, gene expression analysis, epigenetic analysis, GWAS, EWAS, genomic sequencing, and gene editing. Emphasis is placed on rigor and reproducibility throughout, with each section containing laboratory case-studies and classroom activities covering step-by-step protocols, best practices, and common pitfalls. Specific genetic and genomic technologies discussed include microarray analysis, DNA-seq, RNA-seq, Chip-Seq, methyl-seq, CRISPR gene editing, and CRISPR-based genetic analysis. Training exercises, supporting data, and in-depth discussions of rigor, reproducibility, and ethics in research together deliver a solid foundation in research standards for the next generation of genetic and genomic scientists. Provides practical approaches and step-by-step protocols to strengthen genetic and genomic research conducted in the laboratory or classroom Presents illustrative case studies and training exercises, discussing common pitfalls and solutions for genotyping, gene expression analysis, epigenetic analysis, GWAS, genomic sequencing, and gene editing, among other genetic and genomic approaches Examines best practices for microarray analysis, DNA-seq, RNA-seq, gene expression validation, Chip-Seq, methyl-seq, CRISPR gene editing, and CRISPR-based genetic analysis Written to provide trainees and educators with highly applicable tools and strategies to learn or refine a method toward identifying meaningful results with high confidence in their reproducibility

Developing Machine Learning And Statistical Methods For The Analysis Of Genetics And Genomics

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Author : Jiajin Li
language : en
Publisher:
Release Date : 2021

Developing Machine Learning And Statistical Methods For The Analysis Of Genetics And Genomics written by Jiajin Li and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021 with categories.

With the development of next-generation sequencing technologies, we can detect numerous genetic variants associated with many diseases or complex traits over the past decades. Genome-wide association studies (GWAS) have been one of the most effective methods to identify those variants. It discovers disease-associated variants by comparing the genetic information between controls and cases. This approach is simple and effective and has been used by many studies. Before performing GWAS, we need to detect the genetic variants of the sample population. A subset of these variants, however, may have poor sequencing quality due to limitations in NGS or variant callers. In genetic studies that analyze a large number of sequenced individuals, it is critical to detect and remove those variants with poor quality as they may cause spurious findings. Here, I will present ForestQC, an efficient statistical tool for performing quality control on variants identified from NGS data by combining a traditional filtering approach and a machine learning approach, which outperforms widely used methods by considerably improving the quality of variants to be included in the analysis. Once this association is identified, the next step is to understand the genetic mechanism of rare variants on how the variants influence diseases, especially whether or how they regulate gene expression as they may affect diseases through gene regulation. However, it is challenging to identify the regulatory effects of rare variants because it often requires large sample sizes and the existing statistical approaches are not optimized for it. To improve statistical power, I will introduce a new approach, LRT-q, based on a likelihood ratio test that combines effects of multiple rare variants in a nonlinear manner and has higher power than previous approaches. I apply LRT-q to the GTEx dataset and find many novel biological insights. Recent studies have shown that omics data can be used for automatic disease diagnosis with machine learning algorithms. I will introduce an accurate and automated machine learning pipeline for the diagnosis of atopic dermatitis (AD) based on transcriptome and microbiota data. I will demonstrate that this classifier can accurately differentiate subjects with AD and healthy individuals. It also identifies a set of genes and microorganisms that are predictive for AD. I will show that they are directly or indirectly associated with AD.

Handbook Of Statistical Genomics

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Author : David J. Balding
language : en
Publisher: John Wiley & Sons
Release Date : 2019-07-09

Handbook Of Statistical Genomics written by David J. Balding and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-07-09 with Science categories.

A timely update of a highly popular handbook on statistical genomics This new, two-volume edition of a classic text provides a thorough introduction to statistical genomics, a vital resource for advanced graduate students, early-career researchers and new entrants to the field. It introduces new and updated information on developments that have occurred since the 3rd edition. Widely regarded as the reference work in the field, it features new chapters focusing on statistical aspects of data generated by new sequencing technologies, including sequence-based functional assays. It expands on previous coverage of the many processes between genotype and phenotype, including gene expression and epigenetics, as well as metabolomics. It also examines population genetics and evolutionary models and inference, with new chapters on the multi-species coalescent, admixture and ancient DNA, as well as genetic association studies including causal analyses and variant interpretation. The Handbook of Statistical Genomics focuses on explaining the main ideas, analysis methods and algorithms, citing key recent and historic literature for further details and references. It also includes a glossary of terms, acronyms and abbreviations, and features extensive cross-referencing between chapters, tying the different areas together. With heavy use of up-to-date examples and references to web-based resources, this continues to be a must-have reference in a vital area of research. Provides much-needed, timely coverage of new developments in this expanding area of study Numerous, brand new chapters, for example covering bacterial genomics, microbiome and metagenomics Detailed coverage of application areas, with chapters on plant breeding, conservation and forensic genetics Extensive coverage of human genetic epidemiology, including ethical aspects Edited by one of the leading experts in the field along with rising stars as his co-editors Chapter authors are world-renowned experts in the field, and newly emerging leaders. The Handbook of Statistical Genomics is an excellent introductory text for advanced graduate students and early-career researchers involved in statistical genetics.

Topics In Applied Statistics

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Author : Mingxiu Hu
language : en
Publisher: Springer Science & Business Media
Release Date : 2013-09-14

Topics In Applied Statistics written by Mingxiu Hu 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 2013-09-14 with Medical categories.

This volume presents 27 selected papers in topics that range from statistical applications in business and finance to applications in clinical trials and biomarker analysis. All papers feature original, peer-reviewed content. The editors intentionally selected papers that cover many topics so that the volume will serve the whole statistical community and a variety of research interests. The papers represent select contributions to the 21st ICSA Applied Statistics Symposium. The International Chinese Statistical Association (ICSA) Symposium took place between the 23rd and 26th of June, 2012 in Boston, Massachusetts. It was co-sponsored by the International Society for Biopharmaceutical Statistics (ISBS) and American Statistical Association (ASA). This is the inaugural proceedings volume to share research from the ICSA Applied Statistics Symposium.

Biological Knowledge Discovery Handbook

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Author : Mourad Elloumi
language : en
Publisher: John Wiley & Sons
Release Date : 2015-02-04

Biological Knowledge Discovery Handbook written by Mourad Elloumi and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-02-04 with Computers categories.

The first comprehensive overview of preprocessing, mining, and postprocessing of biological data Molecular biology is undergoing exponential growth in both the volume and complexity of biological data and knowledge discovery offers the capacity to automate complex search and data analysis tasks. This book presents a vast overview of the most recent developments on techniques and approaches in the field of biological knowledge discovery and data mining (KDD) providing in-depth fundamental and technical field information on the most important topics encountered. Written by top experts, Biological Knowledge Discovery Handbook: Preprocessing, Mining, and Postprocessing of Biological Data covers the three main phases of knowledge discovery (data preprocessing, data processing also known as data mining and data postprocessing) and analyzes both verification systems and discovery systems. BIOLOGICAL DATA PREPROCESSING Part A: Biological Data Management Part B: Biological Data Modeling Part C: Biological Feature Extraction Part D Biological Feature Selection BIOLOGICAL DATA MINING Part E: Regression Analysis of Biological Data Part F Biological Data Clustering Part G: Biological Data Classification Part H: Association Rules Learning from Biological Data Part I: Text Mining and Application to Biological Data Part J: High-Performance Computing for Biological Data Mining Combining sound theory with practical applications in molecular biology, Biological Knowledge Discovery Handbook is ideal for courses in bioinformatics and biological KDD as well as for practitioners and professional researchers in computer science, life science, and mathematics.

Neither Mind Nor Brain

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Author : CJ ROY
language : en
Publisher: CJ Roy
Release Date : 2020-12-12

Neither Mind Nor Brain written by CJ ROY and has been published by CJ Roy this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-12-12 with Philosophy categories.

This book is an interdisciplinary theoretical effort to explain the mind-body problem. Conscious mind is the hard problem to be explained and is the utmost existential question for any scientific mind. Neither a reductionist identity theory nor a commonsense-religious dualism can answer the problem. Human cognitive system can have a natural explanation rather than a religious description. To reduce the mind as what the brain does is too premature and to separate the mind and brain as two independent realities is too trivial. The hypothesis of the book identifies the conscious mind with the emergent functionality of the human brain. And, this is definitely an approximate guess. This informed guess is a challenge to many previously established theories and is an invitation for further research. It demystifies the age old homunculus mind and does not explains it away. To elaborate the theme, the author has incorporated themes such as complex system dynamics, evolution, cosmology, thermodynamics, information and emergence. The philosophical discussion on the first three chapters govern as an intuitive background for the theoretical development in further chapters. It affirms that the mind and brain are neither two dichotomized substances nor are they one and same substance. Chapters from four to eight deal with various themes from natural science with respect to the theme of mind-brain. they involve system dynamics, cosmology, thermodynamics, evolutionary theory and information model. Last chapter assimilates the discussions of previous chapters to propose the key hypothesis of the book viz. mind-brain is the emergent functionality of the human brain which is the matter-energy-information complex system. The universe, which itself is a matter-energy-information system, at least in one occasion, becomes conscious of itself through humans.

Biological Sequence Analysis Using The Seqan C Library

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Author : Andreas Gogol-Döring
language : en
Publisher: CRC Press
Release Date : 2009-11-11

Biological Sequence Analysis Using The Seqan C Library written by Andreas Gogol-Döring and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-11-11 with Computers categories.

An Easy-to-Use Research Tool for Algorithm Testing and DevelopmentBefore the SeqAn project, there was clearly a lack of available implementations in sequence analysis, even for standard tasks. Implementations of needed algorithmic components were either unavailable or hard to access in third-party monolithic software products. Addressing these conc