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Linking Phenotypes And Genotypes
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Book Synopsis Epigenetics by : Benedikt Hallgrimsson Ph.D.
Download or read book Epigenetics written by Benedikt Hallgrimsson Ph.D. and published by Univ of California Press. This book was released on 2011-04-11 with total page 469 pages. Available in PDF, EPUB and Kindle. Book excerpt: Illuminating the processes and patterns that link genotype to phenotype, epigenetics seeks to explain features, characters, and developmental mechanisms that can only be understood in terms of interactions that arise above the level of the gene. With chapters written by leading authorities, this volume offers a broad integrative survey of epigenetics. Approaching this complex subject from a variety of perspectives, it presents a broad, historically grounded view that demonstrates the utility of this approach for understanding complex biological systems in development, disease, and evolution. Chapters cover such topics as morphogenesis and organ formation, conceptual foundations, and cell differentiation, and together demonstrate that the integration of epigenetics into mainstream developmental biology is essential for answering fundamental questions about how phenotypic traits are produced.
Book Synopsis Phenotypes and Genotypes by : Florian Frommlet
Download or read book Phenotypes and Genotypes written by Florian Frommlet and published by Springer. This book was released on 2016-02-12 with total page 232 pages. Available in PDF, EPUB and Kindle. Book excerpt: This timely text presents a comprehensive guide to genetic association, a new and rapidly expanding field that aims to elucidate how our genetic code (genotypes) influences the traits we possess (phenotypes). The book provides a detailed review of methods of gene mapping used in association with experimental crosses, as well as genome-wide association studies. Emphasis is placed on model selection procedures for analyzing data from large-scale genome scans based on specifically designed modifications of the Bayesian information criterion. Features: presents a thorough introduction to the theoretical background to studies of genetic association (both genetic and statistical); reviews the latest advances in the field; illustrates the properties of methods for mapping quantitative trait loci using computer simulations and the analysis of real data; discusses open challenges; includes an extensive statistical appendix as a reference for those who are not totally familiar with the fundamentals of statistics.
Book Synopsis Systems Genetics by : Florian Markowetz
Download or read book Systems Genetics written by Florian Markowetz and published by Cambridge University Press. This book was released on 2015-07-02 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: Whereas genetic studies have traditionally focused on explaining heritance of single traits and their phenotypes, recent technological advances have made it possible to comprehensively dissect the genetic architecture of complex traits and quantify how genes interact to shape phenotypes. This exciting new area has been termed systems genetics and is born out of a synthesis of multiple fields, integrating a range of approaches and exploiting our increased ability to obtain quantitative and detailed measurements on a broad spectrum of phenotypes. Gathering the contributions of leading scientists, both computational and experimental, this book shows how experimental perturbations can help us to understand the link between genotype and phenotype. A snapshot of current research activity and state-of-the-art approaches to systems genetics are provided, including work from model organisms such as Saccharomyces cerevisiae and Drosophila melanogaster, as well as from human studies.
Book Synopsis Linking Phenotypes and Genotypes by : Florian Markowetz
Download or read book Linking Phenotypes and Genotypes written by Florian Markowetz and published by Cambridge University Press. This book was released on 2015-07-02 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first book to comprehensively cover the field of systems genetics, gathering contributions from leading scientists.
Book Synopsis Environmental Genomics by : C. Cristofre Martin
Download or read book Environmental Genomics written by C. Cristofre Martin and published by Springer Science & Business Media. This book was released on 2008-01-18 with total page 363 pages. Available in PDF, EPUB and Kindle. Book excerpt: Here is a manual for an environmental scientist who wishes to embrace genomics to answer environmental questions. The volume covers: gene expression profiling, whole genome and chromosome mutation detection, and methods to assay genome diversity and polymorphisms within a particular environment. This book provides a systematic framework for determining environmental impact and ensuring human health and the sustainability of natural populations.
Book Synopsis Epigenetics by : Benedikt Hallgrímsson
Download or read book Epigenetics written by Benedikt Hallgrímsson and published by Univ of California Press. This book was released on 2011-04-11 with total page 468 pages. Available in PDF, EPUB and Kindle. Book excerpt: “If you want to understand evolution, you need to understand the murky world of epigenetics. A hearty congratulations should be paid to Hallgrimsson and Hall, who provide reliable and steady illumination.”-Bernard Wood, Center for the Advanced Study of Hominid Paleobiology, George Washington University
Book Synopsis Understanding the Connection Between Genotypes and Phenotypes Using Linkage Analysis and CRISPR Genetic Engineering by : Liangke Gou
Download or read book Understanding the Connection Between Genotypes and Phenotypes Using Linkage Analysis and CRISPR Genetic Engineering written by Liangke Gou and published by . This book was released on 2019 with total page 172 pages. Available in PDF, EPUB and Kindle. Book excerpt: The fundamental goal of genetics is to understand the functional effect of DNA sequence variations on a wide range of phenotypes, from basic biology to genetic diseases. Broadly, there are two major strategies to approach this goal: the first one is to find natural genetic variants underlying the trait of interest through linkage or association studies; the other is experimentally introducing genetic perturbations and assaying the effects of the perturbations in a high-throughput manner. In this dissertation, both approaches were employed to understand the effect of genetic variants. Following the first approach, we used linkage analysis to find the genetic basis of mutation rate variation in yeast. We developed a high-throughput fluctuation assay to enable quantification of spontaneous mutation rate in hundreds of yeast for the first time. We measured the mutation rate of 1040 yeast segregants from a cross between two diverge yeast strains, BY and RM. Combined with the genotype data, we performed linkage analysis in the segregants and identified four quantitative trait loci (QTLs) that contribute to the mutation rate variation in the cross. We fine-mapped two QTLs to the underlying causal genes, RAD5 and MKT1, that contribute to mutation rate variation. For the second approach, we developed three different systems to study the effect of natural variants using the genetic engineering tool CRISPR-Cas9. We constructed ten different CRISPR-Cas9 base editor systems for yeast, aiming to expand the targetable regions and the base converting types by using different base editors. We measured the efficiency of ten base editors in yeast from amplicon sequencing results at ten different sites along the genome and found one base editor that recognized the protospacer adjacent motif (PAM) site NGA with high efficiency. In addition to CRISPR base editor, we constructed a precise genome editing system with trackable genome integrated barcode using CRISPR-Cas9 with gRNA and donor DNA pairs. The integrated barcode enables precise tracking of edited strains with sequencing, ensuring robust downstream phenotyping. We also worked toward developing a CRISPR-directed mitotic recombination mapping panel in human cell lines to narrow down mapped out regions to causal genes by targeted creation of DNA double strand breaks along the chromosome.
Book Synopsis Quantitative Trait Loci (QTL) by : Scott A. Rifkin
Download or read book Quantitative Trait Loci (QTL) written by Scott A. Rifkin and published by Humana Press. This book was released on 2012-05-09 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over the last two decades advances in genotyping technology, and the development of quantitative genetic analytical techniques have made it possible to dissect complex traits and link quantitative variation in traits to allelic variation on chromosomes or quantitative trait loci (QTLs). In Quantitative Trait Loci (QTLs):Methods and Protocols, expert researchers in the field detail methods and techniques that focus on specific components of the entire process of quantitative train loci experiments. These include methods and techniques for the mapping populations, identifying quantitative trait loci, extending the power of quantitative trait locus analysis, and case studies. Written in the highly successful Methods in Molecular BiologyTM series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Thorough and intuitive, Quantitative Trait Loci (QTLs):Methods and Protocols aids scientists in the further study of the links between phenotypic and genotypic variation in fields from medicine to agriculture, from molecular biology to evolution to ecology.
Book Synopsis Quantitative Trait Loci by : Nicola J. Camp
Download or read book Quantitative Trait Loci written by Nicola J. Camp and published by Springer Science & Business Media. This book was released on 2008-02-03 with total page 362 pages. Available in PDF, EPUB and Kindle. Book excerpt: In Quantitative Trait Loci: Methods and Protocols, a panel of highly experienced statistical geneticists demonstrate in a step-by-step fashion how to successfully analyze quantitative trait data using a variety of methods and software for the detection and fine mapping of quantitative trait loci (QTL). Writing for the nonmathematician, these experts guide the investigator from the design stage of a project onwards, providing detailed explanations of how best to proceed with each specific analysis, to find and use appropriate software, and to interpret results. Worked examples, citations to key papers, and variations in method ease the way to understanding and successful studies. Among the cutting-edge techniques presented are QTDT methods, variance components methods, and the Markov Chain Monte Carlo method for joint linkage and segregation analysis.
Book Synopsis Scientific Frontiers in Developmental Toxicology and Risk Assessment by : National Research Council
Download or read book Scientific Frontiers in Developmental Toxicology and Risk Assessment written by National Research Council and published by National Academies Press. This book was released on 2000-12-21 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt: Scientific Frontiers in Developmental Toxicology and Risk Assessment reviews advances made during the last 10-15 years in fields such as developmental biology, molecular biology, and genetics. It describes a novel approach for how these advances might be used in combination with existing methodologies to further the understanding of mechanisms of developmental toxicity, to improve the assessment of chemicals for their ability to cause developmental toxicity, and to improve risk assessment for developmental defects. For example, based on the recent advances, even the smallest, simplest laboratory animals such as the fruit fly, roundworm, and zebrafish might be able to serve as developmental toxicological models for human biological systems. Use of such organisms might allow for rapid and inexpensive testing of large numbers of chemicals for their potential to cause developmental toxicity; presently, there are little or no developmental toxicity data available for the majority of natural and manufactured chemicals in use. This new approach to developmental toxicology and risk assessment will require simultaneous research on several fronts by experts from multiple scientific disciplines, including developmental toxicologists, developmental biologists, geneticists, epidemiologists, and biostatisticians.
Book Synopsis Genetics and Analysis of Quantitative Traits by : Michael Lynch
Download or read book Genetics and Analysis of Quantitative Traits written by Michael Lynch and published by Sinauer Associates Incorporated. This book was released on 1998-01 with total page 980 pages. Available in PDF, EPUB and Kindle. Book excerpt: Professors Lynch and Walsh bring together the diverse array of theoretical and empirical applications of quantitative genetics in a work that is comprehensive and accessible to anyone with a rudimentary understanding of statistics and genetics.
Book Synopsis Linking Genotypes Database with Locus-specific Database and Genotype-phenotype Correlation in Phenylketonuria by : Sarah Beatrice Wettstein
Download or read book Linking Genotypes Database with Locus-specific Database and Genotype-phenotype Correlation in Phenylketonuria written by Sarah Beatrice Wettstein and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Linkage Analysis and Gene Mapping by : Jiankang WANG
Download or read book Linkage Analysis and Gene Mapping written by Jiankang WANG and published by EDP Sciences. This book was released on 2023-07-07T00:00:00+02:00 with total page 532 pages. Available in PDF, EPUB and Kindle. Book excerpt: One major task of genetic studies is to construct the genetic map through linkage analysis, and then locate the genetic loci of important traits on the constructed linkage maps, identify favorable alleles which are of values to human beings, and investigate their biochemical pathways from genotype to phenotype. This book presents the linkage analysis and gene mapping methodologies, which are applicable to self-pollinated, cross-pollinated, and asexual propagated species, and genetic populations derived from two homozygous parents, two heterozygous parents, and multiple homozygous parents. Chapter 1 in this book begins with genetic mating designs and various types of genetic populations, followed by the structure of commonly used populations and analysis methods of phenotypic data. In chapters 2 and 3, estimation of recombination frequency and construction of linkage map are introduced for twenty bi-parental populations. Chapter 4 deals with two classical gene mapping methods, where no background control is considered, while chapters 5 and 6 describe the inclusive composite interval mapping (ICIM) with background control. Chapter 7 is focused on populations derived from two heterozygous parents, which can be two individuals in a random mating population, two clonal cultivars, or two single crosses from four homozygous inbred lines. Chapter 8 provides knowledge on the pure-line progeny populations derived from four to eight homozygous parents. The last two chapters covers populations, methods and commonly asked questions in genetic mapping which cannot be included previously. This book is intended for readers working on plant and animal genetics, population and quantitative genetics, and plant and animal breeding.
Book Synopsis Principles of Biology by : Lisa Bartee
Download or read book Principles of Biology written by Lisa Bartee and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The Principles of Biology sequence (BI 211, 212 and 213) introduces biology as a scientific discipline for students planning to major in biology and other science disciplines. Laboratories and classroom activities introduce techniques used to study biological processes and provide opportunities for students to develop their ability to conduct research.
Book Synopsis Genetics for Surgeons by : Patrick John Morrison
Download or read book Genetics for Surgeons written by Patrick John Morrison and published by Remedica. This book was released on 2005 with total page 237 pages. Available in PDF, EPUB and Kindle. Book excerpt: Morrison (human genetics, University of Ulster, UK) and Spence (biomedical science, University of Ulster, UK) offer an accessible reference on the genetic disorders that surgeons can expect to meet in general surgical practice. Written in non-technical language, with a glossary, list of abbreviations, and color and b&w photos and medical images, the book supplies an introduction to the nomenclature and technology of molecular biology, and will be a useful starting point for those who wish to extend their knowledge. Annotation :2005 Book News, Inc., Portland, OR (booknews.com).
Book Synopsis The Extended Phenotype by : Richard Dawkins
Download or read book The Extended Phenotype written by Richard Dawkins and published by Oxford University Press. This book was released on 2016 with total page 486 pages. Available in PDF, EPUB and Kindle. Book excerpt: In The Selfish Gene, Richard Dawkins crystallized the gene's eye view of evolution developed by W.D. Hamilton and others. The book provoked widespread and heated debate. Written in part as a response, The Extended Phenotype gave a deeper clarification of the central concept of the gene as the unit of selection; but it did much more besides. In it, Dawkins extended the gene's eye view to argue that the genes that sit within an organism have an influence that reaches out beyond the visible traits in that body - the phenotype - to the wider environment, which can include other individuals. So, for instance, the genes of the beaver drive it to gather twigs to produce the substantial physical structure of a dam; and the genes of the cuckoo chick produce effects that manipulate the behaviour of the host bird, making it nurture the intruder as one of its own. This notion of the extended phenotype has proved to be highly influential in the way we understand evolution and the natural world. It represents a key scientific contribution to evolutionary biology, and it continues to play an important role in research in the life sciences. The Extended Phenotype is a conceptually deep book that forms important reading for biologists and students. But Dawkins' clear exposition is accessible to all who are prepared to put in a little effort. Oxford Landmark Science books are 'must-read' classics of modern science writing which have crystallized big ideas, and shaped the way we think.
Book Synopsis Learning Genomic and Molecular Mediators of Genotype-phenotype Associations by : Anna Shcherbina
Download or read book Learning Genomic and Molecular Mediators of Genotype-phenotype Associations written by Anna Shcherbina and published by . This book was released on 2020 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The vast majority of genomic variants are non-coding, and many disrupt regulatory elements, causing dysregulation of gene expression. However, the functional mechanisms by which non-coding variants operate at the molecular level, as well as their tissue-specific downstream effects on cellular, organismal and disease phenotypes remain challenging to decipher. Firstly, complex phenotypes such as physical activity patterns are difficult to characterize and measure. Secondly, even after inferring statistical associations between genetic loci and complex phenotypes, identifying the causal variants is challenging due to the issues posed by linkage disequilibrium. Finally, the elucidation of functional molecular mechanisms that mediate the manifestation of genotypic variation to phenotypic effects remains an open challenge in the field. This thesis attempts to address these three challenges via the development and application of statistical and deep learning approaches to mine large genomic, molecular and phenotypic datasets. The MyHeart Counts study serves as an example of how wearable and mobile technologies enable unobtrusive real-time measurements of complex phenotypes such as exercise and physical activity patterns. These technologies also enable rapid recruitment of large study cohorts and facilitate fully digital randomized controlled trials with low barriers to entry. Such technologies also facilitate the compilation of population-level biobanks, such as the UK Biobank by enabling acquisition of lifestyle and activity data at scale. Having acquired complex phenotypes on large data cohorts, we can begin to investigate the effects of genomic variation on these phenotypes by performing genomewide association studies (GWAS). Functional GWAS SNPs can be identified via in silico interrogation of predictive deep learning models of regulatory DNA. Here, I present convolutional neural network models trained on genome-wide chromatin profiling experiments to interpret and finemap GWAS SNPs by leveraging their ability to learn predictive DNA sequence syntax. Case studies in colorectal cancer and Alzheimer's disease are presented to illustrate the application of these methods. To improve the model stability and interpretability, I developed deep learning models that can predict regulatory chromatin profiles at single base resolution, accounting and correcting for confounding experimental biases. I also contributed to several collaborative investigations of the molecular basis of complex cellular phenotypes. We identified the Sp1 regulatory protein as a key regulator of matrix stiffness and induction of tumorigenic phenotypes in mammary epithelium; the PI3K pathway as a key modulator of efficiency of stem cell differentiation and transcription factor networks that regulate murine muscle stem cell aging through differentiation. In summary, this thesis presents new computational approaches for linking genotype to phenotype through mechanistic molecular mechanisms.
