Interpreting Human Genetic Variations Through Transcriptional Regulation and 3D Genome Organization

Download Interpreting Human Genetic Variations Through Transcriptional Regulation and 3D Genome Organization PDF Online Free

Author :
Publisher :
ISBN 13 :
Total Pages : 196 pages
Book Rating : 4.:/5 (111 download)

DOWNLOAD NOW!


Book Synopsis Interpreting Human Genetic Variations Through Transcriptional Regulation and 3D Genome Organization by : Yunjiang Qiu

Download or read book Interpreting Human Genetic Variations Through Transcriptional Regulation and 3D Genome Organization written by Yunjiang Qiu and published by . This book was released on 2019 with total page 196 pages. Available in PDF, EPUB and Kindle. Book excerpt: It has been more than a decade since the human genome was sequenced, but a complete understanding of the functional elements in the human genome is still lacking, especially for the non-coding part of the genome. The lack of complete understanding of the genome makes interpreting the function of genetic variants a daunting challenge. Here I exploited multiple ways to decipher the function of genetic variants by leveraging knowledge about transcriptional regulation and three-dimension genome organization. First, we developed SNP-SELEX, a high throughput method to assess the effect of SNPs on transcription factor (TF) binding. I demonstrated the superior performance of SNP-SELEX over previous delta PWM models, and applied results of SNP-SELEX to identify putative causal variants for type 2 diabetes. Furthermore, I employed deltaSVM algorithm to develop models that could predict the effect of SNPs on TF binding for any non-coding variants. Those models not only outperform delta PWM models in vitro and in vivo but also could help identify novel master regulator for complex traits and diseases. Next, I co-led a study to investigate the effect of genetic variants on three-dimensional (3D) chromatin conformation. I identified thousands of regions across the genome where 3D chromatin conformation varies between individuals and found those variations often accompany changes in other genome functions. Moreover, I found DNA sequence variations could influence 3D chromatin conformation and mapped hundreds of Quantitative Trait Loci (QTLs) associated with 3D chromatin features, some of which confer disease risk. Finally, I analyzed Hi-C data from human embryonic stem cells differentiated to beta cell progenitors to characterize changes in chromatin organizations during differentiation. I identified chromatin loops that are dynamic during different stages and found those loops are also associated with transcriptional regulation. Further, I revealed that chromatin loops form interaction hubs that are related to the establishment of stage-specific transcriptional programs.

Analysis of 3D Genome Organization and Gene Regulation in Mammalian Cells

Download Analysis of 3D Genome Organization and Gene Regulation in Mammalian Cells PDF Online Free

Author :
Publisher :
ISBN 13 : 9781321138146
Total Pages : 156 pages
Book Rating : 4.1/5 (381 download)

DOWNLOAD NOW!


Book Synopsis Analysis of 3D Genome Organization and Gene Regulation in Mammalian Cells by : Siddarth Gautham Selvaraj

Download or read book Analysis of 3D Genome Organization and Gene Regulation in Mammalian Cells written by Siddarth Gautham Selvaraj and published by . This book was released on 2014 with total page 156 pages. Available in PDF, EPUB and Kindle. Book excerpt: The three-dimensional structure of the genome plays a key role in gene regulation. For example, while highly compacted heterochromatin drives gene silencing, open euchromatin facilitates gene activation. Nevertheless, how chromatin folds within these structures and consequently how it controls access to genomic content is poorly understood. Recent advances in high-throughput sequencing have provided valuable tools, such as Hi-C, for the study of chromatin structure. Using Hi-C datasets, I developed a hidden markov based algorithm to identify self-interacting patterns of chromatin structure termed topological domains. These mega-base sized domains are pervasive throughout the genome and are highly conserved among humans and mouse. At a higher resolution, topological domains encompass individual chromatin interactions between regulatory elements and its target gene. Therefore, in order to mechanistically understand gene regulation, it is essential to elucidate the functional relationship among regulatory elements and their target genes. By exploiting the sequence diversity between homologous chromosomes, it is possible to delineate this relationship. However, this requires the knowledge of haplotypes, which has traditionally been difficult to obtain. As the Hi-C protocol preferentially recovers DNA variants on the same chromosome, I invented HaploSeq to reconstruct chromosome-scale haplotypes. HaploSeq can generate haplotypes with ~99.5% accuracy for >95% of alleles in mouse and 98% accuracy for ~81% of alleles in humans, thus solving a long-standing problem in genetics. By integrating the knowledge of haplotypes, we queried the relationship between regulatory elements and gene expression in human embryonic stem cells and a panel of differentiated cell-types. Across the 5 cell lineages examined, I identified a total of 24% of genes that showed allelic bias in gene expression. While most of the allelic-genes had a correlating allelic-promoter chromatin state, ~29% of genes were exceptions suggesting other mechanisms of gene regulation. Accordingly, I then analyzed histone-acetylation marks to identify 1589 allelic enhancers. By predicting chromatin interactions using Hi-C, we observed allelic enhancers to be spatially proximal to allelic genes, suggesting cooperative activity among genome sequence, structure, and function. Taken together, our studies suggest that gene regulation is facilitated and coordinated by genome structure.

3D Genome Organization and Transcriptional Regulation in Mammalian Cells

Download 3D Genome Organization and Transcriptional Regulation in Mammalian Cells PDF Online Free

Author :
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (119 download)

DOWNLOAD NOW!


Book Synopsis 3D Genome Organization and Transcriptional Regulation in Mammalian Cells by : Emaly Piecuch

Download or read book 3D Genome Organization and Transcriptional Regulation in Mammalian Cells written by Emaly Piecuch and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Remarkably, cell types sharing the same linear genome sequence express different genes and have distinct functions. 3D genomic arrangement has been demonstrated to play a critical role in this process. Fine scale organization of genes and regulatory elements within active and inactive domains underlie gene expression and disruption of this process has been shown to influence development and disease. Yet, the precise dynamics of cell type specific 3D genomic interactions mediating mammalian gene expression, such as those between enhancers and promoters, remain lacking on a genome wide level. Neurons represent a specialized cell type known to respond to a myriad of physiological stimuli by changes in transcription of activity dependent (AD) genes. Neuron specific enhancer activation has been identified genome wide in mouse neurons during AD gene transcription, yet we lack genome wide 3D connectivity information allowing assignment of AD enhancer gene targets. Many questions about chromatin structure and how 3D structural changes influence cell type specificity and function through changes in gene expression remain unanswered due to technological limitations and the nature of biological samples required. This thesis specifically addresses such limitations focusing on application to mammalian genomes.

CELL GEOMETRY.

Download CELL GEOMETRY. PDF Online Free

Author :
Publisher :
ISBN 13 : 9781138628564
Total Pages : pages
Book Rating : 4.6/5 (285 download)

DOWNLOAD NOW!


Book Synopsis CELL GEOMETRY. by : G. V. SHIVASHANKAR

Download or read book CELL GEOMETRY. written by G. V. SHIVASHANKAR and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Long-Range Control of Gene Expression

Download Long-Range Control of Gene Expression PDF Online Free

Author :
Publisher : Academic Press
ISBN 13 : 0080877818
Total Pages : 415 pages
Book Rating : 4.0/5 (88 download)

DOWNLOAD NOW!


Book Synopsis Long-Range Control of Gene Expression by : Veronica van Heyningen

Download or read book Long-Range Control of Gene Expression written by Veronica van Heyningen and published by Academic Press. This book was released on 2011-09-02 with total page 415 pages. Available in PDF, EPUB and Kindle. Book excerpt: Long-Range Control of Gene Expression covers the current progress in understanding the mechanisms for genomic control of gene expression, which has grown considerably in the last few years as insight into genome organization and chromatin regulation has advanced. Discusses the evolution of cis-regulatory sequences in drosophila Includes information on genomic imprinting and imprinting defects in humans Includes a chapter on epigenetic gene regulation in cancer

Hi-C Data Analysis

Download Hi-C Data Analysis PDF Online Free

Author :
Publisher : Humana
ISBN 13 : 9781071613924
Total Pages : 0 pages
Book Rating : 4.6/5 (139 download)

DOWNLOAD NOW!


Book Synopsis Hi-C Data Analysis by : Silvio Bicciato

Download or read book Hi-C Data Analysis written by Silvio Bicciato and published by Humana. This book was released on 2022-09-04 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume details a comprehensive set of methods and tools for Hi-C data processing, analysis, and interpretation. Chapters cover applications of Hi-C to address a variety of biological problems, with a specific focus on state-of-the-art computational procedures adopted for the data analysis. Written in the highly 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 laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Hi-C Data Analysis: Methods and Protocols aims to help computational and molecular biologists working in the field of chromatin 3D architecture and transcription regulation.

Chromosome Structure and Aberrations

Download Chromosome Structure and Aberrations PDF Online Free

Author :
Publisher : Springer
ISBN 13 : 8132236734
Total Pages : 377 pages
Book Rating : 4.1/5 (322 download)

DOWNLOAD NOW!


Book Synopsis Chromosome Structure and Aberrations by : Tariq Ahmad Bhat

Download or read book Chromosome Structure and Aberrations written by Tariq Ahmad Bhat and published by Springer. This book was released on 2017-02-08 with total page 377 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is a compilation of various chapters contributed by a group of leading researchers from different countries and covering up to date information based on published reports and personal experience of authors in the field of cytogenetics. Beginning with the introduction of chromosome, the subsequent chapters on organization of genetic material, karyotype evolution, structural and numerical variations in chromosomes, B-chromosomes and chromosomal aberrations provide an in-depth knowledge and easy understanding of the subject matter. A special feature of the book is the inclusion of a series of chapters on various types of chromosomal aberrations and their impact on breeding behaviour and crop improvement. The possible mechanism, their consequences and role in genetic analysis has been emphasized in these chapters. A few chapters have also been dedicated on various techniques routinely used in the laboratory by students and researchers. Each chapter ends with an extensive bibliography so that the students and researchers may find it relevant to consult more literature on the subject than a book of this size can offer. The book is intended to fulfill the needs of undergraduate and post graduate students of botany, zoology and agriculture besides, teachers and researchers engaged in the field of genetics, cytogenetics, and molecular genetics. In general the readers will find each chapter of the book informative and easy to understand.

Human Chromosome Variation: Heteromorphism, Polymorphism and Pathogenesis

Download Human Chromosome Variation: Heteromorphism, Polymorphism and Pathogenesis PDF Online Free

Author :
Publisher : Springer
ISBN 13 : 9811030359
Total Pages : 500 pages
Book Rating : 4.8/5 (11 download)

DOWNLOAD NOW!


Book Synopsis Human Chromosome Variation: Heteromorphism, Polymorphism and Pathogenesis by : Herman E. Wyandt

Download or read book Human Chromosome Variation: Heteromorphism, Polymorphism and Pathogenesis written by Herman E. Wyandt and published by Springer. This book was released on 2017-03-28 with total page 500 pages. Available in PDF, EPUB and Kindle. Book excerpt: This new edition now titled “Human Chromosome Variation: Heteromorphism, Polymorphism and Pathogenesis” provides the reader with an up-to-date overview of microarrays, fragile sites, copy number variations and whole genome sequencing. Greatly expanding the discussion of microarray analysis in the previous edition of the book, are new chapters on microarray and genomic analysis, plus comprehensive tables on the subtle microdeletions and microduplications that are found on each chromosome, including 235 recurring copy number variants that are associated with well-established or emerging chromosomal syndromes. The current edition features concise information on cytogenetic methods and applications, extending these discussions to DNA analysis and genome sequencing. Sections on euchromatin, heterochromatin, FISH pattern, fragile site, copy number, and DNA sequence variation are integrated with actual clinical examples from cytogenetic laboratories and from clinical practice. The principles that allow for the distinction between benign chromosome / DNA variation and pathogenic heteromorphisms / polymorphisms are discussed and include references to the latest organizational guidelines and genomic or population databases. The two previous incarnations of this book: the ‘Atlas of Human Chromosome Heteromorphism’, and ‘Human Chromosome Variation: Heteromorphism and Polymorphism’ have been standard reference works in most cytogenetic laboratories, used by laboratory directors and clinicians all around the world. While widely used sections from the previous edition on cytogenetic technologies and heteromorphisms are retained intact the present volume adds extensive material on copy number variations (polymorphisms detected by microarray analysis), fragile sites in disease and cancer, and practical views on interpreting emerging technologies, including whole exome sequencing. This book should be of interest to clinicians, technicians and students who are or will be exposed to DNA and/or chromosome analysis and the data derived from these continuously developing techniques. This fully updated book volume will bring the reader up to speed on the latest technologies, their applications, benefits and drawbacks and as such, is a must read for anyone with an interest in DNA and chromosome analysis and the distinction between benign variation and pathogenic mistakes.

Computational Genomics with R

Download Computational Genomics with R PDF Online Free

Author :
Publisher : CRC Press
ISBN 13 : 1498781861
Total Pages : 462 pages
Book Rating : 4.4/5 (987 download)

DOWNLOAD NOW!


Book Synopsis Computational Genomics with R by : Altuna Akalin

Download or read book Computational Genomics with R written by Altuna Akalin and published by CRC Press. This book was released on 2020-12-16 with total page 462 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.

Anatomy of Gene Regulation

Download Anatomy of Gene Regulation PDF Online Free

Author :
Publisher : Cambridge University Press
ISBN 13 : 9780521804745
Total Pages : 300 pages
Book Rating : 4.8/5 (47 download)

DOWNLOAD NOW!


Book Synopsis Anatomy of Gene Regulation by : Panagiotis A. Tsonis

Download or read book Anatomy of Gene Regulation written by Panagiotis A. Tsonis and published by Cambridge University Press. This book was released on 2003-01-13 with total page 300 pages. Available in PDF, EPUB and Kindle. Book excerpt: Table of contents

Modeling the 3D Conformation of Genomes

Download Modeling the 3D Conformation of Genomes PDF Online Free

Author :
Publisher : CRC Press
ISBN 13 : 9780367780456
Total Pages : 370 pages
Book Rating : 4.7/5 (84 download)

DOWNLOAD NOW!


Book Synopsis Modeling the 3D Conformation of Genomes by : G. Tiana

Download or read book Modeling the 3D Conformation of Genomes written by G. Tiana and published by CRC Press. This book was released on 2021-03-31 with total page 370 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a timely summary of physical modeling approaches applied to biological datasets that describe conformational properties of chromosomes in the cell nucleus. The coverage ranges from introductory chapters to modeling aspects related to polymer physics, and data-driven models for genomic domains, and predicting 3D genome structur

HiC-Pro: an Optimized and Flexible Pipeline for Hi-C Data Processing

Download HiC-Pro: an Optimized and Flexible Pipeline for Hi-C Data Processing PDF Online Free

Author :
Publisher :
ISBN 13 : 9781523764426
Total Pages : 40 pages
Book Rating : 4.7/5 (644 download)

DOWNLOAD NOW!


Book Synopsis HiC-Pro: an Optimized and Flexible Pipeline for Hi-C Data Processing by : Oldenburg Oldenburg Press

Download or read book HiC-Pro: an Optimized and Flexible Pipeline for Hi-C Data Processing written by Oldenburg Oldenburg Press and published by . This book was released on 2016-01-29 with total page 40 pages. Available in PDF, EPUB and Kindle. Book excerpt: HiC-Pro is an optimized and flexible pipeline for processing Hi-C data from raw reads to normalized contact maps. HiC-Pro maps reads, detects valid ligation products, performs quality controls and generates intra- and inter-chromosomal contact maps. It includes a fast implementation of the iterative correction method and is based on a memory-efficient data format for Hi-C contact maps. In addition, HiC-Pro can use phased genotype data to build allele-specific contact maps. We applied HiC-Pro to different Hi-C datasets, demonstrating its ability to easily process large data in a reasonable time. Source code and documentation are available at http://github.com/nservant/HiC-Pro.

Epigenetic Mechanisms of Gene Regulation

Download Epigenetic Mechanisms of Gene Regulation PDF Online Free

Author :
Publisher :
ISBN 13 :
Total Pages : 716 pages
Book Rating : 4.3/5 (91 download)

DOWNLOAD NOW!


Book Synopsis Epigenetic Mechanisms of Gene Regulation by : Vincenzo E. A. Russo

Download or read book Epigenetic Mechanisms of Gene Regulation written by Vincenzo E. A. Russo and published by . This book was released on 1996 with total page 716 pages. Available in PDF, EPUB and Kindle. Book excerpt: Many inheritable changes in gene function are not explained by changes in the DNA sequence. Such epigenetic mechanisms are known to influence gene function in most complex organisms and include effects such as transposon function, chromosome imprinting, yeast mating type switching and telomeric silencing. In recent years, epigenetic effects have become a major focus of research activity. This monograph, edited by three well-known biologists from different specialties, is the first to review and synthesize what is known about these effects across all species, particularly from a molecular perspective, and will be of interest to everyone in the fields of molecular biology and genetics.

Human Gene Mutation

Download Human Gene Mutation PDF Online Free

Author :
Publisher : Taylor & Francis
ISBN 13 : 9781859960554
Total Pages : 412 pages
Book Rating : 4.9/5 (65 download)

DOWNLOAD NOW!


Book Synopsis Human Gene Mutation by : David N. Cooper

Download or read book Human Gene Mutation written by David N. Cooper and published by Taylor & Francis. This book was released on 1995 with total page 412 pages. Available in PDF, EPUB and Kindle. Book excerpt: Within the last decade, much progress has been made in the analysis and diagnosis of human inherited disease, and in the characterization of the underlying genes and their associated pathological lesions.

The Mouse Nervous System

Download The Mouse Nervous System PDF Online Free

Author :
Publisher : Academic Press
ISBN 13 : 0123694973
Total Pages : 815 pages
Book Rating : 4.1/5 (236 download)

DOWNLOAD NOW!


Book Synopsis The Mouse Nervous System by : Charles Watson

Download or read book The Mouse Nervous System written by Charles Watson and published by Academic Press. This book was released on 2011-11-28 with total page 815 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Mouse Nervous System provides a comprehensive account of the central nervous system of the mouse. The book is aimed at molecular biologists who need a book that introduces them to the anatomy of the mouse brain and spinal cord, but also takes them into the relevant details of development and organization of the area they have chosen to study. The Mouse Nervous System offers a wealth of new information for experienced anatomists who work on mice. The book serves as a valuable resource for researchers and graduate students in neuroscience. Systematic consideration of the anatomy and connections of all regions of the brain and spinal cord by the authors of the most cited rodent brain atlases A major section (12 chapters) on functional systems related to motor control, sensation, and behavioral and emotional states A detailed analysis of gene expression during development of the forebrain by Luis Puelles, the leading researcher in this area Full coverage of the role of gene expression during development and the new field of genetic neuroanatomy using site-specific recombinases Examples of the use of mouse models in the study of neurological illness

The Fourth Industrial Revolution

Download The Fourth Industrial Revolution PDF Online Free

Author :
Publisher : Currency
ISBN 13 : 1524758876
Total Pages : 192 pages
Book Rating : 4.5/5 (247 download)

DOWNLOAD NOW!


Book Synopsis The Fourth Industrial Revolution by : Klaus Schwab

Download or read book The Fourth Industrial Revolution written by Klaus Schwab and published by Currency. This book was released on 2017-01-03 with total page 192 pages. Available in PDF, EPUB and Kindle. Book excerpt: World-renowned economist Klaus Schwab, Founder and Executive Chairman of the World Economic Forum, explains that we have an opportunity to shape the fourth industrial revolu­tion, which will fundamentally alter how we live and work. Schwab argues that this revolution is different in scale, scope and complexity from any that have come before. Characterized by a range of new technologies that are fusing the physical, digital and biological worlds, the developments are affecting all disciplines, economies, industries and governments, and even challenging ideas about what it means to be human. Artificial intelligence is already all around us, from supercomputers, drones and virtual assistants to 3D printing, DNA sequencing, smart thermostats, wear­able sensors and microchips smaller than a grain of sand. But this is just the beginning: nanomaterials 200 times stronger than steel and a million times thinner than a strand of hair and the first transplant of a 3D printed liver are already in development. Imagine “smart factories” in which global systems of manu­facturing are coordinated virtually, or implantable mobile phones made of biosynthetic materials. The fourth industrial revolution, says Schwab, is more significant, and its ramifications more profound, than in any prior period of human history. He outlines the key technologies driving this revolution and discusses the major impacts expected on government, business, civil society and individu­als. Schwab also offers bold ideas on how to harness these changes and shape a better future—one in which technology empowers people rather than replaces them; progress serves society rather than disrupts it; and in which innovators respect moral and ethical boundaries rather than cross them. We all have the opportunity to contribute to developing new frame­works that advance progress.

Molecular Biology of The Cell

Download Molecular Biology of The Cell PDF Online Free

Author :
Publisher :
ISBN 13 : 9780815332183
Total Pages : 0 pages
Book Rating : 4.3/5 (321 download)

DOWNLOAD NOW!


Book Synopsis Molecular Biology of The Cell by : Bruce Alberts

Download or read book Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: