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Author : Karim Mekhail
Publisher : Frontiers Media SA
ISBN 13 : 288974504X
Total Pages : 139 pages
Book Rating : 4.8/5 (897 download)
Download or read book Spatial Genome Organization written by Karim Mekhail and published by Frontiers Media SA. This book was released on 2022-02-23 with total page 139 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Tom Sexton
Publisher : Springer Nature
ISBN 13 : 1071624970
Total Pages : 332 pages
Book Rating : 4.0/5 (716 download)
Download or read book Spatial Genome Organization written by Tom Sexton and published by Springer Nature. This book was released on 2022-07-22 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed volume explores a variety of cutting-edge techniques used to interrogate spatial genome organization. Beginning with a section covering the vital chromosome conformation capture (3C) technique, this collection continues with chapters on targeted Hi-C approaches, sequencing-based approaches to assess nuclear environment, as well as single-cell technologies to better characterize the heterogeneity and dynamics of nuclear architectures and approaches to visualize them by microscopy. Finally, in order to be able to ask functional questions about the role of spatial chromatin organization in genomic control, the last section provides methods for acute manipulations of chromatin architecture. Written for the highly successful Methods in Molecular Biology series, 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 practical, Spatial Genome Organization: Methods and Protocols is an ideal resource for researchers searching for the best techniques to address their own specific research questions.
Author : Aleksei Anatoliyovych Stepanenko
Publisher : Delve Publishing
ISBN 13 : 9781773610290
Total Pages : 0 pages
Book Rating : 4.6/5 (12 download)
Download or read book Recent Discoveries in Human Genome Organization written by Aleksei Anatoliyovych Stepanenko and published by Delve Publishing. This book was released on 2017-11 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The human body consists of many trillions of cells harboring nearly identical genomes. Yet cells manifest strikingly different cell morphologies and functions, reflecting their distinct patterns of gene expression. One of the most fundamental questions in human biology is how one genome sequence can give rise to so many different cell types. Increasing evidence indicates that the spatial, three-dimensional (3D) organization of chromatin influences gene expression and cell fate. The spatial organization of metazoan genomes has a direct influence on fundamental nuclear processes that include transcription, replication, and DNA repair. Advancements in high-throughput genomics and computational methods in the past 15 years have taken our understanding of the genome to a whole new level by allowing genome-wide assessments of chromatin conformation in the 3D space. General principles guiding the spatial conformation of chromosomes, such as compartmentalization and formation of topologically associating domains and chromatin loops, are now becoming increasingly understood, and this is leading to a better understanding of long-range chromosomal communication. In this book, recent studies concerning the chromatin compaction, local interactions, long-range interactions and the nuclear positioning of each chromatin type are reviewed. The well-established and emerging technologies that are revolutionizing our understanding of higher-order genome architecture are summarized.
Author : Minghua Deng
Publisher : Springer
ISBN 13 : 9783642371943
Total Pages : 346 pages
Book Rating : 4.3/5 (719 download)
Download or read book Research in Computational Molecular Biology written by Minghua Deng and published by Springer. This book was released on 2013-03-22 with total page 346 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 17th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2013, held in Beijing, China, in April 2013. The 32 revised full papers were carefully reviewed and selected from 167 submissions. The papers cover a wide range of topics including molecular sequence analysis; genes and regulatory elements; molecular evolution; gene expression; biological networks; sequencing and genotyping technologies; genomics; epigenomics; metagenomics; population, statistical genetics; systems biology; computational proteomics; computational structural biology; imaging; large-scale data management.
Author : Oldenburg Oldenburg Press
Publisher :
ISBN 13 : 9781523764426
Total Pages : 40 pages
Book Rating : 4.7/5 (644 download)
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.
Author : J. Zlatanova
Publisher : Gulf Professional Publishing
ISBN 13 : 9780444515940
Total Pages : 546 pages
Book Rating : 4.5/5 (159 download)
Download or read book Chromatin Structure and Dynamics written by J. Zlatanova and published by Gulf Professional Publishing. This book was released on 2004 with total page 546 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biological processes that replicate, preserve and use the genetic information encoded in DNA must operate in the context of chromatin, a highly organized complex of DNA and proteins. These proteins do not merely package the DNA in the tiny volume of the nucleus, but impart the structure the ability to change according to the requirements of the specific process the DNA is involved in. Moreover, chromatin structure is used by the cell to control the activity of DNA. In this volume the basics of chromatin structure and dynamics are presented by established experts in the field.
Author : Sergey V. Razin
Publisher :
ISBN 13 : 9783540624554
Total Pages : 195 pages
Book Rating : 4.6/5 (245 download)
Download or read book The Nuclear Matrix and Spatial Organization of Chromosomal DNA Domains written by Sergey V. Razin and published by . This book was released on 1997-01-01 with total page 195 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the first monograph giving an all-round description of different aspects of the eukaryotic genome functional architecture. It focuses on how the spatial organization of a genome within a eukaryotic cell nucleus fulfills the specific needs of the genome functioning. This volume presents an integral view of eukaryotic cell nuclei functional compartmentalization with special emphasis on the genome spatial organization and the functional significance of this organization.
Author : Kurt Binder
Publisher : Springer Science & Business Media
ISBN 13 : 366230273X
Total Pages : 201 pages
Book Rating : 4.6/5 (623 download)
Download or read book Monte Carlo Simulation in Statistical Physics written by Kurt Binder and published by Springer Science & Business Media. This book was released on 2013-11-11 with total page 201 pages. Available in PDF, EPUB and Kindle. Book excerpt: When learning very formal material one comes to a stage where one thinks one has understood the material. Confronted with a "realiife" problem, the passivity of this understanding sometimes becomes painfully elear. To be able to solve the problem, ideas, methods, etc. need to be ready at hand. They must be mastered (become active knowledge) in order to employ them successfully. Starting from this idea, the leitmotif, or aim, of this book has been to elose this gap as much as possible. How can this be done? The material presented here was born out of a series of lectures at the Summer School held at Figueira da Foz (Portugal) in 1987. The series of lectures was split into two concurrent parts. In one part the "formal material" was presented. Since the background of those attending varied widely, the presentation of the formal material was kept as pedagogic as possible. In the formal part the general ideas behind the Monte Carlo method were developed. The Monte Carlo method has now found widespread appli cation in many branches of science such as physics, chemistry, and biology. Because of this, the scope of the lectures had to be narrowed down. We could not give a complete account and restricted the treatment to the ap plication of the Monte Carlo method to the physics of phase transitions. Here particular emphasis is placed on finite-size effects.
Author : Beatrice Bodega
Publisher : Humana
ISBN 13 : 9781071606636
Total Pages : 322 pages
Book Rating : 4.6/5 (66 download)
Download or read book Capturing Chromosome Conformation written by Beatrice Bodega and published by Humana. This book was released on 2020-10-29 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed book collects methods based on the evolution of the chromosome conformation capture (3C) technique and other complementary approaches to dissect chromatin conformation with an emphasis on dissection of nuclear compartmentalization and visualization in imaging. Written for the highly successful Methods in Molecular Biology series, 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 practical, Capturing Chromosome Conformation: Methods and Protocols serves as an ideal guide for researchers working to further understand 3D genome organization.
Author : Eric H. Davidson
Publisher : Elsevier
ISBN 13 : 9780080525594
Total Pages : 261 pages
Book Rating : 4.5/5 (255 download)
Download or read book Genomic Regulatory Systems written by Eric H. Davidson and published by Elsevier. This book was released on 2001-01-24 with total page 261 pages. Available in PDF, EPUB and Kindle. Book excerpt: The interaction between biology and evolution has been the subject of great interest in recent years. Because evolution is such a highly debated topic, a biologically oriented discussion will appeal not only to scientists and biologists but also to the interested lay person. This topic will always be a subject of controversy and therefore any breaking information regarding it is of great interest. The author is a recognized expert in the field of developmental biology and has been instrumental in elucidating the relationship between biology and evolution. The study of evolution is of interest to many different kinds of people and Genomic Regulatory Systems: In Development and Evolution is written at a level that is very easy to read and understand even for the nonscientist. * Contents Include * Regulatory Hardwiring: A Brief Overview of the Genomic Control Apparatus and Its Causal Role in Development and Evolution * Inside the Cis-Regulatory Module: Control Logic and How the Regulatory Environment Is Transduced into Spatial Patterns of Gene Expression * Regulation of Direct Cell-Type Specification in Early Development * The Secret of the Bilaterians: Abstract Regulatory Design in Building Adult Body Parts * Changes That Make New Forms: Gene Regulatory Systems and the Evolution of Body Plans
Author : Ákos Végvári
Publisher : Springer
ISBN 13 : 3319423169
Total Pages : 184 pages
Book Rating : 4.3/5 (194 download)
Download or read book Proteogenomics written by Ákos Végvári and published by Springer. This book was released on 2016-09-29 with total page 184 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book highlights key technologies and identifies areas for further development in proteogenomics. The utility and usefulness of very large Omics data sets (Next Gen Sequencing of DNA, RNA-seq, ribosome profiling, mass spectrometry- and antibody-based proteomics) is discussed and opportunities and challenges of related bioinformatics applications are outlined. The reader will be able to appreciate the interdisciplinary nature of the continuously evolving area of proteogenomics, which has already grown beyond its original concept of verifying gene annotations by proteomics. The chapters presented in this book are arranged to offer a general overview, rather than to provide detailed descriptions of technologies. The selected applications will provide useful insight into the level of detail that can be obtained in relation to certain diseases areas, including cancer biology and personalized medicine. The readers will find that each chapter delivers a comprehensive approach to proteogenomics, each from the point of view of a specific application. Research scientists interested in innovative processes that can offer a unique and at the same time a more complete access to technological developments and concepts that in turn can contribute to a better understand biological functions should read this book.
Author : National Academies of Sciences, Engineering, and Medicine
Publisher : National Academies Press
ISBN 13 : 0309676738
Total Pages : 201 pages
Book Rating : 4.3/5 (96 download)
Download or read book Next Steps for Functional Genomics written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2020-12-18 with total page 201 pages. Available in PDF, EPUB and Kindle. Book excerpt: One of the holy grails in biology is the ability to predict functional characteristics from an organism's genetic sequence. Despite decades of research since the first sequencing of an organism in 1995, scientists still do not understand exactly how the information in genes is converted into an organism's phenotype, its physical characteristics. Functional genomics attempts to make use of the vast wealth of data from "-omics" screens and projects to describe gene and protein functions and interactions. A February 2020 workshop was held to determine research needs to advance the field of functional genomics over the next 10-20 years. Speakers and participants discussed goals, strategies, and technical needs to allow functional genomics to contribute to the advancement of basic knowledge and its applications that would benefit society. This publication summarizes the presentations and discussions from the workshop.
Author : Richard Baldock
Publisher : OUP Oxford
ISBN 13 : 0191565814
Total Pages : 322 pages
Book Rating : 4.1/5 (915 download)
Download or read book Image Processing and Analysis written by Richard Baldock and published by OUP Oxford. This book was released on 1999-12-09 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: A wide range of books on image processing and analysis provide comprehensive descriptions of mathematics and algorithms for image processing practitioners, or introductory material for engineering students. This volume is different in addressing the topic from the point of view of the "user". Standard algorithms, procedures and rules of thumb are explained in the context of successful application to biological or medical images. Early chapters cover the basic topics of image acquisition, processing, analysis and pattern recognition. Much of the explanation is in the form of protocols, which should equip the user in the biological or earth sciences with the background for informed use of image processing software, and sufficient knowledge to write their own programmes if they feel moved to do so. More advanced techniques in the use of explicit models and analysis of 3D images are covered in later chapters, also with reference to specific applications. The coverage of these is not exhaustive, but may inspire the reader to consider applying image analysis to problems beyond those tackled by commercial packages.
Author : Silvio Bicciato
Publisher : Humana
ISBN 13 : 9781071613924
Total Pages : 0 pages
Book Rating : 4.6/5 (139 download)
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.
Author : David P. Bazett-Jones
Publisher : Springer
ISBN 13 : 3319388827
Total Pages : 513 pages
Book Rating : 4.3/5 (193 download)
Download or read book The Functional Nucleus written by David P. Bazett-Jones and published by Springer. This book was released on 2016-10-17 with total page 513 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book gives an in-depth overview on nuclear structure and function. It clearly shows that the epigenome and the three-dimensional organization of the nucleus are not independent properties. The intimate relationship between the location and the epigenetic modifications of gene loci is highlighted. Finally, it shows that the complex three-dimensional organization of the nucleus is not just of academic interest: The structure, composition and function of virtually all of the sub-nuclear compartments identified so far can be implicated to a list of human genetic diseases. Hence, a detailed elucidation of how these domains are assembled and function will provide new opportunities for therapeutic intervention in clinical practice.
Author : Scott Camazine
Publisher : Princeton University Press
ISBN 13 : 0691212929
Total Pages : pages
Book Rating : 4.6/5 (912 download)
Download or read book Self-Organization in Biological Systems written by Scott Camazine and published by Princeton University Press. This book was released on 2020-05-26 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The synchronized flashing of fireflies at night. The spiraling patterns of an aggregating slime mold. The anastomosing network of army-ant trails. The coordinated movements of a school of fish. Researchers are finding in such patterns--phenomena that have fascinated naturalists for centuries--a fertile new approach to understanding biological systems: the study of self-organization. This book, a primer on self-organization in biological systems for students and other enthusiasts, introduces readers to the basic concepts and tools for studying self-organization and then examines numerous examples of self-organization in the natural world. Self-organization refers to diverse pattern formation processes in the physical and biological world, from sand grains assembling into rippled dunes to cells combining to create highly structured tissues to individual insects working to create sophisticated societies. What these diverse systems hold in common is the proximate means by which they acquire order and structure. In self-organizing systems, pattern at the global level emerges solely from interactions among lower-level components. Remarkably, even very complex structures result from the iteration of surprisingly simple behaviors performed by individuals relying on only local information. This striking conclusion suggests important lines of inquiry: To what degree is environmental rather than individual complexity responsible for group complexity? To what extent have widely differing organisms adopted similar, convergent strategies of pattern formation? How, specifically, has natural selection determined the rules governing interactions within biological systems? Broad in scope, thorough yet accessible, this book is a self-contained introduction to self-organization and complexity in biology--a field of study at the forefront of life sciences research.
Author : Natalia V. Botchkareva
Publisher : Humana
ISBN 13 : 9781071606476
Total Pages : 0 pages
Book Rating : 4.6/5 (64 download)
Download or read book Molecular Dermatology written by Natalia V. Botchkareva and published by Humana. This book was released on 2020-04-21 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume delivers the most important laboratory techniques that underlie dermatological investigation, including in situ, in vitro, ex vivo, and in vivo models of skin, its appendages (hair follicles, sebaceous and sweat glands), and immune cells. Also included are unique techniques that unravel epigenetic mechanisms in skin and hair follicle cells, such as gene organization in the nucleus and gene expression regulation by the non-coding transcriptome, which are important recent developments in investigative dermatology. Written for the highly successful Methods in Molecular Biology series, 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 practical, Molecular Dermatology: Methods and Protocols serves as an essential resource for researchers working in the areas of fundamental as well as applied dermatological science.
