Modeling The 3d Conformation Of Genomes

Author : Guido Tiana,Luca Giorgetti
Publisher : CRC Press
Page : 370 pages
File Size : 45,7 Mb
Release : 2019-01-15
Category : Science
ISBN : 9781351387002

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Modeling the 3D Conformation of Genomes by Guido Tiana,Luca Giorgetti Pdf

This book provides a timely summary of physical modeling approaches applied to biological datasets that describe conformational properties of chromosomes in the cell nucleus. Chapters explain how to convert raw experimental data into 3D conformations, and how to use models to better understand biophysical mechanisms that control chromosome conformation. The coverage ranges from introductory chapters to modeling aspects related to polymer physics, and data-driven models for genomic domains, the entire human genome, epigenome folding, chromosome structure and dynamics, and predicting 3D genome structure.

Author : Guido Tiana,Luca Giorgetti
Publisher : CRC Press
Page : 319 pages
File Size : 49,9 Mb
Release : 2019-01-15
Category : Science
ISBN : 9781351386999

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Modeling the 3D Conformation of Genomes by Guido Tiana,Luca Giorgetti Pdf

This book provides a timely summary of physical modeling approaches applied to biological datasets that describe conformational properties of chromosomes in the cell nucleus. Chapters explain how to convert raw experimental data into 3D conformations, and how to use models to better understand biophysical mechanisms that control chromosome conformation. The coverage ranges from introductory chapters to modeling aspects related to polymer physics, and data-driven models for genomic domains, the entire human genome, epigenome folding, chromosome structure and dynamics, and predicting 3D genome structure.

Author : Beatrice Bodega,Chiara Lanzuolo
Publisher : Unknown
Page : 128 pages
File Size : 55,9 Mb
Release : 2020
Category : Chromosomes
ISBN : 1071606646

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Capturing Chromosome Conformation by Beatrice Bodega,Chiara Lanzuolo Pdf

Author : Kirti Prakash
Publisher : Springer
Page : 152 pages
File Size : 45,7 Mb
Release : 2017-02-20
Category : Science
ISBN : 9783319521831

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Chromatin Architecture by Kirti Prakash Pdf

This book sheds new light on the current state of knowledge concerning chromatin organization. Particular emphasis is given to the new imaging potential offered by super-resolution microscopy, which allows DNA imaging with a very high labeling density. From the early work on chromosomes by Walther Flemming in the nineteenth century to recent advances in genomics, the history of chromatin research now spans more than a century. The various milestones, such as the discovery of the double helix structure, the sequencing of the human genome, and the recent description of the genome in 3D space, show that understanding chromatin and chromosome function requires a clear understanding of its structure. Presenting cutting-edge data from super-resolution single molecule microscopy, the book demonstrates that chromatin manifests several levels of folding, from nucleosomes to chromosomes. Chromatin domains emerge as a new fundamental building block of chromatin architecture, with functions possibly related to gene regulation. A detailed description of chromatin folding in the pachytene stage of meiosis serves as a model for exploring this functionality, showing the apparent interplay between structure, function, and epigenetic regulation. Lastly, the book discusses possible new avenues of innovation to describe chromatin’s organization and functions. Gathering essential insights on chromatin architecture, the book offers students an introduction to microscopy and its application to chromatin organization, while also providing advanced readers with new ideas for future research.

Author : Sławomir Filipek
Publisher : Springer Nature
Page : 379 pages
File Size : 41,7 Mb
Release : 2023-03-23
Category : Science
ISBN : 9781071629741

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Homology Modeling by Sławomir Filipek Pdf

This detailed volume provides state-of-the-art methodologies and reviews of important topics in the field of homology modeling. From homology modeling in the twilight zone and improving accuracy through sequence space analysis to approaches to construct multi-protein complex models, the book explores a wide variety of uses and applications of this valuable technique. Written for the highly successful Methods in Molecular Biology series, the chapters include introductions to their respective topics, lists of the necessary programs, webservers, and databases, step-by-step and readily reproducible protocols, as well as tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Homology Modeling: Methods and Protocols serves as an ideal guide to recent homology modeling procedures, assumptions made, and model quality assessment that will illuminate the black box of homology modeling for novice readers and broaden the knowledge of this methodology for professionals.

Author : Silvio Bicciato,Francesco Ferrari
Publisher : Humana
Page : 0 pages
File Size : 50,5 Mb
Release : 2022-09-04
Category : Science
ISBN : 1071613928

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Hi-C Data Analysis by Silvio Bicciato,Francesco Ferrari Pdf

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 : Jason T. L. Wang,Cathy H. Wu,Paul P. Wang
Publisher : World Scientific
Page : 266 pages
File Size : 40,9 Mb
Release : 2003
Category : Science
ISBN : 9789812382573

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Computational Biology and Genome Informatics by Jason T. L. Wang,Cathy H. Wu,Paul P. Wang Pdf

This book contains articles written by experts on a wide range of topics that are associated with the analysis and management of biological information at the molecular level. It contains chapters on RNA and protein structure analysis, DNA computing, sequence mapping, genome comparison, gene expression data mining, metabolic network modeling, and phyloinformatics. The important work of some representative researchers in bioinformatics is brought together for the first time in one volume. The topic is treated in depth and is related to, where applicable, other emerging technologies such as data mining and visualization. The goal of the book is to introduce readers to the principle techniques of bioinformatics in the hope that they will build on them to make new discoveries of their own. Contents: Exploring RNA Intermediate Conformations with the Massively Parallel Genetic Algorithm; Introduction to Self-Assembling DNA Nanostructures for Computation and Nanofabrication; Mapping Sequence to Rice FPC; Graph Theoretic Sequence Clustering Algorithms and their Applications to Genome Comparison; The Protein Information Resource for Functional Genomics and Proteomics; High-Grade Ore for Data Mining in 3D Structures; Protein Classification: A Geometric Hashing Approach; Interrelated Clustering: An Approach for Gene Expression Data Analysis; Creating Metabolic Network Models Using Text Mining and Expert Knowledge; Phyloinformatics and Tree Networks. Readership: Molecular biologists who rely on computers and mathematical scientists with interests in biology.

Author : Stéphane Robin,F. Rodolphe,S. Schbath
Publisher : Cambridge University Press
Page : 168 pages
File Size : 54,9 Mb
Release : 2005-10-13
Category : Computers
ISBN : 052184729X

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DNA, Words and Models by Stéphane Robin,F. Rodolphe,S. Schbath Pdf

Publisher Description

Author : Oldenburg Oldenburg Press
Publisher : Unknown
Page : 40 pages
File Size : 47,8 Mb
Release : 2016-01-29
Category : Electronic
ISBN : 1523764422

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

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 : Gavin Williams,Mélanie Hall
Publisher : Royal Society of Chemistry
Page : 594 pages
File Size : 47,9 Mb
Release : 2018-05-31
Category : Science
ISBN : 9781788014533

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Modern Biocatalysis by Gavin Williams,Mélanie Hall Pdf

The synergy between synthetic biology and biocatalysis is emerging as an important trend for future sustainable processes. This book reviews all modern and novel techniques successfully implemented in biocatalysis, in an effort to provide better performing enzymatic systems and novel biosynthetic routes to (non-)natural products. This includes the use of molecular techniques in protein design and engineering, construction of artificial metabolic pathways, and application of computational methods for enzyme discovery and design. Stress is placed on current ‘hot’ topics in biocatalysis, where recent advances in research are defining new grounds in enzyme-catalyzed processes. With contributions from leading academics around the world, this book makes a ground-breaking contribution to this progressive field and is essential reading for graduates and researchers investigating (bio)catalysis, enzyme engineering, chemical biology, and synthetic biology.

Author : Aleksei Anatoliyovych Stepanenko
Publisher : Delve Publishing
Page : 0 pages
File Size : 50,5 Mb
Release : 2017-11
Category : Electronic
ISBN : 1773610295

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Recent Discoveries in Human Genome Organization by Aleksei Anatoliyovych Stepanenko Pdf

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,Rui Jiang,Fengzhu Sun,Xuegong Zhang
Publisher : Springer
Page : 346 pages
File Size : 46,9 Mb
Release : 2013-03-22
Category : Computers
ISBN : 3642371949

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Research in Computational Molecular Biology by Minghua Deng,Rui Jiang,Fengzhu Sun,Xuegong Zhang Pdf

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 : Bruce Alberts
Publisher : Unknown
Page : 0 pages
File Size : 48,8 Mb
Release : 2002
Category : Cytology
ISBN : 0815332181

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Molecular Biology of The Cell by Bruce Alberts Pdf

Author : Tamar Schlick
Publisher : Springer Science & Business Media
Page : 669 pages
File Size : 55,9 Mb
Release : 2013-04-18
Category : Science
ISBN : 9780387224640

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Molecular Modeling and Simulation by Tamar Schlick Pdf

Very broad overview of the field intended for an interdisciplinary audience; Lively discussion of current challenges written in a colloquial style; Author is a rising star in this discipline; Suitably accessible for beginners and suitably rigorous for experts; Features extensive four-color illustrations; Appendices featuring homework assignments and reading lists complement the material in the main text

Author : Hichem Arioui,Rochdi Merzouki,Hadj Ahmed Abbassi
Publisher : American Institute of Physics
Page : 608 pages
File Size : 54,6 Mb
Release : 2008-06-17
Category : Computers
ISBN : UCSD:31822036956258

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Intelligent Systems and Automation by Hichem Arioui,Rochdi Merzouki,Hadj Ahmed Abbassi Pdf

All papers have been peer-reviewed. The ‘Intelligent Systems and Automation’ conference will be organized for its first edition between June 30th and July 02nd, 2008, where it will be held at Annaba, in Algeria (Africa). CISA encourages the diverse research actors and the industrial one to present the last headways in "Robotics and Automation" fields, notably the experimental demonstration of prototypes. CISA tries to give to the unsupported researchers, a significant access to the new technologies and theories around the topics of Robotics & Automation. The organizers want to give the necessary scientific documents to disposal of the PhD students and researchers of the Mediterranean region. CISA wants to offer to the youth researchers from the south Mediterranean region the opportunities to exchange and to discuss their scientific contributions with the other researchers from all over the world.