Hic Pro An Optimized And Flexible Pipeline For Hi C Data Processing
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Hic Pro An Optimized And Flexible Pipeline For Hi C Data Processing
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Author : Oldenburg Oldenburg Press
language : en
Publisher:
Release Date : 2016-01-29
Hic Pro An Optimized And Flexible Pipeline For Hi C Data Processing written by Oldenburg Oldenburg Press and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-01-29 with categories.
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.
Hi C Data Analysis
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Author : Silvio Bicciato
language : en
Publisher: Humana
Release Date : 2022-09-04
Hi C Data Analysis written by Silvio Bicciato and has been published by Humana this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-09-04 with Science categories.
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.
Bioinformatics Research And Applications
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Author : Zhipeng Cai
language : en
Publisher: Springer
Release Date : 2019-05-27
Bioinformatics Research And Applications written by Zhipeng Cai and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-05-27 with Computers categories.
This book constitutes the proceedings of the 15th International Symposium on Bioinformatics Research and Applications, ISBRA 2019, held in Barcelona, Spain, in June 2019. The 22 full papers presented in this book were carefully reviewed and selected from 95 submissions. They were organized in topical sections named: genome analysis; systems biology; computational proteomics; machine and deep learning; and data analysis and methodology.
Spatial Genome Organization
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Author : Tom Sexton
language : en
Publisher: Springer Nature
Release Date : 2022-07-22
Spatial Genome Organization written by Tom Sexton and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-07-22 with Science categories.
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.
The Role Of High Order Chromatin Organization In Gene Regulation
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Author : Alexey V. Pindyurin
language : en
Publisher: Frontiers Media SA
Release Date : 2022-11-11
The Role Of High Order Chromatin Organization In Gene Regulation written by Alexey V. Pindyurin and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-11-11 with Science categories.
Epigenetics Methods
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Author : Trygve Tollefsbol
language : en
Publisher: Academic Press
Release Date : 2020-07-08
Epigenetics Methods written by Trygve Tollefsbol and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-07-08 with Medical categories.
In recent years, the field of epigenetics has grown significantly, driving new understanding of human developmental processes and disease expression, as well as advances in diagnostics and therapeutics. As the field of epigenetics continues to grow, methods and technologies have multiplied, resulting in a wide range of approaches and tools researchers might employ. Epigenetics Methods offers comprehensive instruction in methods, protocols, and experimental approaches applied in field of epigenetics. Here, across thirty-five chapters, specialists offer step-by-step overviews of methods used to study various epigenetic mechanisms, as employed in basic and translational research. Leading the reader from fundamental to more advanced methods, the book begins with thorough instruction in DNA methylation techniques and gene or locus-specific methylation analyses, followed by histone modification methods, chromatin evaluation, enzyme analyses of histone methylation, and studies of non-coding RNAs as epigenetic modulators. Recently developed techniques and technologies discussed include single-cell epigenomics, epigenetic editing, computational epigenetics, systems biology epigenetic methods, and forensic epigenetic approaches. Epigenetics methods currently in-development, and their implication for future research, are also considered in-depth. In addition, as with the wider life sciences, reproducibility across experiments, labs, and subdisciplines is a growing issue for epigenetics researchers. This volume provides consensus-driven methods instruction and overviews. Tollefsbol and contributing authors survey the range of existing methods; identify best practices, common themes, and challenges; and bring unity of approach to a diverse and ever-evolving field. Includes contributions by leading international investigators involved in epigenetic research and clinical and therapeutic application Integrates technology and translation with fundamental chapters on epigenetics methods, as well as chapters on more novel and advanced epigenetics methods Written at verbal and technical levels that can be understood by scientists and students alike Includes chapters on state-of-the-art techniques such as single-cell epigenomics, use of CRISPR/Cas9 for epigenetic editing, and epigenetics methods applied to forensics
Analyzing Network Data In Biology And Medicine
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Author : Nataša Pržulj
language : en
Publisher: Cambridge University Press
Release Date : 2019-03-28
Analyzing Network Data In Biology And Medicine written by Nataša Pržulj and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-03-28 with Language Arts & Disciplines categories.
Introduces biological concepts and biotechnologies producing the data, graph and network theory, cluster analysis and machine learning, using real-world biological and medical examples.
High Density Sequencing Applications In Microbial Molecular Genetics
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Author :
language : en
Publisher: Academic Press
Release Date : 2018-11-28
High Density Sequencing Applications In Microbial Molecular Genetics 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 2018-11-28 with Science categories.
High-Density Sequencing Applications in Microbial Molecular Genetics, Volume 612 in the Methods of Enzymology series provides the latest on the high-density sequencing of DNA and cDNA libraries and how they have revolutionized contemporary research in biology. Methods permitting tens of millions of sequence reads in a single experiment have paved the way to genome-wide studies that are contributing to our understanding of the complexity of living systems. Chapters in this updated volume include Characterizing the role of exoribonucleases in the control of microbial gene expression: Differential RNA seq., Conformational studies of bacterial chromosomes by high-throughput sequencing methods, Measuring mRNA degradation, and more. Addition sections cover Global recognition patterns of bacterial RNA-binding proteins, High-resolution profiling of NMD targets, and the Generation of a metagenomic 3C/Hi-C library of human gut microbiota, Genome-wide mapping of yeast retrotransposons integration target sites, Measuring protein synthesis rates, Finding unsuspected partners of small RNAs with new screening approaches, Use of multiplexed transcriptomics to define the relationship between promoter sequence and transcription output, RNA-based control of quorum sensing in Vibrio cholerae, amongst other highly regarded topics. Detail methods used in research articles that were recently published in leading journals Provides the latest on the high-density sequencing of DNA and cDNA libraries and how they have revolutionized contemporary research in biology
Computational Epigenomics And Epitranscriptomics
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Author : Pedro H. Oliveira
language : en
Publisher: Springer Nature
Release Date : 2023-02-01
Computational Epigenomics And Epitranscriptomics written by Pedro H. Oliveira and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-02-01 with Science categories.
This volume details state-of-the-art computational methods designed to manage, analyze, and generally leverage epigenomic and epitranscriptomic data. Chapters guide readers through fine-mapping and quantification of modifications, visual analytics, imputation methods, supervised analysis, and integrative approaches for single-cell data. 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. Cutting-edge and thorough, Computational Epigenomics and Epitranscriptomics aims to provide an overview of epiomic protocols, making it easier for researchers to extract impactful biological insight from their data.
Twin And Family Studies Of Epigenetics
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Author : Shuai Li
language : en
Publisher: Academic Press
Release Date : 2021-08-19
Twin And Family Studies Of Epigenetics written by Shuai Li and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-08-19 with Medical categories.
Twin and Family Studies of Epigenetics, Volume 27, the latest release in the Translational Epigenetics series, gathers expert opinions on epigenetic twin and family study research methods, recent findings across various disease areas, and future directions. The book provides in-depth coverage of epigenetics fundamentals, twin and family epigenetic study design, and the broader role of epigenetics in answering questions on the developmental origins of health and disease. Throughout the volume, twin and family studies are employed to examine causes of epigenetic variation, the relationship between epigenetic modifications and mental illness, cancers, cardiovascular disease, diabetes, obesity, high blood pressure, and more. Emerging research methods applied in twin and family studies discussed include imaging epigenetics, exposure-specific DNA methylation changes, and unravelling time trends in epigenetic effects. Offers a practical, interdisciplinary approach across epigenetics, epidemiology and various disease specialties Applies epigenetic twin and family studies to determine the relationship between epigenetics and mental illness, cancers, cardiovascular disease, diabetes, obesity and high blood pressure, among other diseases and disorders Features chapter contributions from a wide range of international researchers in the field
