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Computational Methods for 3D Genome Analysis, 1 Ed.
出版済み 3週間でお届けいたします。
Series: Methods in Molecular Biology, Vol.2856 Author: Ryuichiro Nakato Publisher: Springer ISBN: 9781071641354 Cover: HARDCOVER Date: 2024年09月 DESCRIPTION This volume covers the latest methods and analytical approaches used to study the computational analysis of three-dimensional (3D) genome structure. The chapters in this book are organized into six parts. Part One discusses different NGS assays and the regulatory mechanism of 3D genome folding by SMC complexes. Part Two presents analysis workflows for Hi-C and Micro-C in different species, including human, mouse, medaka, yeast, and prokaryotes. Part Three covers methods for chromatin loop detection, sub-compartment detection, and 3D feature visualization. Part Four explores single-cell Hi-C and the cell-to-cell variability of the dynamic 3D structure. Parts Five talks about the analysis of polymer modelling to simulate the dynamic behavior of the 3D genome structure, and Part Six looks at 3D structure analysis using other omics data, including prediction of 3D genome structure from the epigenome, double-strand break-associated structure, and imaging-based 3D analysis using seqFISH. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and tools, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Computational Methods for 3D Genome Analysis: Methods and Protocols is a valuable resource for researchers interested in using computational methods to further their studies in the nature of 3D genome organization. TABLE OF CONTENTS Introduction Methods for Genome-Wide Chromatin Interaction Analysis Atsushi Okabe Structural Maintenance of Chromosomes Complexes Kristian Jeppsson Workflow for 3D Genome Analysis Read Mapping for Hi-C Analysis Simon Thomas Kelly, Kugui Tanaka, Chiaki Hosaka, Satoshi Yuhara Micro-C Analysis Workflow Using Pairtools and Juicer Toyonori Sakata HOMER for Analysis of Hi-C Data and Assessment of Composite Structure of the X Chromosome Andrea J. Kriz CWL-Based Analysis Pipeline for Hi-C Data: From FASTQ Files to Matrices Hisashi Miura, Rory T. Cerbus, Izumi Noda, Ichiro Hiratani Acquisition and Analysis Methods for Hi-C Data from Medaka Early Embryos Ryohei Nakamura Step-by-Step Protocol to Generate Hi-C Contact Maps Using the rfy_hic2 Pipeline Hideki Tanizawa, Claire Yik-Lok Chung, Shun-ichiro Fuse, Tomomi Hayashi, Peter Weisel, Ken-ichi Noma Hi-C/3C-seq Data Analysis for Prokaryotic Genomes with HiC-Pro Naomichi Takemata Specific Analysis of 3D Genome Data Exploring Contact Distance Distributions with Google Colaboratory Ryuichiro Nakato Supervised Chromatin Loop Detection Using Peakachu Version 2 Xiaotao Wang Systematic Inference of Multi-scale Chromatin Sub-compartments Using Calder2 Yuanlong Liu Analysis and Visualization of Multiple Hi-C and Micro-C Data with CustardPy Yuya Nagaoka, Ryuichiro Nakato Single-Cell Hi-C Single-Cell Hi-C Analysis Workflow with Pairtools Aleksandra Galitsyna Reconstruction of 3D Chromosome Structure from Single-Cell Hi-C Data via Recurrence Plots Yoshito Hirata, Hiroki Sugishita, Yukiko Gotoh 3D Genome Modeling Using Polymer Simulation 4D Genome Analysis Using PHi-C2 Soya Shinkai, Shuichi Onami Construction of Coarse-Grained Molecular Dynamics Model of Nuclear Global Chromosomes Dynamics in Mammalian Cells Akinori Awazu, Tetsushi Komoto Three-Dimensional Simulation of Whole-Genome Structuring Through the Transition from Anaphase to Interphase Shin Fujishiro, Masaki Sasai Integrative Modeling of 3D Genome Organization by Bayesian Molecular Dynamics Simulations with Hi-C Metainference Giovanni B. Brandani Integration with Other Omics Data Prediction of Enhancer-Gene Interactions Using Chromatin-Conformation Capture and Epigenome Data Using STARE Dennis Hecker, Marcel H. Schulz Learning Enhancer-Gene associations from Bulk Transcriptomic and Epigenetic Sequencing Data with STITCHIT Laura Rumpf, Marcel H. Schulz Machine and Deep Learning Methods for Predicting 3D Genome Organization Brydon P. G. Wall, My Nguyen, J. Chuck Harrell, Mikhail G. Dozmorov Processing and Visualization of Protec-Seq Data for the Generation of Calibrated, Genome-Wide Double Double-Strand Break (dDSB) Maps Doris Chen, Martin Xaver, Franz Klein Image Analysis Protocol for DNA/RNA/Immunofluorescence (IF)-seqFISH Data Hiroaki Ohishi, Hiroshi Ochiai Extracting Chromosome Structural Information as One-Dimensional Metrics and Integrating Them with Epigenomics Jiankang Wang, Haoping Chen Exploring Cohesin-Related Multiomics Information in the Web Browser Jiankang Wang
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