Table of contents Initial page Cover Preface Figurelist Chap0 Preparation 0.1 Molecular biology 0.2 Sequencing technologies 0.3 RNA-seq Data Mapping & Gene Quantification 0.4 RNA-seq Differential Analysis Chap1 Why we care about 3D genome 1.1 From 2D to 3D nuclear structure 1.2 From static to dynamic 1.3 From intra to inter chromosomes "talk" 1.4 From aggregation to division - phase separation Chap2 experiment tools for exploring genome interaction 2.1 Image based 2.2 Primary order 2.3 Higher order C-techs Chap3 Computational analysis 3.1 Primary order analysis 3.2 Higer order data analysis 3.2.1 Read mapping consideration 3.2.2 Analytical Pipelines GITAR Pipeline HiC-Pro Pipeline 3.2.3 TAD calling algorithms 3.3 3D structure Chap4 RNA-genome interaction 4.1 Experimental Methods 4.2 Computational Analysis Chap5 Integrative Data Visualization Tools 5.1 GIVE 5.2 HiGlass Chap6 4DN Project Appendix Homework Student's presentation A Brief Introduction to Machine Learning Precision medicine CHIP-Seq