3dgenome
  • 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
Powered by GitBook
On this page

Chap1 Why we care about 3D genome

Better understanding of life from a higher dimension view

Around 15 years ago, one of the greatest feats of exploration in history - The Human Genome Project (HGP) was completed. This inward voyage to explore the sequence and map all of the genes - together known as the genome - of Homo sapiens. It gave us the ability to read nature's complete genetic blueprint for building a human being. By leveraging the comprehensive sequence map, we gained insight of how these simple life codes are associated with life development, disease, evolution so on and so forth.

"two sequence whisper, multiple sequences shout" —— Arthur M. Lesk

However, the mystery of life can never be simply understood in the view of a linear structure. Instead, just as we understand the complexity of a jungle by walking through it, obersving the hierachical niches and biological diversity rather than a birdview with green patches companied with blue lines from the google map, a 3D genome architecture further integrate a time dimension can provide a much more comprehensive knowledge for understanding the life.

“Genes and regulatory elements are like people, They care about and communicate with those in their own domain, and they ignore everything else.” —— Job Dekker

Previous0.4 RNA-seq Differential AnalysisNext1.1 From 2D to 3D nuclear structure

Last updated 6 years ago