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Visually Exploring the Genome at Scale

Fritz Lekschas
October 21, 2018

Visually Exploring the Genome at Scale

The human genome is about 2 meters long and tightly folded into the cell nucleus, a sphere that is 4 million times smaller than a pinhead. How do cells avoid entangling the DNA and ensure accessibility of necessary parts? Biologists study DNA folding through the detection of pairwise physical interactions along the DNA, which results in a 3-by-3 million pixel matrix. Visualized as a heatmap, thousands of local visual patterns become apparent. Studying these patterns is like trying to understand the average layout of parks while viewing countries on a world map. Biologists need to inspect these patterns for sensemaking of biological features. We have developed 3 interactive tools to explore such large datasets at different steps: (1) seamless browsing using HiGlass, (2) local pattern exploration through decomposition in HiPiler, and (3) guided navigation with Scalable Insets. I will present our tools and discuss the generalizability of the underlying concepts. More at http://infoplus.lekschas.de/

Fritz Lekschas

October 21, 2018
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  1. Visually Exploring the
    Genome At Scale
    Fritz Lekschas, PhD Candidate
    Harvard University
    Benjamin Bach, Peter Kerpedjiev, Michael Behrisch, Nils Gehlenborg, and
    Hanspeter Pfister
    Oct 21st, 2018
    INFO+ 2018

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  2. Apple EarPods headphones

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  3. 1.5x Pin Head

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  4. 3D GENOME

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  5. DNA Cell Nucleus
    3D GENOME

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  6. DNA Cell Nucleus Contact
    3D GENOME

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  7. DNA Cell Nucleus Contact Sequencing
    3D GENOME

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  8. DNA Cell Nucleus Contact Sequencing Matrix
    3D GENOME

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  9. HiGlass
    Kerpedjiev, Abdennur, Lekschas, et al. Genome Biology, 2018, 19:125.

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  10. HiGlass
    Kerpedjiev, Abdennur, Lekschas, et al. Genome Biology, 2018, 19:125.

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  11. HiPiler

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  13. CONCLUSION
    Integrate
    Aggregate
    Separate

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  14. CONCLUSION
    Integrate
    Aggregate
    Separate
    Visual Scale
    Information Scale

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  15. Thank You!
    MORE INFORMATION
    infoplus.lekschas.de
    CONTACT
    [email protected]
    @flekschas
    lekschas.de

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