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9th EAI International Conference on Bio-inspired Information and Communications Technologies (formerly BIONETICS)

Research Article

Multiscale Topology of Chromatin Folding

Cite
BibTeX Plain Text
  • @INPROCEEDINGS{10.4108/eai.3-12-2015.2262453,
        author={Kevin Emmett and Benjamin Schweinhart and Raul Rabadan},
        title={Multiscale Topology of Chromatin Folding},
        proceedings={9th EAI International Conference on Bio-inspired Information and Communications Technologies (formerly BIONETICS)},
        publisher={ACM},
        proceedings_a={BICT},
        year={2016},
        month={5},
        keywords={topological data analysis chromatin conformation},
        doi={10.4108/eai.3-12-2015.2262453}
    }
    
  • Kevin Emmett
    Benjamin Schweinhart
    Raul Rabadan
    Year: 2016
    Multiscale Topology of Chromatin Folding
    BICT
    EAI
    DOI: 10.4108/eai.3-12-2015.2262453
Kevin Emmett1,*, Benjamin Schweinhart2, Raul Rabadan1
  • 1: Columbia University
  • 2: Harvard University
*Contact email: kje2109@columbia.edu

Abstract

The three dimensional structure of DNA in the nucleus (chromatin) plays an important role in many cellular processes. Recent experimental advances have led to high-throughput methods of capturing information about chromatin conformation on genome-wide scales. New models are needed to quantitatively interpret this data at a global scale. Here we introduce the use of tools from topological data analysis to study chromatin conformation. We use persistent homology to identify and characterize conserved loops and voids in contact map data and identify scales of interaction. We demonstrate the utility of the approach on simulated data and then look data from both a bacterial genome and a human cell line. We identify substantial multiscale topology in these datasets.

Keywords
topological data analysis chromatin conformation
Published
2016-05-24
Publisher
ACM
http://dx.doi.org/10.4108/eai.3-12-2015.2262453
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