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DOI: 10.4230/LIPIcs.WABI.2017.22

Efficient and Accurate Detection of Topologically Associating Domains from Contact Maps

Authors: Abbas Roayaei Ardakany and Stefano Lonardi

Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)

Abstract

Continuous improvements to high-throughput conformation capture (Hi-C) are revealing richerinformation about the spatial organization of the chromatin and its role in cellular functions.Several studies have confirmed the existence of structural features of the genome 3D organiza-tion that are stable across cell types and conserved across species, calledtopological associatingdomains(TADs). The detection of TADs has become a critical step in the analysis of Hi-C data,e.g., to identify enhancer-promoter associations. Here we presentEast, a novel TAD identifi-cation algorithm based on fast 2D convolution of Haar-like features, that is as accurate as thestate-of-the-art method based on the directionality index, but 75-80x faster.Eastis availablein the public domain at https://github.com/ucrbioinfo/EAST.

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Abbas Roayaei Ardakany and Stefano Lonardi. Efficient and Accurate Detection of Topologically Associating Domains from Contact Maps. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 22:1-22:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{roayaeiardakany_et_al:LIPIcs.WABI.2017.22,
  author =	{Roayaei Ardakany, Abbas and Lonardi, Stefano},
  title =	{{Efficient and Accurate Detection of Topologically Associating Domains from Contact Maps}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{22:1--22:11},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.22},
  URN =		{urn:nbn:de:0030-drops-76446},
  doi =		{10.4230/LIPIcs.WABI.2017.22},
  annote =	{Keywords: Chromatin, TADs, 3D genome, Hi-C, contact maps}
}

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Documents authored by Roayaei Ardakany, Abbas

Efficient and Accurate Detection of Topologically Associating Domains from Contact Maps

Abstract

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