Enhancing Hi-C contact matrices for loop detection with Capricorn: a multiview diffusion model.

Journal: Bioinformatics (Oxford, England)
PMID: 38940142

Abstract

MOTIVATION: High-resolution Hi-C contact matrices reveal the detailed three-dimensional architecture of the genome, but high-coverage experimental Hi-C data are expensive to generate. Simultaneously, chromatin structure analyses struggle with extremely sparse contact matrices. To address this problem, computational methods to enhance low-coverage contact matrices have been developed, but existing methods are largely based on resolution enhancement methods for natural images and hence often employ models that do not distinguish between biologically meaningful contacts, such as loops and other stochastic contacts.

Authors

  • Tangqi Fang
    Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, United States.
  • Yifeng Liu
    Department of Clinical Medicine, Chengdu Medical College, Sichuan, China.
  • Addie Woicik
    Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, United States.
  • Minsi Lu
    Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, United States.
  • Anupama Jha
    Department of Computer and Information Science, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, USA.
  • Xiao Wang
    Research Centre of Basic Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
  • Gang Li
    The Centre for Cyber Resilience and Trust, Deakin University, Australia.
  • Borislav Hristov
    Department of Genome Sciences, University of Washington, Seattle, WA 98195, United States.
  • Zixuan Liu
    Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA.
  • Hanwen Xu
    University of Washington, Seattle, WA, USA.
  • William S Noble
    Department of Genome Sciences, University of Washington , Seattle 98195, Washington, United States.
  • Sheng Wang
    Intensive Care Medical Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, People's Republic of China.

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