title: HSA: integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure.
abstract: Genome-wide 3C technologies (Hi-C) are being increasingly employed to study three-dimensional (3D) genome conformations. Existing computational approaches are unable to integrate accumulating data to facilitate studying 3D chromatin structure and function. We present HSA ( http://ouyanglab.jax.org/hsa/ ), a flexible tool that jointly analyzes multiple contact maps to infer 3D chromatin structure at the genome scale. HSA globally searches the latent structure underlying different cleavage footprints. Its robustness and accuracy outperform or rival existing tools on extensive simulations and orthogonal experiment validations. Applying HSA to recent in situ Hi-C data, we found the 3D chromatin structures are highly conserved across various human cell types.
authors.affiliation: The Jackson Laboratory for Genomic Medicine, Farmington, 06032, CT, USA. chenchen.zou@jax.org.
authors.forename: Chenchen
authors.initials: C
authors.lastname: Zou
authors.affiliation: Department of Statistics, University of Connecticut, Storrs, 06269, CT, USA. yuping.zhang@uconn.edu.|Institute for Systems Genomics, University of Connecticut, Farmington, 06030, CT, USA. yuping.zhang@uconn.edu.|Institute for Collaboration on Health, Intervention, and Policy, University of Connecticut, Storrs, 06269, CT, USA. yuping.zhang@uconn.edu.|Center for Quantitative Medicine, University of Connecticut, Farmington, 06030, CT, USA. yuping.zhang@uconn.edu.|The Connecticut Institute for the Brain and Cognitive Sciences, University of Connecticut, Storrs, 06269, CT, USA. yuping.zhang@uconn.edu.
authors.forename: Yuping
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: The Jackson Laboratory for Genomic Medicine, Farmington, 06032, CT, USA. zhengqing.ouyang@jax.org.|Institute for Systems Genomics, University of Connecticut, Farmington, 06030, CT, USA. zhengqing.ouyang@jax.org.|Department of Biomedical Engineering, University of Connecticut, Storrs, 06269, CT, USA. zhengqing.ouyang@jax.org.|Department of Genetics and Genome Sciences, University of Connecticut, Farmington, 06030, CT, USA. zhengqing.ouyang@jax.org.
authors.forename: Zhengqing
authors.initials: Z
authors.lastname: Ouyang
mesh_terms: D000465:Algorithms; D002843:Chromatin / Q000235:genetics / Q000648:ultrastructure; D015894:Genome, Human; D006801:Humans; D008390:Markov Chains; D008958:Models, Molecular; D008968:Molecular Conformation
chemical_list: D002843:Chromatin