SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data

Seminar Series

Friday, January 14, 2022 - 12:00
Ming Hu, PhD

Abtract: Single-cell Hi-C (scHi-C) analysis has been increasingly used to map chromatin architecture in diverse tissue contexts, but computational tools to define chromatin loops at high resolution from scHi-C data are still lacking. Here, we describe Single-Nucleus Analysis Pipeline for Hi-C (SnapHiC), a method that can identify chromatin loops at high resolution and accuracy from scHi-C data. Using scHi-C data from 742 mouse embryonic stem cells, we benchmark SnapHiC against a number of computational tools developed for mapping chromatin loops and interactions from bulk Hi-C. We further demonstrate its use by analyzing single-nucleus methyl-3C-seq data from 2,869 human prefrontal cortical cells, which uncovers cell type-specific chromatin loops and predicts putative target genes for noncoding sequence variants associated with neuropsychiatric disorders. Our results indicate that SnapHiC could facilitate the analysis of cell type-specific chromatin architecture and gene regulatory programs in complex tissues.

Speaker: Ming Hu, PhD
Assistant Professor Medicine
Cleveland Clinic Foundation

Bio: I am now an Assistant Staff at Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation. I am also an Assistant Professor (non-tenure track) at Department of Medicine, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, an Associate Member of Molecular Oncology Program at Case Comprehensive Cancer Center, and a joint faculty member of Institute for Computational Biology at Case Western Reserve University School of Medicine. As a computational biologist, I am interested in developing statistical models and computational tools to understand chromatin spatial organization and gene regulation mechanisms relevant to human health and diseases.

I got my B.S. in Statistics from University of Science and Technology of China in 2006. I obtained my Ph.D. in Biostatistics from University of Michigan in 2010. Before joining Cleveland Clinic in 2016, I did a three year postdoctoral training (2010 ~ 2013) with Dr. Jun S. Liu at Department of Statistics, Harvard University, and was tenure-track Assistant Professor (2013 ~ 2016) at Department of Population Health, Division of Biostatistics, New York University School of Medicine.