Research Experience

September 2015 – Present
La Jolla, CA

PhD Student

Ludwig Cancer & UC San Diego
(advisor: Bing Ren)

  • Developing snapR, a bioinformatics package that facilitates pre-processing, clustering, annotation for single-nucleus ATAC-seq analysis (in progress).
  • Constructed a cellular taxonomy of motor cortex in adult mouse brain using single cell ATAC sequencing.
  • Applied Latent Dirichlet Allocation (LDA) to single cell ATAC-seq data to identify cell-type specific regulatory modules.
  • Developed network-based analysis methods for analyzing single cell Hi-C datasets.
  • Characterized the dynamic of genome structure at the level of single cell during early neuronal differentiation.
  • Developed and Applied multiplexed single nucleus ATAC-seq to delineate cis-regulatory landscapes of constitute cell types in a frozen complex tissue (Nature Neurosciences).
  • Invented PLAC-seq (aka HiChIP) to map long-range chromatin interaction, improving the cost-efficiency by at least 10 fold compared to the previous method (Cell Research).
  • Developed CREST-seq, a titling deletion based CRISPR screening method to identify DNA regulatory elements, revealing enhancer elements for OCT4 gene (Nature Methods).
  • Applied convolutional neural networks to predict enhancer target genes using multi-omics data.
July 2015 – September 2015
San Diego, CA

Summer Intern

Illumina (advisor: Felix Schlesinger)

  • Developed a RNA-seq aligner within 2 months to detect structural variants in breast cancer using targeted RNA-seq, resulting in Illumina BaseSpace application and integrated into TruSight RNA/Tumor Fusion products (
September 2014 – December 2014
La Jolla, CA

Rotation Student

Salk Institute for Biological Studies (advisor: Joe Ecker)

  • Analyzed whole-genome bisulfite sequencing data.
  • Developed an algorithm to identify DNA methylation footprint.
November 2013 – April 2014
Durham, NC

Research Assistant

Duke University
(advisor: Reluca Gordan)

  • Applied machine learning techniques to predict transcription factor binding specificity using protein binding microarray data.
October 2012 – November 2013
Beijing, China

Research Assistant

Chinese Academy of Sciences
(advisor: Zhihua Zhang)

  • Developed a motif discovery pipeline that identified three CTCF binding motifs and revealed distinctive functional enrichments between the three motifs by integrative analysis of various “omics” datasets.
  • Discovered that methylation status at 12th bp of the CTCF core motif might determine its function (BMC Genomics).

Selected Publications

. Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. Nature Neuroscience, 2018.


. A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells. Nature Methods, 2017.


. Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. Cell Research, 2016.


Recent Publications

. Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function. Cell, 2018.


. MAPS: model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments. bioRxiv, 2018.


. Spatiotemporal DNA Methylome Dynamics of the Developing Mammalian Fetus. bioRxiv, 2017.


. Functional diversity of CTCFs is encoded in their binding motifs. BMC Genomics, 2015.