• MeSiC: A Model-Based Method for Estimating 5 mC Levels at Single-CpG Resolution (Scientific Reports, 2015)
  
  
  
• LnChrom: A database for lncRNA-chromatin interactions (Database, 2018)
  
  
  
• scTPA: single-cell transcriptome analysis of pathway activation signatures (Bioinformatics, 2020)
  
  
  
• CFEA: a cell-free epigenome atlas (Nucleic Acids Research, 2020)
  
  
  
• CUT&RUNTools2.0: A tool for bulk and single-cell CUT&RUN/CUT&Tag data processing and analysis (Bioinformatics, 2021)
  
  
  
• HemeMap: a computational framework to identify putative cisREs and cell type-specific cisRE-gene interactions in human hematopoiesis (bioRxiv, 2021)
  
  
  
• SCAVENGE: Single Cell Analysis of Variant Enrichment through Network propagation of GEnomic data (Nature Biotechnology, 2022)