We are interested in developing bioinformatic methods and resources, and applying them to uncover the underlying principles of RNA regulation. The finished online tools and databases can be accessed here.

  • RNA lifecycle
    • InPACT: A new method for accurate characterization of intronic polyadenylation from RNA-seq data (Method).
    • InPACT is a computational method designed to identify and quantify intronic polyadenylation sites via the examination of contextual sequence patterns and RNA-seq reads alignment(Nature Communications, 2024). InPACT could be accessed at https://doi.org/10.5281/zenodo.10707806

    • CellNetdb: An atlas of cell-type-specific interactome networks across 44 human tumor types (Database).
    • CellNetdb is a comprehensive database containing a large-scale atlas of cell-type-specific interactome networks within tumor microenvironments (Genome Medicine, 2024). We created these networks by analyzing single-cell RNA-seq data from 563 patients, which included over two million cells from 44 different tumor types. The database offers various functionalities designed to provide in-depth biological insights. CellNetdb can be accessed at http://bioailab.com:3838/CellNetdb/

    • scAPAatlas: An atlas of alternative polyadenylation across cell types in human and mouse (Database).
    • scAPAatlas is a user-friendly database for investigating APA at the cell-type level in diverse human and mouse tissues (Nucleic Acids Res, 2022). Versatile functionalities have been developed for investigating cell-type-specific APA events, which could give a hint of the underlying mechanisms of post-transcriptional regulation. scAPAatlas could be accessed at http://bioailab.com:3838/scAPAatlas/

    • SAPAS: Systematic Alternative Polyadenylation Analysis at Single-cell level (Method).
    • SAPAS is a computational method that utilizes 3′-tag-based scRNA-seq data to identify novel polyA sites and quantify APA at the single-cell level. SAPAS also enable detection of cell type-specific APA events and estimation of APA modality (BMC Biology, 2021). SAPAS could be accessed at https://github.com/YY-TMU/SAPAS

  • Noncoding genome
    • eaQTLdb: An atlas of enhancer activity quantitative trait loci (Database).
    • eaQTLdb is a user-friendly database which incorporates multidimensional information of enhancer activity quantitative trait loci in human cancers (Int J Cancer, 2023). eaQTLdb could be accessed at http://bioailab.com:3838/eaQTLdb/

  • Before TMU