Resources

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
    • DIPAN: A method for detecting personalized intronic polyadenylation derived neoantigens from RNA sequencing data (Method).

      • DIPAN is a computational method that incorporates IPA detection, protein fragmentation, and MHC binding predictinon to detect IPA-derived neoantigens from RNA sequencing data (Computational and Structural Biotechnology Journal, 2024).

    • 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