1. csORF-finder:

csORF-finder is a tool for identifying ORFs with small peptides-coding ability.

Reference: Zhang M, Zhao J, Li C, et al. csORF-finder: an effective ensemble learning framework for accurate identification of multi-species coding short open reading frames. Briefings in Bioinformatics, 2022, 23(6): bbac392.

2. DeepIRES:

DeepIRES is a hybird deep learning model for indentifying internal ribosome entry site in mRNA.

Reference: Zhao J, Chen Z, Zhang M, et al. DeepIRES: a hybrid deep learning model for accurate identification of internal ribosome entry sites in cellular and viral mRNAs[J]. Briefings in Bioinformatics, 2024, 25(5): bbae439.

3. UROBORUS:

UROBORUS is a computational pipeline to detect circular RNA supported by junction reads from back spliced exons.

Reference: Song X, Zhang N, Han P, et al. Circular RNA profile in gliomas revealed by identification tool UROBORUS. Nucleic acids research, 2016, 44(9): e87-e87.

4. THOR

The THOR Algorithm is a TMB heterogeneity-adaptive optimization model designed to predict immunotherapy response using clonal genomic features in group-structured data.

Reference: Wang Y, Guan Y, Lai X, et al. THOR: a TMB heterogeneity-adaptive optimization model predicts immunotherapy response using clonal genomic features in group-structured data. Briefings in Bioinformatics, 2025, 26(1): bbae648.

5. LncMiM:

LncMiM isa tool to identify lncRNA-associated competing triplets, especially for large-scale expression data.

Reference: Zhao J, Song X, XuZhao J, Song X, Xu T, et al. Identification of potential prognostic competing triplets in high-grade serous ovarian cancer. Frontiers in Genetics, 2021, 11: 607722.

6. CircAST:

CircAST is a computational tool for circular RNA full-length assembly and quantification using RNA-Seq data.

Reference: Wu J, Li Y, Wang C, et al. CircAST: full-length assembly and quantification of alternatively spliced isoforms in circular RNAs[J]. Genomics, Proteomics and Bioinformatics, 2019, 17(5): 522-534.

7. IRESfinder:

IRESfinder is a python package for the identification of RNA internal ribosome entry site in eukaryotic cell.

Reference: Zhao J, Wu J, Xu T, Yang Q, He J, Song X. IRESfinder: Identifying RNA internal ribosome entry site in eukaryotic cell using framed k-mer features. Journal of genetics and genomics, 2018,45(7), p.403.

8. IRESbase:

IRESbase is a comprehensive database of experimentally verified internal ribosome entry sites.

Reference: Jian Zhao, Yan Li, Cong Wang, Haotian Zhang, Hao Zhang, Bin Jiang, Xuejiang Guo, Xiaofeng Song. IRESbase: A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites. Genomics. Genomics Proteomics Bioinformatics. 2020 Apr;18(2):129-139.

9. circASbase:

circASbase is a comprehensive database of circular RNAs' alternative splicing events and circular RNAs' coding potentials.

10. CircAI:

CircAI is a comprehensive database for A-to-I editing in circRNAs.

11. pHisPred:

pHisPred is a bioinformatic tool for identifying protein histidine phosphorylation sites.

Reference: Zhao J, Zhuang M, Liu J, Zhang M, Zeng C, Jiang B, Wu J, Song X. pHisPred: a tool for the identification of histidine phosphorylation sites by integrating amino acid patterns and properties. BMC Bioinformatics. 2022 Sep 28;23(Suppl 3):399.

12. HisPhosSite:

HisPhosSite is a comprehensive database of protein histidine phosphorylation sites.

Reference: Zhao J, Zou L, Li Y, et al. HisPhosSite: A comprehensive database of histidine phosphorylated proteins and sites. Journal of Proteomics, 2021, 243: 104262.