2020年

英文论文：

1. Zhao J, Li Y, Wang C, Zhang H, Zhang H, Jiang B, Guo X, Song X. IRESbase: A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites. Genomics Proteomics Bioinformatics. 2020 Apr;18(2):129-139.

2. Xu T, Song X, Wang Y, Fu S, Han P. Genome-Wide Analysis of the Expression of Circular RNA Full-Length Transcripts and Construction of the circRNA-miRNA-mRNA Network in Cervical Cancer. Front Cell Dev Biol. 2020 Nov 24;8:603516.

3. Yang Q, Wu J, Zhao J, Xu T, Han P, Song X. The Expression Profiles of lncRNAs and Their Regulatory Network during Smek1/2 Knockout Mouse Neural Stem Cells Differentiation. Current Bioinformatics. 2020 151:77-78.

4. Liu H, Zhou X, Yuan M, Zhou S, Huang YE, Hou F, Song X, Wang L, Jiang W. ncEP: A Manually Curated Database for Experimentally Validated ncRNA-encoded Proteins or Peptides. J Mol Biol. 2020 May 15;432(11):3364-3368.

中文论文：

1、王琮, 赵健, 宋晓峰. 真核生物环形 RNA 编码蛋白的研究进展[J]. 生物信息学, 2020, 18(1): 1-7.

2、王琮, 赵健, 刘晶晶, 宋晓峰. 基于机器学习方法预测环形 RNA 编码蛋白的潜能[J]. 云南民族大学学报 (自然科学版), 2020.

2021年

英文论文：

1. Zhao J, Zou L, Li Y, Liu X, Zeng C, Xu C, Jiang B, Guo X, Song X. HisPhosSite: A comprehensive database of histidine phosphorylated proteins and sites. J Proteomics. 2021 Jul 15;243:104262.

2. Liu J, Dong W, Wong TY, Qiu C, Wu J, Zhao J, Xia J, Xie S, Song X. Proteome-wide analysis of protein alterations in response to aristolochic acids in rat kidney and liver tissues. Mol Omics. 2021 Jun 14;17(3):405-412.

3. Xu T, Wang L, Jia P, Song X, Zhao Z. An Integrative Transcriptomic and Methylation Approach for Identifying Differentially Expressed Circular RNAs Associated with DNA Methylation Change. Biomedicines. 2021 Jun 8;9(6):657.

4. Zhao J, Song X, Xu T, Yang Q, Liu J, Jiang B, Wu J. Identification of Potential Prognostic Competing Triplets in High-Grade Serous Ovarian Cancer. Front Genet. 2021 Jan 13;11:607722.

5. Wu J, Song X. Expression Profiles and Bioinformatics Analysis of Full-length circRNA Isoforms in Gliomas. Current Bioinformatics. 2021 May 16(4), 553-564.

6. Wang Y, Song X, Xu T. Identification and Analysis of RNA Editing Events in Ovarian Serous Cystadenoma Using RNA-seq Data. Curr Gene Ther. 2021;21(3):258-269.

7. Zhuang M, Zhao J, Wu J, Fu S, Han P, Song X. The circular RNA expression profile in ovarian serous cystadenocarcinoma reveals a complex circRNA-miRNA regulatory network. BMC Med Genomics. 2021 Dec 2;14(Suppl 2):276.

中文论文：

1. 曾聪,赵健,吴静,刘晶晶,宋晓峰.蛋白质组氨酸磷酸化研究进展[J].现代生物医学进展,2021,21(12):2396-2400.

2. 谢宏文,吴静,宋晓峰.环形RNA全长组装与定量工具的研究进展[J/OL].生物信息学:1-9[2021-12-06].

2022年

英文论文：

1. 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.

2. Liu J, Dong W, Zhao J, Wu J, Xia J, Xie S, Song X. Gut microbiota profiling variated during colorectal cancer development in mouse. BMC Genomics. 2022 Dec 22;23(Suppl 4):848.

3. Zhang M, Zhao J, Li C, Ge F, Wu J, Jiang B, Song J, Song X. csORF-finder: an effective ensemble learning framework for accurate identification of multi-species coding short open reading frames. Brief Bioinform. 2022 Nov 19;23(6):bbac392.

4. Liu J, Qi M, Qiu C, Wang F, Xie S, Zhao J, Wu J, Song X. Integrative analysis of the mouse fecal microbiome and metabolome reveal dynamic phenotypes in the development of colorectal cancer. Front Microbiol. 2022 Sep 28;13:1021325.

5. Liu J, Qi M, Yuan Z, Wong TY, Song X, Lam H. Nontargeted metabolomics reveals differences in the metabolite profiling among methicillin-resistant and methicillin-susceptible Staphylococcus aureus in response to antibiotics. Mol Omics. 2022 Dec 5;18(10):948-956.

中文论文：

1. 谢宏文,吴静,宋晓峰.环形RNA全长组装与定量工具的研究进展[J].生物信息学,2022,20(3):155-162.

2023年

英文论文

1. Wang Y, Zhao J, Wu J, Liu J, Wang Y, Xu T, Zhang M, Zhuang M, Zou L, Sun W, Han P, Song X. Genome-wide perturbations of A-to-I RNA editing dysregulated circular RNAs promoting the development of cervical cancer. Comput Biol Med. 2023 Nov;166:107546.

2. Zhang M, Zhao J, Wu J, Wang Y, Zhuang M, Zou L, Mao R, Jiang B, Liu J, Song X. In-depth characterization and identification of translatable lncRNAs. Comput Biol Med. 2023 Sep;164:107243.

3. Wang Y, Wang J, Fang W, Xiao X, Wang Q, Zhao J, Liu J, Yang S, Liu Y, Lai X, Song X. TMBserval: a statistical explainable learning model reveals weighted tumor mutation burden better categorizing therapeutic benefits. Front Immunol. 2023 May 10;14:1151755.

4. Wang Y, Liu J, Zhao J, Wang J, Wang Q, Song X. A Statistical Explainable Learning Model Optimizing Co-localization of Multidimensional Positivity Thresholds in Immunotherapy Decision-Supporting. 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2023 4439-4443.

中文论文

1. [1]吴琼,汪玉兰,赵健,等.癌症中lncRNA调控可变剪接的生物信息学研究进展[J/OL].生物信息学,1-17[2024-11-27].

2. 何山,赵健,宋晓峰.N6-甲基腺苷修饰对女性生殖系统功能的影响[J].遗传,2023,45(06):472-487.

3. 严玉娟,赵健,宋晓峰.卵巢癌侵袭转移机制的生物信息学研究进展[J].生物信息学,2023,21(03):161-170.

2024年

英文论文

1. Zhao J, Chen Z, Zhang M, Zou L, He S, Liu J, Wang Q, Song X, Wu J. DeepIRES: a hybrid deep learning model for accurate identification of internal ribosome entry sites in cellular and viral mRNAs. Brief Bioinform. 2024 Jul 25;25(5):bbae439.

2. Zhang M, Cai R, Liu J, Wang Y, He S, Wang Q, Song X, Wu J, Zhao J. Multi-omics integration analysis reveals the role of N6-methyladenosine in lncRNA translation during glioma stem cell differentiation. Brief Funct Genomics. 2024 Oct 8:elae037.

3. Wang Y, Wu J, Zhao J, Xu T, Zhang M, Liu J, Wang Y, Wang Q, Song X. Global characterization of RNA editing in genetic regulation of multiple ovarian cancer subtypes. Mol Ther Nucleic Acids. 2024 Jan 24;35(1):102127.

4. Jingjing Liu, Xinghua Jin, Chengchao Qiu, Ping Han, Yixuan Wang, Jian Zhao, Jing Wu, Neng Yan, and Xiaofeng Song. Journal of Proteome Research 2024 23 (1), 175-184.

中文论文

1. 王以瑄,王嘉寅,赖欣,等.考虑基因检测误差的癌症患者临床用药辅助决策模型研究[J].工程管理科技前沿,2024,43(02):55-61.

2. 轩依然,赵健,宋晓峰.IRES介导的非帽依赖翻译调控研究进展[J].生物信息学,2024,22(01):1-10.

3. 金兴华,祝敬信,丰俊东,等.电磁辐射的微生物效应与疾病[J].微生物学报,2024,64(08):2610-2622.