BioT Future Interdisciplinary Technology Mathematics Information Life Sciences

† first authors with equal contribution, * corresponding authors

[34] Tao Jiang†, Shuqi Cao†, Yadong Liu, Zhendong Zhang, Bo Liu, Ruibang Luo, Guohua Wang*, Yadong Wang*. cuteFC: regenotyping structural variants through an accurate and efficient force-calling method, Genome Biology, 26, 166 (2025). [link, code]

[33] Heng Hu†, Tao Jiang†*, Runtian Gao, Zhongjun Jiang, Shuqi Cao, Yadong Liu, Murong Zhou, Wentao Gao, Shengming Zhou, Guohua Wang*. SVPG: A pangenome-based structural variant detection approach and rapid augmentation of pangenome graphs with new samples, biorxiv. [link, code]

[32] Runtian Gao†, Heng Hu†, Zhongjun Jiang, Shuqi Cao, Guohua Wang, Yuming Zhao, Tao Jiang*. SVHunter Long read based structural variation detection through the transformer model, Briefings in Bioinformatics, Volume 26, Issue 3, May 2025, bbaf203. [link, code]

[31] Wentao Gao†, Sui Wang†, Tao Jiang†, Heng Hu, Runtian Gao, Murong Zhou, Guohua Wang*. Chromosome-scale and haplotype-resolved genome assembly of Populus trichocarpa, Horticulture Research, 2025. [link, code]

[30] Xin Li†, Yadong Liu†, Zhongbo Yang, Yadong Wang* and Tao Jiang*. Comprehensive Benchmarking of Genotype Imputation Tools Using a Large-Scale Chinese Reference Panel, BIBM2024, pp.5218-5223. [link, code]

[29] Zhongbo Yang, Zhenhao Lu, Xin Li, Tao Jiang*, Yadong Wang*, Yadong Liu*. Comprehensive evaluation of haplotype phasing tools with different strategies across diverse sequence technologies, BIBM2024, pp.653-658. [link]

[28] Yadong Liu†, Zhenhao Lu†, Yadong Wang*, Tao Jiang*. GFHunter enables accurate and efficient gene fusion detection in long-read cancer transcriptomes, biorxiv. [link]

[27] Tao Jiang†, Zuji Zhou†, Zhendong Zhang, Shuqi Cao, Yadong Wang*, Yadong Liu*. MEHunter: transformer-based mobile element variant detection from long reads, Bioinformatics, Volume 40, Issue 9, September 2024, btae557. [link, code]

[26] Miao Cui†, Yadong Liu†, Xian Yu, Hongzhe Guo, Tao Jiang, Yadong Wang*, Bo liu*. miniSNV: accurate and fast single nucleotide variant calling from nanopore sequencing data, Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae473. [link, code]

[25] Tao Jiang, Hongzhe Guo, Yadong Liu, Gaoyang Li, Zhe Cui, Xinran Cui, Yue Liu, Yang Li, Anqi Zhang, Shuqi Cao, Tianyi Zhao, Liran Juan, Weize Kong, Ming Chen, Dianming Liu, Hongri Liu, Yixiao Zhang, Kelin Xu, Yongjun Wang, Meian He, Jiancheng Guo, Ming Lu, Jun Chen, Xing Zhao, Genming Zhao, Shaonong Dang, Chao Chen, Xiaojian Wu, Qiyuan Qin, Yixue Li, Hongbing Shen, Li Jin, Bo Liu*, Xingdong Chen*, Yuhong Zhao*, Yadong Wang*. A comprehensive genetic variant reference for the Chinese population. Science Bulletin, 2024. [link]

[24] Heng Hu†, Runtian Gao†, Wentao Gao, Bo Gao, Zhongjun Jiang, Murong Zhou, Guohua Wang*, Tao Jiang*. SVDF: enhancing structural variation detect from long-read sequencing via automatic filtering strategies, Briefings in Bioinformatics, Volume 25, Issue 4, July 2024, bbae336, 2024. [link, code]

[23] Zhendong Zhang†, Yue Liu†, Xin Li, Yadong Liu*, Yadong Wang*, Tao Jiang*. HapKled: a haplotype-aware structural variant calling approach for Oxford Nanopore sequencing data. Frontiers in Genetics, Volume 15, 2024. [link, code]

[22] Yue Liu†, Yuhuan Zhou†, Xiumei Hu†, Wuri Le-Ge†, Haoyan Wang, Tao Jiang, Junyi Li*, Yang Hu*, Yadong Wang*. DIRMC: a database of immunotherapy-related molecular characteristics. Database, Volume 2024, 2024, baae032. [link]

[21] Zhendong Zhang†, Tao Jiang†, Gaoyang Li, Shuqi Cao, Yadong Liu*, Bo Liu*, Yadong Wang*. Kled: an ultra-fast and sensitive structural variant detection tool for long-read sequencing data. Briefings in Bioinformatics, 25 (2), bbae049. [link, code]

[20] Xinran Cui†, Qingyan Lin†, Ming Chen, Yidan Wang, Yiwen Wang, Yadong Wang*, Jiang Tao*, Honglei Yin*, Tianyi Zhao*. Long-read sequencing unveils novel somatic variants and methylation patterns in the genetic information system of early lung cancer. Computers in Biology and Medicine, 171(10299):108174. [link]

[19] Ping Meng, Guohua Wang, Hongzhe Guo*, Tao Jiang*. Identifying cancer driver genes using a two-stage random walk with restart on a gene interaction network. Computers in Biology and Medicine, 158, 106810. [link]

[18] Yadong Liu†, Zhenhao Lu†, Zhongyu Liu, Hongzhe Guo*, Yadong Wang*, Tao Jiang*. Comprehensive evaluation of RNA-seq alignment methods based on long-read sequencing data. BIBM2023. [link, tool]

[17] Tao Jiang, Shiqi Liu, Hongzhe Guo*. Reply: Correspondence on NanoVar's performance outlined by Jiang T. et al. in 'Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation'. BMC Bioinformatics, 24 (1), 352. [link, code]

[16] Anqi Zhang†, Tangchao Kong†, Baiquan Sun†, Shizheng Qiu†, Jiahe Guo, Shuyong Ruan, Yu Guo, Jirui Guo, Zhishuai Zhang, Yue Liu, Zheng Hu, Tao Jiang, Yadong Liu, Shuqi Cao, Shi Sun, Tingting Wu, Huilong Hong, Bingjun Jiang, Maoxiang Yang, Xiangyu Yao, Yang Hu*, Bo Liu*, Tianfu Han*, Yadong Wang*. A telomere-to-telomere genome assembly of Zhonghuang 13, a widely-grown soybean variety from the original center of Glycine max. The Crop Journal. [link]

[15] Pir Noman Ahmad*, Yuanchao Liu, Khalid Khan, Tao Jiang, Umama Burhan. BIR: Biomedical Information Retrieval System for Cancer Treatment in Electronic Health Record Using Transformers. Sensors, 2023 23(23), 9355. [link]

[14] Tao Jiang, Shiqi Liu, Shuqi Cao, Yadong Wang*. (2022). Structural Variant Detection from Long-Read Sequencing Data with cuteSV. Variant Calling. Methods in Molecular Biology, vol 2493. Humana, New York, NY, 2022. [link]

[13] Yadong Liu†; Zhongyu Liu†; Tao Jiang; Tianyi Zang*; Yadong Wang*. Comparison of the Nanopore and PacBio sequencing technologies for DNA 5-methylcytosine detection. BIBM 2022. [link, code]

[12] Hongzhe Guo†, Zhongbo Yang†, Tao Jiang, Shiqi Liu, Yadong Wang*, Zhe Cui*. Evaluation of classification in single cell atac-seq data with machine learning methods. BMC Bioinformatics, 23 (Suppl 5), 249 (2022). [link, code]

[11] Tao Jiang†, Shiqi Liu†, Shuqi Cao, Yadong Liu, Zhe Cui, Yadong Wang*, Hongzhe Guo*. Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation. BMC Bioinformatics, 22 (1), 2021, 1-17. [link, code]

[10] Yadong Liu†, Tao Jiang†, Junhao Su, Bo Liu*, Tianyi Zang*, Yadong Wang*. SKSV: ultrafast structural variation detection from circular consensus sequencing reads. Bioinformatics, 2021, btab341. [link, tool]

[9] Gaoyang Li†, Tao Jiang†, Junyi Li, Yadong Wang*. PanSVR: Pan-Genome Augmented Short Read Realignment for Sensitive Detection of Structural Variations. Frontiers in Genetics, 2021, 1486. [link]

[8] Yadong Liu†, Tao Jiang†, Yan Gao, Bo Liu, Tianyi Zang*, Yadong Wang*. Psi-Caller: A Lightweight Short Read-Based Variant Caller With High Speed and Accuracy. Frontiers in Cell and Developmental Biology, 2021, 2139. [link, code]

[7] Zhe Cui†, Ya Cui†, Yan Gao, Tao Jiang, Tianyi Zang* and Yadong Wang*. Enhancement and Imputation of Peak Signal Enables Accurate Cell-Type Classification in scATAC-seq. Frontiers in Genetics, 12, 345, 2021. ISSN=1664-8021. [link]