[12] Peisen Sun, Stephen J Bush, Songbo Wang, Peng Jia, Mingxuan Li, Tun Xu, Pengyu Zhang, Xiaofei Yang, Chengyao Wang, Linfeng Xu, Tingjie Wang, Kai Ye. STMiner: gene-centric spatial transcriptomics for deciphering tumor tissues. Cell Genomics, 2025,12;5(2):100771.

[11] Songbo Wang, Jiadong Lin, Peng Jia, Tun Xu, Xiujuan Li, Yuezhuangnan Liu, Dan Xu, Stephen J Bush, Deyu Meng, Kai Ye. De novo and somatic structural variant discovery with SVision-pro. Nature Biotechnology, 2024, Mar 22.

[10] Luyao Ren, Xiaoke Duan, Lianhua Dong, Rui Zhang, Jingcheng Yang, Yuechen Gao, Rongxue Peng, Wanwan Hou, Yaqing Liu, Jingjing Li, Ying Yu, Naixin Zhang, Jun Shang, Fan Liang, Depeng Wang, Hui Chen, Lele Sun, Lingtong Hao, Quartet Project Team, Andreas Scherer, Jessica Nordlund, Wenming Xiao, Joshua Xu, Weida Tong, Xin Hu, Peng Jia, Kai Ye, Jinming Li, Li Jin, Huixiao Hong, Jing Wang, Shaohua Fan, Xiang Fang, Yuanting Zheng, Leming Shi. Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance. Genome Biology, 2023, 24, 270. 

[9] Jiadong Lin, Peng Jia, Songbo Wang, Walter Kosters, Kai Ye. Comparison and benchmark of structural variants detected from long read and long-read assembly. Briefings in Bioinformatics,  2023, 24(4), bbad188.

[8] Xiaofei Yang, Gaoyang Zheng, Peng Jia, Songbo Wang, Kai Ye, Pindel-TD: A Tandem Duplication Detector Based on A Pattern Growth Approach, Genomics, Proteomics & Bioinformatics, 22(1), February 2024, qzae008,

[7] Xiaofei Yang, Xixi Zhao, Shoufang Qu, Peng Jia, Bo Wang, Shenghan Gao, Tun Xu, Wenxin Zhang, Jie Huang, Kai Ye. Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing, Fundamental Research, 2022, 2(6): 946-953

[6] Jiadong Lin, Songbo Wang, Peter A Audano, Deyu Meng, Jacob I Flores, Walter Kosters, Xiaofei Yang, Peng Jia, Tobias Marschall, Christine R Beck, Kai Ye. SVision: a deep learning approach to 6resolve complex structural variants. Nature Methods, 2022,19(10), 1230-1233.

[5] Yizhuo Che, Xiaofei Yang, Peng Jia, Tingjie Wang, Dan Xu, Tianxue Guo, Kai Ye, D² Plot, a Matrix of DNA Density and Distance to Periphery, Reveals Functional Genome Regions. Advanced Science, 2022,  9(30)

[4] Bo Wang, Xiaofei Yang, Yanyan Jia, Yu Xu, Peng Jia, Ningxin Dang, Songbo Wang, Tun Xu, Xixi Zhao, Shenghan Gao, Quanbin Dong, Kai Ye. High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads. Genomics, Proteomics & Bioinformatics, 2022, 20(1), 4-13.

[3] Xiaofei Yang, Shenghan Gao, Li Guo, Bo Wang, Yanyan Jia, Jian Zhou, Yizhuo Che, Peng Jia, Jiadong Lin, Tun Xu, Jianyong Sun, Kai Ye. Three chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway. Nature Communications, 2021, 12(1), 6030.

[2] Xiaofei Yang, Tun Xu, Peng Jia, Han Xia, Li Guo, Lei Zhang, Kai Ye, Transportation, germs, culture: a dynamic graph model of COVID-19 outbreak, Quantitative Biology, 2020, 8(3): 238–244, 

[1] Bowen Liu, Xiaofei Yang, Tingjie Wang, Jiadong Lin, Yongyong Kang, Peng Jia, Kai Ye. MEpurity: estimating tumor purity using DNA methylation data. Bioinformatics, 2019, 35(24), 5298-5300.