Identifying overlapping mutated driver pathways by constructing gene networks in cancer. - Hao Wu 062; Lin Gao 006; Feng Li 033; Fei Song; Xiaofei Yang 003; Nikola K. Kasabov (BMC Bioinform., 2015)

MEpurity: estimating tumor purity using DNA methylation data. - Bowen Liu; Xiaofei Yang 003; Tingjie Wang; Jiadong Lin; Yongyong Kang; Peng Jia 004; Kai Ye 001 (Bioinform., 2019)

MSIsensor-pro: Fast, Accurate, and Matched-normal-sample-free Detection of Microsatellite Instability. - Peng Jia 004; Xiaofei Yang 003; Li Guo 012; Bowen Liu; Jiadong Lin; Hao Liang; Jianyong Sun; Chengsheng Zhang; Kai Ye 001 (Genom. Proteom. Bioinform., 2020)

Transportation, germs, culture: a dynamic graph model of COVID-19 outbreak. - Xiaofei Yang 003; Tun Xu; Peng Jia 004; Han Xia; Li Guo 012; Lei Zhang 095; Kai Ye 001 (Quant. Biol., 2020)

Building Fast and Compact Sketches for Approximately Multi-Set Multi-Membership Querying. - Rundong Li 002; Pinghui Wang; Jiongli Zhu; Junzhou Zhao; Jia Di; Xiaofei Yang 003; Kai Ye 001 (SIGMOD Conference, 2021)

Mako: A Graph-based Pattern Growth Approach to Detect Complex Structural Variants. - Jiadong Lin; Xiaofei Yang 003; Walter A. Kosters; Tun Xu; Yanyan Jia; Songbo Wang; Qihui Zhu; Mallory Ryan; Li Guo 012; Chengsheng Zhang (Genom. Proteom. Bioinform., 2022)

High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads. - Bo Wang 119; Xiaofei Yang 003; Yanyan Jia; Yu Xu; Peng Jia 004; Ningxin Dang; Songbo Wang; Tun Xu; Xixi Zhao; Shenghan Gao; Quanbin Dong; Kai Ye 001 (Genom. Proteom. Bioinform., 2022)

JAX-CNV: A Whole-genome Sequencing-based Algorithm for Copy Number Detection at Clinical Grade Level. - Wan-Ping Lee; Qihui Zhu; Xiaofei Yang 003; Silvia Liu; Eliza Cerveira; Mallory Ryan; Adam Mil-Homens; Lauren Bellfy; Kai Ye 001; Charles Lee; Chengsheng Zhang (Genom. Proteom. Bioinform., 2022)

Centromere Landscapes Resolved from Hundreds of Human Genomes. - Shenghan Gao; Yimeng Zhang; Stephen J. Bush; Bo Wang 119; Xiaofei Yang 003; Kai Ye 001 (Genom. Proteom. Bioinform., 2024)

MSIsensor-RNA: Microsatellite Instability Detection for Bulk and Single-cell Gene Expression Data. - Peng Jia 004; Xuanhao Yang; Xiaofei Yang 003; Tingjie Wang; Yu Xu; Kai Ye 001 (Genom. Proteom. Bioinform., 2024)

Pindel-TD: A Tandem Duplication Detector Based on A Pattern Growth Approach. - Xiaofei Yang 003; Gaoyang Zheng; Peng Jia 004; Songbo Wang; Kai Ye 001 (Genom. Proteom. Bioinform., 2024)