Kai Ye

32 papers A 1Journal 30Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
A Telomere-to-telomere Diploid Reference Genome and Centromere Structure of the Chinese Quartet.
Genom. Proteom. Bioinform.
Bo Wang, Peng Jia, Stephen J. Bush, Xia Wang, Yi Yang, Yu Zhang, Shijie Wang, Xiaofei Yang, Pengyu Zhang, Yuanting Zheng, Leming Shi, Lianhua Dong, Kai Ye
2025 J jnl
Deciphering Complex Interactions Between LTR Retrotransposons and Three
Genom. Proteom. Bioinform.
Tun Xu, Stephen J. Bush, Yizhuo Che, Huanhuan Zhao, Tingjie Wang, Peng Jia, Songbo Wang, Peisen Sun, Pengyu Zhang, Shenghan Gao, Yu Xu, Chengyao Wang, Ningxin Dang, Yong E. Zhang, Xiaofei Yang, Kai Ye
2025 J jnl
Long and Accurate: How HiFi Sequencing is Transforming Genomics.
Genom. Proteom. Bioinform.
Bo Wang, Peng Jia, Shenghan Gao, Huanhuan Zhao, Gaoyang Zheng, Linfeng Xu, Kai Ye
2024 J jnl
Centromere Landscapes Resolved from Hundreds of Human Genomes.
Genom. Proteom. Bioinform.
Shenghan Gao, Yimeng Zhang, Stephen J. Bush, Bo Wang, Xiaofei Yang, Kai Ye
2024 J jnl
MSIsensor-RNA: Microsatellite Instability Detection for Bulk and Single-cell Gene Expression Data.
Genom. Proteom. Bioinform.
Peng Jia, Xuanhao Yang, Xiaofei Yang, Tingjie Wang, Yu Xu, Kai Ye
2024 J jnl
NextPolish2: A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads.
Genom. Proteom. Bioinform.
Jiang Hu, Zhuo Wang, Fan Liang, Shanlin Liu, Kai Ye, De-Peng Wang
2024 J jnl
Pindel-TD: A Tandem Duplication Detector Based on A Pattern Growth Approach.
Genom. Proteom. Bioinform.
Xiaofei Yang, Gaoyang Zheng, Peng Jia, Songbo Wang, Kai Ye
2023 J jnl
Comparison and benchmark of structural variants detected from long read and long-read assembly.
Briefings Bioinform.
Jiadong Lin, Peng Jia, Songbo Wang, Walter A. Kosters, Kai Ye
2023 J jnl
DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning.
J. Cheminformatics
Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen
2022 J jnl
High-quality
Genom. Proteom. Bioinform.
Bo Wang, Xiaofei Yang, Yanyan Jia, Yu Xu, Peng Jia, Ningxin Dang, Songbo Wang, Tun Xu, Xixi Zhao, Shenghan Gao, Quanbin Dong, Kai Ye
2022 J jnl
Homotopic Convex Transformation: A New Landscape Smoothing Method for the Traveling Salesman Problem.
IEEE Trans. Cybern.
Jialong Shi, Jianyong Sun, Qingfu Zhang, Kai Ye
2022 J jnl
JAX-CNV: A Whole-genome Sequencing-based Algorithm for Copy Number Detection at Clinical Grade Level.
Genom. Proteom. Bioinform.
Wan-Ping Lee, Qihui Zhu, Xiaofei Yang, Silvia Liu, Eliza Cerveira, Mallory Ryan, Adam Mil-Homens, Lauren Bellfy, Kai Ye, Charles Lee, Chengsheng Zhang
2021 — conf
Building Fast and Compact Sketches for Approximately Multi-Set Multi-Membership Querying.
SIGMOD Conference
Rundong Li, Pinghui Wang, Jiongli Zhu, Junzhou Zhao, Jia Di, Xiaofei Yang, Kai Ye
2021 J jnl
DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology.
J. Cheminformatics
Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Michael T. M. Emmerich, Adriaan P. IJzerman, Gerard J. P. van Westen
2021 J jnl
From Innovations to Prospects: What Is Hidden Behind Cryptocurrencies?
CoRR
Ang Jia, Ming Fan, Xi Xu, Di Cui, Wenying Wei, Zijiang Yang, Kai Ye, Ting Liu
2020 A conf
From Innovations to Prospects: What Is Hidden Behind Cryptocurrencies?
MSR
Ang Jia, Ming Fan, Xi Xu, Di Cui, Wenying Wei, Zijiang Yang, Kai Ye, Ting Liu
2020 J jnl
MSIsensor-pro: Fast, Accurate, and Matched-normal-sample-free Detection of Microsatellite Instability.
Genom. Proteom. Bioinform.
Peng Jia, Xiaofei Yang, Li Guo, Bowen Liu, Jiadong Lin, Hao Liang, Jianyong Sun, Chengsheng Zhang, Kai Ye
2020 J jnl
Transportation, germs, culture: a dynamic graph model of COVID-19 outbreak.
Quant. Biol.
Xiaofei Yang, Tun Xu, Peng Jia, Han Xia, Li Guo, Lei Zhang, Kai Ye
2019 J jnl
An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A2A receptor.
J. Cheminformatics
Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen
2019 J jnl
Learning From a Stream of Nonstationary and Dependent Data in Multiobjective Evolutionary Optimization.
IEEE Trans. Evol. Comput.
Jianyong Sun, Hu Zhang, Aimin Zhou, Qingfu Zhang, Ke Zhang, Zhenbiao Tu, Kai Ye
2019 J jnl
MEpurity: estimating tumor purity using DNA methylation data.
Bioinform.
Bowen Liu, Xiaofei Yang, Tingjie Wang, Jiadong Lin, Yongyong Kang, Peng Jia, Kai Ye
2019 J jnl
Mapping Genome Variants Sheds Light on Genetic and Phenotypic Differentiation in Chinese.
Genom. Proteom. Bioinform.
Li Guo, Kai Ye
2019 J jnl
PRESM: personalized reference editor for somatic mutation discovery in cancer genomics.
Bioinform.
Chen Cao, Lauren Mak, Guangxu Jin, Paul Gordon, Kai Ye, Quan Long
2017 J jnl
BreakPoint Surveyor: a pipeline for structural variant visualization.
Bioinform.
Matthew A. Wyczalkowski, Kristine M. Wylie, Song Cao, Michael D. McLellan, Jennifer Flynn, Mo Huang, Kai Ye, Xian Fan, Ken Chen, Michael C. Wendl, Li Ding
2016 J jnl
Detecting dispersed duplications in high-throughput sequencing data using a database-free approach.
Bioinform.
M. Kroon, Eric-Wubbo Lameijer, N. Lakenberg, Jayne Y. Hehir-Kwa, D. T. Thung, P. Eline Slagboom, Joost N. Kok, Kai Ye
2016 J jnl
Precision Medicine: What Challenges Are We Facing?
Genom. Proteom. Bioinform.
Yu Xue, Eric-Wubbo Lameijer, Kai Ye, Kunlin Zhang, Suhua Chang, Xiaoyue Wang, Jianmin Wu, Ge Gao, Fangqing Zhao, Jian Li, Chunsheng Han, Shuhua Xu, Jing-Fa Xiao, Xuerui Yang, Xiaomin Ying, Xuegong Zhang, Wei-Hua Chen, Yun Liu, Zhang Zhang, Kun Huang, Jun Yu
2014 J jnl
MSIsensor: microsatellite instability detection using paired tumor-normal sequence data.
Bioinform.
Beifang Niu, Kai Ye, Qunyuan Zhang, Charles Lu, Mingchao Xie, Michael D. McLellan, Michael C. Wendl, Li Ding
2012 J jnl
PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data.
Bioinform.
Yanju Zhang, Eric-Wubbo Lameijer, Peter A. C. 't Hoen, Zemin Ning, P. Eline Slagboom, Kai Ye
2009 J jnl
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.
Bioinform.
Kai Ye, Marcel H. Schulz, Quan Long, Rolf Apweiler, Zemin Ning
2008 J jnl
Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting.
Bioinform.
Kai Ye, K. Anton Feenstra, Jaap Heringa, Adriaan P. IJzerman, Elena Marchiori
2008 J jnl
Tracing evolutionary pressure.
Bioinform.
Kai Ye, Gert Vriend, Adriaan P. IJzerman
2007 J jnl
An efficient, versatile and scalable pattern growth approach to mine frequent patterns in unaligned protein sequences.
Bioinform.
Kai Ye, Walter A. Kosters, Adriaan P. IJzerman