mBWA: A Massively Parallel Sequence Reads Aligner. - Yingbo Cui 001; Xiangke Liao; Xiaoqian Zhu; Bingqiang Wang; Shaoliang Peng (PACBB, 2014)

The Challenge of Scaling Genome Big Data Analysis Software on TH-2 Supercomputer. - Shaoliang Peng; Xiangke Liao; Canqun Yang; Yutong Lu; Jie Liu 002; Yingbo Cui 001; Heng Wang; Chengkun Wu; Bingqiang Wang (CCGRID, 2015)

Large-Scale Neo-Heterogeneous Programming and Optimization of SNP Detection on Tianhe-2. - Yingbo Cui 001; Xiangke Liao; Shaoliang Peng; Yutong Lu; Canqun Yang; Bingqiang Wang; Chengkun Wu (ISC, 2015)

Neo-hetergeneous Programming and Parallelized Optimization of a Human Genome Re-sequencing Analysis Software Pipeline on TH-2 Supercomputer. - Xiangke Liao; Shaoliang Peng; Yutong Lu; Yingbo Cui 001; Chengkun Wu; Heng Wang; Jiajun Wen 002 (Supercomput. Front. Innov., 2015)

Efficient computation of motif discovery on Intel Many Integrated Core (MIC) Architecture. - Shaoliang Peng; Minxia Cheng; Kaiwen Huang; Yingbo Cui 001; Zhiqiang Zhang; Runxin Guo; Xiaoyu Zhang 008; Shunyun Yang; Xiangke Liao; Yutong Lu; Quan Zou 001; Benyun Shi (BMC Bioinform., 2018)

mSNP: A Massively Parallel Algorithm for Large-Scale SNP Detection. - Yingbo Cui 001; Shaoliang Peng; Yutong Lu; Xiaoqian Zhu; Bingqiang Wang; Chengkun Wu; Xiangke Liao (IEEE Trans. Parallel Distributed Syst., 2018)

A CPU/MIC Collaborated Parallel Framework for GROMACS on Tianhe-2 Supercomputer. - Shaoliang Peng; Yingbo Cui 001; Shunyun Yang; Wenhe Su; Xiaoyu Zhang 008; Tenglilang Zhang; Weiguo Liu; Xingming Zhao (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

H-VAE: A Hybrid Variational AutoEncoder with Data Augmentation in Predicting CRISPR/Cas9 Off-target. - Weiming Xiang 003; Dong Chen 013; Yingbo Cui 001; Shaoliang Peng (BIBM, 2021)

Large-Scale Parallel Alignment Algorithm for SMRT Reads. - Zeyu Xia; Yingbo Cui 001; Ang Zhang; Peng Zhang 061; Sifan Long; Tao Tang 001; Lin Peng 001; Chun Huang; Canqun Yang; Xiangke Liao (ICA3PP (2), 2021)

VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments. - Yingbo Cui 001; Zihang Wang; Johannes Köster; Xiangke Liao; Shaoliang Peng; Tao Tang 001; Chun Huang; Canqun Yang (BMC Bioinform., 2021)

CRISP-view: a database of functional genetic screens spanning multiple phenotypes. - Yingbo Cui 001; Xiaolong Cheng; Qing Chen; Bicna Song; Anthony Chiu; Yuan Gao; Tyson Dawson; Lumen Chao; Wubing Zhang; Dian Li; Zexiang Zeng; Jijun Yu; et al. (Nucleic Acids Res., 2021)

MSVF: Multi-task Structure Variation Filter with Transfer Learning in High-throughput Sequencing. - Weiming Xiang 003; Yingbo Cui 001; Yaning Yang; Ang Zhang; Boya Ji; Shaoliang Peng (BIBM, 2022)

MinimapR: A parallel alignment tool for the analysis of large-scale third-generation sequencing data. - Zihang Wang; Yingbo Cui 001; Shaoliang Peng; Xiangke Liao; Yangbo Yu (Comput. Biol. Chem., 2022)

MTMap: A Long-Read Alignment Tool based on Multi-Core DSPs. - Yufei Guo; Xinjie An; Shijie Li; Yingbo Cui 001; Peng Zhang 061; Biao Long; Shanshan Li (BIBM, 2023)

DrugProtKGE: Weakly Supervised Knowledge Graph Embedding for Highly-Effective Drug-Protein Interaction Representation. - Yanlong Qiu; Siqi Wang 001; Xi Yang 020; Xinyuan Qiu; Chengkun Wu; Yingbo Cui 001; Canqun Yang (BIBM, 2023)

Performance Evaluation of Spark, Ray and MPI: A Case Study on Long Read Alignment Algorithm. - Kun Ran; Yingbo Cui 001; Zihang Wang; Shaoliang Peng (ICA3PP (3), 2023)

WFA-vect: a SIMD wavefront algorithm for gap-affine pairwise alignment. - Yifei Guo; Tao Tang 001; Qingzhe Wang; Canqun Yang; Zeyu Xia; Chenchen Peng; Yufei Guo; Yingbo Cui 001 (BIBM, 2024)

MinimapPool: an improved flexible and efficient parallel algorithm based on minimap2. - Zhenang Wang; Yingbo Cui 001; Jiandong Shang; Boya Ji; Jianan Li; Shaoliang Peng (BIBM, 2024)

A Vectorized Sequence-to-Graph Alignment Algorithm. - Chenchen Peng; Shengbo Tang; Yifei Guo; Zeyu Xia; Canqun Yang; Yingbo Cui 001 (ICA3PP (1), 2024)

SNCL: a supernode OpenCL implementation for hybrid computing arrays. - Tao Tang 001; Kai Lu 001; Lin Peng 001; Yingbo Cui 001; Jianbin Fang; Chun Huang; Ruibo Wang; Canqun Yang; Yifei Guo (J. Supercomput., 2024)

PVGwfa: a multi-level parallel sequence-to-graph alignment algorithm. - Chenchen Peng; Zeyu Xia; Shengbo Tang; Yifei Guo; Canqun Yang; Tao Tang 001; Yingbo Cui 001 (J. Supercomput., 2025)

Fast noisy long read alignment with multi-level parallelism. - Zeyu Xia; Canqun Yang; Chenchen Peng; Yifei Guo; Yufei Guo; Tao Tang 001; Yingbo Cui 001 (BMC Bioinform., 2025)