ScBioGrid: a commodity supercomputing environment supporting bioinformatics research. - Beifang Niu; Xianyu Lang; Zhonghua Lu; Xuebin Chi (Int. J. Comput. Math., 2007)

CD-HIT Suite: a web server for clustering and comparing biological sequences. - Ying Huang; Beifang Niu; Ying Gao; Limin Fu; Weizhong Li 002 (Bioinform., 2010)

Artificial and natural duplicates in pyrosequencing reads of metagenomic data. - Beifang Niu; Limin Fu; Shulei Sun; Weizhong Li 002 (BMC Bioinform., 2010)

FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes. - Beifang Niu; Zhengwei Zhu 001; Limin Fu; Sitao Wu; Weizhong Li 002 (Bioinform., 2011)

Ultrafast clustering algorithms for metagenomic sequence analysis. - Weizhong Li 002; Limin Fu; Beifang Niu; Sitao Wu; John C. Wooley (Briefings Bioinform., 2012)

CD-HIT: accelerated for clustering the next-generation sequencing data. - Limin Fu; Beifang Niu; Zhengwei Zhu 001; Sitao Wu; Weizhong Li 002 (Bioinform., 2012)

MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data. - Zhengwei Zhu 001; Beifang Niu; Jing Chen; Sitao Wu; Shulei Sun; Weizhong Li 002 (Bioinform., 2013)

MSIsensor: microsatellite instability detection using paired tumor-normal sequence data. - Beifang Niu; Kai Ye 001; Qunyuan Zhang; Charles Lu 002; Mingchao Xie; Michael D. McLellan; Michael C. Wendl; Li Ding (Bioinform., 2014)

DGCF: A Distributed Greedy Clustering Framework for Large-scale Genomic Sequences. - Zekun Yin; Xiaoming Xu; Kaichao Fan; Ruilin Li; Weizhong Li 002; Weiguo Liu; Beifang Niu (BIBM, 2019)

Distributed Parameter Optimization Scheduling Strategy and System Design Based on Mesos. - Shuo Li; Zhonghua Lu; Yongze Sun; Sungen Deng; Beifang Niu (BigDataSecurity/HPSC/IDS, 2019)

How Big Data and High-performance Computing Drive Brain Science. - Shanyu Chen; Zhipeng He 003; Xinyin Han; Xiaoyu He; Ruilin Li; Haidong Zhu; Dan Zhao; Chuangchuang Dai; Yu Zhang 130; Zhonghua Lu; Xuebin Chi; Beifang Niu (Genom. Proteom. Bioinform., 2019)

Gclust: A Parallel Clustering Tool for Microbial Genomic Data. - Ruilin Li; Xiaoyu He; Chuangchuang Dai; Haidong Zhu; Xianyu Lang; Wei Chen 033; Xiaodong Li; Dan Zhao; Yu Zhang 130; Xinyin Han; Tie Niu; Yi Zhao; et al. (Genom. Proteom. Bioinform., 2019)

Change-Encryption: Encryption Using Spatiotemporal Information as a Function Model. - Chuangchuang Dai; Haijing Luan; Qingbing Yu; Xiaoyu He; Yunhao Wang; Bincheng Shuai; Xiaobing Guo; Zhonghua Lu; Beifang Niu (CSCloud/EdgeCom, 2020)

Digital Currency Investment Strategy Framework Based on Ranking. - Chuangchuang Dai; Xueying Yang; Meikang Qiu; Xiaobing Guo; Zhonghua Lu; Beifang Niu (ICA3PP (3), 2020)

HotSpot3D web server: an integrated resource for mutation analysis in protein 3D structures. - Shanyu Chen; Xiaoyu He; Ruilin Li; Xiaohong Duan; Beifang Niu (Bioinform., 2020)

MSIsensor-ct: microsatellite instability detection using cfDNA sequencing data. - Xinyin Han; Shuying Zhang; Daniel Cui Zhou; Dongliang Wang; Xiaoyu He; Danyang Yuan; Ruilin Li; Jiayin He; Xiaohong Duan; Michael C. Wendl; Li Ding; Beifang Niu (Briefings Bioinform., 2021)

Comprehensive fundamental somatic variant calling and quality management strategies for human cancer genomes. - Xiaoyu He; Shanyu Chen; Ruilin Li; Xinyin Han; Zhipeng He 003; Danyang Yuan; Shuying Zhang; Xiaohong Duan; Beifang Niu (Briefings Bioinform., 2021)

Comprehensive review and evaluation of computational methods for identifying FLT3-internal tandem duplication in acute myeloid leukaemia. - Danyang Yuan; Xiaoyu He; Xinyin Han; Chunyan Yang; Fei Liu; Shuying Zhang; Haijing Luan; Ruilin Li; Jiayin He; Xiaohong Duan; Dongliang Wang; Qiming Zhou; et al. (Briefings Bioinform., 2021)

RabbitQC: high-speed scalable quality control for sequencing data. - Zekun Yin; Hao Zhang 142; Meiyang Liu; Wen Zhang; Honglei Song; Haidong Lan; Yanjie Wei; Beifang Niu; Bertil Schmidt; Weiguo Liu (Bioinform., 2021)

Visual analysis of meteorological satellite data via model-agnostic meta-learning. - Shiyu Cheng; Han-Wei Shen; Guihua Shan; Beifang Niu; Weihua Bai (J. Vis., 2021)

RabbitQCPlus: More Efficient Quality Control for Sequencing Data. - Lifeng Yan; Zekun Yin; Hao Zhang 142; Zhan Zhao; Mingkai Wang; André Müller; Robin Kobus; Yanjie Wei; Beifang Niu; Bertil Schmidt; Weiguo Liu (BIBM, 2022)

OncoPubMiner: a platform for mining oncology publications. - Quan Xu; Yueyue Liu; Jifang Hu; Xiaohong Duan; Niuben Song; Jiale Zhou; Jincheng Zhai; Junyan Su; Siyao Liu; Fan Chen; Wei Zheng; Zhongjia Guo; et al. (Briefings Bioinform., 2022)

ACMViz: a visual analytics approach to understand DRL-based autonomous control model. - Shiyu Cheng; Xiaochen Li; Guihua Shan; Beifang Niu; Yang Wang 121; Maokang Luo (J. Vis., 2022)

Multi-class Cancer Classification of Whole Slide Images Through Transformer and Multiple Instance Learning. - Haijing Luan; Taiyuan Hu; Jifang Hu; Ruilin Li; Detao Ji; Jiayin He; Xiaohong Duan; Chunyan Yang; Yajun Gao; Fan Chen; Beifang Niu (ISBRA, 2023)

OncoCTMiner: streamlining precision oncology trial matching via molecular profile analysis. - Quan Xu; Yueyue Liu; Dawei Sun; Xiaoqian Huang; Feihong Li; Jincheng Zhai; Yang Li; Qiming Zhou; Niansong Qian; Beifang Niu (Database J. Biol. Databases Curation, 2023)

Transformer-Based Multi-Scale Fusion for Robust Predicting Microsatellite Instability from Pathological Images. - Taiyuan Hu; Haijing Luan; Rui Yan; Jifang Hu; Kaixing Yang; Xinyin Han; Weier Liu; Jiayin He; Xiaohong Duan; Ruilin Li; Fa Zhang; Beifang Niu (BIBM, 2024)

Peridynamic modeling for multiscale heat transport of phonon Boltzmann transport equation. - Weier Liu; Yangde Feng; Ruilin Li; Chenhan Bai; Beifang Niu (Comput. Phys. Commun., 2024)

A comprehensive performance evaluation, comparison, and integration of computational methods for detecting and estimating cross-contamination of human samples in cancer next-generation sequencing analysis. - Huijuan Chen; Bing Wang; Lili Cai; Xiaotian Yang; Yali Hu; Yiran Zhang; Xue Leng; Wen Liu; Dongjie Fan; Beifang Niu; Qiming Zhou (J. Biomed. Informatics, 2024)

Review of deep learning-based pathological image classification: From task-specific models to foundation models. - Haijing Luan; Kaixing Yang; Taiyuan Hu; Jifang Hu; Siyao Liu; Ruilin Li; Jiayin He; Rui Yan; Xiaobing Guo; Niansong Qian; Beifang Niu (Future Gener. Comput. Syst., 2025)