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2020 – today
- 2025
[j22]Haijing Luan, Kaixing Yang, Taiyuan Hu, Jifang Hu, Siyao Liu, Ruilin Li, Jiayin He, Rui Yan, Xiaobing Guo, Niansong Qian, Beifang Niu:
Review of deep learning-based pathological image classification: From task-specific models to foundation models. Future Gener. Comput. Syst. 164: 107578 (2025)- 2024
- [j21]Weier Liu
, Yangde Feng, Ruilin Li, Chenhan Bai, Beifang Niu:
Peridynamic modeling for multiscale heat transport of phonon Boltzmann transport equation. Comput. Phys. Commun. 299: 109157 (2024) - [j20]Huijuan Chen, Bing Wang, Lili Cai, Xiaotian Yang, Yali Hu, Yiran Zhang, Xue Leng, Wen Liu, Dongjie Fan, Beifang Niu, Qiming Zhou:
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. J. Biomed. Informatics 152: 104625 (2024) - 2023
- [j19]Quan Xu, Yueyue Liu, Dawei Sun, Xiaoqian Huang, Feihong Li, Jincheng Zhai, Yang Li, Qiming Zhou, Niansong Qian, Beifang Niu:
OncoCTMiner: streamlining precision oncology trial matching via molecular profile analysis. Database J. Biol. Databases Curation 2023 (2023) - [c6]Haijing Luan, Taiyuan Hu, Jifang Hu, Ruilin Li, Detao Ji, Jiayin He, Xiaohong Duan, Chunyan Yang, Yajun Gao, Fan Chen, Beifang Niu:
Multi-class Cancer Classification of Whole Slide Images Through Transformer and Multiple Instance Learning. ISBRA 2023: 150-164 - 2022
- [j18]Quan Xu, Yueyue Liu, Jifang Hu, Xiaohong Duan, Niuben Song, Jiale Zhou, Jincheng Zhai, Junyan Su, Siyao Liu, Fan Chen, Wei Zheng, Zhongjia Guo, Hexiang Li, Qiming Zhou, Beifang Niu:
OncoPubMiner: a platform for mining oncology publications. Briefings Bioinform. 23(5) (2022) - [j17]Shiyu Cheng, Xiaochen Li, Guihua Shan, Beifang Niu, Yang Wang, Maokang Luo:
ACMViz: a visual analytics approach to understand DRL-based autonomous control model. J. Vis. 25(2): 427-442 (2022) - [c5]Lifeng Yan, Zekun Yin, Hao Zhang, Zhan Zhao, Mingkai Wang, André Müller, Robin Kobus, Yanjie Wei, Beifang Niu, Bertil Schmidt, Weiguo Liu:
RabbitQCPlus: More Efficient Quality Control for Sequencing Data. BIBM 2022: 619-626 - 2021
- [j16]Xiaoyu He, Shanyu Chen, Ruilin Li, Xinyin Han, Zhipeng He, Danyang Yuan, Shuying Zhang, Xiaohong Duan, Beifang Niu:
Comprehensive fundamental somatic variant calling and quality management strategies for human cancer genomes. Briefings Bioinform. 22(3) (2021) - [j15]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:
MSIsensor-ct: microsatellite instability detection using cfDNA sequencing data. Briefings Bioinform. 22(5) (2021) - [j14]Danyang Yuan, Xiaoyu He, Xinyin Han, Chunyan Yang, Fei Liu, Shuying Zhang, Haijing Luan, Ruilin Li, Jiayin He, Xiaohong Duan, Dongliang Wang, Qiming Zhou, Sujun Gao, Beifang Niu:
Comprehensive review and evaluation of computational methods for identifying FLT3-internal tandem duplication in acute myeloid leukaemia. Briefings Bioinform. 22(5) (2021) - [j13]Zekun Yin, Hao Zhang, Meiyang Liu, Wen Zhang, Honglei Song, Haidong Lan, Yanjie Wei, Beifang Niu, Bertil Schmidt, Weiguo Liu:
RabbitQC: high-speed scalable quality control for sequencing data. Bioinform. 37(4): 573-574 (2021) - [j12]Shiyu Cheng, Han-Wei Shen, Guihua Shan, Beifang Niu, Weihua Bai:
Visual analysis of meteorological satellite data via model-agnostic meta-learning. J. Vis. 24(2): 301-315 (2021) - 2020
- [j11]Shanyu Chen, Xiaoyu He, Ruilin Li, Xiaohong Duan, Beifang Niu:
HotSpot3D web server: an integrated resource for mutation analysis in protein 3D structures. Bioinform. 36(12): 3944-3946 (2020) - [c4]Chuangchuang Dai, Haijing Luan, Qingbing Yu, Xiaoyu He, Yunhao Wang, Bincheng Shuai, Xiaobing Guo, Zhonghua Lu, Beifang Niu:
Change-Encryption: Encryption Using Spatiotemporal Information as a Function Model. CSCloud/EdgeCom 2020: 281-287 - [c3]Chuangchuang Dai, Xueying Yang, Meikang Qiu, Xiaobing Guo, Zhonghua Lu, Beifang Niu:
Digital Currency Investment Strategy Framework Based on Ranking. ICA3PP (3) 2020: 654-662
2010 – 2019
- 2019
- [j10]Shanyu Chen, Zhipeng He, Xinyin Han, Xiaoyu He, Ruilin Li, Haidong Zhu, Dan Zhao, Chuangchuang Dai, Yu Zhang, Zhonghua Lu, Xuebin Chi, Beifang Niu:
How Big Data and High-performance Computing Drive Brain Science. Genom. Proteom. Bioinform. 17(4): 381-392 (2019) - [j9]Ruilin Li, Xiaoyu He, Chuangchuang Dai, Haidong Zhu, Xianyu Lang, Wei Chen, Xiaodong Li, Dan Zhao, Yu Zhang, Xinyin Han, Tie Niu, Yi Zhao, Rongqiang Cao, Rong He, Zhonghua Lu, Xuebin Chi, Weizhong Li, Beifang Niu:
Gclust: A Parallel Clustering Tool for Microbial Genomic Data. Genom. Proteom. Bioinform. 17(5): 496-502 (2019) - [c2]Zekun Yin, Xiaoming Xu, Kaichao Fan, Ruilin Li, Weizhong Li, Weiguo Liu, Beifang Niu:
DGCF: A Distributed Greedy Clustering Framework for Large-scale Genomic Sequences. BIBM 2019: 2272-2279 - [c1]Shuo Li, Zhonghua Lu, Yongze Sun, Sungen Deng, Beifang Niu:
Distributed Parameter Optimization Scheduling Strategy and System Design Based on Mesos. BigDataSecurity/HPSC/IDS 2019: 218-224 - 2014
- [j8]Beifang Niu, Kai Ye, Qunyuan Zhang, Charles Lu, Mingchao Xie, Michael D. McLellan, Michael C. Wendl, Li Ding:
MSIsensor: microsatellite instability detection using paired tumor-normal sequence data. Bioinform. 30(7): 1015-1016 (2014) - 2013
- [j7]Zhengwei Zhu, Beifang Niu, Jing Chen, Sitao Wu, Shulei Sun, Weizhong Li:
MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data. Bioinform. 29(1): 122-123 (2013) - 2012
- [j6]Weizhong Li, Limin Fu, Beifang Niu, Sitao Wu, John C. Wooley:
Ultrafast clustering algorithms for metagenomic sequence analysis. Briefings Bioinform. 13(6): 656-668 (2012) - [j5]Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu, Weizhong Li:
CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinform. 28(23): 3150-3152 (2012) - 2011
- [j4]Beifang Niu, Zhengwei Zhu, Limin Fu, Sitao Wu, Weizhong Li:
FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes. Bioinform. 27(12): 1704-1705 (2011) - 2010
- [j3]Ying Huang, Beifang Niu, Ying Gao, Limin Fu, Weizhong Li:
CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinform. 26(5): 680-682 (2010) - [j2]Beifang Niu, Limin Fu, Shulei Sun, Weizhong Li:
Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinform. 11: 187 (2010)
2000 – 2009
- 2007
- [j1]Beifang Niu, Xianyu Lang, Zhonghua Lu, Xuebin Chi:
ScBioGrid: a commodity supercomputing environment supporting bioinformatics research. Int. J. Comput. Math. 84(2): 177-182 (2007)
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