长期从事临床肿瘤基因组学、医学生物信息学与高性能计算交叉领域的研究工作。聚焦于肿瘤驱动信号及免疫治疗标志物的发现算法和软件技术研发，开发基因组数据建模和机器学习新模型。是MSIsensor、MuSiC/MuSiC2、HotSpot3D、CD-HIT系列等流行癌症基因检测软件的主要作者。其中代表性算法体系MSIsensor在2017年获得美国FDA批准，被国际上700余个临床研究项目所应用。迄今发表同行评审论文70余篇，包括Nature、Nature Genetics等期刊，总被引用30000余次。曾获2015年美国10大临床研究成就奖（排名：8/33），入选2022年美国斯坦福大学发布的“全球前2%科学家榜单”。

   

081202-计算机软件与理论

高性能计算与生物信息学
计算基因组学

2002-09--2009-02   中国科学院计算机网络信息中心   工学博士
1998-09--2002-07   山东农业大学计算机系   工学学士

研究生

博士

   

2012-08~2015-01,美国圣路易斯华盛顿大学（WUSTL）, Research Scientist
2009-03~2012-07,美国加州大学圣迭戈（UCSD）, 博士后

2019-10-23-今,中国科学院计算技术研究所西部高等研究院, 特聘研究员
2018-10-20-今,中国计算机学会高性能计算专业委员会, 会员
2018-10-13-今,中国计算机学会生物信息专业委员会, 会员
2017-09-30-今,贵州大学特聘教授, 兼职教授
2016-11-30-今,中国计算机学会, 会员
2015-08-13-今,中国运筹学会计算生物学分会, 理事
2015-08-11-今,中国运筹学会, 会员

   

（1） Top 10 Clinical Research Achievement Awards for 2015（2015年美国10大临床研究成就奖）, , 国家级, 2015

[1] 陈义夫, 冯仰德, 牛北方, 刘威尔. 基于国家高性能计算环境的中小企业计算社区系统. CN: CN112416565A, 2021-02-26.
[2] 陆忠华, 李铄, 孙永泽, 代闯闯, 邓笋根, 牛北方. 一种基于Mesos的分布式超参数优化系统及方法. CN: CN110046046A, 2019-07-23.

   

[1] Weier Liu, Yangde Feng, Ruilin Li, Chenhan Bai, Beifang Niu. Peridynamic modeling for multiscale heat transport of phonon Boltzmann transport equation. Computer Physics Communications[J]. 2024, 第 5 作者  通讯作者  299: https://doi.org/10.1016/j.cpc.2024.109157.
[2] HuiJuan Chen, YiRan Zhang, Bing Wang, Rui Liao, XiaoHong Duan, ChunYan Yang, Jing Chen, YanTong Hao, YingShuang Shu, LiLi Cai, Xue Leng, Nian-Song Qian, DaWei Sun, Beifang Niu, Qiming Zhou. Characterization and mitigation of artifacts derived from NGS library preparation due to structure-specific sequences in the human genome. BMC Genomics[J]. 2024, 第 14 作者  通讯作者  25: https://doi.org/10.1186/s12864-024-10157-w.
[3] 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: The Journal of Biological Databases and Curation[J]. 2023, 第 10 作者  通讯作者  https://academic.oup.com/database/article/doi/10.1093/database/baad077/7343996?login=true.
[4] 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. International Symposium on Bioinformatics Research and Applications. 2023, 第 11 作者  通讯作者  https://link.springer.com/chapter/10.1007/978-981-99-7074-2_12#chapter-info.
[5] Zhang, Hui, Jiang, Da, Meng, Erhong, Zhao, Meng, Niu, Beifang. Long-term response to camrelizumab in a pretreated metastatic mixed testicular germ-cell tumor patient with co-mutations in DNA damage-repair genes. IMMUNOTHERAPY[J]. 2023, 第 5 作者15(1): 17-25, 
[6] Xiaoming Xu, Zekun Yin, Lifeng Yan, Hao Zhang, Borui Xu, Yanjie Wei, Beifang Niu, Bertil Schmidt, Weiguo Liu. RabbitTClust: enabling fast clustering analysis of millions of bacteria genomes with MinHash sketches. GENOME BIOLOGY[J]. 2023, 第 7 作者24(1): 1-20, http://dx.doi.org/10.1186/s13059-023-02961-6.
[7] Mengyuan Liu, Yuting Hong, Xiaohong Duan, Qiming Zhou, Jing Chen, Siyao Liu, Junyan Su, Li Han, Jiali Zhang, Beifang Niu. Unveiling the metal mutation nexus: Exploring the genomic impacts of heavy metal exposure in lung adenocarcinoma and colorectal cancer. Journal of Hazardous Materials[J]. 2023, 第 10 作者  通讯作者  461: https://www.sciencedirect.com/science/article/abs/pii/S0304389423018733?via%3Dihub.
[8] Yan, Lifeng, Yin, Zekun, Zhang, Hao, Zhao, Zhan, Wang, Mingkai, Mueller, Andre, Kallenborn, Felix, Wichmann, Alexander, Wei, Yanjie, Niu, Beifang, Schmidt, Bertil, Liu, Weiguo. RabbitQCPlus 2.0: More efficient and versatile quality control for sequencing data. METHODS[J]. 2023, 第 10 作者216: 39-50, http://dx.doi.org/10.1016/j.ymeth.2023.06.007.
[9] Cui, Zhi, Wang, Qi, Deng, Muhong, Meng, Erhong, Liu, Sheng, Niu, Beifang, Han, Quanli. Long-term response to sintilimab, bevacizumab and chemotherapy in heavily pretreated microsatellite stable colon cancer. IMMUNOTHERAPY[J]. 2023, 第 6 作者  通讯作者  15(3): 
[10] Huiqun Hao, Jinrong Jiang, Tianyi Wang, Hailong Liu, Pengfei Lin, Ziyang Zhang, Beifang Niu. Deep Parallel Optimizations on an LASG/IAP Climate System Ocean Model and Its Large-Scale Parallelization. APPLIED SCIENCES[J]. 2023, 第 7 作者  通讯作者  13(4): https://doaj.org/article/798522b2ca114c6e827314d58fbbb3b5.
[11] Xi Cheng, Haiming Yu, Jinying Li, Xiaona Han, Erhong Meng, Houqing Zhou, Dongliang Wang, Beifang Niu, Xiaotao Zhang. Dramatic response to local radiotherapy in a refractory metastatic mediastinal yolk sac tumor patient harboring a germline BRCA2 frameshift mutation: a case report. Cancer Biology & Therapy[J]. 2022, 第 8 作者  通讯作者  
[12] Xiaoli Shi, Fa Cui, Xinyin Han, Yilin He, Long Zhao, Na Zhang, Hao Zhang, Haidong Zhu, Zhexin Liu, Bin Ma, Shusong Zheng, Wei Zhang, Jiajia Liu, Xiaoli Fan, Yaoqi Si, Shuiquan Tian, Jianqing Niu, Huilan Wu, Xuemei Liu, Zhuo Chen, Deyuan Meng, Xiaoyan Wang, Liqiang Song, Lijing Sun, Jie Han, Hui Zhao, Jun Ji, Zhiguo Wang, Xiaoyu He, Ruilin Li, Xuebin Chi, Chengzhi Liang, Beifang Niu, Jun Xiao, Junming Li, HongQing Ling. Comparative genomic and transcriptomic analyses uncover the molecular basis of high nitrogen-use efficiency in the wheat cultivar Kenong 9204. Molecular Plant[J]. 2022, 第 33 作者  通讯作者  15(9): 1440-1456, http://dx.doi.org/10.1016/j.molp.2022.07.008.
[13] Quan Xu, Yueyue Liu, Jifang Hu, Duan, Xiaohong, 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 in Bioinformatics[J]. 2022, 第 15 作者  通讯作者  23(5): https://academic.oup.com/bib/article/23/5/bbac383/6691792?searchresult=1#.
[14] Lifeng Yan, Zekun Yin, Hao Zhang, Mingkai Wang, Andre Muller, Robin Kobus, Yanjie Wei, Beifang Niu, Bertil Schmidt, Weiguo Liu. RabbitQCPlus: More Efficient Quality Control for Sequencing Data. International Conference on Bioinformatics and Biomedicine (BIBM). 2022, 第 8 作者
[15] Xie, Xuehua, You, Mengxing, Meng, Erhong, Wang, Shunyou, Niu, Beifang, Huang, Weiming. Complete and durable response to crizotinib in a patient with malignant pleural mesothelioma harboring CD74-ROS1 fusion. JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY[J]. 2022, 第 5 作者148(9): 2561-2566, http://dx.doi.org/10.1007/s00432-022-04076-0.
[16] Han, Xinyin, Zhang, Shuying, Zhou, Daniel Cui, Wang, Dongliang, He, Xiaoyu, Yuan, Danyang, Li, Ruilin, He, Jiayin, Duan, Xiaohong, Wendl, Michael C, Ding, Li, Niu, Beifang. MSIsensor-ct: microsatellite instability detection using cfDNA sequencing data. Briefings in Bioinformatics[J]. 2021, 第 12 作者  通讯作者  22(5): 
[17] 何小雨, 韩鑫胤, 牛北方. 肿瘤突变印记的求解算法比较. 计算机系统应用[J]. 2021, 第 3 作者  通讯作者  30(12): 46-54, 
[18] He, Xiaoyu, Chen, Shanyu, Li, Ruilin, Han, Xinyin, He, Zhipeng, Yuan, Danyang, Zhang, Shuying, Duan, Xiaohong, Niu, Beifang. Comprehensive fundamental somatic variant calling and quality management strategies for human cancer genomes. Briefings in Bioinformatics[J]. 2021, 第 9 作者  通讯作者  22(3): 
[19] 代闯闯, 栾海晶, 杨雪莹, 过晓冰, 陆忠华, 牛北方. 区块链技术研究综述. 计算机科学[J]. 2021, 第 6 作者  通讯作者  48(11A): 500-508, 
[20] 何小雨, 邓笋根, 栾海晶, 牛北方. 国家高性能计算环境的虚拟数据空间运行支撑技术研究. 大数据[J]. 2021, 第 4 作者  通讯作者  7(2): 158-171, http://lib.cqvip.com/Qikan/Article/Detail?id=7104093237.
[21] Danyang Yuan, Xiaoyu He, Xinyin Han, Chunyan Yang, Fei Liu, Shuying Zhang, Haijing Luan, Ruilin Li, Jiayin He, Duan, Xiaohong, Dongliang Wang, Qiming Zhou, Sujun Gao, Beifang Niu. Comprehensive review and evaluation of computational methods for identifying FLT3-internal tenderm duplication in acute myeloid leukaemia. Briefings in Bioinformatics[J]. 2021, 第 14 作者  通讯作者  22(5): 
[22] Yin, Zekun, Zhang, Hao, Liu, Meiyang, Zhang, Wen, Song, Honglei, Lan, Haidong, Wei, Yanjie, Niu, Beifang, Schmidt, Bertil, Liu, Weiguo. RabbitQC: high-speed scalable quality control for sequencing data. BIOINFORMATICS[J]. 2021, 第 8 作者37(4): 573-574, http://dx.doi.org/10.1093/bioinformatics/btaa719.
[23] 秦广军, 肖利民, 张广艳, 牛北方, 陈志广. 面向国家高性能计算环境的虚拟数据空间系统. 大数据[J]. 2021, 第 4 作者7(2): 101-122, http://lib.cqvip.com/Qikan/Article/Detail?id=7104093234.
[24] 张舒莹, 韩鑫胤, 何小雨, 袁丹阳, 栾海晶, 李瑞琳, 何佳茵, 牛北方. 基于机器学习的基因组微卫星状态探测方法综述. 数据与计算发展前沿[J]. 2021, 第 8 作者  通讯作者  126-135, https://t.cnki.net/kcms/detail?v=3uoqIhG8C46NmWw7YpEsKMypi3qVj28LEUDxQXHYyS3fbyEOrIfBzA0n_znVSGEh23VTYlquiImaTFULhBrMsbV5ietEVNWu.
[25] Cheng, Shiyu, Shen, Hanwei, Shan, Guihua, Niu, Beifang, Bai, Weihua. Visual analysis of meteorological satellite data via model-agnostic meta-learning. JOURNAL OF VISUALIZATION[J]. 2021, 第 4 作者24(2): 301-315, http://dx.doi.org/10.1007/s12650-020-00704-4.
[26] Yulia Rubanova, Ruian Shi, Caitlin F. Harrigan, Roujia Li, Jeff Wintersinger, Nil Sahin, Amit G. Deshwar, , Quaid D. Morris, . Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig. NATURE COMMUNICATIONS[J]. 2020, 11(1): 1-12, 
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[28] Paczkowska, Marta, Barenboim, Jonathan, Sintupisut, Nardnisa, Fox, Natalie S, Zhu, Helen, AbdRabbo, Diala, Mee, Miles W, Boutros, Paul C, Reimand, Juri, PCAWG Drivers Functional Interpret, PCAWG Consortium. Integrative pathway enrichment analysis of multivariate omics data. NATURE COMMUNICATIONS[J]. 2020, 11(1): 
[29] Constance H Li, Stephenie D Prokopec, Ren X Sun, Fouad Yousif, Nathaniel Schmitz, PCAWG Tumour Subtypes and Clinical Translation, Paul C Boutros, PCAWG Consortium. Sex differences in oncogenic mutational processes. NATURE COMMUNICATIONS[J]. 2020, 11(1): https://doaj.org/article/675a0b63db164a13bc463d8f773c85d4.
[30] Dai, Chuangchuang, Yang, Xueying, Qiu, Meikang, Guo, Xiaobing, Lu, Zhonghua, Niu, Beifang. Digital Currency Investment Strategy Framework Based on Ranking. ALGORITHMS AND ARCHITECTURES FOR PARALLEL PROCESSING, ICA3PP 2020, PT III. 2020, 第 6 作者  通讯作者  12454: 654-662, 
[31] Zapatka, Marc, Borozan, Ivan, Brewer, Daniel S, Iskar, Murat, Grundhoff, Adam, Alawi, Malik, Desai, Nikita, Sueltmann, Holger, Moch, Holger, Cooper, Colin S, Eils, Roland, Ferretti, Vincent, Lichter, Peter, PCAWG Pathogens, PCAWG Consortium. The landscape of viral associations in human cancers. NATURE GENETICS[J]. 2020, 52(3): 320-+, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8076016/.
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[33] Chen, Shanyu, He, Xiaoyu, Li, Ruilin, Duan, Xiaohong, Niu, Beifang. HotSpot3D web server: an integrated resource for mutation analysis in protein 3D structures. Bioinformatics[J]. 2020, 第 5 作者  通讯作者  36(12): 3944-3946, https://www.webofscience.com/wos/woscc/full-record/WOS:000550127500061.
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（1） FR-HIT Overview, SpringerReference, 2014-06, 第 1 作者
（2） Clustering-based HMP Sequence Comparison, SpringerReference, 2014-06, 第 1 作者
（3） Fast program for clustering and comparing large sets of protein or nucleotide sequences, SpringerReference, 2014-06, 第 2 作者

   

（ 1 ） 泛癌体细胞突变热点分析算法研究, 负责人, 国家任务, 2018-05--2021-12
（ 2 ） 国家高性能计算环境中虚拟数据空间运行支撑技术, 负责人, 国家任务, 2018-05--2021-04
（ 3 ） 生态环境损害鉴定评估业务化技术研究, 负责人, 国家任务, 2016-07--2021-06
（ 4 ） 组学数据挖掘的高性能开源软件系统, 负责人, 中国科学院计划, 2016-01--2018-12
（ 5 ） 大尺度基因组重构与注释的高性能软件系统, 负责人, 中国科学院计划, 2017-01--2020-12
（ 6 ） 个性化药物—基于疾病分子分型的惠普新药研发, 参与, 中国科学院计划, 2015-10--2018-12
（ 7 ） 基于高通量测序技术的新生儿出生缺陷筛查新技术研究与示范, 负责人, 地方任务, 2016-01--2018-12
（ 8 ） 宫颈癌组学数据深度挖掘分析, 负责人, 其他国际合作项目, 2017-05--2019-12
（ 9 ） 面向生命健康大数据分析的新计算架构与人工智能方法, 负责人, 中国科学院计划, 2020-01--2024-12
（ 10 ） 肿瘤微环境三维重建及动态演进的智能可视模拟研究, 负责人, 国家任务, 2023-01--2025-12

（1）MSI及TMB高表达人群数据挖掘算法   第二十二届“全国临床肿瘤学大会暨2019年CSCO学术年”   2018-09-18
（2）Pan-cancer Analysis of Genomics Sequencing Big Data   International Workshop on CO-DESIGN   2016-10-27
（3）Protein-structure-guided discovery of functional mutations across 19 cancer types   International Symposium on Clinical and Translational Medicine   2016-09-22
（4）Mutational Landscape and Significance Across Pan-Cancer   第四届“数学、计算机与生命科学交叉研究”青年学者论坛   2016-05-21

The  McDonnell Genome Institute, School of Medicine, Washington University in St. Louis, Missouri, US.

San Diego Supercomputer Center(SDSC), University of California, San Diego, California, US.

The J. Craig Venter Institute (JCVI), La Jolla, San Diego, California, US. 

The General Hospital of the People's Liberation Army (PLAGH), Beijing, China.

已指导学生

李瑞琳  博士研究生  081202-计算机软件与理论  

赵丹  硕士研究生  085211-计算机技术  

张裕  硕士研究生  081202-计算机软件与理论  

祝海栋  硕士研究生  081203-计算机应用技术  

何小雨  博士研究生  081202-计算机软件与理论  

陈玮  硕士研究生  081202-计算机软件与理论  

陈珊羽  硕士研究生  085211-计算机技术  

何志鹏  硕士研究生  085211-计算机技术  

张舒莹  硕士研究生  085211-计算机技术  

袁丹阳  硕士研究生  081202-计算机软件与理论  

代闯闯  博士研究生  081202-计算机软件与理论  

余果  硕士研究生  025100-金融  

刘月琳  硕士研究生  025100-金融  

冀德韬  硕士研究生  081202-计算机软件与理论  

李安可  硕士研究生  025100-金融  

现指导学生

郝卉群  博士研究生  081202-计算机软件与理论  

程世宇  博士研究生  081202-计算机软件与理论  

胡季芳  硕士研究生  081202-计算机软件与理论  

栾海晶  博士研究生  081202-计算机软件与理论  

刘威尔  博士研究生  081202-计算机软件与理论  

杨开星  硕士研究生  1001Z1-精准医学