中国人民大学数学科学研究院
English中文
龚新奇
时间:2015-01-19  浏览:17694次

数学智能应用实验室

MIALAB

(Mathematical Intelligence Application)



龚新奇,中国人民大学数学科学研究院教授、博士生导师,清华大学结构生物学高精尖创新中心合作研究员,中国人民大学数学学院学术委员会委员、学位委员会委员、师德监督建设委员会委员。开展生物信息学和应用数学的科研和教学。教育经历有本科毕业于北京航空航天大学和博士毕业于北京工业大学(博士导师:王存新教授),并在清华大学从事博士后研究(合作导师:施一公教授)。哈佛大学丘成桐先生和IBM公司高性能计算的访问学者。中国人民大学2018年优秀课外指导教师、2017年十佳班主任、2016年优秀班主任和优秀学生军训工作者。中国生物信息学会(筹)理事,中国运筹学会计算系统生物学分会理事,中国计算机学会高级会员、生物信息学专业委员,第一、二届中国计算机学会生物信息学大会程序委员,第十、十一届国际系统生物学与生物信息学大会程序委员,2015年11月在中国人民大学负责举办全国生物信息学与计算生物学大会。


在生物信息学方向的科研和教学包括构建数学模型、开发计算方法和应用它们来研究多体超大蛋白质相互作用复合物的结构、网络和动力学等。在机器学习方向利用深度学习和大数据方法设计新的算法框架解决生物大分子和医疗图像的计算。已经发表的SCI学术论文有50多篇,包括理论模型、计算方法和生物应用三部分,发表的杂志包括NatureSciencePNASCell ResearchProteinsScience in China等学术刊物,论文被引用次数已超过2300多次,H指数22。


主持课题:国家自然科学基金面上项目、中国人民大学科学研究基金、国家重点实验室合作项目、国家自然科学基金重点集成项目子课题。

讲授课程:本科的高等代数、数学软件的原理与实践、随机优化和研究生的生物信息学前沿专题、学术论文写作规范与方法等课程。

发表论文:详见学术网页 https://www.researchgate.net/profile/Xinqi_Gong


1.        Daiwen Sun, Xinqi Gong*. Tetramer protein complex interface residue pairs prediction with LSTM combined with graph representations. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 2020. 1868(11):14054. https://doi.org/10.1016/j.bbapap.2020.140504.

2.        Hongmei Yang, Qin Peng, Jun Zhou, Guojun Song, Xinqi Gong*. The unidirectional causality influence of factors on PM2.5 in Shenyang city of China. Scientific Reports. 2020,10: 8403.

3.        Jian Li, William Terzaghi, Yanyan Gong,Congran Li,Jun-Jie Ling, Yangyang Fan1, Nanxun Qin, Xinqi Gong*, Danmeng Zhu*, Xingwang Deng*. Modulation of BIN2 kinase activity by HY5 controls hypocotyl elongation in the light. Nature Communications. 2020. 11(1):1234567890. DOI: 10.1038/s41467-020-15394-7.

4.        He Huang, Xinqi Gong*. A Review of Protein Inter-Residue Distance Prediction. Current Bioinformatics. 2020. DOI: 10.2174/1574893615999200425230056.

5.        Yu Chen, Wei Wang*, Jiale Liu, Jinping Feng, Xinqi Gong*. Protein interface complementarity and gene duplication improve link prediction of protein-protein interaction network. Frontiers in Genetics, section Bioinformatics and Computational Biology. 2020. Frontiers in Genetics, https://doi.org/10.3389/fgene.2020.00291.

6.        Yanfen Lyu, He Huang, Xinqi Gong*. A novel index of contact frequency from noise protein-protein interaction data help for accurate interface residue pair prediction. Interdisciplinary Sciences: Computational Life Sciences. 2020, Mar 17. doi: 10.1007/s12539-020-00364-w.

7.        Zhenni Zhao, Xinqi Gong*. Protein-protein interaction interface residue pair prediction based on deep learning architecture. IEEE-ACM Transactions on Computational Biology and Bioinformatics. 2019: 16(5):1753-1759.

8.        Jiale Liu, Xinqi Gong*. Attention mechanism enhanced LSTM with residual architecture and its application for protein-protein interaction residue pair prediction. BMC Bioinformatics 2019, 20:609, https://doi.org/10.1186/s12859-019-3199-1.

9.        Fang Kong, Xirong Li, Qing Liu, Chuangye Yan, Xinqi Gong*. An automatic particle picking method based on generative adversarial network. Communications in Information and Systems. 2019, 19(3): 321-341.

10.     Lu Su, Linkang Zhou, Fengjung Chen, Huimin Wang, Hui Qian, Yuanyuan Sheng, Yuangang Zhu, Hua Yu, Xinqi Gong, Li’e Cai, etc, & Peng Li*. Cideb controls sterol- regulated ER export of SREBP by promoting cargo loading at ER exit sites. EMBO Journal. 2019, 38(8): e100156.

11.     Zhenni Zhao, Xinqi Gong*. Trimer Protein-Protein Complex Interface Interacting Residue Pairs Prediction Using Deep Learning Approach. ACM bioinformatics conference, NY, USA. 2019, September 7-10.

12.     Qiuhua Liu, Min Fu, Hao Jiang, Xinqi Gong*. Densely Dilated Spatial Pooling Convolutional Network Using Benign Loss Functions for Imbalanced Volumetric Prostate Segmentation. Current Bioinformatics, 2019. http://www.currentbioinformatics.com/articles/178647/Dens.

13.     Yu Chen, Wei Wang*, Rongyan Cai, Jinping Feng, Xinqi Gong. A new and more flexible median ranked set sampling for Horvitz-Thompson estimation of population mean. Mathematics in practice and theory. 2019, 49(20):235-247. (In Chinese)

14.     Xingheng Yu, Xinqi Gong*, Hao Jiang*. Heterogeneous multiple kernel learning for breast cancer outcome prediction. BMC Bioinformatics. 2020. 21:155.

15.     Yu Chen, Wei Wang*, Xinqi Gong*. Maximizing multiple influences and fair seed allocation on multilayer social networks. PLOS ONE. 2020, e0229201. https://doi.org/10.1371/journal.pone.0229201.

16.     Wei Wang, Yongxiao Yang, Jianxin Yin, Xinqi Gong*. Different protein- protein interface patterns predicted by different machine learning methods. Scientific Reports. 2017, 7:16023.

17.     Qiuhua Liu, Min Fu, Hao Jiang, Xinqi Gong*. Densely Dilated Spatial Pooling Convolutional Network Using Benign Loss Functions for Imbalanced Volumetric Prostate Segmentation. Accepted by Current Bioinformatics. DOI:10.2174/1574893615666200127124145.

18.     Min Fu, Wenming Wu, Xiafei Hong, Qiuhua Liu, Jialin Jiang, Yaobin Ou*, Yupei Zhao* & Xinqi Gong*. Hierarchical combinatorial deep learning architecture for pancreas segmentation of medical computed tomography cancer images. BMC Systems Biology. 2018, 12(S4), 56.

19.     Wenzhi Feng, Tong Wu, Xiaoyu Dan, Yuling Chen, Lin Li, She Chen, Di Miao, Haiteng Deng, Xinqi Gong*, Li Yu, Phosphorylation of Atg31 is required for autophagy. Protein Cell 2015,6:288-296.

20.     Jiao Tang, Zhifu Han, Yadong Sun, Heqiao Zhang, Xinqi Gong and Jijie Chai. Sructural basis for recognition of an endogenous peptide by the plant receptor kinase PEPR1. Cell Research 2015, 25:110-120.

21.     Lu Gao, Xiafei Hong, Xiaopeng Guo, Xinqi Gong, Rongrong Chen, Wenying Qiu, Xiaojing Qiao, Jianjiao Ni, Xi Chen, Yanfang Guan, Ling Yang, Renzhi Wang, Yong Yao, Bing Xing. Targeted next-generation sequencing of dedifferentiated chondrosarcoma in the skull base reveals combined TP53 and PTEN mutations with increased proliferation index, an implication for pathogenesis. Oncotarget. 2016, 7(28): 43557-43569.

22.     Simiao Liu, Jizong Wang, Zhifu Han, Xinqi Gong, Heqiao Zhang, Jijie Chai. Molecular Mechanism for Fungal Cell Wall Recognition by Rice Chitin Receptor OsCEBiP. Structure. 2016, 24(7):1192-1200.

23.     Xinqi Gong*, Tingyi Cao. Five Dimensional Feature Space for Protein Binding Site Residue Prediction. Journal of Beijing University of Technology 2017, 43(12):254-3712.

24.     Yongxiao Yang, Xinqi Gong*. A new probability method to understand protein-protein interface formation mechanism at amino acid level. Journal of Theoretical Biology. 2017, doi:10.1016/j.jtbi.2017.09.026.

25.     Yongxiao Yang, Xinqi Gong*. Understanding Protein-Protein Interface Formation Mechanism in a New Probability Way at Amino Acid Level. Lecture Notes in Bioinformatics. 2017, doi: 10.1007/978-3-319-59575- 7_36.

26.     Fangfang Chen, Chunxiao Zhang, Haonan Wu, Yue Ma, Xiaomin Luo, Xinqi Gong, Fan Jiang, Yaoting Gui, Hui Zhang, Fei Lu. The E3 ubiquitin ligase SCF FBXL14 complex stimulates neuronal differentiation by targeting the Notch signaling factor HES1 for proteolysis. Journal of Biological Chemistry. 2017, 292(49):jbc.M117.815001.

27.     Sixue Ren, Antonella Caforio, Qin Yang, Bo Sun, Feng Yu, Xiaofeng Zhu, Jinjing Wang, Chao Dou, Qiuyu Fu, Niu Huang, Qiu Sun, Chunlai Nie, Shiqian Qi, Xinqi Gong, Jianhua He,Yuquan Wei, Arnold JM Driessen, Wei Cheng. Structural and mechanistic insights into the biosynthesis of CDP-archaeol in membranes. Cell Research. 2017,27(11).

28.     Shulin Mou, Xiaoxiao Zhang, Zhifu Han, Jiawei Wang, Xinqi Gong, Jijie Chai. CLE42 binding induces PXL2 interaction with SERK2. Protein Cell. 2017, DOI 10.1007/s13238-017-0435-1.

29.     Shuaihua Gao, Yu Zhou, Weiwei Zhang, Wenhe Wang, You Yu, Yajuan Mu, Hao Wang, Xinqi Gong, Guojun Zheng, Yue Feng. Structural insights into the γ-lactamase activity and substrate enantio-selectivity of an isochorimatase-like hydrolase from Microbacterium hydrocarbonoxydans. Scientific Reports. 2017,7:44542.

30.     Zhuomaji, Xinqi Gong*. Natural distinct inter-preference between genetic codon and protein secondary structure combinations. Communications in Information and Systems. 2018, 18(4): 331-347.

31.     Yongxiao Yang, Wei Wang, Yuan Lou, Jianxin Yin, Xinqi Gong*. Geometric and amino acid type determinants for protein-protein interaction interfaces. Quantitative Biology. 2018, 6(2).

32.     Ni Zhan, Chun Wang, Lichao Chen, Huanjie Yang, Jian Feng, Xinqi Gong, etc, & Jianru, Zuo. S-nitrosylation targets gsno reductase for selective autophagy during hypoxia responses in plants. Molecular Cell. 2018, 71(1):142-154.e6.

33.     Lu Su, Linkang Zhou, Fengjung Chen, Huimin Wang, Hui Qian, Yuanyuan Sheng, Yuangang Zhu, Hua Yu, Xinqi Gong, Li’e Cai, etc, & Peng Li. Cideb controls sterol- regulated ER export of SREBP by promoting cargo loading at ER exit sites. EMBO Journal. 2019, 38(8): e100156.

34.     Panwen Wang+, Xinqi Gong+, Chunhua Li, Weizu Chen, Cunxin Wang. Division of Protein Surface Patches and Its Application in Protein Binding Site Prediction. Acta Physico-Chimica Sinic, 2012, 28:2729-34.

35.     Cunxin Wang, Shan Chang, Xinqi Gong, Feng Yang, Chunhua Li, Weizu Chen. Progress in the Scoring Functions of Protein-Protein Docking. Acta Physico-Chimica Sinica. 2012, 28(4):751-758.

36.     杨峰,曹立彬,龚新奇,常珊,陈慰祖,王存新,李春华. 蛋白质-蛋白质分子对接方法中分子柔性处理与近天然结构筛选的研究. 生物物理学报. 2012, 28(1):15-22. (In Chinese)

37.     Fleishman SJ, etc., Xinqi Gong, etc., Wodak SJ, Janin Joel, Baker David. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. Journal of Molecular Biology. 2011, 414(2):289-302.

38.     Xinqi Gong, Liu Bin, Chang Shan, Cunxin Wang. A holistic molecular docking approach for predicting protein-protein complex structure. Sci China Life Sci. 2010, 53(9):1152-61.

39.     Xinqi Gong, Wang Panwen, Yang Feng, Chang Shan, etc, & Cunxin Wang. Protein-protein docking with binding site patch prediction and network-based terms enhanced combinatorial scoring. Proteins: Structure Function and Bioinformatics. 2010,15;78(15):3150-5.

40.     Shan Chang, Xinqi Gong, Xiong Jiao, Chunhua Li, Weizu Chen, Cunxin Wang. Network analysis of protein-protein interaction. Chinese Science Bulletin. 2010, 55: 814-822.

41.     龚新奇, 刘斌, 常珊, 李春华, 陈慰祖, 王存新. 蛋白质复合物结构预测的集成分子对接方法. 中国科学2009, 39 (10):963-973.

42.     Jianping Hu, Xinqi Gong, Jiguo Su, Weizu Chen, Cunxin Wang. Study on the molecular mechanism of inhibiting HIV-1 integrase by EBR28 peptide via molecular modeling approach. Biophysical chemistry. 2008, 132: 69-80.

43.     Shan Chang, Xiong Jiao, Xinqi Gong, Chunhua Li, Weizu Chen, Cunxin Wang. Evolving model of amino acid networks. Physical Review E. 2008, 77(6): 061920.

44.     Xinqi Gong, Shan Chang, Qinghua Zhang, Chunhua Li, Longzhu Shen, Xiaohui Ma, Minghui Wang, Bin Liu, Hongqiu He, Weizu Chen, Cunxin Wang. A filter enhanced sampling and combinatorial scoring study for protein docking in CAPRI. Proteins: Structure Function and Bioinformatics. 2007, 69(4): 859-865.

45.     Shan Chang, Xiong Jiao, Chunhua Li, Xinqi Gong, Weizu Chen, Cunxin Wang. Amino acid network and its scoring application in protein-protein docking. Biophysical Chemistry. 2008, 134(3):111-8.

46.     Xiaohui Ma, Chunhua Li, Longzhu Shen, Xinqi Gong, Weizu Chen, Cunxin Wang. Biologically Enhanced Sampling Geometric Docking and Backbone Flexibility Treatment with Multiconformational Superposition. Proteins: Structure, Function, and Bioinformatics. 2005, 60: 319-323.

47.     Xiao Ge, Xiang Zhao, Akihisa Nakagawa, Xinqi Gong, Riley Robert Skeen-Gaar, Yong Shi, Haipeng Gong, Xinquan Wang, and Ding Xue. A novel mechanism underlies caspase-dependent conversion of the dicer ribonuclease into a deoxyribonuclease during apoptosis. Cell Research. 2014, 24:218-32.

48.     Yangmeng Wang, etc., Xinqi Gong, Yonggong Zhai, etc., Zhijie Chang. GdX/UBL4A Specifically Stabilizes the TC45/STAT3 Association and Promotes Dephosphorylation of STAT3 to Repress Tumorigenesis. Molecular Cell, 13 February 2014. 10.1016/j.molcel.2014.01.020.

49.     Peilong Lu, Dan Ma, Chuangye Yan, Mingjian Du, Xinqi Gong, Yigong Shi. Structure and mechanism of a eukaryotic transmembrane ascorbate-dependent oxidoreductase. PNAS. 2014, 11(5):1813-1818.

50.     Tian Xie, Wei Peng, Chuangye Yan, Jianping Wu, Xinqi Gong, Yigong Shi. Structural Insights into RIP3-Mediated Necroptotic Signaling. Cell Reports. 2013, 5(1):70-78.

51.     Tingliang Wang, Guobin Fu, Xiaojing Pan, Jianping Wu, Xinqi Gong, Jiawei Wang, Yigong Shi. Structure of a bacterial energy-coupling factor transporter. Nature. 2013, 497:272-276.

52.     Hanchi Yan, Weiyun Huang, Chuangye Yan, Xinqi Gong, Sirui Jiang, Yu Zhao, Jiawei Wang, Yigong Shi. Structure and Mechanism of a Nitrate Transporter. Cell Reports. 2013,3(3):716-723.

53.     Weijiao Huang, Tianyu Jiang, Wooyoung Choi, Shiqian Qi, Yuxuan Pang, Qi Hu, Yanhui Xu, Xinqi Gong, Philip D Jeffrey, Jiawei Wang, Yigong Shi. Mechanistic insights into CED-4-mediated activation of CED-3. Genes & development. 2013, 27(18):2039-48.

54.     Xie Tian, Ren R, Zhang YY, Pang Yuxuan, Yan Chuangye, Xinqi Gong, etc., Nieng Yan. Molecular mechanism for inhibition of a critical component in the Arabidopsis thaliana abscisic acid signal transduction pathways, SnRK2.6, by protein phosphatase ABI1. Journal of Biological Chemistry. 2012, 287(1):794-802.

55.     Xiaochun Li, Shangyu Dang, Chuangye Yan, Xinqi Gong, Jiawei Wang, Yigong Shi. Structure of a presenilin family intramembrane aspartate protease. Nature. 2012, 493:56-61.

56.     Dongxing Guo, Xuanling Shi, Kelly C Arledge, Dingka Song, Liwei Jiang, Lili Fu, Xinqi Gong, Senyan Zhang, Xinquan Wang, Linqi Zhang. A single residue within the V5 region of HIV-1 envelope facilitates viral escape from the broadly neutralizing monoclonal antibody VRC01. J Biol Chem. 2012, 287(51):43170-9.

57.     Linfeng Sun, Xin Zeng, Chuangye Yan, Xiuyun Sun, Xinqi Gong, Yu Rao, Nieng Yan. Crystal structure of a bacterial homologue of glucose transporters GLUT1-4. Nature. 2012, 490:361-366. Nature. 2013, 497:272-276.

58.     Dong Deng, Ping Yin, Chuangye Yan, Xiaojing Pan, Xinqi Gong, Shiqian Qi,Tian Xie, Magdy Mahfouz, Jian-Kang Zhu, Nieng Yan, Yigong Shi. Recognition of methylated DNA by TAL effectors. Cell Research. 2012, 22(10):1502-4.

59.     Cong Yi, Meisheng Ma, etc., Xinqi Gong, etc., Haiteng Deng, Li Yu. Function and molecular mechanism of acetylation in autophagy regulation. Science. 2012, 336:474-477.

60.     He W, Brumos J, Li H, Ji Y, Ke Meng, Xinqi Gong, etc., Yang Z, Stepanova AN, Alonso JM, Guo H. A small-molecule screen identifies L-kynurenine as a competitive inhibitor of TAA1/TAR activity in ethylene-directed auxin biosynthesis and root growth in Arabidopsis. Plant Cell. 2011, 23(11):3944-60.




课题组活动安排:

组   会:每周六晚18:00-20:00,每周三中午12:00-13:00技术午餐会,中国人民大学数学科学研究院(环境楼)316会议室。

羽毛球:每周二晚19:30-21:30,中国人民大学世纪馆。


合作者:刘青、卢志武(计算机);姜昊、欧耀彬、丘成栋(数学);周春来(理论计算);俞立(生物);尹建鑫(统计);宋国君(环境)。

博士生:吕艳芬,赵翠翠、杨红梅、黄鹤、孙黛雯、李佳珊

硕士生:于赞,赵楠,栗晓宇、曾诚实、刘世婕

已毕业:刘一宁(卡内基梅隆)、陶冠华(英国)、王思齐(卡内基梅隆)、薛力荣(普林斯顿)、刘小晴(航天科工)、廖钊坡(清华大学)、肖臻杰、赵珍妮、曹婷颐、卓玛机、付敏(数学合作)、左清瞳(计算机合作)王伟(统计合作)、余幸恒、刘佳乐、施畅、刘秋华、张若靖、张黄涛、田昊坤


招聘:博士后,欢迎数学、计算机、生物和物理等背景的优秀博士应聘,共创科研新成果。

招生:生物信息学、生物数学和机器学习等三个方向招收志向于科学研究的博士生、硕士生和做实习毕业设计的本科生等。

(1)生物信息学方向简介:本招生专业属于应用数学,研究方向是开发新的数学模型和计算方法,并应用它们来计算蛋白质等生物大分子的结构和功能。目前重点关注用复杂网络、图论和统计等知识来构建应用于多体蛋白质相互作用的新模型和新算法。也在开展用压缩感知和机器学习等知识来构建用于超大分子结构的拓扑分析和精确定位的模型和算法。

(2)应用数学方向简介:本招生专业属于应用数学,目前重点关注构建新的微分方程模型来解决分子生物学在系综和个体两种尺度上的脱节难题。在系综水平上,实验操作能调节溶液浓度,而在个体水平上,理论计算能研究单个原子和分子的行为,但它们俩之间的关系还不清楚。我们致力于搭建数学桥梁来融合这两种尺度。

(3)机器学习方向简介:本招生专业属于应用数学,目前重点关注构建新的深度学习算法和图像识别算法来解决多体蛋白质相互作用超大复合物结构和自闭症、胰腺肿瘤的计算和预测等难题。


办公室:中国人民大学数学科学研究院(环境楼)309室

地   址:北京市海淀区中关村大街59号,100872

Email: xinqigong AT ruc.edu.cn

微   信: xinqigong3701