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龔新奇
時間:2015-01-19  浏覽:16899次

數學智能應用實驗室

MIALAB

(Mathematical Intelligence Application)



龔新奇,唐人娱乐教授、博士生導師,清華大學結構生物學高精尖創新中心合作研究員。開展生物信息學和應用數學的科研和教學。教育經曆有本科畢業于北京航空航天大學和博士畢業于北京工業大學(博士導師:王存新教授),並在清華大學從事博士後研究(合作導師:施一公教授)。哈佛大學丘成桐先生和IBM公司高性能計算的訪問學者。中國人民大學2018年優秀課外指導教師、2017年十佳班主任、2016年優秀班主任和優秀學生軍訓工作者。中國計算機學會高級會員、生物信息學專業委員,第一、二屆中國計算機學會生物信息學大會程序委員,第十、十一屆國際系統生物學與生物信息學大會程序委員,2015年11月在中國人民大學負責舉辦全國生物信息學與計算生物學大會。


在生物信息學方向的科研和教學包括構建數學模型、開發計算方法和應用它們來研究多體超大蛋白質相互作用複合物的結構、網絡和動力學等。在機器學習方向利用深度學習和大數據方法設計新的算法框架解決生物大分子和醫療圖像的計算。已經發表的SCI學術論文有50多篇,包括理論模型、計算方法和生物應用三部分,發表的雜志包括NatureSciencePNASCell ResearchProteinsScience in China等學術刊物,論文被引用次數已超過2300多次,H指數22。


主持課題:國家自然科學基金面上項目、中國人民大學科學研究基金、國家重點實驗室合作項目、國家自然科學基金重點集成項目子課題。

講授課程:本科的高等代數、數學軟件的原理與實踐、隨機優化和研究生的生物信息學前沿專題、學術論文寫作規範與方法等課程。

發表論文:詳見学术网页 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,龔新奇,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.     龔新奇, 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.




課題組活動安排:

组   会:每周六晚18:00-20:00,每周三中午12:00-13:00技术午餐会,中国人民大学數學科學研究院(環境樓)316會議室。

羽毛球:每周二晚19:30-21:30,中國人民大學世紀館。


合作者:劉青、盧志武(計算機);姜昊、歐耀彬、丘成棟(數學);周春來(理論計算);俞立(生物);尹建鑫(統計);宋國君(環境)。

博士生:呂豔芬,趙翠翠、楊紅梅、黃鶴、孫黛雯、李佳珊

碩士生:于贊,趙楠,栗曉宇、曾誠實、劉世婕

已畢業:劉一甯(卡內基梅隆)、陶冠華(英國)、王思齊(卡內基梅隆)、薛力榮(普林斯頓)、劉小晴(航天科工)、廖钊坡(清華大學)、肖臻傑、趙珍妮、曹婷頤、卓瑪機、付敏(數學合作)、左清瞳(計算機合作)王偉(統計合作)、余幸恒、劉佳樂、施暢、劉秋華、張若靖、張黃濤、田昊坤


招聘:博士後,歡迎數學、計算機、生物和物理等背景的優秀博士應聘,共創科研新成果。

招生:生物信息學、生物數學和機器學習等三個方向招收志向于科學研究的博士生、碩士生和做實習畢業設計的本科生等。

(1)生物信息學方向簡介:本招生專業屬于應用數學,研究方向是開發新的數學模型和計算方法,並應用它們來計算蛋白質等生物大分子的結構和功能。目前重點關注用複雜網絡、圖論和統計等知識來構建應用于多體蛋白質相互作用的新模型和新算法。也在開展用壓縮感知和機器學習等知識來構建用于超大分子結構的拓撲分析和精確定位的模型和算法。

(2)應用數學方向簡介:本招生專業屬于應用數學,目前重點關注構建新的微分方程模型來解決分子生物學在系綜和個體兩種尺度上的脫節難題。在系綜水平上,實驗操作能調節溶液濃度,而在個體水平上,理論計算能研究單個原子和分子的行爲,但它們倆之間的關系還不清楚。我們致力于搭建數學橋梁來融合這兩種尺度。

(3)機器學習方向簡介:本招生專業屬于應用數學,目前重點關注構建新的深度學習算法和圖像識別算法來解決多體蛋白質相互作用超大複合物結構和自閉症、胰腺腫瘤的計算和預測等難題。


办公室:唐人娱乐(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