Bioinformatics & Intelligent Information Processing Research Group @ Information Science

生物信息学与智能信息处理研究小组

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古槿 工学博士, 博导

生物信息学教育部重点实验室

清华信息国家实验室生物信息学研究部

清华大学自动化系 北京 100084

 

联系方式

电子邮件: jgu@tsinghua.edu.cn

电话: +86 10 62794294866

传真: +86 10 62773552

学术博客: 科学网博客

 


 

主要研究方向

1)    生物信息学与机器学习

        单细胞转录组数据分析 (SCRL, NAR 2017)

        基于海量组学信息的癌症分型和分层 (LRAcluster, BMC Genomics 2015)

        生物网络分析 (ClustEx, BMC Syst Biol 2010; NP-miRNA, BMC Bioinformatics 2014)

        癌症基因组研究工具与资源  (FastDMA, PLoS ONE 2013; oncomiRDB, Bioinformatics 2014)

 

2)    精准肿瘤学与癌症生物学(应用案例)

        建立随机重采样的计算框架,评价基于分子信息的抗癌药物临床响应的预测性能 (Bioinformatics 2016) (博文)

        利用基因模块与主要调控因子分析,发现具有抑癌作用的miR-139-5p调控子网 (Mol BioSyst 2014)

        基于动态基因模块分析,揭示在血管新生过程中TNF-αVEGF-A信号的动态协同作用 (Bioinformatics 2012)

 


 

开设课程
 

概率图模型理论与方法(研究生专业基础课, 2011秋季学期起)

计算分子生物学导论(研究生专业课, 2015秋季学期起)

2017年秋季学期开发交流时间:每周五上午1000~1130,地点:FIT大楼1-112C

 


 

研究小组成员
 

博士研究生: 王东方(2016级)、武桂英(2014/联合指导)、连秋宇(2015/联合指导) 、郭文博(2017级)

硕士研究生: 黄倩倩(2015/联合指导)、冯晨(2016级)、王事成(2017级)

 

已毕业研究生:王霆(博士/2014.7)、武丁明(博士/2016.1)、丁子建(博士/2017.7)、张谷超(硕士/2017.7

 


 

工具软件与数据库

HCCDB: expression atlas of hepatocellular carcinoma [Updated: 2016/11/02 (v1.21)]
Drug_response: the dataset of clinical drug responses curated from TCGA [Updated: 2016/04/28]

LRAcluster: a low-rank regularized model for fast dimension reduction and integrative clustering of multi-omics data [Updated: 2015/09/21]

NP-miRNA: a network propagation based method for inferring perturbed miRNA regulatory networks [Updated: 2014/06/23]

OncomiRDB: a database for the experimentally verified oncogenic and tumor-suppressive microRNAs [Updated: 2014/03/14]

FastDMA: an Infinium HumanMethylation450 beadchip (450k methylation array) analyzer [Updated: 2014/05/24]

miRHiC: enrichment analysis of a set of genes in hierarchical gene co-expression signatures [Updated: 2013/03/19]

sGSCA: signature-based gene set co-expression analysis (using sparse canonical correlation analysis) [Updated: 2013/11/22]

ClustEx: responsive gene module identification package (v0.32) [Updated: 2012/05/03]

PCS: de novo k-mer analysis package (v1.5) [Updated: 2009/10/8]

 


 

主要论文(按发表时间排序)
 

Xiangyu Li, Weizheng Chen, Yang Chen, Xuegong Zhang, Jin Gu#, Michael Q Zhang#. Network embedding based representation learning for single cell RNA-seq data. Nucleic Acids Research 2017, 45(19):e166.

Xi-Meng Lin*, Liang Hu*, Jin Gu*, Ruo-Yu Wang*, Liang Li, Jing Tang, Bao-Hua Zhang, Xing-Zhou Yan, Yan-Jing Zhu, Cong-Li Hu, Wei-Ping Zhou, Shao Li, Jing-Feng Liu, Frank J Gonzalez, Meng-Chao Wu, Hong-Yang Wang#, Lei Chen#. Choline kinase alpha mediates interactions between the epidermal growth factor receptor and mTORC2 in hepatocellular carcinoma cells to promote drug resistance and xenograft tumor progression. Gastroenterology 2017, 152:1187-1202.

Yang Yang*, Lei Chen*#, Jin Gu*, Hanshuo Zhang*, Jiapei Yuan, Qiuyu Lian, Gui-Shuai Lv, Siqi Wang, Yang Wu, Yucheng Yang, Dongfang Wang, Yang Liu, Jing Tang, Guijuan Luo, Yang Li, Long Hu, Xinbao Sun, Dong Wang, Mingzhou Guo, Qiaoran Xi, Jianzhong Xi, Hongyang Wang#, Michael Q Zhang#, Zhi John Lu#. Recurrently deregulated lncRNAs in hepatocellular carcinoma. Nature Communications 2017, 8:14421.

Zijian Ding, Songpeng Zu, Jin Gu#. Evaluating the molecule-based prediction of clinical drug responses in cancer. Bioinformatics 2016, 32(19):2891-2895.

Dongfang Wang, Jin Gu#. Integrative clustering methods of multi-omics data for molecule-based cancer classifications. Quantitative Biology 2016, 4(1):58-67.

Dingming Wu, Dongfang Wang, Michael Q Zhang#, Jin Gu#. Fast dimension reduction and integrative clustering of large-scale multi-omics data using low-rank approximation: application to cancer molecular classification. BMC Genomics 2015, 16:1022.

Jin Gu*#, Yang Chen*, Huiya Huang, Lingyun Yin, Zhen Xie, Michael Q Zhang#. Gene module based regulator inference identifying miR-139 as a tumor suppressor in colorectal cancer. Molecular BioSystems 2014, 10(12):3249-3254.

Ting Wang, Jin Gu#, Yanda Li. Inferring the perturbed microRNA regulatory networks from gene expression data using a network propagation based method. BMC Bioinformatics 2014, 15:255.

Dongfang Wang, Jin Gu#, Ting Wang, Zijian Ding. OncomiRDB: a database for the experimentally verified oncogenic and tumor-suppressive microRNAs. Bioinformatics 2014, 30(15):2237-2238.

Jin Gu#, Zhenyu Xuan. Inferring the perturbed microRNA regulatory networks in cancer using hierarchical gene co-expression signatures. PLoS ONE 2013, 8(11):e81032.

Dingming Wu, Jin Gu#, Michael Zhang#. FastDMA: An Infinium HumanMethylation450 BeadChip analyzer. PLoS ONE 2013, 8(9):e74275.

Jin Gu#, Shao Li#. Towards integrative annotating the cell-type specific gene functional and signaling map in vascular endothelial cells. Molecular BioSystems 2012, 8(8):2041-2049.

Yang Chen*, Jin Gu*, Dan Li, Shao Li. Time-course network analysis reveals TNF-alpha can promote G1/S transition of cell cycle in vascular endothelial cells. Bioinformatics 2012, 28(1):1-4.

Jin Gu, Yang Chen, Shao Li, Yanda Li. Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis. BMC Systems Biology 2010, 4:47.

Jin Gu, Hu Fu, Xuegong Zhang, Yanda Li. Identifications of conserved 7-mers in 3'-UTRs and microRNAs in Drosophila. BMC Bioinformatics 2007, 8:32.

Jin Gu*, Tao He*, Yunfei Pei, Fei Li, Jing Zhang, Xiaowo Wang, Xuegong Zhang, Yanda Li. Primary transcripts and expressions of mammal intergenic microRNAs detected by mapping ESTs to their flanking sequences. Mammalian Genome 2006, 17(10):1033-1041.


 

其它论文(按发表时间排序)
 

张学工, 江瑞, 汪小我, 古槿, 陈挺. 从生物大数据到知识大发现: 十年进展与未来展望. 科学通报 2016, 61(36): 3869-3877.

Adwait Sathe, Yu-An Zhang, Xiaotu Ma, Pradipta Ray, Daniela Cadinu, Yi-Wei Wang, Xiao Yao, Xiaoyun Liu, Hao Tang, Yunfei Wang, Ying Huang, Changning Liu, Jin Gu, Martin Akerman, Yifan Mo, Chao Cheng, Zhenyu Xuan, Lei Chen, Guanghua Xiao, Yang Xie, Luc Girard, Hongyang Wang, Stephen Lam, Ignacio I Wistuba, Li Zhang, Adi F Gazdar, Michael Q Zhang. SCT promoter methylation is a highly discriminative biomarker for lung and many other cancers. IEEE Life Sciences Letters 2015, 1(3):30-33.

Liang Li, Jing Tang, Baohua Zhang, Wen Yang, Gaomiyang Liu, Ruoyu Wang, Yexiong Tan, Jianling Fan, Yanxin Chang, Jing Fu, Feng Jiang, Caiyang Chen, Yingcheng Yang, Jin Gu, Dingming Wu, Linna Guo, Dan Cao, Hengyu Li, Guangwen Cao, Mengchao Wu, Michael Q Zhang, Lei Chen, Hongyang Wang. Epigenetic modification of miR-429 promotes liver tumour-initiating cell properties by targeting Rb binding protein 4. Gut 2015, 64(1):156-167.

Rui Li, Tao Ma, Jin Gu, Xujun Liang, Shao Li. Imbalanced network biomarkers for traditional Chinese medicine syndrome in gastritis patients. Scientific Reports 2013, 3:1543.

Ting Wang, Jin Gu, Jun Yuan, Ran Tao, Yanda Li, Shao Li. Inferring pathway crosstalk networks using gene set co-expression signatures. Molecular BioSystems 2013, 9(7):1822-1888.

Ruijuan Li, Weilong Guo, Jin Gu, Michael Q Zhang, Xiaowo Wang. Chromatin state and microRNA determine different gene expression dynamics responsive to TNF stimulation. Genomics 2012, 100(5):297-302.

Jin Gu. A multiple-instance scoring method to predict tissue-specific cis-regulatory motifs and regions. The International MultiConference of Engineers and Computer Scientists (IMECS'10) 2010, Vol I:186-190. (Oral Presentation)

Jin Gu, Shao Li, Yang Chen, Yanda Li. Integrative computational identifications of the signaling pathway network related to TNF-alpha stimulus in vascular endothelial cells. International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing (IJCBS'09) 2009, 422-427.

Jin Gu. Brief review: frontiers in the computational studies of gene regulations. Frontier of Electrical Electronic Engineering in China 2008, 3(3):251-259.

Xiaowo Wang, Jin Gu, Michael Zhang, Yanda Li. Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species. Bioinformatics 2008, 24(2):165-171.

Tao He, Fei Li, Jin Gu, Ruiqiang Li, Fei Li. Computational identification of 99 invertebrate microRNAs with comparative genomics. Tsinghua Science and Technology 2008, 13(4):425-432.

Xiaowo Wang, Jing Zhang, Fei Li, Jin Gu, Tao He, Xuegong Zhang, Yanda Li. MicroRNA identification based on sequence and structure alignment. Bioinformatics 2005, 21(18):3610-3614.


 

学术大会口头报告
 

单细胞基因表达数据的低维表示. 第六届青年生物信息PI研讨会 (西安), 2017/09.

癌症组学数据的低维表示. 生物信息学与智能信息处理2017学术年会 (上海), 2017/06.

肝癌基因表达图谱构建与分析. 中国生物工程学会第二届青年科技论坛暨首届青年工作委员会学术年会 (广州), 2017/04.

基于分子特征预测化疗药物临床响应的性能评价. 生物信息学与智能信息处理2016学术年会 (长春), 2016/07.

Integrative clustering of cancer multi-omics data. CSHA/AACR Joint Meeting: Big Data, Computation and Systems Biology in Cancer (Suzhou), 2015/12.

Integrative analysis of heterogeneous and high-dimensional cancer-ome. 生物信息学与智能信息处理2015学术年会 (厦门), 2015/06.

LRAcluster: fast dimension reduction of multi-omics data using low-rank approximation for cancer molecular classification. 第二届全国计算生物学与生物信息学学术会议 (北京), 2015/04.

差异基因表达模块及其在血管新生等过程中的应用, 全国生物信息学联合会议 (西安), 2012/05.