Welcome to Jin Gu’s Homepage

Bioinformatics & Machine Learning Research Group


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Jin Gu Ph.D. (古槿), Assistant Professor

MOE Key Laboratory of Bioinformatics

TNLIST Bioinformatics Division / Center for Synthetic and Systems Biology

Department of Automation

Tsinghua University, Beijing 100084, China

 

Contact Information:

Email: wellgoo at gmail dot com

Phone (Lab): +86 10 62794294-866

Fax (Lab): +86 10 62773552

 Last Update: June 1 (Happy International Children's Day), 2016


Group News

[2016/06/01] The first study for evaluating the molecule-based predictions of clinical drug responses using TCGA data is accepted by Bioinformatics.

[2015/12/01] LRAcluster, a fast tool for integrative clustering of large-scale multi-omics data is published by BMC Genomics.

[2015/08/30] Qiuyu Lian and Qianqian Huang join our research group! Welcome!

 


Research Interests

1)    Bioinformatics & Machine Learning

       Methods for molecule-based cancer classification and stratification (LRAcluster, BMC Genomics 2015)
Biological network analysis (ClustEx: BMC Syst Biol 2010
; NP-miRNA: BMC Bioinformatics 2014)
Bioinformatics tools and resources for cancer genomics  (FastDMA: PLoS ONE 2013; oncomiRDB, Bioinformatics 2014)

2)    Applications to Precision Oncology & Cancer Biology

       Evaluation of the molecule-based clinical drug responses in multiple cancer (Bioinformatics 2016)
Identification of a tumor-suppressive master regulatory network mediated by miR-139-5p
(Mol BioSyst 2014)
Revealing the dynamic interaction between TNF-α & VEGF-A signaling in angiogenesis (Bioinformatics 2012)

 


Teaching

Probabilistic Graphical Models: Principles and Techniques (Graduate core course, from Fall 2011, with Dr Michael Q Zhang)

Introduction to Computational Biology (Graduate course, from Fall 2015, with Dr Xiaowo Wang)

 


Resources

[NEW!!] LRAcluster: a low-rank regularized method 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 DNA 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]

 


Books

Bioinformatics Applications in Signaling Transduction Research
//Cell Signaling: Fundamental Theory and Practical Techniques [In Chinese], Edited by Hongyang Wang

Shanghai: Shanghai Scientific & Technological Education Publisher 2013.
Jin Gu, Bo Zhang, Shao Li.


Publications

Integrative genomic analysis identifies recurrent molecular alterations of metastatic hepatocellular carcinoma.

Submitted.
Jin Gu*, Yanjing Zhu*, Jing Tang, Dingming Wu, Qiuyu Lian, Dongfang Wang, Guiying Wu, Guijuan Luo, Wen Wen, Yang Yang, Zhi John Lu, Lei Chen#, Hongyang Wang#, Michael Q Zhang#


Evaluating the molecule-based prediction of clinical drug responses in cancer.

Bioinformatics 2016, Accepted. [Abstract] [Dataset]
Zijian Ding, Songpeng Zu, Jin Gu#.


Integrative clustering methods of multi-omics data for molecule-based cancer classifications.

Quantitative Biology 2016, 4(1):58-67. [Abstract]
Dongfang Wang, Jin Gu#.


SCT promoter methylation is a highly discriminative biomarker for lung and many other cancers.

IEEE Life Sciences Letters 2015, 1(3):30-33. [Abstract]
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.


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. [Abstract] [Free_Full_Text] [Software]
Dingming Wu, Dongfang Wang, Michael Q Zhang#, Jin Gu#.


Gene module based regulator inference identifying miR-139 as a tumor suppressor in colorectal cancer.

Molecular BioSystems 2014, 10(12):3249-3254. [Abstract] [Free_Full_Text]
Jin Gu*#, Yang Chen*, Huiya Huang, Lingyun Yin, Zhen Xie, Michael Zhang#.


Inferring the perturbed microRNA regulatory networks from gene expression data using a network propagation based method.

BMC Bioinformatics 2014, 15:255. [Abstract] [Software]
Ting Wang, Jin Gu#, Yanda Li.


OncomiRDB: a database for the experimentally verified oncogenic and tumor-suppressive microRNAs.

Bioinformatics 2014, 30(15):2237-2238. [Abstract] [Database]
Dongfang Wang, Jin Gu#, Ting Wang, Zijian Ding.


Epigenetic modification of miR-429 promotes liver tumour-initiating cell properties by targeting Rb binding protein 4.

Gut 2015, 64(1):156-167. [Abstract]
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.


Inferring the perturbed microRNA regulatory networks in cancer using hierarchical gene co-expression signatures.

PLoS ONE 2013, 8(11):e81032. [Abstract] [Software]
Jin Gu#, Zhenyu Xuan.


FastDMA: An Infinium HumanMethylation450 BeadChip analyzer.

PLoS ONE 2013, 8(9):e74275. [Abstract] [Software]
Dingming Wu, Jin Gu#, Michael Zhang#.


Imbalanced network biomarkers for traditional Chinese medicine Syndrome in gastritis patients.

Scientific Reports 2013, 3:1543. [Full Text]
Rui Li, Tao Ma, Jin Gu, Xujun Liang, Shao Li.


Inferring pathway crosstalk networks using gene set co-expression signatures.

Molecular BioSystems 2013, 9(7):1822-1888. [Abstract] [Software]
Ting Wang, Jin Gu, Jun Yuan, Ran Tao, Yanda Li, Shao Li.


Chromatin state and microRNA determine different gene expression dynamics responsive to TNF stimulation.

Genomics 2012, 100(5):297-302. [Abstract]
Ruijuan Li, Weilong Guo, Jin Gu, Michael Q Zhang, Xiaowo Wang.


Towards integrative annotating the cell-type specific gene functional and signaling map in vascular endothelial cells.

Molecular BioSystems 2012, 8(8):2041-2049. [Abstract] [Database]
Jin Gu#, 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. [Abstract] [Full Text] [Software]
Yang Chen*, Jin Gu*, Dan Li, Shao Li.


Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis.

BMC Systems Biology 2010, 4:47. [Abstract] [Free_Full Text] [Software]
Jin Gu, Yang Chen, Shao Li, Yanda Li.


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) [Manuscript] [Nature_Precedings]
Jin Gu.


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. (Oral Presentation) [Abstract] [Manuscript]
Jin Gu, Shao Li, Yang Chen, Yanda Li.


Brief review: frontiers in the computational studies of gene regulations.

Frontier of Electrical Electronic Engineering in China 2008, 3(3):251-259. [Abstract] [Full Text] [Manuscript]
Jin Gu.


Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species.

Bioinformatics 2008, 24(2):165-171. [Abstract] [Free Full Text]
Xiaowo Wang, Jin Gu, Michael Zhang, Yanda Li.


Computational identification of 99 invertebrate microRNAs with comparative genomics.

Tsinghua Science and Technology 2008, 13(4):425-432. [Abstract] [Full Text]
Tao He, Fei Li, Jin Gu, Ruiqiang Li, Fei Li.


Identifications of conserved 7-mers in 3'-UTRs and microRNAs in Drosophila.

BMC Bioinformatics 2007, 8:32. [Abstract] [Free Full Text] [Software]
Jin Gu, Hu Fu, 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. [Abstract] [Full Text] [Supplementary Materials]
Jin Gu*, Tao He*, Yunfei Pei, Fei Li, Jing Zhang, Xiaowo Wang, Xuegong Zhang, Yanda Li.


MicroRNA identification based on sequence and structure alignment.

Bioinformatics 2005, 21(18):3610-3614. [Abstract] [Free Full Text]
Xiaowo Wang, Jing Zhang, Fei Li, Jin Gu, Tao He, Xuegong Zhang, Yanda Li.