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Bioinformatics & Systems Biology 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 62786911

 Last Update: Jul 31, 2014


Group News

[2014/05/24] A new version of FastDMA (v1.2.1) is released. The and output formats for region-based analyses are improved. A Win32 version is provided.

[2014/03/18] OncomiRDB, a database for the experimentally verified oncogenic and tumor-suppressive microRNAs, is accepted for publication by Bioinformatics.


Research Interests

1)    MicroRNAs (miRNAs) regulatory networks. MiRNAs, a class of ~22nt endogenous small regulatory RNAs, play essential roles in multiple cellular processes. Most of the annotated protein-coding genes are predicted to be regulated by these tiny molecules through 3'-UTR sequence specific binding sites. Till now, ~1400 miRNAs are identified in human, but most of them are lack of functional annotations. We aim to develop new computational methods and theories to understand the principles of miRNA regulations and their functions during multiple biological processes, such as angiogenesis, inflammation and cancer. Now, we are trying to integrate gene expression data, protein-protein interaction (PPI) network data and miRNA target gene data to infer the dys-regulated miRNA pathways in cancers. We proposed to analyze the miRNA functions based on their target gene modularity in gene co-expression and PPI networks (BMC Syst Biol 2010; Bioinformatics 2012). We also work on building reference resources for studying cancer related miRNAs (oncomiRs) (oncomiRDB, Bioinformatics 2014).

2)    Analyzing and modeling the regulatory and functional networks in cancers. Dys-regulated biological networks (including genetics, epigenetics, transcription regulation and miRNA regulation, etc.) in cancer development provide important information for cancer diagnosis and therapy. We are developing methods to identify the dys-regulated networks by integrating genomic, epigenomic, transcriptomic and proteomic data produced by high-throughput technology. Now, we mainly focus on: the methods and tools to analyze DNA methylation data (FastDMA, PLoS ONE 2013); learning the hidden patterns and deep structures from large-scale cancer omic data; and the characteristics of cancer genomic and epigenomic landscapes.


Teaching

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

Selected Topics in Bioinformatics (Graduate course, Spring 2010, with Dr. Shao Li)


Resources

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

[NEW!!] ClustEx2: finding gene modules based on a set of pre-defined seed genes [Updated: 2013/11/15]

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

[HOT!!] 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]

LQ_Bioinfo: a collection for useful resources in Bioinformatics and Systems Biology [Updated: 2011/10/07] (Click Here)


Publications

Selected Publications:

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. [Abstract] [Software]

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. [Abstract] [Database]

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

Dingming Wu, Jin Gu#, Michael Zhang#. FastDMA: An Infinium HumanMethylation450 Beadchip Analyzer. PLoS ONE 2013, 8(9):e74275. [Abstract] [Software]

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. [Abstract] [Software]

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. [Abstract] [Database]

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. [Abstract] [Full Text] [Software]

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. [Abstract] [Free_Full Text] [Software]

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. [Abstract] [Free Full Text] [Software]

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. [Abstract] [Full Text] [Supplementary Materials]

 

Other Publications:

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 Tumor-Initiating Cells Properties by Targeting Rb Binding Protein 4. Gut 2014, Accepted.

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. [Full Text]

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. [Abstract]

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) [Manuscript] [Nature_Precedings]

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. (Oral Presentation) [Abstract] [Manuscript]

Jin Gu. 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]

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. [Abstract] [Free Full Text]

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. [Abstract] [Full Text]

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. [Abstract] [Free Full Text]