to Jin Gu’s Homepage
Systems Biology Research Group
Jin Gu Ph.D. (古槿), Assistant
MOE Key Laboratory of
Bioinformatics Division / Center for
Synthetic and Systems Biology
Tsinghua University, Beijing 100084,
Email: wellgoo at gmail dot com
Phone (Lab): +86
Fax (Lab): +86
Last Update: Nov. 16, 2015
LRAcluster, a fast tool for unsupervised clustering of large-scale multi-omics
data is accepted for publication by BMC Genomics.
[2015/08/30] Qiuyu Lian and Qianqian
Huang join our research group! Welcome!
MicroRNAs (miRNAs) regulatory networks. MiRNAs, a class
of ~22nt endogenous small regulatory RNAs, play
essential roles in multiple cellular processes. 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, especially in
cancers (BMC Syst Biol
BioSyst 2014). We also work on building reference resources for studying
cancer related miRNAs (oncomiRs) (oncomiRDB,
2) Analyzing and
modeling the regulatory and functional networks in
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 (BMC Syst Biol
BioSyst 2014). Now, we mainly focus on: the methods and tools to
analyze DNA methylation data (FastDMA,
ONE 2013); learning the hidden patterns and deep structures
from large-scale cancer omic data (LRAcluster,
BMC Genomics 2015); and the characteristics of cancer genomic and epigenomic landscapes.
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)
LRAcluster: a low-rank
regularized method for fast dimension reduction and integrative clustering of multi-omics data
a network propagation based method for inferring perturbed miRNA regulatory
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]
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:
PCS: de novo k-mer analysis package (v1.5) [Updated: 2009/10/8]
Applications in Signaling Transduction Research
//Cell Signaling: Fundamental Theory and Practical Techniques [In
Chinese], Edited by Hongyang Wang
Scientific & Technological Education Publisher
Jin Gu, Bo Zhang, Shao Li.
SCT promoter methylation is a highly
discriminative biomarker for lung and many other cancers.
IEEE Life Sciences Letters 2015, Accepted. [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
Fast dimension reduction and integrative
clustering of large-scale multi-omics data using low-rank approximation:
application to cancer molecular classification.
BMC Genomics 2015, Accepted. [Abstract] [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.
2014, 10(12):3249-3254. [Abstract]
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.
2014, 15:255. [Abstract]
Ting Wang, Jin Gu#, Yanda Li.
|OncomiRDB: a database for the experimentally verified
oncogenic and tumor-suppressive microRNAs.
30(15):2237-2238. [Abstract] [Database]
Dongfang Wang, Jin Gu#,
Ting Wang, Zijian Ding.
|Epigenetic modification of
liver tumour-initiating cell properties by targeting Rb binding protein
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,
|Inferring the perturbed microRNA regulatory networks in cancer
using hierarchical gene co-expression signatures.
PLoS ONE 2013,
8(11):e81032. [Abstract] [Software]
|FastDMA: An Infinium
HumanMethylation450 Beadchip Analyzer.
2013, 8(9):e74275. [Abstract]
Dingming Wu, Jin Gu#, Michael Zhang#.
|Imbalanced network biomarkers for traditional Chinese medicine Syndrome
in gastritis patients.
Scientific Reports 2013, 3:1543. [Full
Rui Li, Tao Ma, Jin Gu, Xujun Liang, Shao
|Inferring pathway crosstalk networks using gene set co-expression
Molecular BioSystems 2013, 9(7):1822-1888. [Abstract]
Ting Wang, Jin Gu, Jun Yuan, Ran Tao, Yanda Li, Shao
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.
annotating the cell-type specific gene functional and signaling map in vascular
Molecular BioSystems 2012,
[Database] Jin Gu#, Shao Li#.
network analysis reveals TNF-alpha can promote G1/S transition of cell cycle in
vascular endothelial cells.
Bioinformatics 2012, 28(1):1-4. [Abstract]
Yang Chen*, Jin Gu*, Dan
Li, Shao Li.
responsive gene modules by network-based gene clustering and extending:
application to inflammation and angiogenesis.
BMC Systems Biology 2010, 4:47. [Abstract] [Free_Full
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
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,
Identification of phylogenetically
conserved microRNA cis-regulatory elements across 12 Drosophila species.
Bioinformatics 2008, 24(2):165-171. [Abstract]
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]
Tao He, Fei
Li, Jin Gu, Ruiqiang Li, Fei Li.
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
Mammalian Genome 2006,
17(10):1033-1041. [Abstract] [Full
Jin Gu*, Tao He*, Yunfei
Pei, Fei Li, Jing Zhang, Xiaowo Wang, Xuegong Zhang, Yanda Li.
Identification Based on Sequence and Structure Alignment.
Bioinformatics 2005, 21(18):3610-3614. [Abstract]
Jing Zhang, Fei Li, Jin Gu, Tao He,
Xuegong Zhang, Yanda Li.