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.

2) Dys-regulated biological networks in cancer development by integrating high-throughput sequencing data. 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 multi-layer gene regulation data produced by high-throughput sequencing technology. Now, we focus on the differentially DNA methylated regions (DMRs) and the corresponding downstream regulatory networks in cancers. These functional DMRs and their directly regulated genes may be highly related to cancer early development stages.

3) Developing the integrative computational platform and database for angiogenesis, inflammation, cancer, etc. Lab-mates have developed dozens of software and databases in network analysis, pathway analysis, literature mining, association analysis, etc. For better maintenance and broader use of these resources, we are developing flexible computational and storage platform to achieve the integration.

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)

Tools and Database

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

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

Mamm miR-EST: the ESTs mapped to the flanking sequences of miRNAs [Updated: 2006/06/22] (Download)

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

Nanno-Angiogenesis: an integrative database for the gene functional and signaling map in vascular endothelial cells [Updated: 2012/05/03] (Browse)

Publications

In Progress (sorted by submission date):

Jin Gu, Shao Li. Towards integrative annotating the cell-type specific gene functional and signaling map in vascular endothelial cells. Molecular BioSystems, 2012 Accepted.

Yang Chen, Jin Gu (co-first author), 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]

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]

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]

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 (co-first author), 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]

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]

Dingming Wu, Michael Q Zhang, Jin Gu. A new gene network clustering algorithm based on minimum spanning tree. The 4th Chinese National Bioinformatics and Systems Biology Conference, 2010, Hangzhou. (Poster)

Ting Wang, Jin Gu, Rui Li, Shiwen Zhao, Yanda Li. Defining gene expression adaptive responses regulated by microRNAs and transcription factors in human umbilical vein endothelial cells. Computational Biology 2010, Suzhou Dushu Lake Conference Center. (Abstract & Oral Presentation)

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]