Welcome
to Jin Gu’s Homepage on
Computational
Systems Biology!
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
Latest Update: Feb 2, 2012
Research
Interests:
1) microRNAs (miRNAs) and
the regulatory networks. MiRNAs are a class
of endogenous regulatory small noncoding RNAs. At
least 30% protein-coding genes are regulated by these tiny molecules. Using
deep sequencing technology, we aim at developing the computational pipeline to
analyze the miRNA expressions. Then, we try to
develop network-based multi-layer association analysis methods (funded by NSFC)
to identify the miRNA sub-networks regulating the
cell phenotypes or diseases.
2) The complex biological networks. We are very interested in
developing new theories and methods to establish the association (may be casual)
between network states and cell/disease phenotypes. It is expected that we can
use network states to explain or predict the disease occurrence and
progression. We are also interested in developing new tools integrating gene
expressions, biological networks and literature information, such as network
clustering-based gene set analysis, gene function prediction and the simplified
equivalent model of biological networks.
3) Developing the integrative computational platform and database
for angiogenesis, inflammation, 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. We welcome the students with good software engineering/programming
background to join our team.
Teaching:
Probabilistic Graphical Models: (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 (v0.3) [Updated:
2010/11/21] (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)
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. Submitted, 2011
Oct.
Journal Papers:
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]
Conference Papers and Posters:
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]