Welcome to Jin Gu’s Homepage
Bioinformatics
& Intelligent Information Processing Research Group
Group
News
[Announcement]
Open Positions for Post Doctoral
Research Fellows on Bioinformatics and Medicine!
[2020/05/25] The paper about the
fantastic scRNAseq analysis package for cancer,
scCancer, get
accepted!
[2020/04/25] Congratulations to
the acceptance of our work about the spatial immune heterogeneity in HCC.
[2020/04/14] Congratulations to
lab's first ISMB paper about CITE-sort for analyzing CITE-seq data.
[2019/08/16] Awarded by NSFC for
Excellent Young Scholar!
Research
Interests
1)
Methods & Algorithms
Methods
for scRNA-seq data (SRCL, Nucleic Acids Res
2017; VASC, GPB 2018)
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)
2) Applications to
Precision Oncology & Cancer Biology
HCC
spatial immune microenvironment analysis identifies CD4+CD8+ T cells
enriched in tumor leading edge (Advanced
Science 2020)
A
large-scale DNA methylation analysis identifies candidate epigenetic markers
and drivers of HCCs (Briefings
in Bioinformatics 2018)
Evaluation of the molecule-based clinical drug responses in multiple cancer (Bioinformatics
2016)
3) Databases & Tools
scCancer: a package for automated processing of single cell RNA-seq
data in cancer (Briefings
in Bioinformatics 2020)
HCCDB:
integrative molecular database of hepatocellular carcinoma (GPB 2018)
OncomiRDB: a database for the experimentally verified oncogenic and
tumor-suppressive microRNAs (Bioinformatics
2014)
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)
Group
Members
PhD Students:
Guiying Wu (2014),
Wenbo Guo (2017), Yiran Shan (2018), Xinqi Li (2019), Yanhong Wu (2020), Qifan
Hu (2020)
Master Students:
Changyi Liu (2018),
Siyu Bao (2019), Jinyan Li (2020)
Graduated PhD Students: Ting Wang (2014.07),
Dingming Wu (2016.01),
Zijian Ding (2017.07), Dongfang Wang (2019.07),
Qiuyu Lian (2020.08)
Graduated Master Students: Guchao Zhang (2017.07), Qianqian Huang
(2018.07), Chen Feng (2019.07),
Wenfang Guan (2019.07), Shicheng Wang (2020.07)
Resources
scCancer:
a package for automated processing of single cell RNA-seq data in cancer
[Updated: 2020/05/08]
VASC:
a deep variational autoencoder for single cell RNA-seq data analysis
[Updated: 2018/08/15]
HCCDB: integrative molecular database of
hepatocellular carcinoma [Updated: 2018/07/21]
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]
Publications
Integrative genomic analysis of gemcitabine resistance in pancreatic cancer
by patient-derived xenograft models.
Clinical Cancer Research, In Revision.
Gang Yang, Wenfang Guan, Zhe Cao, Wenbo Guo, Guangbing Xiong, Fangyu Zhao,
Mengyu Feng, Jiangdong Qiu, Yueze Liu, Michael Q Zhang, Lei You, Taiping
Zhang, Yupei Zhao, Jin Gu.
|
scCancer: a package for automated processing of single cell RNA-seq data in
cancer.
Briefings in
Bioinformatics 2020 (Published Online). [Abstract] [Software]
Wenbo Guo, Dongfang Wang, Shicheng Wang, Yiran Shan, Changyi Liu,
Jin Gu#.
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Artificial-cell-type aware cell type classification in CITE-seq.
Bioinformatics 2020, 36(S1):i542-i550. (ISMB 2020)
[Full Text]
Qiuyu Lian*, Hongyi Xin*, Jianzhu Ma, Liza Konnikova, Wei Chen#,
Jin Gu#, Kong Chen#.
|
Trajectory and
functional analysis of PD-1high CD4+CD8+ T cells in hepatocellular carcinoma
by single-cell cytometry and transcriptome sequencing.
Advanced Science
2020, 7(13):2000224. [Full
Text]
Bo Zheng*, Dongfang Wang*, Xinyao Qiu*, Guijuan Luo*, Tong Wu,
Shuai Yang, Zhixuan Li, Yanjing Zhu, Xuan Wu, Shan Wang, Ziqi Gu, Siyun
Shen, Seogsong Jeong, Rui Wu, Yang Ge, Jin Gu#, Hongyang Wang#, Lei
Chen#.
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Targeted
sequencing reveals mutational landscape responsible for sorafenib therapy in
advanced hepatocellular carcinoma.
Theranostics 2020,
10(12):5384-5397. [Abstract]
Jing Tang*, Cheng-Jun Sui*, Dong-Fang Wang*, Xin-Yuan Lu*, Gui-Juan
Luo, Qing Zhao, Qiuyu Lian, Seogsong Jeong, Xi-Meng Lin, Yan-Jing
Zhu, Bo Zheng, Rui Wu, Qing Wang, Xiao-Long Liu, Jing-Feng Liu, Qiang Xia,
Gang Wu, Jin Gu#, Hong-Yang Wang#, Lei Chen#.
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Hexosamine
pathway inhibition overcomes pancreatic cancer resistance to gemcitabine
through Unfolded Protein Response and EGFR-Akt pathway modulation.
Oncogene 2020, 39(20):4103-4117. [Abstract]
Francesca Ricciardiello*, Yang Gang*, Roberta Palorini, Quanxiao Li, Marco
Giampà, Fangyu Zhao, Lei You, Barbara La Ferla, Humberto De Vitto,
Wenfang Guan, Jin Gu, Taiping Zhang#, Yupei Zhao#, Ferdinando
Chiaradonna#.
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Integrative molecular anlaysis of metastatic
hepatocellular carcinoma.
BMC Medical Genomics 2019, 12:164. [Abstract]
Dongfang Wang#, Yanjing Zhu#, Jing Tang, Qiuyu Lian, Guijuan
Luo, Wen Wen, Michael Q Zhang, Hongyang Wang*, Lei Chen*, Jin Gu*.
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Effects of somatic alterations at pathway
level are more mechanism-explanatory and clinically applicable to quantity
of liver metastases of colorectal cancer.
Cancer Medicine 2019, 8(10):4732-4742. [Abstract]
Zhong-guo Zhang, Fei Ma, Shuang Zhao, Xiaoyu Yang, Fang Liu, Chenghai Xue,
Liren Liu#, Jin Gu#, Haozhe Piao#.
|
VASC:
dimension reduction and visualization of single cell RNA sequencing data by
deep variational autoencoder.
Genomics, Proteomics & Bioinformatics
2018, 16(5):320-331. [Abstract]
[Software]
Dongfang Wang, Jin Gu#.
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ClustEx2: gene
module identification using density-based network hierarchical clustering.
Proceedings of 2018
Chinese Automation Congress
(CAC), Xi'An, 2018, 2407-2412. [Abstract]
Zijian Ding, Wenbo Guo, Jin Gu#.
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HCCDB: a database
of hepatocellular carcinoma expression atlas.
Genomics, Proteomics &
Bioinformatics 2018, 16(4):269-275. [Abstract] [Database]
Qiuyu Lian*, Shicheng Wang*, Guchao Zhang, Dongfang Wang, Guijuan Luo, Jing
Tang, Lei Chen#, Jin Gu#.
|
Genome-wide DNA
methylation analysis identifies candidate epigenetic markers and drivers of
hepatocellular carcinoma.
Briefings
in Bioinformatics 2018, 19(1):101-108. [Abstract] [Dataset]
Yongchang Zheng*, Qianqian Huang*, Zijian Ding, Chenghai Xue,
Tingting Liu, Xinting Sang, Jin Gu#.
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Network embedding
based representation learning for single cell RNA-seq data.
Nucleic
Acids Research 2017, 45(19):e166. [Abstract]
Xiangyu Li, Weizheng Chen, Yang Chen, Xuegong Zhang, Jin Gu#,
Michael Q Zhang#.
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Choline kinase
alpha mediates interactions between the epidermal growth factor receptor
and mTORC2 in hepatocellular carcinoma cells to promote drug resistance and
xenograft tumor progression.
Gastroenterology
2017, 152:1187-1202. [Abstract]
Xi-Meng Lin*, Liang Hu*, Jin Gu*, Ruo-Yu Wang*, Liang Li, Jing Tang,
Bao-Hua Zhang, Xing-Zhou Yan, Yan-Jing Zhu, Cong-Li Hu, Wei-Ping Zhou, Shao
Li, Jing-Feng Liu, Frank J Gonzalez, Meng-Chao Wu, Hong-Yang Wang#, Lei
Chen#
|
Recurrently
deregulated lncRNAs in hepatocellular carcinoma.
Nature
Communications 2017, 8:14421. [Abstract]
Yang Yang*, Lei Chen*#, Jin Gu*, Hanshuo Zhang*, Jiapei Yuan, Qiuyu
Lian, Gui-Shuai Lv, Siqi Wang, Yang Wu, Yucheng Yang, Dongfang Wang,
Yang Liu, Jing Tang, Guijuan Luo, Yang Li, Long Hu, Xinbao Sun, Dong Wang,
Mingzhou Guo, Qiaoran Xi, Jianzhong Xi, Hongyang Wang#, Michael Q Zhang#,
Zhi John Lu#
|
How will big
pictures emerge from a sea of biological data? (In Chinese)
Chin
Sci Bull 2016, 61(36):3869-3877. [Abstract]
Xuegong Zhang#, Rui Jiang, Xiaowo Wang, Jin Gu, Tim Chen
|
Evaluating the
molecule-based prediction of clinical drug responses in cancer.
Bioinformatics
2016, 32(19):2891-2895. [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.
|
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.
|
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#.
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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.
|
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]
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.
|
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.
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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.
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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.
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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.
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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.
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