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#.

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#.

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#.

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#.

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*.

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#.

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#.

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#.

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#.

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#.

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.

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.

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.

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.

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.