Group News

[Announcement] Open Positions for Post Doctoral Research Fellows on Bioinformatics and Medicine!

[2021/08/04] Hepatology: the publication of our work about big omics data based CPS1-deficieny HCC subtype identification and analysis!

[2021/06/13] Clincial Cancer Research: the publication of our work about the gemcitabine resistance in pancreatic cancer by multi-omics analysis!

[2020/07/06] Briefings in Bioinformatics: The paper about the fantastic scRNAseq analysis package for cancer, scCancer, get online published!

Research Interests

1) Large-scale omics data processing and analysis

2) Biological systems modeling and network analysis

3) Applications to precision oncology

4) Databases and tools

Teaching

Probabilistic Graphical Models: Principles and Techniques (Graduate core course, from Fall 2011)

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), Yuxin Miao (2021), Nan Yan (2021)

Master Students: 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 (2020.07)

Graduated Master Students: Guchao Zhang (2017.07), Qianqian Huang (2018.07), Chen Feng (2019.07), Wenfang Guan (2019.07), Shicheng Wang (2020.07), Changyi Liu (2021.07)

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]

Journal Publications Since 2016 [Full List @ Google Scholar]

Elucidating minimal residual disease of pediatric B cell acute lymphoblastic leukemia by single cell analysis.

In Revision on Nature Cell Biology.
Yingchi Zhang#, Shicheng Wang#, Jingliao Zhang#, Chao Liu#, Xinqi Li#, Wenbo Guo, Yongjuan Duan, Suyu Zong, Jiarui Zheng, Yixuan Wu, Xiaoli Chen, Xiaoyan Chen, Xuelian Cheng, Yanxia Chang, Yue Wang, Feng Ding, Wenyu Yang, Xiaojuan Chen, Ye Guo, Li Zhang, Yumei Chen, Yao Zou, Xiaofan Zhu*, Jin Gu*, Tao Cheng*.

Comprehensive analysis of spatial architecture in primary liver cancer.

In Revision on Science Advances. [BioRvix: https://doi.org/10.1101/2021.05.24.445446]
Rui Wu#, Wenbo Guo#, Xinyao Qiu#, Shicheng Wang, Chengjun Sui, Qiuyu Lian, Jianmin Wu, Yiran Shan, Zhao Yang, Shuai Yang, Tong Wu, Kaiting Wang, Yanjing Zhu, Shan Wang, Changyi Liu, Yangqianwen Zhang, Bo Zheng, Zhixuan Li, Yani Zhang, Siyun Shen, Yan Zhao, Wenwen Wang, Jinxia Bao, Ji Hu, Xuan Wu, Xiaoqing Jiang, Hongyang Wang*, Jin Gu*, Lei Chen*.

Discovery of a CPS1-deficient HCC subtype with therapeutic potential via integrative genomic and experimental analysis.

Hepatology 2021, Advanced Access. [Abstract]
Tong Wu#, Guijuan Luo#, Qiuyu Lian#, Chengjun Sui#, Jing Tang#, Yanjing Zhu, Bo Zheng, Zhixuan Li, Yani Zhang, Yangqianwen Zhang, Jinxia Bao, Ji Hu, Siyun Shen, Zhao Yang, Jianmin Wu, Kaiting Wang, Yan Zhao, Shuai Yang, Shan Wang, Xinyao Qiu, Wenwen Wang, Xuan Wu, Hongyang Wang*, Jin Gu*, Lei Chen*.

Integrative genomic analysis of gemcitabine resistance in pancreatic cancer by patient-derived xenograft models.

Clinical Cancer Research 2021, 27:3383-3396. [Abstract] [Dataset]
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 2021, 22(3):bbaa127. [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*.