Group News

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

[2022/02/10] Nature Cell Biology: decode the MRD of pediatric B-ALL by scRNA-seq & scBCR-seq analyses.
[2022/01/18] JGG: HighlyRegionalGenes: a human-like feature gene selection for scRNA-seq & spatial RNA-seq data. [Software]
[2021/12/18] Science Advances: a high resolution (55um) spatial transcriptome atlas of liver cancer.
[2021/08/04] Hepatology: integrative analysis of large-scale gene expression datasets identifies the CPS1-deficieny HCC subtype.

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

Post Doctoral: Qinglin Mei (2022.01), Wenbo Guo (2022)
PhD Students: Yiran Shan (2018), Xinqi Li (2019), Yanhong Wu (2020), Qifan Hu (2020), Yuxin Miao (2021), Nan Yan (2021), Zeyu Chen (2022), Yuhan Fan (2022)

Master Students: 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), Guiying Wu (2021.04), Wenbo Guo (2022.07)

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), Siyu Bao (2022.07)

Tools, Databases & Datasets

[Software] HiglyRegionalGenes: graph-based gene selection for scRNA-seq & spatial transcriptomics data [Updated: 2022/01/04]
[Software] JEBIN: learning the consensus representations of genes by joint embedding of multiple bipitite networks [Updated: 2021/07/11]
[Software] scCancer: a package for automated processing of single cell RNA-seq data in cancer [Updated: 2020/05/08]

[Software] VASC: a deep variational autoencoder for single cell RNA-seq data analysis [Updated: 2018/08/15]

[Software] LRAcluster: a low-rank regularized method for fast dimension reduction and integrative clustering of multi-omics data [Updated: 2015/09/21]

[Software] NP-miRNA: a network propagation based method for inferring perturbed miRNA regulatory networks [Updated: 2014/06/23]

[Software] FastDMA: an Infinium HumanMethylation450 beadchip (450k DNA methylation array) analyzer [Updated: 2014/05/24]

[Software] miRHiC: enrichment analysis of a set of genes in hierarchical gene co-expression signatures [Updated: 2013/03/19]

[Software] sGSCA: signature-based gene set co-expression analysis (using sparse canonical correlation analysis) [Updated: 2013/11/22]

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

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

[Database] HCCDB: integrative molecular database of hepatocellular carcinoma [Updated: 2018/07/21]
[Database] OncomiRDB: a database for the experimentally verified oncogenic and tumor-suppressive microRNAs [Updated: 2014/03/14]

[Dataset] scRNA-seq & scBCR-seq datasets for the bone marrow of pediatric B-ALL patients and healthy donors (Nature Cell Biology 2022) [Raw]
[Dataset] 10X Visuim Spatial Transcriptomics datasets of liver cancer (Science Advances 2021) [SpatialRanger] [Raw]
[Dataset] Multi-omics datasets for gemcitabine treated pancreatic cancer mouse PDXs (Clinical Cancer Research 2021) [Raw1] [Raw2]
[Dataset] Drug_response: the dataset of clinical drug responses curated from TCGA (Bioinformatics 2016) [Processed]

Selected Publications Since 2016 [Full List @ Google Scholar]

Elucidating minimal residual disease of paediatric B-cell acute lymphoblastic leukaemia by single-cell analysis.

Nature Cell Biology, 2022, 24(2):242-252. [Abstract]
Yingchi Zhang#, Shicheng Wang#, Jingliao Zhang#, Chao Liu#, Xinqi Li#, Wenbo Guo, Yongjuan Duan, Xiaoyan Chen, Suyu Zong, Jiarui Zheng, Yixuan Wu, Xiaoli 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.

Science Advances 2021, 7:eabg3750. [Abstract] [Full Text] [Dataset]
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 Carbamoyl Phosphate Synthetase 1–Deficient HCC Subtype With Therapeutic Potential Through Integrative Genomic and Experimental Analysis.

Hepatology 2021, 74(6):3249-3268. [Abstract] [Database]
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*.

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*.

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*.

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*.

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*.