Group News

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

[2024/12/13] Genome Biology: scStateDynamics: deciphering the drug-responsive tumor cell state dynamics by modeling single-cell level expression changes.
[2024/05/10] Nature Communications: develop a patient-specific lung cancer assembloid model with heterogeneous tumor microenvironments.

Research Interests

1) Large-scale omics data processing and analysis

2) Multi-scale molecular portrait for precision oncology

3) Cancer systems dynamics & cancer cybernetics

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: Xinqi Li (2019), Yanhong Wu (2020), Qifan Hu (2020), Yuxin Miao (2021), Nan Yan (2021), Zeyu Chen (2022), Yuhan Fan (2022), Zikang Yin (2023), Yuman Li (2024)

Master Students: Yifan Sun (2023), Jingmin Huang (2024)

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), Yiran Shan (2023.07)

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), Jinyan Li (2023.07)

Tools, Databases & Datasets

HOT!! [Software] scStateDynamics: deciphering the drug-responsive tumor cell state dynamics by modeling single-cell level expression changes [Updated: 2024/11/23]

[Software] scCancer2: supervised and in-depth annotations of the tumor microenvironment [Updated: 2023/08/23]

[Software] TIST: Transcritpome and histopathological Image integrative analysis for Spatial Transcriptomics [Updated: 2022/07/25]
[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]

HOT!! [Database] uniLIVER: a unified human liver cell atlas for cell state mapping [Updated: 2023/08/31]
HOT!! [Database] HCCDBv2: decompose the expression variations by scRNA-seq and spatial transcriptomics in HCC [Updated: 2023/06/18]
[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]

HOT!! [Dataset] scRNA-seq dataset for the normal pituitary gland and pituitary neuroendocrine tumors (Genome Medicine 2024) [Processed] [Raw]

[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 2020 [Full List @ Google Scholar]

scStateDynamics: deciphering the drug-responsive tumor cell state dynamics by modeling single-cell level expression changes.

Genome Biology 2024, 25:297 [Abstract] [Software]
Wenbo Guo, Xinqi Li, Dongfang Wang, Nan Yan, Qifan Hu, Fan Yang, Xuegong Zhang, Jianhua Yao*, Jin Gu*.

A patient-specific lung cancer assembloid model with heterogeneous tumor microenvironments.

Nature Communications 2024, 15:3382 [Abstract]
Yanmei Zhang#, Qifan Hu#, Yuquan Pei#, Hao Luo, Zixuan Wang, Xinxin Xu, Qing Zhang, Jianli Dai, Qianqian Wang, Zilian Fan, Yongcong Fang, Min Ye, Binhan Li, Mailin Chen, Qi Xue, Qingfeng Zheng, Shulin Zhang, Miao Huang, Ting Zhang, Jin Gu*, Zhuo Xiong*.

Region-specific cellular and molecular basis of liver regeneration after acute pericentral injury.

Cell Stem Cell 2024, 31(3):341-358 [Abstract]
Shuyong Wang#, Xuan Wang#, Yiran Shan#, Zuolong Tan, Yuxin Su, Yannan Cao, Shuang Wang, Jiahong Dong, Jin Gu*, Yunfang Wang*.

scCancer2: data-driven in-depth annotations of the tumor microenvironment at single-level resolution.

Bioinformatics 2024, 40(2):btae028 [Full_Text]
Zeyu Chen#, Yuxin Miao#, Zhiyuan Tan, Qifan Hu, Yanhong Wu, Xinqi Li, Wenbo Guo*, Jin Gu*.

Single cell transcriptomic analysis reveals tumor cell heterogeneity and immune microenvironment features of pituitary neuroendocrine tumors.

Genome Medicine 2024, 16:2 [Full_Text]
Nan Yan#, Weiyan Xie#, Dongfang Wang#, Qiuyue Fang, Jing Guo, Yiyuan Chen, Xinqi Li, Lei Gong, Jialin Wang, Wenbo Guo, Xuegong Zhang, Yazhuo Zhang*, Jin Gu*, Chuzhong Li*.

TIST: transcriptome and histopathological image integrative analysis for spatial transcriptomics.

Genomics Proteomics & Bioinformatics, 2022, 20(5):974-988 [Full_Text] [Software]
Yiran Shan#, Qian Zhang#, Wenbo Guo, Yanhong Wu, Yuxin Miao, Hongyi Xin, Qiuyu Lian*, Jin Gu*.

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

Nature Cell Biology, 2022, 24(2):242-252 [Abstract] [Dataset]
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*.