Group News

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

[2025/09/17] Cell Systems: scTrace+, computational lineage-tracing data enhancement by kernelized pNMF for more robust biological discovery and inferences.

[2025/06/26] Nature Genetics: Multi-omic analysis of gallbladder cancer identifies distinct tumor microenvironments associated with disease progression.

[2025/04/26] Cancer Letters: Decipher the single-cell level responses to chemotherapy in pancreatic ductal adenocarcinoma by a cross-time context graph model.

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 Digital Biology (Graduate course, from Fall 2015, with Dr Xiaowo Wang)

Group Members

Post Doctoral: Xinqi Li

PhD Student: Nan Yan (2021), Zeyu Chen (2022), Yuhan Fan (2022), Zikang Yin (2023), Yuman Li (2024), Xingye Cai (2025), Shihao Chu (2026)

Master Student: Jingmin Huang (2024), Yiming Gao (2025)

Tools, Databases & Datasets

HOT!! [Software] scTrace+: improving the cell fate analysis by computational lineage-tracing data enhancement via kernelized pNMF [Updated: 2025/09/17]

[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] the dataset for the gallbladder cancer cell atlas (Nature Genetics 2025) [Processed] [Raw]

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 2021 [Full List @ Google Scholar]

Wenbo Guo#, Zeyu Chen#, Xinqi Li, Jingmin Huang, Qifan Hu, Jin Gu*. scTrace+: Enhancing cell fate inference by integrating the lineage-tracing and multi-faceted transcriptomic similarity information. Cell Systems 2025, 16(9):101398

Tao Zhou*, Yanhong Wu*, Shuai Li*, Xinyao Qiu*, Erdong Liu*, Zhihua Xie*, Xuebing Shi, Yani Zhang, Guosheng Ma, Wenbo Guo, Xiang Wang, Kaiting Wang, Xiaomeng Yao, Ji Hu, Siyun Shen, Shuai Yang, Xiaoqing Jiang#, Jing Fu#, Hongyang Wang#, Jin Gu#, Lei Chen#. Multi-omic analysis of gallbladder cancer identifies distinct tumor microenvironments associated with disease progression. Nature Genetics 2025, 57(8):1935-1949

Xinqi Li#, Yueze Liu#, Feihan Zhou#, Wenbo Guo, Guangyu Chen, Jinxin Tao, Jingmin Huang, Jiangdong Qiu, Hao Chen, Bo Ren, Lei You, Yanan Shi, Gang Yang*, Taiping Zhang*, Jin Gu*, Yupei Zhao*. Decipher the single-cell level responses to chemotherapy in pancreatic ductal adenocarcinoma by a cross-time context graph model. Cancer Letters 2025, 626:217751

Wenbo Guo, Xinqi Li, Dongfang Wang, Nan Yan, Qifan Hu, Fan Yang, Xuegong Zhang, Jianhua Yao*, Jin Gu*. scStateDynamics: deciphering the drug-responsive tumor cell state dynamics by modeling single-cell level expression changes. Genome Biology 2024, 25:297

Zeyu Chen#, Yuxin Miao#, Zhiyuan Tan, Qifan Hu, Yanhong Wu, Xinqi Li, Wenbo Guo*, Jin Gu*. scCancer2: data-driven in-depth annotations of the tumor microenvironment at single-level resolution. Bioinformatics 2024, 40(2):btae028

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*. Single cell transcriptomic analysis reveals tumor cell heterogeneity and immune microenvironment features of pituitary neuroendocrine tumors. Genome Medicine 2024, 16:2

Yiran Shan#, Qian Zhang#, Wenbo Guo, Yanhong Wu, Yuxin Miao, Hongyi Xin, Qiuyu Lian*, Jin Gu*. TIST: transcriptome and histopathological image integrative analysis for spatial transcriptomics.Genomics Proteomics & Bioinformatics, 2022, 20(5):974-988

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*. Elucidating minimal residual disease of paediatric B-cell acute lymphoblastic leukaemia by single-cell analysis. Nature Cell Biology, 2022, 24(2):242-252

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*. Comprehensive analysis of spatial architecture in primary liver cancer. Science Advances 2021, 7:eabg3750

Wenbo Guo, Dongfang Wang, Shicheng Wang, Yiran Shan, Changyi Liu, Jin Gu*. scCancer: a package for automated processing of single cell RNA-seq data in cancer. Briefings in Bioinformatics 2021, 22(3):bbaa127

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*. Integrative genomic analysis of gemcitabine resistance in pancreatic cancer by patient-derived xenograft models. Clinical Cancer Research 2021, 27:3383-3396