Welcome to Jin Gu’s Homepage
Bioinformatics
& Intelligent Information Processing Research Group
[点击此处查看 中文版]

Jin Gu Ph.D. (古槿),
Principal Investigator
MOE
Key Laboratory of Bioinformatics
BNRIST
Bioinformatics
Division
Department of Automation
Tsinghua University, Beijing
100084, China
Contact Information:
Email: jgu@tsinghua.edu.cn
Phone (Lab): +86 10 62794294-866
Fax (Lab): +86 10 62773552
Last Update: Sept 06, 2025
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Group
News
[Announcement] Open
Positions for Post Doctoral Research Fellows on Bioinformatics and Medicine!
[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: Qinglin Mei, Wenbo
Guo
PhD Student: Xinqi Li (2019), Yuxin Miao (2021), Nan Yan
(2021), Zeyu Chen (2022), Yuhan Fan (2022), Zikang Yin (2023), Yuman Li
(2024), Xingye Cai (2025)
Master Student: Yifan Sun (2023), Jingmin
Huang (2024), Yiming Gao (2025)
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] 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]
uniLIVER: a human liver cell atlas for data-driven cellular
state mapping.
Journal
of Genetics and Genomics 2025, 52(9):1133-1147 [Abstract]
[Database]
Yanhong Wu#, Yuhan Fan#, Yuxin Miao#, Yuman Li, Guifang Du, Zeyu Chen, Jinmei
Diao, Yu-Ann Chen, Mingli Ye, Renke You, Amin Chen, Yixin Chen, Wenrui Li, Wenbo Guo, Jiahong Dong, Xuegong Zhang, Yunfang Wang*, Jin Gu*.
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Multi-omic analysis of gallbladder cancer identifies distinct
tumor microenvironments associated with disease progression.
Nature
Genetics 2025, 57(8):1935-1949 [Abstract]
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#.
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Decipher the single-cell level
responses to chemotherapy in pancreatic ductal adenocarcinoma by a
cross-time context graph model.
Cancer
Letters 2025, 626:217751 [Abstract]
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*.
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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*.
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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*.
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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*.
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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*.
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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*.
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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*.
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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*.
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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*.
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