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Bioinformatics & Intelligent Information Processing Research Group @ Information Science 生物信息学与智能信息处理研究小组 [Click Here for English Version]
古槿
工学博士,
研究组负责人
生物信息学教育部重点实验室 北京信息科学与技术国家研究中心 生物信息学研究部 清华大学自动化系 北京 100084
联系方式 电子邮件: jgu@tsinghua.edu.cn 电话: +86 10 62794294转866 传真: +86 10 62773552 学术博客: 科学网博客
研究组负责人简介
课题组主要从事生物信息学与机器学习方向的研究，
针对生命遗传密码与复杂系统调控规律解析的关键难题，发展新的信息理论与智能技术，推动恶性肿瘤等重大疾病诊疗的精准化与个体化。近年来在Nature
Cell Biology、Science Advances、Nature Communications等期刊上发表学术论文60余篇，担任GPB、BMC
Bioinformatics等期刊的编委。现任中国自动化学会智能健康与生物信息专业委员会秘书长、中国人工智能学会生物信息学与人工智能专业委员会常务委员。主持国家自然科学基金优秀青年科学基金、重点项目、国家重点研发计划课题等国家级科研项目。
最新消息 [公告] 招聘博士后研究员，欢迎生物信息学、机器学习、细胞生物学、分子生物学、医学等方向的青年学者！
[2024/12/13] 热烈祝贺基于动态单细胞转录组数据的肿瘤细胞命运解析算法scStateDynamics发表于发表于Genome Bioolgy！
主要研究方向 1) 时空组学大数据智能处理的理论与方法 2) 多尺度分子画像技术与精准肿瘤医学 3) 生物信息数据库、计算分析工具与软件平台
开设课程 概率图模型理论与方法（研究生专业基础课、校级精品课，2011秋季学期起） 计算分子生物学引论（研究生专业课，2015秋季学期起） 交叉项目综合训练-合成生物学（本科实践课，2020秋季学期起）
研究小组成员 博士后在站：梅清琳（2022年）
、郭文博（2022年） 硕士研究生：孙一凡（2023级）、黄静民（2024级）
已毕业博士生：王霆（2014.7）、武丁明（2016.1）、丁子建（2017.7）、王东方（2019.7）、连秋宇（2020.7）、武桂英（2021.4） 、郭文博（2022.7）、单怡然（2023.7） 已毕业硕士生：张谷超（2017.7）、黄倩倩（2018.7）、冯晨（2019.7）、关雯方（2019.7）、王事成（2020.7） 、刘昌毅（2021.7）、鲍思羽（2022.7）、李晋砚（2023.7）
工具软件与数据库 HOT!! [软件] scStateDynamics: deciphering the drug-responsive tumor cell state dynamics by modeling single-cell level expression changes [Updated: 2024/11/23] HOT!! [软件] scCancer2: supervised and in-depth annotations of the tumor microenvironment [Updated: 2023/08/23]
[软件]
TIST: Transcritpome and
histopathological Image integrative analysis for Spatial Transcriptomics
[Updated: 2022/07/25] [软件] VASC: a deep variational autoencoder for single cell RNA-seq data analysis [Updated: 2018/08/15] [软件] LRAcluster: a low-rank regularized method for fast dimension reduction and integrative clustering of multi-omics data [Updated: 2015/09/21] [软件] NP-miRNA: a network propagation based method for inferring perturbed miRNA regulatory networks [Updated: 2014/06/23] [软件] FastDMA: an Infinium HumanMethylation450 beadchip (450k DNA methylation array) analyzer [Updated: 2014/05/24] [软件] miRHiC: enrichment analysis of a set of genes in hierarchical gene co-expression signatures [Updated: 2013/03/19] [软件] sGSCA: signature-based gene set co-expression analysis (using sparse canonical correlation analysis) [Updated: 2013/11/22] [软件] ClustEx: responsive gene module identification package (v0.32) [Updated: 2012/05/03]
[软件]
PCS: de novo k-mer analysis package (v1.5) [Updated:
2009/10/8]
[数据集] scRNA-seq &
scBCR-seq datasets for the bone marrow of pediatric B-ALL patients and
healthy donors (Nature Cell Biology 2022) [Raw]
近期代表性论文（按发表时间排序） 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 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*. A patient-specific lung cancer assembloid model with heterogeneous tumor microenvironments. Nature Communications 2024, 15:3382 Shuyong Wang#, Xuan Wang#, Yiran Shan#, Zuolong Tan, Yuxin Su, Yannan Cao, Shuang Wang, Jiahong Dong, Jin Gu*, Yunfang Wang*. Region-specific cellular and molecular basis of liver regeneration after acute pericentral injury. Cell Stem Cell 2024, 31(3):341-358 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 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*. 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 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
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*.
Trajectory and
functional analysis of PD-1high CD4+CD8+ T cells in hepatocellular carcinoma
by single-cell cytometry and transcriptome sequencing. |
