Bioinformatics Server

Database and Software Tools

Knowledge Network Insight Platform for Drug Discovery

Insight Platform for pan-cancer prognostic genes analysis

OmicsViz

COVID-19 drug research insights from omics data

MafViz

Visualize TCGA mutations or user-uploaded MAFs

HeatmapViz

Powerful cluster analysis and heatmap visualization tool

ClusterProfilerViz

Over-Representation analysis and GSEA analysis. It often crashes. Please use X-enrich in CancerPro.

AIViz

Interactive Data Visualization with AI, Please contact wangzg@pumc.edu.cn to obtain a username and password.

DrugInsight LLM

An intelligent platform that integrates knowledge graphs with large language models to extract and explain drug mechanisms of action, supporting drug research and similarity analysis.

IBDLinker: An LLM- and expert-curated database integrating gene, drug, mutation and disease relationships for enhanced understanding of IBD mechanisms and therapies.

Publications

Wang Z*, Li XX, Zheng J, He Y*, Unveiling Differential Adverse Event Profiles in Vaccines via LLM Text Embeddings and Ontology Semantic Analysis. Journal of Biomedical Semantics, 2025:16(10) https://link.springer.com/article/10.1186/s13326-025-00331-8.
Wang Z*, Yuan Y, Yang XL*, et al. CancerPro: deciphering the pan-cancer prognostic landscape through combinatorial enrichment analysis and knowledge network insights. NAR Genomics and Bioinformatics, 2024, 6(4): lqae157.
Wang Z, Zhang ZG, Peng Y. Charactrerization of congestive heart failure by the pattern of diurnal rhythm based on heart rate variability. Chinese Journal of Biomedical Engineering (English edition), 2022, 31(2): 47-55.
Wang Z*, He Y*. Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research. Brief Funct Genomics, 2021: 1-14.
Wang Z, He Y, Huang J, et al. Integrative web-based analysis of omics data for study of drugs against SARS-CoV-2. Scientific Reports, 2021, 11(1): 10763.
Wang Z, Liu W, Chen C, et al. Low mutation and neoantigen burden and fewer effector tumor infiltrating lymphocytes correlate with breast cancer metastasization to lymph nodes. Scientific Reports, 2019, 9(1): 253.
Liu Y, Hur J, Wang Z, et al. Ontological modeling and analysis of experimentally or clinically verified drugs against coronavirus infection. Scientific Data, 2021, 8(1): 16.
Zhang Q, Bai B, Wang Z, et al. Elevated H3K79 homocysteinylation causes abnormal gene expression during neural development and subsequent neural tube defects. Nature Communications, 2018, 9(1): 3436.
Lai Z, Wang Z, Yuan Z, et al. Disease-Specific haptoglobin N-Glycosylation in inflammatory disorders between cancers and benign diseases of 3 types of female internal genital organs. Clinica Chimica Acta, 2023, 547: 117420.
Zhang W, Lai Z, Liang X, Wang Z et al. Metabolomic biomarkers for benign conditions and malignant ovarian cancer: Advancing early diagnosis. Clinica Chimica Acta, 2023, 560: 119734.

Liu Y, Chan W, Wang Z, et al. Ontological and bioinformatic analysis of anti-coronavirus drugs and their implication for drug repurposing against COVID-19. MDPI AG, 2020.
Hu Q, Wang ZG, Zhang ZG. FSim: a novel functional similarity search algorithm and tool for discovering functionally related gene products. BioMed Research International, 2014: 509149.
Zhu Y, Yang X, Wang Z, Peng Y. An evaluating method for autonomic nerve activity by means of estimating the consistency of heart rate variability and QT variability. IEEE Transactions on Biomedical Engineering, 2013, 61(3): 938-945.
Zhu Y, Yang X, Wang Z, Peng Y. Comparative analysis of short-term variability of RR and QT intervals for the assessment of autonomic nerve activity. Computing in Cardiology, 2013: 73-76.
袁一泽, 王志刚, 王哲, 等. 知识图谱驱动的人类蛋白质组知识注释与知识探索研究. 中国生物医学工程学报, 2024, 43(3): 315-326.
王志刚*, 杨啸林, 张文佳, 等. 应用大语言模型实现疫苗不良反应文本到本体的映射. 中国生物医学工程大会暨创新医疗峰会, 深圳, 2024.
Wang Z*, Yuan Y, Liu Z, et al. An interactive ontology-based web server for data visualization in SARS-CoV-2 drug repurposing research. 中国生物医学工程大会暨创新医疗峰会, 2023.
孙德伟, 王志刚, 杨啸林, 等. 基于深度学习的肺腺癌肿瘤突变负荷的预测. 中国生物医学工程学报, 2021, 40(6): 681-690.
张艳丽, 王志刚, 史涪仁, 等. 基于 Moodle 的混合式教学在医学教育中的应用. 基础医学与临床, 2021, 41(11): 1701.
杨啸林, 杨晟, 潘虹洁, 等. FAIR 准则与生物医学数据标准应用服务. 中国医学伦理学, 2020, 33(2): 153-159.
Wang Z, et al. Comprehensive comparison of immune features between ultra-low and ultra-high mutation burden non-small cell lung cancers. Preprint, 2020.
Chang S, Lu X, Wang S, et al. The effect of folic acid deficiency on FGF pathway via Brachyury regulation in neural tube defects. The FASEB Journal, 2019, 33(4): 4688-4702.
王志刚. 应用转录组和外显子组测序分析不同年龄组的胶质母细胞瘤中基因表达与变异的差异. 解剖学报, 2019, 50(1).
Pan H, Zhu Y, Yang S, et al. Biomedical ontologies and their development, management, and applications in and beyond China. Journal of Bio-X Research, 2019, 2(04): 178-184.
张璐璐, 杨晟, 史涪仁, 等. 本体支持的生物医学领域元数据异质性与可兼容性研究. 中国生物医学工程学报, 2019, 38(3): 324-331.
潘越, 王志刚, 张正国, 等. 正常人短时心率变异性指标在长时序列中的分布特性及其年龄的影响. 中国生物医学工程学报, 2019, 38(3): 291-297.
李晨曦, 潘越, 王志刚, 等. 以线性参数模型和信息分解方法评价 QT 变异性对心率变异性的响应. 中国生物医学工程学报, 2018, 37(3): 305-312.
湛萍, 李晨曦, 王志刚, 等. 直立倾斜引起的心率和血压的耦合性变化分析. 中国生物医学工程学报, 2017, 36(3): 284-292.
Zhang Z, Li Q, Diao M, et al. Sporadic Hirschsprung disease: mutational spectrum and novel candidate genes revealed by next-generation sequencing. Scientific Reports, 2017, 7(1): 14796.
Li C, Pan Y, Zhan P, et al. Information theory based evaluation of interactions between RR and QT intervals in the normal and people with high risk for cardiac arrhythmias. Computing in Cardiology, 2017: 1-4.
刘红夺儿, 湛萍, 王志刚, 等. 以短时心率变异性反映充血性心力衰竭患者自主神经活动的改变. 中国生物医学工程学报, 2016, 35(2): 155-161.
Cui H, Li N, Li X, et al. Tongxinluo modulates cytokine secretion by cardiac microvascular endothelial cells in ischemia/reperfusion injury. American Journal of Translational Research, 2016, 8(10): 4370.
Liu H, Zhan P, Wang Z, Peng Y. Assessment of autonomic nerve activity by circadian rhythm at different stages after acute myocardial infarction based on holter data. Computing in Cardiology Conference, 2015: 613-616.
王志刚, 陈鑫, 王茜, 等. FlexDB: 在线个人健康评估系统. 医学信息学杂志, 2012, 33(2): 18-21.
王志刚, 谢丽芳, 陈鑫, 等. 基于语义的疾病表型相似性. 生物信息学, 2012, 10(3): 154-157.
王志刚, 陈鑫, 谢丽芳, 等. 药物化学结构在线分析系统. 药物生物技术, 2012, 19(2): 153-155.
王志刚, 陈鑫, 谢丽芳, 等. 药物功能模式相似度及其聚类. 中国生物医学工程学报, 2011, 30(6): 807-812.
Shao C, Li M, Li X, et al. A tool for biomarker discovery in the urinary proteome: a manually curated human and animal urine protein biomarker database. Molecular & Cellular Proteomics, 2011, 10(11).
王志刚, 翟天野, 张正国. 乳腺影像数据库及其纹理特征的机器学习分类. 中国仪器仪表学会医疗仪器分会 2010 两岸四地生物医学工程学术年会论文集, 2010.
杨啸林, 张靖, 徐铖, 等. 基于大规模人群调查的心电数据库的构建. 中国生物医学工程学报, 2010, 29(3): 326-330.
Hu Q, Zhang Z. An online system for functional relationship analysis of genome-wide gene products. 4th International Conference on Bioinformatics and Biomedical Engineering, 2010: 1-4.
王志刚, 张正国. 应用 MPEG.7 建立乳腺 X 线影像数据库. 中国生物医学工程学报, 2008, 27(2): 260-264.