黄茉莉，博士，苏州大学基础医学院教授，北京大学生物学（生物信息学）博士。兼任江苏省生物信息学学会理事、多个专委会委员；若干TOP期刊审稿人和编委、杰出编委；国内和国际基金评审人。
研究方向
用系统信息学的观点、方法研究生命科学和医学的基础问题。
1）通过表观遗传学、基因组学和转录组学的整合分析，寻找决定细胞命运的关键因子及其可能的分子机制；
2）网站和webserver的构建；
3）方法和软件开发。
主持的科技项目和人才项目
1）国家自然科学基金面上项目，2024.1-2027.12，主持；
2）国家自然科学基金面上项目，2020.1-2023.12，主持；
3）国家重点专项，课题骨干；
4）苏州市产业技术创新专项（应用基础研究），2015.7-2018.6，结题；
5）亚非国家杰出青年科学家来华工作计划，2015.12-2016.12，结题；
6）国家自然科学基金青年基金，2012.1-2014.12，结题；
7）江苏省自然科学基金，2011.7-2014.6，结题；
8）江苏省高校面上项目，2009.09-2011.12，结题；
9）苏州市高层次紧缺人才。
主要围绕多基因多器官发病的肿瘤，以表观基因组学为切入点，整合多种生物医学信息资源，揭示不同细胞的核心调控基因及其可能的肿瘤驱动机制。近几年在Gut 、Nucleic Acids Res、Oncogenesis、Nat Commun、Bioinformatics、Oncogene、Genes & Diseases等多个期刊发表相应结果。
发表论文
2018年至今部分期刊论文(共)第一或通讯作者(#共同第一；*共同通讯)
1. Jiang R, Lu Z, Li F, Zhu Y, Yang M, Zhang S, Wu P, Gong C, Fei Y, Sang Y, Huang Y, Guo JJ*, Huang M*(2025) scCirclehunter delineates ecDNA-containing cells using single-cell ATAC-seq, with a focus on glioblastoma. Cell Discov 11(1): 98. PMID: 41360770
2. Wang Q, Huang M*, Guo JJ* (2025) From cells to clinic: Single-cell transcriptomics shaping the future of orthopedics. J Orthop Translat 53: 1-11. PMID: 38021216
3. Zhang S, Jiang R, Yang M, Wang T, Cui J, Li G, Chen S, Huang M (2025) Transcriptional programs associated with luminal play a vital role in invasive mucinous lung adenocarcinoma. Genes & Diseases 12(2): 101278. PMID: 39584073
4. Wang Y, Lu Y, Li F, Huang M (2024) Pyroptosis: A promising biomarker for predicting colorectal cancer prognosis and enhancing immunotherapy efficacy. World Journal of Clinical Oncology 15(8): 968-974. PMID: 39193165
5. Jiang R#, Yang M#, Zhang S, Huang M (2023) Advances in sequencing-based studies of microDNA and ecDNA: Databases, identification methods, and integration with single-cell analysis. Computational and Structural Biotechnology Journal 21: 3073-3080. PMID: 37273851
6. Yang M, Zhang S, Jiang R, Chen S*, Huang M* (2023) Circlehunter: a tool to identify extrachromosomal circular DNA from ATAC-Seq data. Oncogenesis 12(1): 28. PMID: 37217468
7. Zhang S, Jiang R, Yang M, Wang T, Chen H, Shi Y, Liu W*, Huang M* (2023) Identification of a novel eighteen‑gene signature of recurrent metastasis neuroblastoma. Journal of Molecular Medicine 101(4): 403-417 PMID: 36856811
8. Liu Z, Meng M, Zhang S, Qiu H, Liu Z, Huang M (2021) Rhythmic Component Analysis Tool (RCAT): A Precise, Efficient and User-Friendly Tool for Circadian Clock Genes Analysis. Interdiscip Sci 14(1): 269-278 PMID: 34374039
9. Huang M, Wang Y, Yang M, Yan J, Yang H, Zhuang W, Xu Y, Koeffler HP, Lin DC*, Chen X* (2020) dbInDel: a database of enhancer-associated insertion and deletion variants by analysis of H3K27ac ChIP-Seq. Bioinformatics 36(5): 1649-1651. PMID: 31603498
10. Chen L#, Huang M#,*, Plummer J#, Pan J#, Jiang YY#, Yang Q, Silva TC, Gull N, Chen S, Ding LW, An O, Yang H, Cheng Y, Said JW, Doan N, Dinjens WN, Waters KM, Tuli R, Gayther SA, Klempner SJ, Berman BP, Meltzer SJ, Lin DC*, Koeffler HP (2020) Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in oesophageal adenocarcinoma. Gut 69(4): 630-640. PMID: 31409603
11. Chen Y#, Xu L#,*, Mayakonda A#, Huang ML#, Kanojia D#, Tan TZ, Dakle P, Lin RY, Ke XY, Said JW, Chen J, Gery S, Ding LW, Jiang YY, Pang A, Puhaindran ME, Goh BC, Koeffler HP (2019) Bromodomain and extraterminal proteins foster the core transcriptional regulatory programs and confer vulnerability in liposarcoma. Nat Commun 10(1): 1353. PMID: 30903020
12. Lin L#, Huang M#,*, Shi X#, Mayakonda A, Hu K, Jiang YY, Guo X, Chen L, Pang B, Doan N, Said JW, Xie J, Gery S, Cheng X, Lin Z, Li J, Berman BP, Yin D*, Lin DC*, Koeffler HP (2019) Super-enhancer-associated MEIS1 promotes transcriptional dysregulation in Ewing sarcoma in co-operation with EWS-FLI1. Nucleic Acids Res 47(3): 1255-1267 PMID: 30496486
13. Huang M*, Chen Y, Yang M, Guo A, Xu Y, Xu L*, Koeffler HP (2018) dbCoRC: a database of core transcriptional regulatory circuitries modeled by H3K27ac ChIP-seq signals. Nucleic Acids Res 46(D1): D71-D77. PMID: 28977473
14. Li B, Xu H, Han H, Song S, Zhang X, Ouyang L, Qian C, Hong Y, Qiu Y, Zhou W, Huang M*, Zhuang W* (2018) Exosome-mediated transfer of lncRUNX2-AS1 from multiple myeloma cells to MSCs contributes to osteogenesis. Oncogene 37(41): 5508-5519 PMID: 29895968
2018年至今部分期刊论文 参与
15. Liu Z, Zheng Q, Li Z, Huang M, Zhong C, Yu R, Jiang R, Dai H, Zhang J, Gu X, Xu Y, Li C, Shan S, Xu F, Hong Y, Ren T (2025) Epithelial stem cells from human small bronchi offer a potential for therapy of idiopathic pulmonary fibrosis. EBioMedicine PMID: 39753035
16. Lu Y, Sun Y, Zhang J, Kong M, Zhao Z, Sun B, Wang Y, Jiang Y, Chen S, Wang C, Tong Y, Wen L, Huang M, Wu F, Zhang L (2024) The deubiquitinase USP2a promotes tumor immunosuppression by stabilizing immune checkpoint B7-H4 in lung adenocarcinoma harboring EGFR-activating mutants. Cancer Lett PMID: 38849009
17. Li C, Feng Y, Fu Z, Deng J, Gu Y, Wang H, Wu X, Huang Z, Zhu Y, Liu Z, Huang M, Wang T, Hu S, Yao B, Zeng Y, Zhou CJ, Brown SDM, Liu Y, Vidal-Puig A, Dong Y, Xu Y (2022) Human-specific gene CT47 blocks PRMT5 degradation to lead to meiosis arrest. Cell Death Discov PMID: 35918318
18. Liu Z, Huang M, Hong Y, Wang S, Xu Y, Zhong C, Zhang J, Zhuang Z, Shan S, Ren T (2022) Isovalerylspiramycin I suppresses non-small cell lung carcinoma growth through ROS-mediated inhibition of PI3K/AKT signaling pathway. Int J Biol Sci PMID: 35813464.
19. Li C, Feng Y, Fu Z, Deng J, Gu Y, Wang H, Wu X, Huang Z, Zhu Y, Liu Z, Huang M, Wang T, Hu S, Yao B, Zeng Y, Zhou CJ, Brown SDM, Liu Y, Vidal-Puig A, Dong Y, Xu Y (2022) Human-specific gene CT47 blocks PRMT5 degradation to lead to meiosis arrest. Cell Death Discov PMID: 35918318
20. Hong Y, Shan S, Gu Y, Huang H, Zhang Q, Han Y, Dong Y, Liu Z, Huang M, Ren T (2022) Malfunction of airway basal stem cells plays a crucial role in pathophysiology of tracheobronchopathia osteoplastica. Nat Commun 13(1):1309 PMID: 35288560.
21. Lu Y, Wu F, Cao Q, Sun Y, Huang M, Xiao J, Zhou B, Zhang L (2021) B7-H4 is increased in lung adenocarcinoma harboring EGFR-activating mutations and contributes to immunosuppression. Oncogene PMID: 34839353.
22. Xu L, Chen Y, Huang Y, Sandanaraj E, Yu JS, Lin RY, Dakle P, Ke XY, Chong YK, Koh L, Mayakonda A, Nacro K, Hill J, Huang ML, Gery S, Lim SW, Huang Z, Xu Y, Chen J, Bai L, Wang S, Wakimoto H, Yeo TT, Ang BT, Müschen M, Tang C, Tan TZ, Koeffler HP (2021) Topography of transcriptionally active chromatin in glioblastoma. Sci Adv PMID: 33931443.
23. Shi X, Zheng Y, Jiang L, Zhou B, Yang W, Li L, Ding L, Huang M, Gery S, Lin DC, Koeffler HP (2020) EWS-FLI1 regulates and cooperates with core regulatory circuitry in Ewing sarcoma. Nucleic Acids Res 48(20):11434-11451.PMID: 33080033
24. Zhao Z, Zhang N, Li A, Zhou B, Chen Y, Chen S, Huang M, Wu F, Zhang L (2020) Insulin-like growth factor-1 receptor induces immunosuppression in lung cancer by upregulating B7-H4 expression through the MEK/ERK signaling pathway. Cancer Lett 485: 14-26. (IF:7.36)
25. Jiang Y, Jiang YY, Xie JJ, Mayakonda A, Hazawa M, Chen L, Xiao JF, Li CQ, Huang ML, Ding LW, Sun QY, Xu L, Kanojia D, Jeitany M, Deng JW, Liao LD, Soukiasian HJ, Berman BP, Hao JJ, Xu LY, Li EM, Wang MR, Bi XG, Lin DC, Koeffler HP (2018) Co-activation of super-enhancer-driven CCAT1 by TP63 and SOX2 promotes squamous cancer progression. Nat Commun 9(1): 3619. PMID: 30190462.
26. Shi J, Song S, Han H, Xu H, Huang M, Qian C, Zhang X, Ouyang L, Hong Y, Zhuang W, Li B (2018) Potent Activity of the Bromodomain Inhibitor OTX015 in Multiple Myeloma. Mol Pharm 15(9): 4139-4147. PMID: 30048594
27. Ding LW, Tan KT, Sun QY, Lao ZT, Yang H, Jiang N, Chien W, Xiao JF, Loh XY, Huang ML, Lill M, Lin DC, Yeoh AEJ, Koeffler HP (2018) Clonality and clonal evolution analysis of paediatric ALL based on B-cell receptor/T-cell receptor rearrangement. Br J Haematol PMID: 29532914.
28. Xu L, Chen Y, Mayakonda A, Koh L, Chong YK, Buckley DL, Sandanaraj E, Lim SW, Lin RY, Ke XY, Huang ML, Chen J, Sun W, Wang LZ, Goh BC, Dinh HQ, Kappei D, Winter GE, Ding LW, Ang BT, Berman BP, Bradner JE, Tang C, Koeffler HP. (2018) Targetable BET proteins- and E2F1-dependent transcriptional program maintains the malignancy of glioblastoma. Proc Natl Acad Sci U S A 115(22): E5086-E5095. PMID: 29764999.
2018年至今部分书籍
1. Trends in Insect Molecular Biology and Biotechnology. Chapter 15, Correlation of Insects with Forensic Sciences. Mian Sahib Zarand Moli Huang. DOI: 10.1007/978-3-319-61343-7. Springer International Publishing. 2018. ISBN: 978-3-319-61342-0. I
医学系统生物学-生物信息学
黄茉莉，博士，苏州大学基础医学院教授，北京大学生物学（生物信息学）博士。兼任江苏省生物信息学学会理事、多个专委会委员；若干TOP期刊审稿人和编委、杰出编委；国内和国际基金评审人。
研究方向
用系统信息学的观点、方法研究生命科学和医学的基础问题。
1）通过表观遗传学、基因组学和转录组学的整合分析，寻找决定细胞命运的关键因子及其可能的分子机制；
2）网站和webserver的构建；
3）方法和软件开发。
主持的科技项目和人才项目
1）国家自然科学基金面上项目，2024.1-2027.12，主持；
2）国家自然科学基金面上项目，2020.1-2023.12，主持；
3）国家重点专项，课题骨干；
4）苏州市产业技术创新专项（应用基础研究），2015.7-2018.6，结题；
5）亚非国家杰出青年科学家来华工作计划，2015.12-2016.12，结题；
6）国家自然科学基金青年基金，2012.1-2014.12，结题；
7）江苏省自然科学基金，2011.7-2014.6，结题；
8）江苏省高校面上项目，2009.09-2011.12，结题；
9）苏州市高层次紧缺人才。
主要围绕多基因多器官发病的肿瘤，以表观基因组学为切入点，整合多种生物医学信息资源，揭示不同细胞的核心调控基因及其可能的肿瘤驱动机制。近几年在Gut 、Nucleic Acids Res、Oncogenesis、Nat Commun、Bioinformatics、Oncogene、Genes & Diseases等多个期刊发表相应结果。
发表论文
2018年至今部分期刊论文(共)第一或通讯作者(#共同第一；*共同通讯)
1. Jiang R, Lu Z, Li F, Zhu Y, Yang M, Zhang S, Wu P, Gong C, Fei Y, Sang Y, Huang Y, Guo JJ*, Huang M*(2025) scCirclehunter delineates ecDNA-containing cells using single-cell ATAC-seq, with a focus on glioblastoma. Cell Discov 11(1): 98. PMID: 41360770
2. Wang Q, Huang M*, Guo JJ* (2025) From cells to clinic: Single-cell transcriptomics shaping the future of orthopedics. J Orthop Translat 53: 1-11. PMID: 38021216
3. Zhang S, Jiang R, Yang M, Wang T, Cui J, Li G, Chen S, Huang M (2025) Transcriptional programs associated with luminal play a vital role in invasive mucinous lung adenocarcinoma. Genes & Diseases 12(2): 101278. PMID: 39584073
4. Wang Y, Lu Y, Li F, Huang M (2024) Pyroptosis: A promising biomarker for predicting colorectal cancer prognosis and enhancing immunotherapy efficacy. World Journal of Clinical Oncology 15(8): 968-974. PMID: 39193165
5. Jiang R#, Yang M#, Zhang S, Huang M (2023) Advances in sequencing-based studies of microDNA and ecDNA: Databases, identification methods, and integration with single-cell analysis. Computational and Structural Biotechnology Journal 21: 3073-3080. PMID: 37273851
6. Yang M, Zhang S, Jiang R, Chen S*, Huang M* (2023) Circlehunter: a tool to identify extrachromosomal circular DNA from ATAC-Seq data. Oncogenesis 12(1): 28. PMID: 37217468
7. Zhang S, Jiang R, Yang M, Wang T, Chen H, Shi Y, Liu W*, Huang M* (2023) Identification of a novel eighteen‑gene signature of recurrent metastasis neuroblastoma. Journal of Molecular Medicine 101(4): 403-417 PMID: 36856811
8. Liu Z, Meng M, Zhang S, Qiu H, Liu Z, Huang M (2021) Rhythmic Component Analysis Tool (RCAT): A Precise, Efficient and User-Friendly Tool for Circadian Clock Genes Analysis. Interdiscip Sci 14(1): 269-278 PMID: 34374039
9. Huang M, Wang Y, Yang M, Yan J, Yang H, Zhuang W, Xu Y, Koeffler HP, Lin DC*, Chen X* (2020) dbInDel: a database of enhancer-associated insertion and deletion variants by analysis of H3K27ac ChIP-Seq. Bioinformatics 36(5): 1649-1651. PMID: 31603498
10. Chen L#, Huang M#,*, Plummer J#, Pan J#, Jiang YY#, Yang Q, Silva TC, Gull N, Chen S, Ding LW, An O, Yang H, Cheng Y, Said JW, Doan N, Dinjens WN, Waters KM, Tuli R, Gayther SA, Klempner SJ, Berman BP, Meltzer SJ, Lin DC*, Koeffler HP (2020) Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in oesophageal adenocarcinoma. Gut 69(4): 630-640. PMID: 31409603
11. Chen Y#, Xu L#,*, Mayakonda A#, Huang ML#, Kanojia D#, Tan TZ, Dakle P, Lin RY, Ke XY, Said JW, Chen J, Gery S, Ding LW, Jiang YY, Pang A, Puhaindran ME, Goh BC, Koeffler HP (2019) Bromodomain and extraterminal proteins foster the core transcriptional regulatory programs and confer vulnerability in liposarcoma. Nat Commun 10(1): 1353. PMID: 30903020
12. Lin L#, Huang M#,*, Shi X#, Mayakonda A, Hu K, Jiang YY, Guo X, Chen L, Pang B, Doan N, Said JW, Xie J, Gery S, Cheng X, Lin Z, Li J, Berman BP, Yin D*, Lin DC*, Koeffler HP (2019) Super-enhancer-associated MEIS1 promotes transcriptional dysregulation in Ewing sarcoma in co-operation with EWS-FLI1. Nucleic Acids Res 47(3): 1255-1267 PMID: 30496486
13. Huang M*, Chen Y, Yang M, Guo A, Xu Y, Xu L*, Koeffler HP (2018) dbCoRC: a database of core transcriptional regulatory circuitries modeled by H3K27ac ChIP-seq signals. Nucleic Acids Res 46(D1): D71-D77. PMID: 28977473
14. Li B, Xu H, Han H, Song S, Zhang X, Ouyang L, Qian C, Hong Y, Qiu Y, Zhou W, Huang M*, Zhuang W* (2018) Exosome-mediated transfer of lncRUNX2-AS1 from multiple myeloma cells to MSCs contributes to osteogenesis. Oncogene 37(41): 5508-5519 PMID: 29895968
2018年至今部分期刊论文 参与
15. Liu Z, Zheng Q, Li Z, Huang M, Zhong C, Yu R, Jiang R, Dai H, Zhang J, Gu X, Xu Y, Li C, Shan S, Xu F, Hong Y, Ren T (2025) Epithelial stem cells from human small bronchi offer a potential for therapy of idiopathic pulmonary fibrosis. EBioMedicine PMID: 39753035
16. Lu Y, Sun Y, Zhang J, Kong M, Zhao Z, Sun B, Wang Y, Jiang Y, Chen S, Wang C, Tong Y, Wen L, Huang M, Wu F, Zhang L (2024) The deubiquitinase USP2a promotes tumor immunosuppression by stabilizing immune checkpoint B7-H4 in lung adenocarcinoma harboring EGFR-activating mutants. Cancer Lett PMID: 38849009
17. Li C, Feng Y, Fu Z, Deng J, Gu Y, Wang H, Wu X, Huang Z, Zhu Y, Liu Z, Huang M, Wang T, Hu S, Yao B, Zeng Y, Zhou CJ, Brown SDM, Liu Y, Vidal-Puig A, Dong Y, Xu Y (2022) Human-specific gene CT47 blocks PRMT5 degradation to lead to meiosis arrest. Cell Death Discov PMID: 35918318
18. Liu Z, Huang M, Hong Y, Wang S, Xu Y, Zhong C, Zhang J, Zhuang Z, Shan S, Ren T (2022) Isovalerylspiramycin I suppresses non-small cell lung carcinoma growth through ROS-mediated inhibition of PI3K/AKT signaling pathway. Int J Biol Sci PMID: 35813464.
19. Li C, Feng Y, Fu Z, Deng J, Gu Y, Wang H, Wu X, Huang Z, Zhu Y, Liu Z, Huang M, Wang T, Hu S, Yao B, Zeng Y, Zhou CJ, Brown SDM, Liu Y, Vidal-Puig A, Dong Y, Xu Y (2022) Human-specific gene CT47 blocks PRMT5 degradation to lead to meiosis arrest. Cell Death Discov PMID: 35918318
20. Hong Y, Shan S, Gu Y, Huang H, Zhang Q, Han Y, Dong Y, Liu Z, Huang M, Ren T (2022) Malfunction of airway basal stem cells plays a crucial role in pathophysiology of tracheobronchopathia osteoplastica. Nat Commun 13(1):1309 PMID: 35288560.
21. Lu Y, Wu F, Cao Q, Sun Y, Huang M, Xiao J, Zhou B, Zhang L (2021) B7-H4 is increased in lung adenocarcinoma harboring EGFR-activating mutations and contributes to immunosuppression. Oncogene PMID: 34839353.
22. Xu L, Chen Y, Huang Y, Sandanaraj E, Yu JS, Lin RY, Dakle P, Ke XY, Chong YK, Koh L, Mayakonda A, Nacro K, Hill J, Huang ML, Gery S, Lim SW, Huang Z, Xu Y, Chen J, Bai L, Wang S, Wakimoto H, Yeo TT, Ang BT, Müschen M, Tang C, Tan TZ, Koeffler HP (2021) Topography of transcriptionally active chromatin in glioblastoma. Sci Adv PMID: 33931443.
23. Shi X, Zheng Y, Jiang L, Zhou B, Yang W, Li L, Ding L, Huang M, Gery S, Lin DC, Koeffler HP (2020) EWS-FLI1 regulates and cooperates with core regulatory circuitry in Ewing sarcoma. Nucleic Acids Res 48(20):11434-11451.PMID: 33080033
24. Zhao Z, Zhang N, Li A, Zhou B, Chen Y, Chen S, Huang M, Wu F, Zhang L (2020) Insulin-like growth factor-1 receptor induces immunosuppression in lung cancer by upregulating B7-H4 expression through the MEK/ERK signaling pathway. Cancer Lett 485: 14-26. (IF:7.36)
25. Jiang Y, Jiang YY, Xie JJ, Mayakonda A, Hazawa M, Chen L, Xiao JF, Li CQ, Huang ML, Ding LW, Sun QY, Xu L, Kanojia D, Jeitany M, Deng JW, Liao LD, Soukiasian HJ, Berman BP, Hao JJ, Xu LY, Li EM, Wang MR, Bi XG, Lin DC, Koeffler HP (2018) Co-activation of super-enhancer-driven CCAT1 by TP63 and SOX2 promotes squamous cancer progression. Nat Commun 9(1): 3619. PMID: 30190462.
26. Shi J, Song S, Han H, Xu H, Huang M, Qian C, Zhang X, Ouyang L, Hong Y, Zhuang W, Li B (2018) Potent Activity of the Bromodomain Inhibitor OTX015 in Multiple Myeloma. Mol Pharm 15(9): 4139-4147. PMID: 30048594
27. Ding LW, Tan KT, Sun QY, Lao ZT, Yang H, Jiang N, Chien W, Xiao JF, Loh XY, Huang ML, Lill M, Lin DC, Yeoh AEJ, Koeffler HP (2018) Clonality and clonal evolution analysis of paediatric ALL based on B-cell receptor/T-cell receptor rearrangement. Br J Haematol PMID: 29532914.
28. Xu L, Chen Y, Mayakonda A, Koh L, Chong YK, Buckley DL, Sandanaraj E, Lim SW, Lin RY, Ke XY, Huang ML, Chen J, Sun W, Wang LZ, Goh BC, Dinh HQ, Kappei D, Winter GE, Ding LW, Ang BT, Berman BP, Bradner JE, Tang C, Koeffler HP. (2018) Targetable BET proteins- and E2F1-dependent transcriptional program maintains the malignancy of glioblastoma. Proc Natl Acad Sci U S A 115(22): E5086-E5095. PMID: 29764999.
2018年至今部分书籍
1. Trends in Insect Molecular Biology and Biotechnology. Chapter 15, Correlation of Insects with Forensic Sciences. Mian Sahib Zarand Moli Huang. DOI: 10.1007/978-3-319-61343-7. Springer International Publishing. 2018. ISBN: 978-3-319-61342-0. I
医学系统生物学-生物信息学