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、计算生物学与生物信息学委员、多组学与整合生物学专委会委员、肿瘤测序及大数据分析专家委员会委员；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
近5年部分期刊论文(共)第一或通讯作者(#共同第一；*共同通讯)
1. Jiang R, 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
2. 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
3. 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
4. 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
5. 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
6. 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
7. 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
8. 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
9. 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
10. Li B, Xu H, Han H, Song S, Zhang X, Ouyang L, Qian C, Hong Y, Qiu Y, Zhou W, Huang M*, Zhuang W*. Exosome-mediated transfer of lncRUNX2-AS1 from multiple myeloma cells to MSCs contributes to osteogenesis. Oncogene. 2018 Jun 12. PMID: 29895968 (IF: 7.971)
近5年部分期刊论文 参与
1. 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.
2. 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
3. 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.
4. 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.
5. 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.
6. 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.
7. 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)
8. 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.
9. 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
10. 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.
11. 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.
近5年部分书籍
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、计算生物学与生物信息学委员、多组学与整合生物学专委会委员、肿瘤测序及大数据分析专家委员会委员；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
近5年部分期刊论文(共)第一或通讯作者(#共同第一；*共同通讯)
1. Jiang R, 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
2. 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
3. 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
4. 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
5. 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
6. 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
7. 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
8. 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
9. 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
10. Li B, Xu H, Han H, Song S, Zhang X, Ouyang L, Qian C, Hong Y, Qiu Y, Zhou W, Huang M*, Zhuang W*. Exosome-mediated transfer of lncRUNX2-AS1 from multiple myeloma cells to MSCs contributes to osteogenesis. Oncogene. 2018 Jun 12. PMID: 29895968 (IF: 7.971)
近5年部分期刊论文 参与
1. 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.
2. 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
3. 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.
4. 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.
5. 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.
6. 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.
7. 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)
8. 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.
9. 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
10. 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.
11. 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.
近5年部分书籍
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