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朱瑞新
来源:  作者:  发表时间:2012-12-29  阅读次数:14668次

 

姓 名:朱瑞新

学 位:博士

导师情况:博士生导师

研究领域:生物信息学

研究方向:宏基因组、整合组学和药物设计

课题组网站:cadd.tongji.edu.cn

招生方向:欢迎对生物信息学和计算机辅助药物设计感兴趣的同学报考

E-mailrxzhu@tongji.edu.cn

通讯地址:上海市杨浦区四平路1239号同济大学生命科学与技术学院

 

个人简介:

     现任同济大学生命科学与技术学院副教授,博士生导师。2001年毕业于兰州大学化学化工学院,获化学学士学位。2007年毕业于中国科学院上海有机化学研究所,获计算机化学博士学位。2007-2008年在上海生物信息技术研究中心从事科研工作。2008年至今在同济大学生命科学与技术学院从事教学和科研工作。2011年至今兼任辽宁中医药大学药学院研究生导师。近5年发表SCI检索论文56篇(其中33篇为第一作者/通讯作者)。主编出版了国内“计算机辅助药物设计”第一本本科生专业教材:《计算机辅助药物设计:基本方法原理概要与实践详解》,朱瑞新编著,大连理工大学出版社,2011年,ISBN 978-7-5611-6104-3,任期刊Frontiers in Pharmacology(IF=4.4)副主编。

 

科研工作情况(详情参考cadd.tongji.edu.cn)

      我所领导的团队运用信息学方法致力于两个主要研究方向:
1、宏基因组分析方法的发展及其在人类活动等领域的应用:
(1)  寻找真核生物的古菌祖先:综合利用宏基因组数据分析、进化分析和生化分析探讨真核生物细胞功能的进化动力和过程。
(2)“关键菌种(Keystone species)”确定:国际上目前尚无成熟可靠的方法,是与菌群(微生物)相关的环境修复和疾病治疗的瓶颈问题。
2、重大疾病心血管和脂肪肝的病理研究及药物开发:
(1)  阐述心血管和脂肪肝两类主要疾病发病机制:结合高通量组学分析和分子生物学验证,从Host和Microbiome及两者相互作用三个层面系统研究心血管和脂肪肝的发病机制,为后续药物研发确定靶标。
(2)  从深海代谢产物和中药资源中开发相关的治疗药物:充分挖掘深海代谢产物和中药资源,综合运用虚拟筛选、有机合成和药理测试开发心血管和脂肪肝治疗和预防药物或保健品。
 
主持的科研项目
1.2018-2021,国家自然科学基金(编号: 81774152),主持
2.2016-2019,上海市自然科学基金-探索类项目(编号:16ZR1449800),主持
3.2015-2016,中央高校基本科研业务费专项资金-跨学科交叉项目(编号:10247201546),主持
4.2013-2014,中央高校基本科研业务费专项资金-英才计划(编号:2000219083),主持
5.2013-2015,国家自然科学基金(编号:31200986),主持
6.2010-2012,教育部高等学校博士学科点专项科研基金(编号:2010-0072120050),主持
7.2008-2009,同济大学青年优秀人才培养行动计划(编号:2008KJ073),主持
8.2007-2010,上海市自然科学基金项目(编号:07ZR14085),主持
9.2015-至今,各种横向项目,主持
 

同行评议论文(2010年以来发表SCI检索论文56篇(其中33篇为第一作者/通讯作者))
*通讯作者
1.Jiao, N., Baker, S.S., Chapa-Rodriguez, A., Liu, W., Nugent, C. A., Tsompana, M., Mastrandrea, L., Buck, M.J., Baker, R.D., Genco, R.J., Zhu, R.*, Zhu, L. (2017). Suppressed Hepatic Bile Acid Signaling Despite Elevated Production of Primary and Secondary Bile Acids in NAFLD. Gut, gutjnl-2017.
2.Zhu, L., Baker, R.D., Zhu, R., Baker, S.S. (2017). Sequencing the gut metagenome as a non-invasive diagnosis for advanced nonalcoholic steatohepatitis. Hepatology.
3.Xie, W., Jiao, N., Ma, C., Fang, S., Phelps, T. J., Zhu, R.*, & Zhang, C. (2017). The response of archaeal species to seasonal variables in a subtropical aerated soil: insight into the low abundant methanogens. Applied Microbiology and Biotechnology, 1-11.
4.Wang, Y., Lin, W., Li, C., Singhal, S., Jain, G., Zhu, L., Lu, L., Zhu, R*., and Wang, W.(2017). Multipronged Therapeutic Effects of Chinese Herbal Medicine Qishenyiqi in the Treatment of Acute Myocardial Infarction. Frontier in pharmacology,8:98. doi: 10.3389/fphar.2017.00098.
5.Feng, Q., Liu, W., Baker, S.S., Li, H., Chen, C., Liu, Q., Tang, S., Guan, L., Tsompana, M., Kozielski, R., Baker, R.D., Peng, J., Liu, P., Zhu, R.,  Hu, Y. and Zhu, L. (2017). Multi-targeting Therapeutic Mechanisms of the Chinese Herbal Medicine QHD in the Treatment of Non-alcoholic Fatty Liver Disease." Oncotarget, in press.
6.Liu, L., Tsompana, M., Wang, Y., Wu, D., Zhu, L., & Zhu, R*. (2016). Connection Map for Compounds (CMC): A Server for Combinatorial Drug Toxicity and Efficacy Analysis. Journal of Chemical Information and Modeling, 56(9), 1615-1621.
7.Gao, J., Zhang, Q., Liu, M., Zhu, L., Wu, D., Cao, Z., & Zhu, R*. (2016). bSiteFinder, an improved protein-binding sites prediction server based on structural alignment: more accurate and less time-consuming. Journal of Cheminformatics, 8(1), 1-10.
8.Qiu, T., Qiu, J.,Feng, J., Wu, D., Yang, Y., Tang, K., Cao, Z.,& Zhu, R*. (2016).The recent progress in proteochemometric modelling: focusing on target descriptors, cross-term descriptors and application scope. Briefings in Bioinformatics,bbw004. 
9.Zhu, R., Baker, S. S., Moylan, C. A., Abdelmalek, M. F., Guy, C. D., Zamboni, F., ... & Zhu, L. (2016). Systematic Transcriptome Analysis Reveals Elevated Expression of Alcohol Metabolizing Genes in NAFLD Livers. The Journal of Pathology,238(4): 531-542.
10.Zhu, L., Baker, R. D., Zhu, R., & Baker, S. S. (2016). Gut microbiota produce alcohol and contribute to NAFLD. Gut,gutjnl-2016.
11.Yan, X., Kang, H., Feng, J., Yang, Y., Tang, K., Zhu, R., ... & Cao, Z. (2016). Identification of Toxic Pyrrolizidine Alkaloids and Their Common Hepatotoxicity Mechanism. International Journal of Molecular Sciences,17(3), 318.
12.Xu, H., Yang, Y., Wang, S., Zhu, R., Qiu, T., Qiu, J., ... & Cao, Z. (2016). Predicting the Mutating Distribution at Antigenic Sites of the Influenza Virus. Scientific Reports,6.
13.Sheng, Z., Sun, Y., Zhu, R., Jiao, N., Tang, K., Cao, Z., & Ma, C. (2015). Functional Cross-Talking between Differentially Expressed and Alternatively Spliced Genes in Human Liver Cancer Cells Treated with Berberine. PLoS ONE,10(11).
14.Sun, Y., Sheng, Z., Ma, C., Tang, K., Zhu, R., Wu, Z., ... & Cao, Z. (2015). Combining genomic and network characteristics for extended capability in predicting synergistic drugs for cancer. Nature Communications, 6.
15.Qiu, T., Xiao, H., Zhang, Q., Qiu, J., Yang, Y., Wu, D., Cao, Z., and Zhu, R*.(2015). Proteochemometric modeling of the antigen-antibody interaction: new fingerprints for antigen, antibody and epitope-paratope interaction. PLoS ONE. 22;10(4):e0122416. 
16.Cui, Z., Kang, H., Tang, K., Liu, Q., Cao, Z., and Zhu, R*. (2015) “Screening Ingredients from Herbs against Pregnane X Receptor in the Study of Inductive Herb-Drug Interactions: Combining Pharmacophore and Docking-Based Rank Aggregation,” BioMed Research International, vol. 2015, Article ID 657159, 8 pages, doi:10.1155/2015/657159. 
17.Kang, H., Zhao, Y., Li, C., Chen, Y., Tang, K., Yang, L., Ma, C., Peng, J., Zhu, R., Liu, Q., Hu, Y., and Cao, Z.(2015). Integrating clinical indexes into four-diagnostic information contributes to the Traditional Chinese Medicine (TCM) syndrome diagnosis of chronic hepatitis B. Scientific Reports,23;5:9395.
18.Zhang, W., Ji L., Chen, Y., Tang, K., Wang, H., Zhu, R., Jia, W., Cao, Z. and Liu, Q.(2015). When drug discovery meets web search: Learning to Rank for ligand-based virtual screening. Journal of Cheminformatics,13;7:5.
19.Wu, D., Qiu, T., Zhang, Q., Kang, H., Yuan, S., Zhu, L., and Zhu, R*.(2015). Systematic toxicity mechanism analysis of proton pump inhibitors: an in silico study. Chemical Research In Toxicology,16;28(3):419-30. 
20.Qi, T., Qiu, T., Zhang, Q., Tang, K., Fan, Y., Qiu, J., Wu, D., Zhang, W., Chen, Y., Gao, J., Zhu, R*., and Cao, Z.(2014). SEPPA 2.0--more refined server to predict spatial epitope considering species of immune host and subcellular localization of protein antigen. Nucleic Acids Research,2014 Jul;42(Web Server issue):W59-63. 
21.Tian, C., Zhu, R., Zhu, L., Qiu, T., Cao, Z., and Kang, T. (2014). Potassium Channels: Structures, Diseases, and Modulators. Chemical Biology & Drug Design,83, 1-26.(co-first)
22.Tian, C., Zhu, L., Yu, D., Cao, Z., Kang, T., and Zhu, R*. (2014). The Stereoselectivity of CYP2C19 on R‐and S‐isomers of Proton Pump Inhibitors. Chemical Biology & Drug Design,83, 610-621.
23.Sun, H., Wang, H., Zhu, R., Tang, K., Gong, Q., Cui, J., Cao, Z., and Liu, Q. (2014). iPEAP: integrating multiple omics and genetic data for pathway enrichment analysis. Bioinformatics,30, 737-739.
24.Liu, Q., Zhou, H., Zhu, R., Xu, Y., and Cao, Z. (2014). Reconsideration of in silico siRNA design from a perspective of heterogeneous data integration: problems and solutions. Briefings in Bioinformatics 15, 292-305.
25.Wu, Q., Kang, H., Tian, C., Huang, Q. and Zhu, R*. (2013), Binding Mechanism of Inhibitors to CDK5/p25 Complex: Free Energy Calculation and Ranking Aggregation Analysis. Molecular Informatics, 32: 251–260. doi: 10.1002/minf.201200139. 
26.Sun, Y., Zhu, R., Ye, H., Tang, K., Zhao, J., Chen, Y., Liu, Q., and Cao, Z. (2013). Towards a bioinformatics analysis of anti-Alzheimer’s herbal medicines from a target network perspective. Briefings in Bioinformatics,14, 327-343.
27.Ma, C., Tang, K., Liu, Q., Zhu, R*., and Cao, Z. (2013). Calmodulin as a potential target by which Berberine induces cell cycle arrest in human hepatoma bel7402 cells. Chemical Biology & Drug Design,81, 775-783.
28.Kang, H., Tang, K., Liu, Q., Sun, Y., Huang, Q., Zhu, R., Gao, J., Zhang, D., Huang, C., and Cao, Z. (2013). HIM-herbal ingredients in-vivo metabolism database. Journal of Cheminformatics,5, 28.
29.Gao, J., Huang, Q., Wu, D., Zhang, Q., Zhang, Y., Chen, T., Liu, Q., Zhu, R., Cao, Z., and He, Y. (2013). Study on human GPCR–inhibitor interactions by proteochemometric modeling. Gene,518, 124-131.
30.Zhang, Y., Baker, S.S., Baker, R.D., Zhu, R*., and Zhu, L. (2012). Systematic analysis of the gene expression in the livers of nonalcoholic steatohepatitis: implications on potential biomarkers and molecular pathological mechanism. PLoS ONE,7, e51131.
31.Zhang, C., Fan, K., Zhang, W., Zhu, R., Zhang, L., and Wei, D. (2012). Structure-based characterization of canine–human chimeric uricases and its evolutionary implications. Biochimie,94, 1412-1420.
32.Xu, T., Zhu, R., Liu, Q., and Cao, Z. (2012). Quantitatively integrating molecular structure and bioactivity profile evidence into drug-target relationship analysis. BMC Bioinformatics,13, 75.
33.Wu, D., Huang, Q., Zhang, Y., Zhang, Q., Liu, Q., Gao, J., Cao, Z., and Zhu, R*. (2012). Screening of selective histone deacetylase inhibitors by proteochemometric modeling. BMC Bioinformatics,13, 212.
34.Wang, H., Wu, P., Kang, H., Xu, L., Zhu, R*., and Kang, T. (2012). Modify a Fragment of Arctigenin with Pyrimidine Derivatives. CHINESE JOURNAL OF ORGANIC CHEMISTRY,32, 1894-1898.
35.Wu, Q., Kang, H., Wang, H., Gao, J., Zhu, R*., and Kang, T. (2012). AT1R-based Virtual Screening Model for Bioactive Components from Traditional Chinese Medicines and Its Mechanism Study. ACTA CHIMICA SINICA,70, 796-802. 
36.Liu, Q., Zhou, H., Zhang, K., Shi, X., Fan, W., Zhu, R., Philip, S.Y., and Cao, Z. (2012). In Silico Target-Specific siRNA Design Based on Domain Transfer in Heterogeneous Data. PLoS ONE,7, e50697.
37.Kang, H., Sheng, Z., Zhu, R., Huang, Q., Liu, Q., and Cao, Z. (2012). Virtual drug screen schema based on multiview similarity integration and ranking aggregation.Journal of Chemical Information and Modeling,52, 834-843.
38.Huang, Q., Jin, H., Liu, Q., Wu, Q., Kang, H., Cao, Z., and Zhu, R*. (2012). Proteochemometric modeling of the bioactivity spectra of HIV-1 protease inhibitors by introducing protein-ligand interaction fingerprint. PLoS ONE,7, e41698.
39.Gao, J., Liu, Q., Kang, H., Cao, Z., and Zhu, R*. (2012). Comparison of different ranking methods in protein-ligand binding site prediction. International Journal of Molecular Sciences,13, 8752-8761.
40.Gao, J., Che, D., Zheng, V.W., Zhu, R., and Liu, Q. (2012). Integrated QSAR study for inhibitors of hedgehog signal pathway against multiple cell lines: a collaborative filtering method. BMC Bioinformatics,13, 186.
41.Zhu, R., Liu, Q., Tang, J., Li, H., and Cao, Z. (2011). Investigations on inhibitors of hedgehog signal pathway: a quantitative structure-activity relationship study. International Journal of Molecular Sciences,12, 3018-3033.
42.Zhu, R., Hu, L., Li, H., Su, J., Cao, Z., and Zhang, W. (2011). Novel natural inhibitors of CYP1A2 identified by in silico and in vitro screening. International Journal of Molecular Sciences,12, 3250-3262.
43.Shen, Z., Huang, Q., Kang, H., Liu, Q., Cao, Z., and Zhu, R*. (2011). A new fingerprint of chemical compounds and its application to drugs virtual screening. ACTA CHIMICA SINICA,69, 1845-1850.
44.Ye, H., Ye, L., Kang, H., Zhang, D., Tao, L., Tang, K., Liu, X., Zhu, R., Liu, Q., and Chen, Y. (2011). HIT: linking herbal active ingredients to targets. Nucleic Acids Research,39, D1055-D1059.
45.Tang, K., Zhu, R., Li, Y., and Cao, Z. (2011). Discrimination of approved drugs from experimental drugs by learning methods. BMC Bioinformatics,12, 157.
46.Zhu, R., Wang, F., Liu, Q., and Kang, T. (2011). Quantitative Structure-Activity Relationship of IOPY/ISPY Analogues as HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors. ACTA CHIMICA SINICA,69, 1731-1736.
47.Huang, Q., Kang, H., Zhang, D., Shen, Z., Liu, Q., Zhu, R*., and Cao, Z. (2011). Comparison of ligand-, target structure-, and protein-ligand interaction fingerprint-based virtual screening methods. ACTA CHIMICA SINICA,69, 515-522.
48.Ma, C., Kang, H., Liu, Q., Zhu, R*., and Cao, Z. (2011). Insight into potential toxicity mechanisms of melamine: an in silico study. Toxicology,283, 96-100.
49.Liu, Q., Zhou, H., Liu, L., Chen, X., Zhu, R*., and Cao, Z. (2011). Multi-target QSAR modelling in the analysis and design of HIV-HCV co-inhibitors: an in-silico study.BMC Bioinformatics,12, 294.
50.Gao, J., Zhu, R., Liu, Q., and Cao, Z. (2011). Petri Net Based Metabolic Network Parameters Fitting with GPU Acceleration. Chinese Journal of Chemistry,29, 1805-1810.(co-first)
51.Dai, T., Liu, Q., Gao, J., Cao, Z., and Zhu, R*. (2011). A new protein-ligand binding sites prediction method based on the integration of protein sequence conservation information. BMC Bioinformatics,12, S9.
52.Zhu, R., Xie, M., Wang, F., Liu, Q., and Kang, T. (2010). An Efficient and Economical Method for the Preparation of Fmoc‐Argω, ω′(Boc) 2‐OH. Chinese Journal of Chemistry,28, 1508-1509.
53.Zhao, J., Geng, C., Tao, L., Zhang, D., Jiang, Y., Tang, K., Zhu, R., Yu, H., Zhang, W., and He, F. (2010). Reconstruction and analysis of human liver-specific metabolic network based on CNHLPP data. Journal of Proteome Research,9, 1648-1658.
54.Xu, X., Sun, J., Liu, Q., Wang, X., Xu, T., Zhu, R., Wu, D., and Cao, Z. (2010). Evaluation of spatial epitope computational tools based on experimentally-confirmed dataset for protein antigens. Chinese Science Bulletin,55, 2169-2174.
55.Sheng, Z., Kang, H., Dai, T., Liu, Q., and Zhu, R*. (2010). Complementary study of structure features and gene profile features for chemical compounds. ACTA CHIMICA SINICA,68, 2395-2400.
56.Liu, Q., Che, D., Huang, Q., Cao, Z., and Zhu, R*. (2010). Multi‐target QSAR Study in the Analysis and Design of HIV‐1 Inhibitors. Chinese Journal of Chemistry,28, 1587-1592.

主编教材

《计算机辅助药物设计:基本方法原理概要与实践详解》,朱瑞新编著,大连理工大学出版社,2011年,ISBN 978-7-5611-6104-3。
(国内“计算机辅助药物设计”第一本本科生专业教材,获同济大学首届本科生优秀教材奖)

教学情况
1.2015-,计算基因组学(生物信息专业)
2.2014-2015,生物信息学II(拔尖班)
3.2011-2014,生物信息学实验(生物技术专业)
4.2010-,课程设计(生物信息专业)
5.2009-,计算机辅助药物设计(生物信息专业)

获得荣誉情况
1.2017年,同济大学“优秀毕业设计指导教师”(生物信息专业唯一名额,再次蝉联)。
2.2016年,同济大学“优秀本科生教材二等奖”。
3.2016年,同济大学“优秀毕业设计指导教师”(生物信息专业唯一名额,蝉联)。
4.2015年,同济大学生命科学与技术学院“先进工作者”。
5.2015年,同济大学生命科学与技术学院“年度考核优秀教师”。
6.2015年,同济大学年度考核被评为“校优”(排名第一)。
7.2015年,同济大学“优秀毕业设计指导教师” (生物信息专业唯一名额)。
8.2013年,同济大学生命科学与技术学院首届“优秀班主任奖”。
9.2012年,同济大学“教学奖二等奖”。
10.2012年,同济大学“优秀青年教师优青计划” (英才计划)。
11.2012年,同济大学生命科学与技术学院首届“教学贡献奖二等奖”。
12.2010年,首届同济大学“优秀青年教师培育计划” (英才计划)。

 

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