研究方向新药创制方法学及现代中药设计技术
药品质量检测方法学及质量控制技术
工业药学及先进制药技术研究
药物分析信息学与临床药学研究学院副院长、浙江大学药物信息学研究所所长、国家中医药管理局计算机辅助中药分析III级实验室主任
社会兼职国家药典委员会委员、国家药品审评专家、教育部高等学校药学类中药专业教学指导委员会委员、中国药学会中药及天然药物专业委员会理事、中国中医药信息数字化专业委员会副主任、中国中医药研究促进会理事、中国药材GAP研究促进会理事、浙江省药学会常务理事及制药工程专业委员会主任、浙江省中医药学会博士学术委员会副主任；
《化学学报》、《中国中药杂志》、《中草药》、《药物分析杂志》等刊物编委；
上海交通大学计算机系兼职教授、上海中医药大学兼职教授、中药标准化教育部重点实验室学术委员
主要荣誉国务院政府特殊津贴专家，天津市人民政府特聘专家，浙江省有突出贡献中青年专家，浙江省151人才工程重点资助人员、浙江省新世纪学术和技术带头人第一层次。
作为第一获奖者获国家科技进步二等奖1项、省级科技进步二等奖5项、省级科技进步三等奖2项、中华中医药学会科学技术奖3项；作为第二获奖者获浙江省教学成果二等奖及高校优秀教材二等奖各1项；作为第三获奖者获2005年天津市自然科学一等奖。指导的博士生获2005年全国优秀博士论文提名论文。
研究课题近5年主持研究或负责完成国家973计划项目、国家自然科学基金重点项目、国家科技攻关重点项目等国家重要课题5项。此外，还承担了一批国家级普通课题及横向科研重大课题10余项。
主要论文近年作为责任作者发表论文200余篇，其中被SCI收录120余篇，IF>3论文20篇。代表性论文有：
1. Ma, GL; Cheng, YY*，Predicting Caco-2 permeability using support vector machine and Chemistry Development Kit，JOURNAL OF PHARMACY AND PHARMACEUTICAL SCIENCES, 9 (2): 210-221 MAY-AUG 2006
2. Zhang, YF; Shi, QR; Shi, PY; Zhang, WD; Cheng, YY*，Characterization of isoquinoline alkaloids, diterpenoids and steroids in the Chinese herb Jin-Guo-Lan (Tinospora sagittata and Tinospora capillipes) by high-performance liquid chromatography/electrospray ionization with multistage mass spectrometry，RAPID COMMUNICATIONS IN MASS SPECTROMETRY, 20 (15): 2328-2342 2006
3. Luo, PH; He, QJ; He, XG; Hu, YZ; Lu, W; Cheng, YY*; Yang, B，Potent antitumor activity of 10-methoxy-9-nitrocamptothecin，MOLECULAR CANCER THERAPEUTICS, 5 (4): 962-968 APR 2006
4. Cheng, YY*; Wang, Y; Wang, XW，A causal relationship discovery-based approach to identifying active components of herbal medicin，COMPUTATIONAL BIOLOGY AND CHEMISTRY, 30 (2): 148-154 APR 2006
5. Cheng, YY*; Yuan, H，A simple approach to the prediction of electrophoretic mobilities of diverse organic acids，ANALYTICA CHIMICA ACTA, 565 (1): 112-120 APR 13 2006
6. Wang, SF; Ye, S; Cheng, YY*，Separation and on-line concentration of saponins from Panax notoginseng by micellar electrokinetic chromatograph，JOURNAL OF CHROMATOGRAPHY A, 1109 (2): 279-284 MAR 24 2006
7. Yu, K; Lin, ZY; Cheng, YY*，Optimization of the buffer system of micellar electrokinetic capillary chromatography for the separation of the active components in Chinese medicine 'SHUANGDAN' granule by genetic algorithm，ANALYTICA CHIMICA ACTA, 562 (1): 66-72 MAR 9 2006
8. Fan, XH; Wang, Y; Cheng, YY*，LC/MS fingerprinting of Shenmai injection: A novel approach to quality control of herbal medicines，JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS, 40 (3): 591-597 FEB 24 2006
9. Cheng, YY*; Yuan, H，Quantitative study of electrostatic and steric effects on physicochemical property and biological activity，JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 24 (4): 219-226 JAN 2006
10. Fan, XH; Cheng, YY*; Ye, ZL; Lin, RC; Qian, ZZ，Multiple chromatographic fingerprinting and its application to the quality control of herbal medicines，ANALYTICA CHIMICA ACTA, 555 (2): 217-224 JAN 12 2006
11. Liu, L; Ning, ZQ; Shan, S; Zhang, K; Deng, T; Lu, XP; Cheng, YY*，Phthalide lactones from Ligusticum chuanxiong inhibit lipopolysaccharide-induced TNF-alpha production and TNF-alpha-mediated NF-kappa B activation，PLANTA MEDICA, 71 (9): 808-813 SEP 2005
12. Shen, P; Fan, XH; Zeng, Z; Cheng, YY*，Two-dimensional electrophoresis analysis of proteomics based on image feature and mathematical morphology，SCIENCE IN CHINA SERIES B-CHEMISTRY, 48 (4): 361-367 AUG 2005
13. Yan, SK; Xin, WF; Luo, GA; Wang, YM; Cheng, YY*，An approach to develop two-dimensional fingerprint for the quality control of Qingkailing injection by high-performance liquid chromatography with diode array detection，JOURNAL OF CHROMATOGRAPHY A, 1090 (1-2): 90-97 OCT 7 2005
14. Wu, YJ; Chen, JJ; Cheng, YY*，A sensitive and specific HPLC-MS method for the determination of sophoridine, sophocarpine and matrine in rabbit plasma，ANALYTICAL AND BIOANALYTICAL CHEMISTRY, 382 (7): 1595-1600 AUG 2005
15. Cheng, YY*; Chen, MJ; Welsh, WJ，Fractal fingerprinting of chromatographic profiles based on wavelet analysis and its application to characterize the quality grade of medicinal herbs，JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES, 43 (6): 1959-1965 NOV-DEC 2003
16. Cheng, YY*; Chen, MJ; Tong, WD，An approach to comparative analysis of chromatographic fingerprints for assuring the quality of botanical drugs，JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES, 43 (3): 1068-1076 MAY-JUN 2003
17. Yang, NL; Cheng, YY*; Wu, YJ，A new method for fast and nondestructive analysis of saponins in Panax notoginseng herb by near infrared spectroscopy，ACTA CHIMICA SINICA, 61 (3): 393-398 MAR 2003
18. Zhang, HJ; Wu, YJ; Cheng, YY*，Analysis of 'SHENMAI' injection by HPLC/MS/MS，JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS, 31 (1): 175-183 FEB 5 2003
19. Cheng, YY*; Chen, MJ; Wu, YJ，Measures for determining the similarity of chemical fingerprint and a method of evaluating the measures，ACTA CHIMICA SINICA, 60 (11): 2017-2021 NOV 2002
20. Cheng, YY*; Yu, J; Wu, YJ，A visualization method of chromatographic data for discovering fingerprint features of natural herbal medicines，ACTA CHIMICA SINICA, 60 (2): 328-333 FEB 2002
21. Cheng, YY*; Zhao, MJ，A type of fuzzy classification neural networks for complex nonlinear chemical pattern recognition，CHEMICAL JOURNAL OF CHINESE UNIVERSITIES, 22 (11): 1813-1818 NOV 2001
22. Zhao, MJ; Cheng, YY*; Chen, WZ，A stepwise method for extracting the characteristic of complex chemical pattern in natural plants，ACTA CHIMICA SINICA, 59 (6): 842-846 2001
