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导师简介
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曹东升副教授
2016-11-21 16:28  


曹东升,男,1983年生,工学博士,副教授。师承著名化学计量学专家梁逸曾教授,研究方向为化学计量学、化学信息学、计算机辅助药物设计及系统生物学,主要从事基于人工智能系统的计算机药物发现和疾病诊断研究。2014年中南大学升华猎英人才计划引进到药学院工作。至今发表SCI科研论文90多篇,其中第一作者和通讯作者41篇,影响因子总和约310,累计引用次数1357次,H因子18,36篇文章引用次数超过10次。单篇最高引用135次,进入ESI高引前0.1%行列。合著外文专著一部(第四作者),此书共八章,主要撰写三章,书名《Support Vector Machines and Their Application in Chemistry and Biotechnology》;参编中文书籍一部,书名《复杂体系仪器分析-白、灰、黑分析体系及其多变量解析方法》。工作至今获得多项荣誉和奖励:湖湘青年科技创新人才(湖湘英才),湖南省优秀博士论文获得者,教育部学术新人奖,宝钢教育特等奖学金(全国50名获奖者中排名第七),国家奖学金,中南大学全国优秀博士资助基金,湖南省博士论文创新基金,中南大学十佳博士称号,中南大学优秀共产党员等。现应邀为"BMC Bioinformatics", "Bioinformatics","Journal of Chemoinformatics","Journal of Chemical Information and Modeling","Journal of Chemometrics", "Chemometrics and Intelligent Laboratory Systems", "Journal of Chromatography A", "Analytica Chimica Acta","PLOS ONE",“Talanta”, “Molecular Informatics”, "OMICS Group"和"Analytical Letters"等杂志审稿人。

个人邮箱:oriental-cds@163.com

课题组网站首页:http://home.scbdd.com/

教育经历:

2009年-2013年,中南大学化学化工学院,博士毕业/工学博士学位,导师:梁逸曾教授

2006年-2009年,中南大学化学化工学院,硕士毕业/理学硕士学位,导师:梁逸曾教授

2002年-2006年,中南大学化学化工学院,大学毕业/制药工程工学学士学位

研究方向:

计算生物学和药物设计实验室致力于运用和发展一些新的概念,算法和软件在海量数据中快速的筛选具有生物活性的先导化合物,以及对复杂疾病系统实现快速的诊断和评估。药物分子设计过程涉及到多种科学原理的运用,而且需要严密的跨学科交叉研究的思维方式。我们运用了各种机器学习方法、化学信息学以及生物信息学技术来实现自动的问题假设生成,活性预测和验证研究。疾病诊断旨在研究疾病显型与各种组学(基因组学/转录组学/蛋白组学/代谢组学/显型组学)的关系。一个好的疾病诊断模型需要整合多种组学数据进行建模分析和评估。我们运用了各种人工智能方法、生物信息学以及系统生物学技术来实现自动的问题假设生成,疾病诊断和潜在生物标记物的发现。

本课题组主要开展以下四方面研究工作:

1:新型人工智能算法及机器学习算法在药物发现和疾病诊断研究中的发展和应用

2:基于人工智能系统和系统药理学的计算机辅助分子设计研究

3:复杂疾病系统中显型组与基因组关系的大标度计算研究

4:系统生物学和药物发现过程中软件、Web服务及数据库的发展

在研项目:

1. 国家自然科学基金青年基金,81402853,基于多尺度系统生物学的药物-

副作用相互作用网络预测研究,2015.01-2017.01,23万,在研,主持。

2.国家青年973项目,2015CB910700,蛋白激酶R在脓毒症中导致免疫抑制

的分子调控机制,2015.01-2019.01,80万,在研,子课题负责人。

3.国家博士后基金特别资助基金,2014T70794,基于多尺度系统药理学的

组合药物研究,2014.08-2016.08,15.00万,在研,主持。

4.国家博士后基金面上资助基金,2014M562142,基于系统药理学的多尺

度融合模型方法研究,2014.09-2016.09,5万,在研,主持。

5.湖南省优秀博士论文基金,基于多尺度系统药理学的组合药物研究,

2015.05-2017.05,3万,在研,主持。

6.国家香江学者计划,2015.02-2017.02,60.00万,在研,主持。

7.中南大学升华猎英学者计划,2014.05-2019.05,50.00万,在研,主持。

8.中南大学创新驱动计划(第二批),2015.09-2017.12, 95万, 在研,主持。

9.湖南省湖湘青年英才计划,2015.05-2017.05, 20万, 在研,主持。

近五年已发表SCI期刊论文(第一作者或通讯作者):

[1]Dong-Sheng Cao, Qing-Song Xu, Yi-Zeng Liang*. propy: a tool to generate various modes of Chou's PseAAC.Bioinformatics, 29(7),960-962, 2013. (影响因子:5.766)

[2]Dong-Sheng Cao*, Nan Xiao, Yuan-Jian Li, Wen-Bin Zeng, Yi-Zeng Liang, Ai-Ping Lu, Qing-Song Xu, Alex F Chen. Integrating multiple evidence sources to predict adverse drug reactions based on a systems pharmacology model.CPT: Pharmacometrics & Systems Pharmacology. 4(9), 498-506, 2015.(影响因子:7.268)

[3]Dong-Sheng Cao, Qing-Song Xu, Q.N. Hu, Yi-Zeng Liang*. chemopy: freely available python package for computational biology and chemoinformatics.Bioinformatics, 29(8), 1092-1094, 2013. (影响因子:5.766)

[4]Dong-Sheng Cao*,Nan Xiao, Qing-Song Xu, Alex F Chen.Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds, and their interactions.Bioinformatics, btu624, 2015. (影响因子:5.766)

[5]Dong-Sheng Cao, Qing-Song Xu, Liang-Xiao Zhang, Jian-Hua Huang, Yi-Zeng Liang*. Tree-based ensemble methods and their applications in analytical chemistry.Trends in Analytical Chemistry, 40, 158-167, 2012. (影响因子:7.487)

[6] Nan Xiao,Dong-Sheng Cao*,Min-Feng Zhu, Qing-Song Xu.protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences.Bioinformatics, btv042, 2015. (影响因子:5.766)

[7]Dong-Sheng Cao*, Gua-Hua Zhou, Shao Liu, Liu-Xia Zhang, Qing-Song Xu, Min He, Yi-Zeng Liang. Large-scale prediction of human kinase-inhibitor interactions using protein sequences and molecular topological structures.Analytica Chimica Acta, 792, 10-18, 2013. (影响因子:4.712)

[8]Dong-Sheng Cao, Yi-Zeng Liang*, Zhe Deng, Qian-Nan Hu, Min He, Guang-Hua Zhou, Liu-Xia Zhang, Qing-Song Xu, Shao Liu. Genome-scale screening of drug-target associations relevant to Ki binding affinity using a chemogenomics approach.PLOS ONE, 8, e57680, 2013. (影响因子:3.057)

[9]Jie Dong, Zhi-Jiang Yao, Ming Wen, Min-Feng Zhu, Ning-Ning Wang, Hong-Yu Miao, Ai-Ping Lu, Wen-Bin Zeng,Dong-Sheng Cao*. BioTriangle: a web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions.Journal of Cheminformatics, 8(1), 1-13.,2016.(影响因子:3.949)

[10] Zhi-Jiang Yao, Jie Dong, Yu-Jing Che, Min-Feng Zhu, Ming Wen, Ning-Ning Wang, Shan Wang, Ai-Ping Lu,Dong-Sheng Cao*. TargetNet: a web service for predicting potential drug–target interaction profiling via multi-target SAR models.Journal of Computer-aided Molecular Design.30, 413-424, 2016.(影响因子:3.199)

[11]Ning-Ning Wang, Jie Dong, Yin-Hua Deng, Min-Feng Zhu, Ming Wen, Zhi-Jiang Yao, Ai-Ping Lu, Jian-Bing Wang,Dong-Sheng Cao*. ADME Properties Evaluation in Drug Discovery: Prediction of Caco-2 Cell Permeability Using a Combination of NSGA-II and Boosting.Journal of Chemical Information and Modeling. 56(4), 763-773, 2016.(影响因子:3.657)

[12] Bai-Chuan Deng, Yong-Huan Yun,Dong-Sheng Cao*, Yu-Long Yin, Wei-Ting Wang, Hong-Mei Lu, Qian-Yi Luo, Yi-Zeng Liang*. A bootstrapping soft shrinkage approach for variable selection in chemical modeling.Analytica Chimica Acta, 908, 63-74, 2016.(影响因子:4.712)

[13] Ming Wen, Bai-Chuan Deng,Dong-Sheng Cao*, Rui-Han Yang, Yong-Huan Yun, Hong-Mei Lu, Yi-Zeng Liang. The model adaptive space shrinkage (MASS) approach: a new method for simultaneous variable selection and outlier detection based on model population analysis.Analyst, DOI: 10.1039/c6an00764c, 2016. (影响因子:4.033)

[14]Dong-Sheng Cao, Shao Liu, Qing-Song Xu, Hong-Mei Lu, Jian-Hua Huang, Qian-Nan Hu, Yi-Zeng Liang*.Large-scale prediction of drug-target interactions using protein sequences and drug topological structures.Analytica Chimica Acta, 752, 1-10, 2012. (封面文章,影响因子:4.712)

[15] Jie Dong,Dong-Sheng Cao*, Hong-Yu Miao, Shao Liu, Bai-Chuan Deng, Yong-Huan Yun, Ning-Ning Wang, Ai-Ping Lu, Wen-Bin Zeng*, Alex F Chen. ChemDes: an integrated web-based platform for molecular descriptor and fingerprint computation,Journal of Cheminformatics. 7(1), 1-10, 2015.(影响因子:3.949)

[16]Dong-Sheng Cao, Yi-Zeng Liang*, Qing-Song Xu, Hong-Dong Li, Xian Chen. A new strategy of outlier detection for QSAR/QSPR.Journal of Computational Chemistry, 31(3), 592-602, 2010. (影响因子:3.648)

[17]Dong-Sheng Cao*, Yi-Zeng Liang, Jun Yan, Gui-Shan Tan, Qing-Song Xu, Shao Liu. PyDPI: a powerful tool for chemoinformatics, bioinformatics and chemogenomics study.Journal of Chemical Information and Modeling, 53, 3086-3096, 2013. (影响因子:3.657)

[18]Dong-Sheng Cao, Mao-Mao Zeng, Lun-Zhao Yi, Bing Wang, Qing-Song Xu, Hong-Mei Lu, Yi-Zeng Liang*. A Novel Kernel Fisher Discriminant Analysis: Constructing Informative Kernel by Decision Tree Ensemble for Metabolomics Data Analysis.Analytica Chimica Acta, 706(1), 97-104, 2012.(影响因子:4.712)

[19] Bai-Chuan Deng, Yong-Huan Yun, Yi-Zeng Liang*,Dong-Sheng Cao*, Qing-Song Xu, Lun-Zhao Yi, Xin Huang. A new strategy to prevent over-fitting in partial least squares models based on model population analysis.Analytica Chimica Acta. 880, 32-41, 2015.(影响因子:4.712)

[20]Dong-Sheng Cao, Bing Wang, Mao-Mao Zeng, Yi-Zeng Liang*,Qing-Song Xu, Liang-Xiao Zhang, Hong-Dong Li, Qian-Nan Hu. A new strategy of exploring metabonomics data using Monte Carlo Tree.Analyst, 136, 947-954, 2011.(影响因子:4.033)

[21]Dong-Sheng Cao*, Liu-Xia Zhang, Gui-Shan Tan, Zheng Xiang, Wen-Bin Zeng, Qing-Song Xu, Alex F Chen.Computational Prediction of Drug-Target Interactions Using Chemical, Biological, and Network Features.Molecular Informatics, 33 (10), 669-681, 2014. (影响因子:1.57)

[22] Liang Shen,Dongsheng Cao(共同第一作者), Qingsong Xu, Xin Huang, Nan Xiao, Yizeng Liang. A novel local manifold-ranking based K-NN for modeling the regression between bioactivity and molecular descriptors.Chemometrics and Intelligent Laboratory Systems, 151, 71-77, 2016.(影响因子:2.217)

[23] Yong Wang, Jing‐Jing Huang, Neng Zhou,Dong-Sheng Cao*, Jie Dong, Han-Xiong Li. Incorporating PLS model information into particle swarm optimization for descriptor selection in QSAR/QSPR.Journal of Chemometrics.29(12), 627-636, 2015.(影响因子:1.873)

[24] Jian‐Bing Wang,Dong-Sheng Cao*, Min‐Feng Zhu, Yong‐Huan Yun, Nan Xiao, Yi‐Zeng Liang*. In silico evaluation of logD7. 4 and comparison with other prediction methods.Journal of Chemometrics. 29(7), 389-398, 2015.(影响因子:1.949)

[25]Dong-Sheng Cao*, Shao Liu, Wen‐Bin Zeng, Yi‐Zeng Liang. Sparse canonical correlation analysis applied to‐omics studies for integrative analysis and biomarker discovery.Journal of Chemometrics. 29(6), 371-378, 2015.(影响因子:1.873)

[26]Dong-Sheng Cao*, Jie Dong, Ning-Ning Wang, Ming Wen, Bai-Chuan Deng, Wen-Bin Zeng, Qing-Song Xu, Yi-Zeng Liang, Ai-Ping Lu, Alex F Chen.In silicotoxicity prediction of chemicals from EPA toxicity database by kernel fusion-based support vector machines.Chemometrics and Intelligent Laboratory Systems. 146, 494-502, 2015.(影响因子:2.217)

[27]Dong-Sheng Cao, Qian-Nan Hu, Qing-Song Xu, Yi-Zeng Liang*, Liang-Xiao Zhang.In silicoestimation of human maximum recommended daily dose based on adaptive random forest and substructure fingerprint.Analytica Chimica Acta, 692, 50-56, 2011.(影响因子:4.712)

[28]Dong-Sheng Cao, Qing-Song Xu, Yi-Zeng Liang*, Yi-Feng Yun, Hong-Dong Li. Toward Clean QSAR/QSPR Datasets: Simultaneous Outlier Detection and Variable Selection Using Distribution of Model Features.Journal of Computer-aided Molecular Design, 25, 67-80, 2011. (影响因子:3.199)

[29]Dong-Sheng Cao, Yan-Ning Yang, Jian-Chao Zhao, Jun Yan, Qing-Song Xu, Yi-Zeng Liang*. Computer-Aided Prediction of Toxicity with Substructure Pattern and Random Forest.Journal of Chemometrics, 26, 7-15, 2012. (影响因子:1.873)

[30]Dong-Sheng Cao, Jian-Hua Huang, Jun Yan, Liang-Xiao Zhang, Qian-Nan Hu, Qing-Song Xu, Yi-Zeng Liang*. Kernelk-nearest neighbor algorithm as a flexible SAR modeling tool.Chemometrics and Intelligent Laboratory Systems, 114, 19-23, 2012. (影响因子:2.217)

[31]Dong-Sheng Cao, Qing-Song Xu, Yi-Zeng Liang*, Lian-Xiao Zhang, Hong-Dong Li. The boosting: A new idea of building models.Chemometrics and Intelligent Laboratory Systems, 100, 1-11, 2010. (影响因子:2.217)

[32]Dong-Sheng Cao, Qing-Song Xu, Yi-Zeng Liang*, Xian Chen, Hong-Dong Li. Prediction of aqueous solubility of druglike organic compounds using partial least squares, back-propagation network and support vector machine.Journal of chemometrics, 24, 584-595, 2010. (影响因子:1.873)

[33]Dong-Sheng Cao, Qing-Song Xu, Yi-Zeng Liang*, Hong-Dong Li. Automatic Feature Subset Selection for Decision Tree-Bsaed Ensemble Methods in the Prediction of Bioactivity.Chemometrics and Intelligent Laboratory Systems, 103, 129-136, 2010.(影响因子:2.217)

[34]Dong-Sheng Cao, Qing-Song Xu, Yi-Zeng Liang*, Hong-Dong Li. Feature importance sampling-based adaptive random forest as a useful tool to screen underlying lead compounds.Journal of Chemometrics, 25, 201-207, 2011.(影响因子:1.873)

[35]Dong-Sheng Cao, Qing-Song Xu, Yi-Zeng Liang*, Hong-Dong Li. Exploring nonlinear relationships in chemical data using kernel-based methods.Chemometrics and Intelligent Laboratory Systems, 107, 106-115, 2011.(影响因子:2.217)

[36]Dong-Sheng Cao, Jian-Chao Zhao, Yan-Ning Yang, Chen-Xi Zhao, Jun Yan, Shao Liu, Qian-Nan Hu, Qing-Song Xu, Yi-Zeng Liang*.In silicotoxicity prediction by support vector machine and SMILES representation-based string kernel.SAR and QSAR in Environmental Research, 23, 141-153, 2012. (影响因子:1.897)

[37]Dong-Sheng Cao*, Shao Liu, Lan Fan, Chen-Xi Zhao, Qing-Song Xu, Yi-Zeng Liang. QSAR analysis of the effects of OATP1B1 transporter by structurally diverse natural products using a particle swarm optimization-combined multiple linear regression approach.Chemometrics and Intelligent Laboratory Systems, 130, 84-90, 2014. (影响因子:2.217)

[38]Jun Yan,Dong-Sheng Cao(共同第一作者), Fang-Qiu Guo, Liang-Xiao Zhang, Jian-Hua Huang, Min He, Qing-Song Xu, Yi-Zeng Liang*. Comparison of QSRR models on four stationary phases with different polarity for a diverse set of flavor compounds.Journal of Chromatography A, 1223, 118-125, 2012. (影响因子:3.926)

[39]Jian-Hua Huang,Dong-Sheng Cao(共同第一作者), Jun Yan, Qing-Song Xu, Qian-Nan Hu, Yi-Zeng Liang*. Using core hydrophobicity to identify phosphorylation sites of human G protein-coupled receptors.Biochime, 94, 1697-1704, 2012. (影响因子:2.474)

[40] Min He,Dong-Sheng Cao (共同第一作者), Yi-Zeng Liang*, Ya-Ping Li, Qing-Song Xu, Han Wu, Chen-Xi Zhao, Ren-Bin Huang. Pressor mechanism evaluation for phytochemical compounds usingin silicocompound-protein interaction prediction.Regulatory Toxicology and Pharmacology, 67, 115-124, 2013. (影响因子:2.227)

[41]Xin Huang,Dong-Sheng Cao(共同第一作者), Qing-Song Xu, Liang Shen, Jian-Hua Huang, Yi-Zeng Liang*. A novel tree kernel support vector machine classifier for modeling the relationship between bioactivity and molecular descriptors.Chemometrics and Intelligent Laboratory Systems, 120, 71-76, 2013. (影响因子:2.217)

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