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HU Qian-Nan

Ph.D.

Professor, Principal Investigator

Laboratory of Microbial Cell Factory Design

Lab Page Link : http://hulab.rxnfinder.org/

Email: qnhu@sibs.ac.cn

Research Areas

Dr. Qian-Nan Hu has been devoted to developing microbial cell factory design platform. Dr. Hu developed a data-driven one-stop biosynthetic design technology system at www.rxnfinder.org. Dr. Hu has outstanding achievements on:

(1) organizing more than 100 people curating more than 250, 000 biochemical reactions from more than 500,000 biosynthetic publications, which represents the most comprehensive biochemical reaction database (RxnFinder).

(2) enzyme discovery using reaction difference fingerprints considering chemical transformations and substrate specificity (ECAssigner).

(3) interactive biosynthetic pathway design web server using the most comprehensive biochemical reactions (BioSynther-Router).

(4) biosynthetic potentials of low-value chemical precursors using greedy search algorithms (BioSynther).

(5) biosynthetic target molecule selection using network pharmacology database and models, in which more than 500,000 biological active compounds are integrated with more than thousands of diseases, thousands of drug targets or potential targets (VNP, FIM, preDPI-ki, DiTaD).

(6) microbial cell strain optimization using metabolic networks and enormous heterologous reactions, and probability optimization models (EcoSynther, SynBioEcoli).

(7) implementation of one-stop microbial cell factory design techniques using big data, chemoinformatics, bioinformatics, systems biology and various IT tools, methods and models (www.rxnfinder.org).

(8) creating a novel chassis-based biosynthetic pathway design tool (EcoSynther) to design new pathways for different target molecules using heterogeneous reactions.

 

Brief Biography

2017-Present: Principal Investigator, Professor, CAS-MPG Partner Institute of Computational Biology (PICB), CAS, China

2014-2017: Professor, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China.

2010-2014: Associate Professor, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan, China.

2008-2010: Institute Research Fellow, Bioinformatics Center, Institute of Chemical Research, Kyoto University, Kyoto, Japan.

2007-2008: Postdoc., Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, CA, U.S.A.

2004-2007: Postdoc., Computer Chemistry Center, University of Erlangen-Nurnberg, Erlangen, Germany.

2001-2004: Ph.D. Applied Chemistry (Chemoinformatics), Central South University

1997-2001: MS. Analytical Chemistry (Chemometrics), Central South University

1994-1997: BS. Analytical Chemistry, Central South University

 

Selected Publications: (*Corresponding Author)

  1. Tong Zhang, Yu Tian, Le Yuan, Fu Chen, Ailin Ren, Qian-Nan Hu*. Bio2Rxn: Sequence-Based Enzymatic Reaction Predictions by a Consensus Strategy. Bioinformatics 2020 Feb 28. DOI: 10.1093/bioinformatics/btaa135.
  2. Dachuan Zhang et al Qian-Nan Hu*. FRCD: A Comprehensive Food Risk Component Database With Molecular Scaffold, Chemical Diversity, Toxicity, and Biodegradability Analysis. Food Chem 318, 126470 2020 Feb 24.
  3. Cheng X, Sun D, Zhang D, Tian Y, Ding S, Cai P, Qian-Nan Hu*. RxnBLAST: Molecular Scaffold and Reactive Chemical Environment Feature Extractor for Biochemical Reactions. Bioinformatics 2020 Jan 17. pii: btaa036.
  4. Dachuan Zhang et al Qian-Nan Hu*. AdditiveChem: a comprehensive bioinformatic knowledge-base for food additive chemicals. Food Chemistry 2020, 308:125519.
  5. Yu Tian et al Qian-Nan Hu*. BCSExplorer: A Customized Biosynthetic Chemical Space Explorer with Multifunctional Objective Function Analysis. Bioinformatics 2019, pii: btz755.
  6. Shaozhen Ding et al Qian-Nan Hu*. CF-Targeter: a rational biological cell factory targeting platform for biosynthetic target chemicals. ACS Synthetic Biology 2019, 8(10):2280-2286.
  7. Fu Chen et al Qian-Nan Hu*. Data-Driven Rational Biosynthesis Design: From Molecules to Cell Factories. Briefings in Bioinformatics 2019, pii: bbz065.
  8. Le Yuan, Weizhong Tu, et al Qian-Nan Hu*. PrecursorFinder: a customized biosynthetic precursor explorer. Bioinformatics2019,35(9):1603-1604.
  9. Shaozhen Ding, Xiaoping Liao, Weizhong Tu, Ling Wu, Yu Tian, Qiuping Sun, Junni Chen, Qian-Nan Hu*. EcoSynther: A customized platform to explore biosynthetic potential in E. coli. ACS Chemical Biology 2017, 12(11):2823-2829.
  10. Deng Zhe, WeiZhong Tu, ZiXin Deng*, Qian-Nan Hu*. PhID: an open-access integrated pharmacology interactions database for drugs, targets, diseases, genes, side-effects and pathways. Journal of Chemical Information and Modeling 2017, 57(10):2395-2400.
  11. Weizhong Tu, Qian-Nan Hu*. SynBioEcoli a comprehensive metabolism network of engineered E. coli in three dimensional visualization. Quantitative Biology 2017, doi:10.1007/s40484-017-0098-1.
  12. 张国庆, 宁康, 职晓阳, 刘婉, 徐萍, 周豪魁, 胡黔楠, 赵国屏. 建设微生物组大数据中心发挥长期科学影响. 中国科学院院刊杂志 2017, 3:280-289.
  13. Tu W, Zhang H, Liu J, Qian-Nan Hu*. BioSynther: a customized biosynthetic potential explorer. Bioinformatics 2016, 32:472-473.
  14. Caihua Wang, Juan Liu, Fei Luo, Qian-Nan Hu*. Multi-fields model for predicting target-ligand interaction. Neurocomputing 2016, 206:58-65.
  15. Wang CH, Liu J, Luo F, Deng ZX, Qian-Nan Hu*. Predicting target-ligand interactions using protein ligand-binding site and ligand substructures. BMC Systems Biology 2015, 9:S2.
  16. 胡黔楠*, 吴玲, 涂伟忠, 丁邵珍, 张红雨. 微生物药物生物合成知识库研究进展,生物产业技术 2015, 6:59-62.
  17. Qian-Nan Hu*, Zhe Deng, Weizhong Tu, Xiaoyan Yang, Zhibin Meng, Zixin Deng and Juan Liu. VNP: Interactive Visual Network Pharmacology of Diseases, Targets and Drugs. CPT: Pharmacometrics & Systems Pharmacology 2014, 3, e105.
  18. Jinmei Zhu, Chunfeng Wu, Xiaobing Li, Guisheng Wu, Shan Xie, Qian-Nan Hu, Zixin Deng, Micheal X. Zhu, Huairong Luo, Xuechuan Hong. Synthesis, biological ? evaluation and molecular modeling of substituted 2-butyryliocholine aminobenzimidazoles as new dual inhibitors of acetylchlinesterase and butyrylcholinesterase. Bioorganic & Medicinal Chemistry 2013, 21(14):4218-4224.
  19. Dong-Sheng Cao, Qing-Song Xu, Qian-Nan Hu, Yi-Zeng Liang. ChemoPy: freely available python package for computational biology and chemoinformatics. Bioinformatics 2013, 29(8):1092-1094.
  20. Dong-Sheng Cao, Yi-Zeng Liang, Zhe Deng, Qian-Nan Hu*, Min He, Qing-Song Xu, Guang-Hua Zhou, Liu-Xia Zhang, Zi-xin Deng, Shao Liu. Genome-Scale Screening of Drug-Target Associations Relevant to Ki Using a Chemogenomics Approach. PLoS One 2013, 8(4):e57680.
  21. Qian-Nan Hu*, Hui Zhu, Xiaobing Li, Manman Zhang, Zhe Deng, Xiaoyan Yang and Zixin Deng. Assignment of EC Numbers to Enzymatic Reactions with Reaction Difference Fingerprints. PLoS One 2012, 7(12):e52901.
  22. 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. Anal Chim Acta 2012, 752:1-10.
  23. Dong-Sheng Cao, Jian-Hua Huang, Jun Yan, Liang-Xiao Zhang, Qian-Nan Hu, Qing-Song Xu, Yi-Zeng Liang. Kernel k-nearest neighbor algorithm as a flexible SAR modeling tool. Chemometrics and Intelligent Laboratory Systems 2012, 114:19-23.
  24. Jian-Hua Huang, Dong-Sheng Cao, Jun Yan, Qing-Song Xu, Qian-Nan Hu, Yi-Zeng Liang. Using core hydrophobicity to identify phosphorylation sites of human G protein-coupled receptors. Biochimie 2012, 94(8):1697-1704.
  25. Dong-Sheng Cao, Jian-Chao Zhao, Yan-Ning Yang, Jun Yan, Shao Liu, Qian-Nan Hu, Qing-Song Xu, Yi-Zeng Liang. In silico toxicity prediction by support vector machine and SMILES representation-based string kernel. SAR QSAR Environ Res 2012, 23(1-2):141-53.
  26. Dong-Sheng Cao, Yan-Ning Yang, Jian-Chao Zhao, Jun Yan, Shao Liu, Qian-Nan Hu, Qing-Song Xu, Yi-Zeng Liang. Computer-aided prediction of toxicity with substructure pattern and random forest. Journal of Chemometrics 2012, 26(1-2):7-15.
  27. Dong-Sheng Cao, Mao-Mao Zeng, Lun-Zhao Yi, Bing Wang, Qing-Song Xu, Qian-Nan Hu, Liang-Xiao Zhang, Hong-Mei Lu, Yi-Zeng Liang. A novel kernel Fisher discriminant analysis: constructing informative kernel by decision tree ensemble for metabolomics data analysis. Anal Chim Acta 2011, 706(1):97-104.
  28. Qian-Nan Hu*, Zhe Deng, Huanan Hu, Dong-Sheng Cao, Yi-Zeng Liang. RxnFinder: Biochemical Reaction Search Engines Using Molecular Structures, Molecular Fragments, and Reaction Similarity. Bioinformatics 2011, 27(17):2465-2467.
  29. Dong-Sheng Cao, Qian-Nan Hu, Qing-Song Xu, Yan-Ning Yang, Jian-Chao Zhao, Hong-Mei Lu, Liang-Xiao Zhang, Yi-Zeng Liang. In silico classification of human maximum recommended daily dose based on modified random forest and substructure fingerprint. Analytica Chimica Acta 2011, 692:50-56.
  30. 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 metabolomics data using Monte Carlo tree. Analyst 2011, 136(5):947-954.
  31. Dong-Sheng Cao, Yi-Zeng Liang, Qing-Song Xu, Qian-Nan Hu, Liang-Xiao Zhang, Guang-Hui Fu. Exploring nonlinear relationships in chemical data using kernel-based methods. Chemometrics and Intelligent Laboratory Systems 2011, 107(1):106-115.
  32. Dong-Sheng Cao, Yi-Zeng Liang, Qing-Song Xu, Liang-Xiao Zhang, Qian-Nan Hu and Hong-Dong Li. Feature importance sampling-based adaptive random forest as a useful tool to screen underlying lead compounds. Journal of Chemometrics 2011, 25(4):201-207.
  33. Emrin Zitha-Bovens, Peter Maas, Dick Wife, Johan Tijhuis, Qian-Nan Hu, Thomas Klein?der, Johann Gasteiger. COMDECOM: Predicting the Lifetime of Screening Compounds in DMSO Solution. Journal of Biomolecular Screening 2009, 14:557-565.
  34. Jonathan Chen, Qian-Nan Hu, Pierre Baldi. Organic Chemical Reaction Expert Systems. Annual Am Chem Soc Conference April, 2008.
  35. 向铮, 卫涛, 梁逸曾, 胡黔楠. 拓扑指数计算软件的开发与设计. 计算机与应用化学, 2007, 24(7):25.
    (Zheng Xiang, Tao Wei, Yi-zeng Liang, Qian-Nan Hu. Design of calculation software of topological index by MATLAB for application. Computers and Applied Chemistry (in Chinese) 2007, 24(7):25.)
  36. Qian-Nan Hu, Yi-Zeng Liang, Xu QS, Fang KT, Peng XL and Yin H. Structural Features within Degree Distributions of Topological Graphs. J Math Chem 2005, 37(1):37-56.
  37. Xiao-Ling Peng, Qian-Nan Hu, Yi-Zeng Liang. Variable Selection via Nonconcave Penalty Function in Structure-Boiling Points Correlations. J Mol Str: THEOCHEM 2005, 714(2-3):235-242.
  38. Shansheng Yang, Wencong Lu, Nianyi Chen, Qian-Nan Hu. Support vector regression based QSPR for the prediction of some physicochemical properties of alkyl benzenes. J Mol Str: THEOCHEM 2005, 719(1-3):119-127.
  39. 向铮, 梁逸曾, 胡黔楠. 基于HQN编码的芳香性识别算法 (Aromaticity Identification Using HQN methods). 计算机与应用化学 Computers and Applied Chemistry (in Chinese) 2005, 10:27-29.
  40. 王亚丽, 梁逸曾, 李博岩, 胡芸, 胡黔楠. 当归补血汤中组分的变化及归属分析 (Relative adscription of components between complex and single herb in Danggui Buxue Decoction). 中草药 (CHINESE TRADITIONAL AND HERBAL DRUGS) 2005, 10:21-24.
  41. 沈菊文, 胡黔楠, 梁逸曾. 子空间比较法研究拓扑块的变量关系及变量选择. 高等学校化学学报 2005, 26(1):39-54.
    (Ju-Wen Shen, Qian-Nan Hu, Yi-Zeng Liang. Application of Subspace Comparison Method in Studying the Relationship between Topological Block Variables and Variable Selection. Chemical Journal of Chinese Universities (in Chinese) 2005, 26(1):39-54.)
  42. 向铮, 梁逸曾, 胡黔楠. 甲基烷烃结构与色谱保留指数相关性的拓扑指数法研究. 色谱 2005, 23(2):117-122.
    (XIANG Zheng, Yi-Zeng Liang, Qian-Nan Hu. Study on Topological Index of Methylalkane Structures and Chromatographic Retention Index. Chromatography (in Chinese) 2005, 23(2):117-122.)
  43. 赵晨曦, 梁逸曾, 胡黔楠, 张泰铭. 气相色谱保留指数定性方法研究进展. 分析化学 2005, 5:129-135.
    (Chen-Xi Zhao, Yi-Zeng Liang, Qian-Nan Hu. Review on gas chromatographic retention index. Chinese J Anal Chem (in Chinese) 2005, 5:129-135.)
  44. Ya-Li Wang, Yi-Zeng Liang, Ben-Mei Chen, Bo-Yan Li, Qian-Nan Hu. LC-DAD-APCI-MS-based screening and analysis of the absorption and metabolite components in plasma from a rabbit administered an oral solution of danggui. Analytical and Bioanalytical Chemistry 2005, 383(2):247-254.
  45. 贠栋, 梁逸曾, 徐承建, 胡黔楠, 梁江龙. 结构描述符正交化及典型相关分析在饱和醇、醚质谱分类中的应用. 应用化学 2004, 21(3):223-226.
    (Yun D, Yi-Zeng Liang, Xu CJ, Qian-Nan Hu, Liang JH. Application of orthogonal computation of block variables and canonical correlation analysis in Mass spectral classification of saturated alcohol and ether. Chinese Journal of Applied Chemistry (in Chinese) 2004, 21(3):223-226.)
  46. 刘伟, 胡黔楠, 梁逸曾. 化学标识语言(CML)在QSAR/QSPR研究中的应用. 计算机与应用化学 2004, 4:521-524.
    (Wei Liu, Qian-Nan Hu, Yi-Zeng Liang. Application of Chemical Markup Language (CML) in QSAR/QSPR Research. Computers and Applied Chemistry (in Chinese) 2004, 4:521-524.)
  47. Qian-Nan Hu, Yi-Zeng Liang, Hong Yin, Xiao-Ling Peng, Kai-Tai Fang. Structure Interpretation of Topological Index (2) Molecular Connectivity Index, Kappa Index and E-State Index. J Chem Inf Comput Sci 2004, 44:1193-1201.
  48. Qian-Nan Hu, Yi-Zeng Liang. The branch number of a topological graph. Internet Electronic Journal of Molecular Design 2004, 3(6):335-349.
  49. Xiao-Ling Peng, Kai-Tai Fang, Qian-Nan Hu, Yi-Zeng Liang. Impersonality of the Connectivity Index and Recomposition of Topological Indices According to Different Properties. Molecule 2004, 9:1089-1099.
  50. Qian-Nan Hu, Yi-Zeng Liang, Xiao-Ling Peng, Hong Yin, Kai-Tai Fang. Structure Interpretation of Topological Index (1) External Factor Variable Connectivity Index. J Chem Inf Comput Sci 2004, 44:437-446.
  51. Qian-Nan Hu, Yi-Zeng Liang, Feng-Liang Ren. Molecular Graph Center, A Novel Approach to Locate the Center of a Molecule and a New Centric Index. J Mol Str: THEOCHEM 2003, 635:105-113.
  52. 胡黔楠, 梁逸曾, 王亚丽, 郭方遒, 黄兰芳. 直观队列命名法的基本原理及其在矩阵与拓扑指数计算中的应用. 计算机与应用化学 2003, 20:386-390.
    (Qian-Nan Hu, Yi-Zeng Liang, Ya-Li Wang, Fang-Qiu Guo, Lan-Fang Huang. The basic principles of heuristic queue notation (H.Q.N.) and its applications in calculation of matrix and topological index for topological graphs. Computers and Applied Chemistry (in Chinese) 2003, 20:386-390.)
  53. Qian-Nan Hu, Yi-Zeng Liang, Xiao-Ling Peng, Hong Yin, Zhu L. Application of Orthogonal Block Variables and Canonical Correlation Analysis in Modeling Pharmacological Activity of Alkaloids from Plant Medicines. J Data Sci 2003, 1(4):405-423.
  54. Huang LF, Liang YZ, Guo FQ, Qian-Nan Hu, Chen BM. Rapid simultaneous determination of arginine and methylated arginines in human urine by high-performance liquid chromatographymass spectrometry. Anal Chem Acta 2003, 487:145-153.
  55. Qian-Nan Hu, Yi-Zeng Liang, Ya-Li Wang, Cheng-Jian Xu, Zhong-Da Zeng, Kai-Tai Fang, Xiao-Ling Peng, Yin Hong. External Factor Variable Connectivity Index. J Chem Inf Comput Sci 2003, 43:773-778.