纪宏超课题组

Ji Hongchao Lab

　　课题组长

纪宏超，副研究员，硕士生导师。理学博士。2020年博士毕业于中南大学化学化工学院，2020-2022年于南方科技大学依次从事博士后研究，2022年加入深圳农业尊龙凯时 人生就是博。长期专注于化学信息学与人工智能算法开发及其在复杂体系分析，尤其是代谢组学中的应用。以第一/通讯作者（含并列）在Nature Communications、Cell Chemical Biology、Analytical Chemistry、Briefings in Bioinformatics等国际学术期刊上发表论文9篇。累计参与发表论文19篇，H指数为11。申请国家发明专利1项，PCT国际专利1项。担任Journal of Chemical Information and Modeling, Analytical and Bioanalytical Chemistry, Chemometrics and Intelligent Laboratory Systems等期刊审稿人，Metabolites期刊客座编辑。

联系方式：[email protected]

　　工作经历

2022.05 - 至今           中国农业科学院深圳农业基因组研究所   副研究员

2020.07 – 2022.05     南方科技大学                                        博士后

　　教育经历

2015.09 – 2020.06  中南大学 化学化工学院 理学博士

2011.09 - 2015.07  中南大学 化学化工学院 工学学士　

研究方向

1）化学信息学与人工智能算法开发

2）代谢组学质谱数据解析算法与软件开发

3）未知小分子代谢物结构注释与功能解析

研究进展

重要进展成果1：针对复杂体系质谱分析，率先提出了基于机器学习的策略的特征提取、质量控制、校准及模式识别等子�？�，并整合为数据处理软件；有效减少噪声干扰，对特征信号，尤其是低强度特征进行准确的定量。

重要进展成果2：针对未知小分子结构注释，开发了基于深度学习模型的从已知预测未知的解决思路，挖掘化合物结构与质谱碎片、色谱保留时间等分析化学性质的关联性，开发了一系列用于注释未知小分子化合物二维结构的方法。

重要进展成果3：针对潜在药物小分子靶标解析，率先提出了机器学习与热转变实验相结合的策略。大幅提高了实验通量，单次实验可以解析15 - 30个待筛化合物在细胞内的作用靶点，将筛选效率提高 15 - 60 倍。

代表论著

(1) Ji, H.#; Lu, X.#; Zhao, S.; Wang, Q.; Bin, L.; Huber, K. V. M.; Luo, R.; Tian, R.; Tan, C. S. H. Matrix-Augmented Pooling Strategy for High-Throughput Target Deconvolution Reveals Cell Type Specific Off-Targets and Responses. Cell Chem. Biol. 2023, Just Accepted. (#Co-first author)

(2) Yang, Q.#; Ji, H.#; Xu, Z.; Li, Y.; Wang, P.; Sun, J.; Fan, X.; Zhang, H.; Lu, H.; Zhang, Z. Ultra-Fast and Accurate Electron Ionization Mass Spectrum Matching for Compound Identification with Million-Scale in-Silico Library. Nat. Commun. 2023, 14 (1), 3722. (#Co-first author)

(3) Ji, H.; Tian, J. Deep Denoising Autoencoder-Assisted Continuous Scoring of Peak Quality in High-Resolution LC?MS Data. Chemometrics and Intelligent Laboratory Systems 2022, 231, 104694.

(4) Ji, H.; Lu, X.; Zheng, Z.; Sun, S.; Tan, C. S. H. ProSAP: A GUI Software Tool for Statistical Analysis and Assessment of Thermal Stability Data. Brief. Bioinform. 2022, 23 (3), bbac057.

(5) Ji, H.; Deng, H.; Lu, H.; Zhang, Z. Predicting a Molecular Fingerprint from an Electron Ionization Mass Spectrum with Deep Neural Networks. Anal. Chem. 2020, 92 (13), 8649–8653.

(6) Ji, H.; Zhang, Z.; Lu, H. TarMet: A Reactive GUI Tool for Efficient and Confident Quantification of MS Based Targeted Metabolic and Stable Isotope Tracer Analysis. Metabolomics 2018, 14 (5), 68.

(7) Ji, H.; Zeng, F.; Xu, Y.; Lu, H.; Zhang, Z. KPIC2: An Effective Framework for Mass Spectrometry-Based Metabolomics Using Pure Ion Chromatograms. Anal. Chem. 2017, 89 (14), 7631–7640.

(8) Ji, H.; Xu, Y.; Lu, H.; Zhang, Z. Deep MS/MS-Aided Structural-Similarity Scoring for Unknown Metabolite Identification. Anal. Chem. 2019, 91 (9), 5629–5637.

(9) Ji, H.; Lu, H.; Zhang, Z. Pure Ion Chromatogram Extraction: Via Optimal k -Means Clustering. RSC Adv. 2016, 6 (62), 56977–56985.

(10) Yang, Q.; Ji, H.; Lu, H.; Zhang, Z. Prediction of Liquid Chromatographic Retention Time with Graph Neural Networks to Assist in Small Molecule Identification. Anal. Chem. 2021, 93 (4), 2200–2206.

(11) Yang, Q.; Ji, H.; Fan, X.; Zhang, Z.; Lu, H. Retention Time Prediction in Hydrophilic Interaction Liquid Chromatography with Graph Neural Network and Transfer Learning. J. Chromatogr. A 2021, 1656.

(12) Wu, Q.; Xu, Y.; Ji, H.; Wang, Y.; Zhang, Z.; Lu, H. Enhancing Coverage in LC–MS-Based Untargeted Metabolomics by a New Sample Preparation Procedure Using Mixed-Mode Solid-Phase Extraction and Two Derivatizations. Anal Bioanal Chem 2019, 411 (23), 6189–6202.

(13) Zhu, H.; Chen, Y.; Liu, C.; Wang, R.; Zhao, G.; Hu, B.; Ji, H.; Zhang, Z.-M.; Lu, H. Feature Extraction for LC-MS via Hierarchical Density Clustering. Chromatographia 2019, 82 (10), 1449–1457.

(14) Fu, C.; Wu, Q.; Zhang, Z.; Xia, Z.; Ji, H.; Lu, H.; Wang, Y. UPLC-ESI-IT-TOF-MS Metabolomic Study of the Therapeutic Effect of Xuefu Zhuyu Decoction on Rats with Traumatic Brain Injury. Journal of Ethnopharmacology 2019, 245, 112149.

(15) Li, W.; Ye, H.; Liu, G.; Ji, H.; Zhou, Y.; Han, K. The Role of Graphene Coating on Cordierite-Supported Pd Monolithic Catalysts for Low-Temperature Combustion of Toluene. Cuihua Xuebao/Chinese Journal of Catalysis 2018, 39 (5), 946–954.

(16) He, Y.; Zhang, Z. ; Ma, P.; Ji, H. .; Lu, H. GC-MS Profiling of Leukemia Cells: An Optimized Preparation Protocol for the Intracellular Metabolome. Anal. Methods 2018, 10 (10), 1266–1274.

(17) Zeng, F.; Ji, H.; Zhang, Z.; Luo, J.; Lu, H. ; Wang, Y. Metabolic Profiling Putatively Identifies Plasma Biomarkers of Male Infertility Using UPLC-ESI-IT-TOFMS. RSC Adv. 2018, 8 (46), 25974–25982.

(18) Wang, R.; Ji, H.; Ma, P.; Zeng, H.; Xu, Y.; Zhang, Z.-M.; Lu, H.-M. Fast Pure Ion Chromatograms Extraction Method for LC-MS. Chemom. Intell. Lab. Syst. 2017, 170, 68–74.

(19) Lin, Z.; Vicente Gon?alves, C. M.; Dai, L.; Lu, H.; Huang, J.; Ji, H.; Wang, D.; Yi, L.; Liang, Y. Exploring Metabolic Syndrome Serum Profiling Based on Gas Chromatography Mass Spectrometry and Random Forest Models. Analytica Chimica Acta 2014, 827, 22–27.

纪宏超课题组更新于2023年7月