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Publications

2024

  • Li, H., Fotouhi, N., Liu, F., Ji, H., Wu, Q. Early detection of dark-affected plant mechanical responses using enhanced electrical signals. Plant Methods. 2024, 22 (1) 49. link

  • Xue, J., Wang, B., Ji, H., Li, W. RT-Transformer: retention time prediction for metabolite annotation to assist in metabolite identification. Bioinformatics*. 2024, 40(3) btae084. link

  • Wu, Q., Zheng, J., Sui, X., Fu, C., Cui, X., Liao, B., Ji, H., Luo, Y., He, A., Lu, X., Xue, X., Tan, C.S.H.,. Tian, R., High-throughput drug target discovery using a fully automated proteomics sample preparation platform. Chem. Sci. 15 (8) 2833-2847. link

2023

  • Ji, H.#; Lu, X.#; Zhao, S.; Wang, Q.; Bin, L.; Huber, K. V. M.; Luo, R.; Tian, R.; Tan, C. S. H. Target deconvolution with matrix-augmented pooling strategy reveals cell-specific drug-protein interactions. Cell Chem. Biol. 2023, 30(11) 1478-1487. link

  • 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. link

  • Song, Y., Chang, S., Tian, J., Pan, W., Feng L,. Ji, H., A Comprehensive Comparative Analysis of Deep Learning Based Feature Representations for Molecular Taste Prediction. Foods. 2023, 12(18), 3386 link

2014 - 2022

  • Ji, H.; Tian, J. Deep Denoising Autoencoder-Assisted Continuous Scoring of Peak Quality in High-Resolution LC−MS Data. Chemo. Intell. Lab*. 2022, 231, 104694. link

  • 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. link

  • 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. link

  • 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. link

  • 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. link

  • 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. link

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

  • 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. link

  • 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. link

  • 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. link

  • 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. link

  • 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. link

  • 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. link

  • 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. link

  • 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. link

  • 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. link

  • Lin, Z.; Vicente Gonçalves, 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. link