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Publications

# Co-first author, * Corresponding author

2026

  1. Jiang S.; Yang Q.; Xiong Z.; Li K.; Dai Q.; Su M.; Lyu Y.; Peng Y.; Du R.; Yan J.; Ji H.* DeepMASS v2: An enhanced deep learning platform for large-scale discovery and structural annotation of unknown plant metabolites. Plant Communications. 2026, 101976, 2590-3462.

  2. Liu W.; Zheng Z.; Wang X.; Ji H.* FiLM-Enhanced Biologically Informed Neural Networks for Multiclass Omics Analysis and Biomarker Discovery. Anal. Chem. 2026, 98(17), 12851–12861.

  3. Wang Q.; Yu N.; Song Y.; Fan X.; Tian J.; Chang S.; Guo Y.; Tan C.S.H.; Ji H.* Thermal Proteomics and AI-assisted Target Deconvolution Identify ACLY as a Direct Target of Demethylzeylasteral in Psoriasis. Anal. Chem. 2026.

  4. Xiong, Z.; Wang, X.; Liu, J.; Cong, S.; Yang, Q.; Ji H.* Unified Multitask Modeling for Retention Time Prediction Across Chromatographic Conditions. Anal. Chem. 2026, 98(13), 9500–9507.

  5. Fan, X.; Li, Z.; Shang, L.; Zhang, J.; Liu, B.; Ren, X.; Liu, G.; Li, X.; Yang, T.; Ji, H.* DeepHSI: A transferable and expandable hyperspectral framework for industrial plant origin identification: A case study of Pogostemon cablin (Blanco) Benth. Talanta. 2026, 303, 129474.

2025

  1. Fan, X.; Liu, Y.; Zhang, Z.; Zhao, P.; Li, Z.; Zhou, J.; Zhai, D.; Hu, Y.; Li, P.; Ji, H.* DeepPHSI: attention-driven CNN-LSTM fusion for hyperspectral origin traceability across Pogostemon cablin batches. RSC Advances. 2025, 15(44), 37039–37049.

  2. Fan, X.; Shang, L.; Zhao, S.; Fan, J.; Zhang, S.; Yang, Q.; Wu, C.; Liu, Y.; Yang, T.; Ji, H.* PLSELM: A lightweight modeling approach for low-data calibration in near-infrared spectroscopy. Analytica Chimica Acta. 2025, 1379, 344728.

  3. Fan, X.; Gao, L.; Lv, J.; Li, B.; Xu, K.; Li, X.; Shao, Y.; Yang, T.; Chen, X.; Ji, H.* A systematic calibration transfer and quantification method based on principal components extreme learning machine for near-infrared spectroscopy. Analytica Chimica Acta. 2025, 1361, 344151.

  4. Chen, Y.; Zeng, H.; Song, Y.; Li, Z.; Chu, G.; Tian, J.; Ji, H.* Development of StatMS platform coupled with MS metabolomics identifies altitude-responsive metabolites in Coreopsis tinctoria Nutt. Chinese Journal of Analytical Chemistry. 2025, 53(9), 100569.

  5. Song, Y.; Zhang, M.; Chang, S.; Chu, G.; Ji, H.* DerivaPredict: A User-Friendly Tool for Predicting and Evaluating Active Derivatives of Natural Products. Molecules. 2025, 30(8), 1683.

  6. Cong, S.; Zhang, M.; Song, Y.; Chang, S.; Tian, J.; Zeng, H.; Ji, H.* Graph-sequence enhanced transformer for template-free prediction of natural product biosynthesis. Patterns. 2025, 6(8), 101259.

2024

  1. Chen J.; Yang Q.; Dai Q.; Chang S.; Tian J.; Cong S.*; Ji, H.* FederEI: Federated Library Matching Framework for Electron Ionization Mass Spectrum Based Compound Identification. Anal. Chem. 2024, 96(40), 15840–15845.

  2. 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.

2022–2023

  1. 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. (Cell 子刊)

  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. (Nature 子刊, Nature Index 期刊)

  3. 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.

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

  5. 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.

2014–2021

  1. 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. (Nature Index 期刊)

  2. 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.

  3. 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. (Nature Index 期刊)

  4. 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. (Nature Index 期刊)

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