2025 July 20

Our publications




2026

  1. Shi, P., Huang, X., Ke, Q., Kou, X., Zhang, D.* Mapping sleep-promoting volatiles in aromatic plants with machine learning: A comprehensive survey of 2,300 molecules. Digital Discovery 2026, accepted.

 

2025

  1. Zhang, D.*, Liu, M., Yu, Z., Xu, H., Pfister, S., Menichetti, G., . . . Rao, P. Domain knowledge, just evaluation, and robust data standards are required to advance AI in food science. Trends in Food Science & Technology 2025, 105272. DOI: 10.1016/j.tifs.2025.105272.
  2. Qiu, Y.#; Zhang, D.#; Long, M.; Zhou, Z.; Gao, C.; Ma, S.; Qin, J.; Chen, K.; Chen, C.; Zhao, Z.; Deng, H. Coassembly of hybrid microscale biomatter for robust, water-processable, and sustainable bioplastics. Science Advances 2025, 11 (14), eadr1596. DOI: 10.1126/sciadv.adr1596.
  3. Ye, T.#; Zhang, D.#; Xing, H#.; .. Hu, Q-N; Wu, A. Computational glycosyltransferases masked deoxynivalenol toxicity and halted FHB spread in wheat grains. Journal of Advanced Research 2025.
  4. Jiao, X.; Zhu, J.; Ye, W.; Zou, H.; Yan, B.; Zhang, N.; Qiang, J.; Tao, Y.; Zhang, H.; Zhang, D.*; Fan, D. Artificial intelligence in smart seafood safety across the supply chains: Recent advances and future prospects. Trends in Food Science & Technology 2025, 163. DOI: 10.1016/j.tifs.2025.105161.
  5. Qiao, G.; Zhang, D.; Zhang, N.; Shen, X.; Jiao, X.; Lu, W.; Fan, D.; Zhao, J.; Zhang, H.; Chen, W.; Jin, Z.. Food recommendation towards personalized wellbeing. Trends in Food Science & Technology 2025, 156. DOI: 10.1016/j.tifs.2025.104877.
  6. Qiu, Y.; Zhang, D; ... Zhao, Z.; Deng, H. Hierarchical assembly of biomass fiber-lamella-macromolecule networks for biocomposites with high strength and water-resistant sealing. Proceedings of the National Academy of Sciences of the United States of America (PNAS) 2025.DOI: 10.1073/pnas.2521173122.
  7. Schmid, C.; Kastner, F.; Zhang, D.; Langenberg, S.; Hellweg, S. Spatiotemporal mapping of Swiss exterior wall material stock using a large language model and architectural history. Journal of Industrial Ecology 2025. DOI: 10.1111/jiec.70058.
  8. Ding, S.; Tian, Y.; Liu, D.; Zhang, D.; Xing, H.; Chen, J.; Liu, Z.; Hu, Q. N.. RxnCluster: A web-based tool for exploring reaction clusters leading to target molecules by digitalizing typical biosynthetic patterns. ACS Synthetic Biology 2025.
  9. Tian, Y.; Yang, L.; Ding, S.; Zhang, D.; Yuan, L.; Liu, Z.; Hu, Q. N. BioTRY: A comprehensive knowledge base for titer, rate, and yield of biosynthesis. ACS Synthetic Biology 2025 14, 285-289.
  10. Ding, S.; Liu, D.; Tian, Y.; Zhang, D.; Xing, H.; Chen, J.; Liu, Z.; Hu, Q. N. From reactants to products: computational methods for biosynthetic pathway design. Synthetic and Systems Biotechnology 2025, 10 (3), 1038-1049. DOI: 10.1016/j.synbio.2025.05.005.
  11. Cai, P.; Liu, D.; Xing, H.; Zhang, D.; Le, Y.; Wu, A.; Hu, Q. N. DeepMBEnzy: An AI-driven database of mycotoxin biotransformation enzymes. J Agric Food Chem 2025. DOI: 10.1021/acs.jafc.5c02477.
  12. Qian, J.; Wang, X.; Song, F.; Liang, Y.; Zhu, Y.; Fang, Y.; Zeng, W.; Zhang, D.; Dong, J. ChemSweet: An AI-driven computational platform for next-gen sweetener discovery. Food Chemistry 2025, 463, 141362. DOI: 10.1016/j.foodchem.2024.141362.
  13. Zhang, D.*, From molecules to perception: A benchmark dataset for AI in sensory science, NeurIPS2025-AI4Science, 2025.

 

2024

  1. Zhang, D.*; Wang, Z.; Oberschelp, C.; Bradford, E.; Hellweg, S. Enhanced Deep-Learning Model for Carbon Footprints of Chemicals. ACS Sustainable Chemistry & Engineering 2024, 12 (7), 2700-2708. DOI: 10.1021/acssuschemeng.3c07038.
  2. Zhang, D.; Xing, H.; Liu, D.; Han, M.; Cai, P.; Lin, H.; Tian, Y.; Guo, Y.; Sun, B.; Le, Y.; et al. Discovery of Toxin-Degrading Enzymes with Positive Unlabeled Deep Learning. ACS Catalysis 2024, 14, 3336-3348. DOI: 10.1021/acscatal.3c04461.
  3. Zhang, D.*; Liu, D.; Jing, J.; Jia, B.; Tian, Y.; Le, Y.; Yu, Y.; Hu, Q.-N. Unveiling the chemical complexity of food-risk components: A comprehensive data resource guide in 2024. Trends in Food Science & Technology 2024, 148. DOI: 10.1016/j.tifs.2024.104513.
  4. Xing, H.; Cai, P.; Liu, D.; Han, M.; Liu, J.; Le, Y.; Zhang, D.*; Hu, Q.-N. High-throughput prediction of enzyme promiscuity based on substrate–product pairs. Briefings in Bioinformatics 2024, 25 (2). DOI: 10.1093/bib/bbae089.

 

2023

  1. Kou, X.; Shi, P.; Gao, C.; Ma, P.; Xing, H.; Ke, Q.; Zhang, D.* Data-Driven Elucidation of Flavor Chemistry. J Agric Food Chem 2023, 71 (18), 6789-6802. DOI: 10.1021/acs.jafc.3c00909.
  2. Zhang, D.*; Jia, C.; Sun, D.; Gao, C.; Fu, D.; Cai, P.; Hu, Q. N. Data-Driven Prediction of Molecular Biotransformations in Food Fermentation. J Agric Food Chem 2023, 71 (22), 8488-8496. DOI: 10.1021/acs.jafc.3c01172. 
  3. Ji, J.#; Zhang, D.#; Ye, J.; Zheng, Y.; Cui, J.; Sun, X. MycotoxinDB: A Data-Driven Platform for Investigating Masked Forms of Mycotoxins. J Agric Food Chem 2023, 71 (24), 9501-9507. DOI: 10.1021/acs.jafc.3c01403.
  4. Zhang, H.; Zhang, D.*; Wei, Z.; Li, Y.; Wu, S.; Mao, Z.; He, C.; Ma, H.; Zeng, X.; Xie, X.; et al. Analysis of public opinion on food safety in Greater China with big data and machine learning. Current Research in Food Science 2023, 6. DOI: 10.1016/j.crfs.2023.100468.
  5. Xing, H.; Zhang, D.; Cai, P.; Zhang, R.; Hu, Q. N. RDBridge: a knowledge graph of rare diseases based on large-scale text mining. Bioinformatics 2023, 39 (7). DOI: 10.1093/bioinformatics/btad440.
  6. Cai, P.; Liu, S.; Zhang, D.; Xing, H.; Han, M.; Liu, D.; Gong, L.; Hu, Q. N. SynBioTools: a one-stop facility for searching and selecting synthetic biology tools. BMC Bioinformatics 2023, 24 (1), 152. DOI: 10.1186/s12859-023-05281-5.
  7. Cai, P.; Liu, S.; Zhang, D.; Hu, Q. N. MCF2Chem: A manually curated knowledge base of biosynthetic compound production. Biotechnol Biofuels Bioprod 2023, 16 (1), 167. DOI: 10.1186/s13068-023-02419-8.
  8. Zhang D, Xing H, Liu D, Han M, Cai P, Lin H, et al. Deep Learning Enables Rapid Identification of Mycotoxin-Degrading Enzymes. ChemRxiv. 2023; doi:10.26434/chemrxiv-2023-g6qb5.

 

2022

  1. Tian, Y.#; Zhang, D.#; Cai, P.; Lin, H.; Ying, H.; Hu, Q.-N.; Wu, A. Elimination of Fusarium mycotoxin deoxynivalenol (DON) via microbial and enzymatic strategies: Current status and future perspectives. Trends in Food Science & Technology 2022, 124, 96-107. DOI: 10.1016/j.tifs.2022.04.002.
  2. Sun, D.; Ding, S.; Cai, P.; Zhang, D.; Han, M.; Hu, Q. N. BioBulkFoundary: A customized webserver for exploring biosynthetic potentials of bulk chemicals. Bioinformatics 2022. DOI: 10.1093/bioinformatics/btac640.
  3. Han, M.; Liu, S.; Zhang, D.; Zhang, R.; Liu, D.; Xing, H.; Sun, D.; Gong, L.; Cai, P.; Tu, W.; et al. AddictedChem: A Data-Driven Integrated Platform for New Psychoactive Substance Identification. Molecules 2022, 27 (12). DOI: 10.3390/molecules27123931.
  4. Cai, P.; Han, M.; Zhang, R.; Ding, S.; Zhang, D.; Liu, D.; Liu, S.; Hu, Q. N. SynBioStrainFinder: A microbial strain database of manually curated CRISPR/Cas genetic manipulation system information for biomanufacturing. Microb Cell Fact 2022, 21 (1), 87. DOI: 10.1186/s12934-022-01813-5.

 

2021

  1. Zhang, D.; Tian, Y.; Tian, Y.; Xing, H.; Liu, S.; Zhang, H.; Ding, S.; Cai, P.; Sun, D.; Zhang, T.; et al. A data-driven integrative platform for computational prediction of toxin biotransformation with a case study. Journal of Hazardous Materials 2021, 408, 124810. DOI: 10.1016/j.jhazmat.2020.124810.
  2. Zhang, D.; Zhang, T.; Liu, S.; Sun, D.; Ding, S.; Cheng, X.; Cai, P.; Ren, A.; Han, M.; Liu, D.; et al. An integrated platform for identification of novel coronavirus by a consensus sequence-function model. Bioinformatics 2021, 37 (8), 1182-1183. DOI: 10.1093/bioinformatics/btaa767.
  3. Han, M.#; Zhang, D.#; Ding, S.; Tian, Y.; Cheng, X.; Yuan, L.; Sun, D.; Liu, D.; Gong, L.; Jia, C.; et al. ChemHub: a knowledgebase of functional chemicals for synthetic biology studies. Bioinformatics 2021. DOI: 10.1093/bioinformatics/btab360.
  4. Ouyang, S.#; Zhang, D.#; Zhu, T.; Yu, S.; Wunier; Hu, Q. N.; Le, Y. Development of 3D-QSAR models for predicting the activities of chemicals to stimulate muscle growth via beta2-adrenoceptor. Toxicol In Vitro 2021, 77, 105251. DOI: 10.1016/j.tiv.2021.105251.
  5. Ren, A.; Zhang, D.; Tian, Y.; Cai, P.; Zhang, T.; Hu, Q. N. Transcriptor: a comprehensive platform for annotation of the enzymatic functions of transcripts. Bioinformatics 2021, 37 (3), 434-435. DOI: 10.1093/bioinformatics/btaa685.
  6. Zhang, D., et al. IFoodCloud: A Platform for Real-time Sentiment Analysis of Public Opinion about Food Safety in China. arxiv 2021.

 

2020

  1. Zhang, D.; Ouyang, S.; Cai, M.; Zhang, H.; Ding, S.; Liu, D.; Cai, P.; Le, Y.; Hu, Q. N. FADB-China: A molecular-level food adulteration database in China based on molecular fingerprints and similarity algorithms prediction expansion. Food Chemistry 2020, 327, 127010. DOI: 10.1016/j.foodchem.2020.127010.
  2. Zhang, D.; Gong, L.; Ding, S.; Tian, Y.; Jia, C.; Liu, D.; Han, M.; Cheng, X.; Sun, D.; Cai, P.; et al. FRCD: A comprehensive food risk component database with molecular scaffold, chemical diversity, toxicity, and biodegradability analysis. Food Chemistry 2020, 318, 126470. DOI: 10.1016/j.foodchem.2020.126470.
  3. Cheng, X.; Sun, D.; Zhang, D.; Tian, Y.; Ding, S.; Cai, P.; Hu, Q. N. RxnBLAST: molecular scaffold and reactive chemical environment feature extractor for biochemical reactions. Bioinformatics 2020, 36 (9), 2946-2947. DOI: 10.1093/bioinformatics/btaa036.
  4. Ding, S.; Tian, Y.; Cai, P.; Zhang, D.; Cheng, X.; Sun, D.; Yuan, L.; Chen, J.; Tu, W.; Wei, D. Q.; et al. novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model. Nucleic Acids Res 2020. DOI: 10.1093/nar/gkaa230.
  5. Sun, D.; Cheng, X.; Tian, Y.; Ding, S.; Zhang, D.; Cai, P.; Hu, Q. N. EnzyMine: a comprehensive database for enzyme function annotation with enzymatic reaction chemical feature. Database (Oxford) 2020. DOI: 10.1093/database/baaa065.

 

2019

  1. Zhang, D.; Cheng, X.; Sun, D.; Ding, S.; Cai, P.; Yuan, L.; Tian, Y.; Tu, W.; Hu, Q. N. AdditiveChem: A comprehensive bioinformatics knowledge-base for food additive chemicals. Food Chemistry 2019, 308, 125519. DOI: 10.1016/j.foodchem.2019.125519.
  2. Ding, S.; Cai, P.; Yuan, L.; Tian, Y.; Tu, W.; Zhang, D.; Cheng, X.; Sun, D.; Chen, J.; Hu, Q. N. CF-Targeter: A Rational Biological Cell Factory Targeting Platform for Biosynthetic Target Chemicals. ACS Synthetic Biology 2019, 8 (10), 2280-2286. DOI: 10.1021/acssynbio.9b00070.
  3. Tian, Y.; Wu, L.; Yuan, L.; Ding, S.; Chen, F.; Zhang, T.; Ren, A.; Zhang, D.; Tu, W.; Chen, J.; et al. BCSExplorer: a customized biosynthetic chemical space explorer with multifunctional objective function analysis. Bioinformatics 2019, 36 (5), 1642-1643. DOI: 10.1093/bioinformatics/btz755.

 

Peer-review for data science journals

Bioinformatics, Briefings in Bioinformatics, Bioinformatics Advances, Computational and Structural Biotechnology Journal, Digital Discovery, Journal of Cheminformatics, Journal of Chemical Information and Modeling, Journal of Autonomous Intelligence, Engineering Applications of Artificial Intelligence, Applied Artificial Intelligence, Advances in Multimedia, Nucleic Acids Research, Scientific Data, NeurIPS

 

Peer-review for food science journals

Comprehensive Reviews in Food Science and Food Safety, Trends in Food Science and Technology, Nature Food, npj Science of Food, Journal of Food Science, Journal of Agricultural and Food Chemistry, Food Chemistry, Food Chemistry Advances, Journal of Food Composition and Analysis, Food Chemical Toxicology, Food Function, Food Science and Human Wellness, Current Research in Food Science, Chemical Research in Toxicology, Nutrition journal, Reviews of Environmental Contamination and Toxicology, Environmental Science & Technology, Environmental Science & Technology Letters, Journal of Hazardous Materials, Journal of Hazardous Materials Advances, Research, iScience, Scientific Reports, F1000Research