2025 July 20

Our publications




2025

  1. Qiu, Y.#; Zhang, D.#; Long, M.; Zhou, Z.; Gao, C.; Ma, S.; Qin, J.; Chen, K.; Chen, C.; Zhao, Z.; et al. Coassembly of hybrid microscale biomatter for robust, water-processable, and sustainable bioplastics. Science Advances 2025, 11 (14), eadr1596. DOI: doi:10.1126/sciadv.adr1596.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.

 

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.