| Deep learning based kcat prediction enables improved enzyme constrained model reconstruction F Li, L Yuan, H Lu, G Li, Y Chen, MKM Engqvist, EJ Kerkhoven, J Nielsen Nature Catalysis 5, 662–672, 2022 | 137 | 2022 |
| novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model S Ding, Y Tian, P Cai, D Zhang, X Cheng, D Sun, L Yuan, J Chen, W Tu, ... Nucleic acids research 48 (W1), W477-W487, 2020 | 33 | 2020 |
| AdditiveChem: a comprehensive bioinformatics knowledge-base for food additive chemicals D Zhang, X Cheng, D Sun, S Ding, P Cai, L Yuan, Y Tian, W Tu, QN Hu Food chemistry 308, 125519, 2020 | 32 | 2020 |
| Improving recombinant protein production by yeast through genome-scale modeling using proteome constraints F Li, Y Chen, Q Qi, Y Wang, L Yuan, M Huang, IE Elsemman, A Feizi, ... Nature communications 13 (1), 2969, 2022 | 23 | 2022 |
| FRCD: A comprehensive food risk component database with molecular scaffold, chemical diversity, toxicity, and biodegradability analysis D Zhang, L Gong, S Ding, Y Tian, C Jia, D Liu, M Han, X Cheng, D Sun, ... Food chemistry 318, 126470, 2020 | 23 | 2020 |
| PrecursorFinder: a customized biosynthetic precursor explorer L Yuan, Y Tian, S Ding, Y Liu, F Chen, T Zhang, W Tu, J Chen, QN Hu Bioinformatics 35 (9), 1603-1604, 2019 | 19 | 2019 |
| Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection H Lu, F Li, L Yuan, I Domenzain, R Yu, H Wang, G Li, Y Chen, B Ji, ... Molecular Systems Biology 17 (10), e10427, 2021 | 18 | 2021 |
| Bio2Rxn: sequence-based enzymatic reaction predictions by a consensus strategy T Zhang, Y Tian, L Yuan, F Chen, A Ren, QN Hu Bioinformatics 36 (11), 3600-3601, 2020 | 18 | 2020 |
| Data-driven rational biosynthesis design: from molecules to cell factories F Chen, L Yuan, S Ding, Y Tian, QN Hu Briefings in Bioinformatics 21 (4), 1238-1248, 2020 | 12 | 2020 |
| BCSExplorer: a customized biosynthetic chemical space explorer with multifunctional objective function analysis Y Tian, L Wu, L Yuan, S Ding, F Chen, T Zhang, A Ren, D Zhang, W Tu, ... Bioinformatics 36 (5), 1642-1643, 2020 | 12 | 2020 |
| CF-targeter: a rational biological cell factory targeting platform for biosynthetic target chemicals S Ding, P Cai, L Yuan, Y Tian, W Tu, D Zhang, X Cheng, D Sun, J Chen, ... ACS Synthetic Biology 8 (10), 2280-2286, 2019 | 6 | 2019 |
| HGTphyloDetect: facilitating the identification and phylogenetic analysis of horizontal gene transfer L Yuan, H Lu, F Li, J Nielsen, EJ Kerkhoven Briefings in Bioinformatics 24 (2), bbad035, 2023 | 5 | 2023 |
| Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0 Y Chen, J Gustafsson, A Tafur Rangel, M Anton, I Domenzain, ... Nature Protocols, 1-39, 2024 | 4 | 2024 |
| ChemHub: a knowledgebase of functional chemicals for synthetic biology studies M Han, D Zhang, S Ding, Y Tian, X Cheng, L Yuan, D Sun, D Liu, L Gong, ... Bioinformatics 37 (22), 4275-4276, 2021 | 3 | 2021 |
