| Methodology-centered review of molecular modeling, simulation, and prediction of SARS-CoV-2 K Gao, R Wang, J Chen, L Cheng, J Frishcosy, Y Huzumi, Y Qiu, ... Chemical Reviews 122 (13), 11287-11368, 2022 | 49 | 2022 |
| Persistent Laplacian projected Omicron BA. 4 and BA. 5 to become new dominating variants J Chen, Y Qiu, R Wang, GW Wei Computers in biology and medicine 151, 106262, 2022 | 43 | 2022 |
| Scaling a Dpp morphogen gradient through feedback control of receptors and co-receptors Y Zhu, Y Qiu, W Chen, Q Nie, AD Lander Developmental cell 53 (6), 724-739. e14, 2020 | 34 | 2020 |
| Cluster learning-assisted directed evolution Y Qiu, J Hu, GW Wei Nature computational science 1 (12), 809-818, 2021 | 30 | 2021 |
| Persistent spectral theory-guided protein engineering Y Qiu, GW Wei Nature computational science 3 (2), 149-163, 2023 | 28 | 2023 |
| A multiscale hybrid mathematical model of epidermal‐dermal interactions during skin wound healing Y Wang, CF Guerrero‐Juarez, Y Qiu, H Du, W Chen, S Figueroa, ... Experimental dermatology 28 (4), 493-502, 2019 | 20 | 2019 |
| Noise control and utility: from regulatory network to spatial patterning Q Nie, L Qiao, Y Qiu, L Zhang, W Zhao Science China Mathematics 63, 425-440, 2020 | 18 | 2020 |
| Emerging dominant SARS-CoV-2 variants J Chen, R Wang, Y Hozumi, G Liu, Y Qiu, X Wei, GW Wei Journal of chemical information and modeling 63 (1), 335-342, 2022 | 17 | 2022 |
| Artificial intelligence-aided protein engineering: from topological data analysis to deep protein language models Y Qiu, GW Wei Briefings in Bioinformatics 24 (5), bbad289, 2023 | 15 | 2023 |
| Review of applications and challenges of quantitative systems pharmacology modeling and machine learning for heart failure L Cheng, Y Qiu, BJ Schmidt, GW Wei Journal of pharmacokinetics and pharmacodynamics, 1-12, 2022 | 12 | 2022 |
| CLADE 2.0: evolution-driven cluster learning-assisted directed evolution Y Qiu, GW Wei Journal of chemical information and modeling 62 (19), 4629-4641, 2022 | 11 | 2022 |
| Multiple morphogens and rapid elongation promote segmental patterning during development Yuchi Qiu, F Lianna, FS Thomas, Q Nie PLoS Computational Biology 17 (e1009077), e1009077, 2021 | 8 | 2021 |
| Stochastic dynamics of cell lineage in tissue homeostasis Y Qiu, W Chen, Q Nie Discrete and continuous dynamical systems. Series B 24 (8), 3971, 2019 | 8 | 2019 |
| A hybrid method for stiff reaction–diffusion equations Y Qiu, W Chen, Q Nie Discrete and continuous dynamical systems. Series B 24 (12), 6387, 2019 | 6 | 2019 |
| SVSBI: sequence-based virtual screening of biomolecular interactions L Shen, H Feng, Y Qiu, GW Wei Communications biology 6 (1), 536, 2023 | 5 | 2023 |
| Reconstructing growth and dynamic trajectories from single-cell transcriptomics data Y Sha, Y Qiu, P Zhou, Q Nie Nature Machine Intelligence 6 (1), 25-39, 2024 | 4 | 2024 |
| Mathematics-assisted directed evolution and protein engineering Y Qiu, GW Wei arXiv preprint arXiv:2306.04658, 2023 | | 2023 |
| Corrections & amendments Y Sha, Y Qiu, P Zhou, Q Nie | | 2023 |
| NEURALGENE: INFERRING GENE REGULATION AND CELL-FATE DYNAMICS FROM NEURAL ODES Y Sha, Y Qiu, Q Nie Journal of Machine Learning for Modeling and Computing 4 (3), 2023 | | 2023 |
| Multiscale Modeling for Tissue Patterning: Growth and Stochasticity Y Qiu University of California, Irvine, 2020 | | 2020 |
