Publications

FULL LIST of publications are available in my google scholar.

Selected publications:

Data-driven modeling for spatio-temporal dynamics of single-cell omics data

• Reconstructing growth and dynamic trajectories from single-cell transcriptomics data.
  Yutong Sha, Yuchi Qiu, Peijie Zhou, Qing Nie.
  Nature Machine Intelligence, 2023.
• NeuralGene: Inferring gene regulation and cell fate dynamics from Neural ODEs.
  Yutong Sha^#, Yuchi Qiu^#, and Qing Nie. (#: co-first)
  Journal of Machine Learning for Modeling and Computing, 2023.

AI-aided protein designs

• Artificial intelligence-aided protein engineering: from topological data analysis to deep protein language models,
  Yuchi Qiu and Guo-Wei Wei.
  Briefings in Bioinformatics, 2023.
• Persistent spectral theory-guided protein engineering,
  Yuchi Qiu and Guo-Wei Wei.
  Nature Computational Science, 2023.
• Persistent Laplacian projected Omicron BA. 4 and BA. 5 to become new dominating variants,
  Jiahui Chen, Yuchi Qiu, Rui Wang, and Guo-Wei Wei.
  Computers in Biology and Medicine, 2022.
• Cluster learning-assisted directed evolution,
  Yuchi Qiu, Jian Hu, and Guo-Wei Wei.
  Nature Computational Science, 2021.
• CLADE 2.0: Evolution-driven cluster learning-assisted directed evolution,
  Yuchi Qiu, Guo-Wei Wei.
  Journal of Chemical Information and Modeling, 2022.

Multi-scale Modeling for embryonic spatial pattern formation:

• Multiple morphogens and rapid elongation promote segmental patterning during development,
  Yuchi Qiu, Lianna Fung, Thomas Schilling, Qing Nie
  PLoS Computational Biology, 2021.
• Scaling a Dpp morphogen gradient through feedback control of receptors and co-receptors,
  Yilun Zhu, Yuchi Qiu, Weitao Chen, Qing Nie, and Arthur Lander.
  Developmental Cell, 2020.
• Stochastic dynamics of cell lineage in tissue homeostasis,
  Yuchi Qiu, Weitao Chen, Qing Nie.
  Discrete and Continuous Dynamical System -B, 2019.

Numerical methods:

• A hybrid method for stiff reaction–diffusion equations,
  Yuchi Qiu, Weitao Chen, Qing Nie.
  Discrete and Continuous Dynamical System -B, 2019.