Publications

Author profiles on Google Scholar.

Preprints

• On E-values, Multiple Testing and Beyond.
  Li, G. and Zhang, X. (arXiv)

• Importance is Important: A Guide to Informed Importance Tempering Methods.
  Li, G., Smith, A. and Zhou, Q., 2023. arXiv preprint arXiv:2304.06251. (arXiv)

• Fast Replica Exchange Stochastic Gradient Langevin Dynamics.
  Li, G., Lin, G., Zhang, Z. and Zhou, Q., 2023. arXiv preprint arXiv:2301.01898. (arXiv)

Journal Publications

• Robust Differential Abundance Analysis of Microbiome Sequencing Data.
  Li, G., Yang, L., Chen, J. and Zhang, X., 2023. Accepted by Genes.

• Bayesian Multi-task Variable Selection with an Application to Differential DAG Analysis.
  Li. G. and Zhou. Q., 2023. Accepted by Journal of Computational and Graphical Statistics. (arXiv)

• Interpretable modeling of time-resolved single-cell gene-protein expression using CrossmodalNet.
  Yang, Y., Lin, Y.T., Li, G., Zhong, Y., Xu, Q. and Cai, J.J., 2023. Briefings in Bioinformatics, 24(6), p.bbad342. (bioRxiv)

• Gene knockout inference with variational graph autoencoder learning single-cell gene regulatory networks.
  Yang, Y., Li, G., Zhong, Y., Xu, Q., Chen, B.J., Lin, Y.T., Chapkin, R.S. and Cai, J.J., 2023. Nucleic Acids Research, p.gkad450. (link)

• scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs.
  Yang, Y., Li, G., Zhong, Y., Xu, Q., Lin, Y.T., Roman-Vicharra, C., Chapkin, R.S. and Cai, J.J., 2023. Cell Systems, 14(4), pp.302-311. (link)

• scTenifoldKnk: An efficient virtual knockout tool for gene function predictions via single-cell gene regulatory network perturbation.
  Osorio, D., Zhong, Y., Li, G., Xu, Q., Yang, Y., Tian, Y., Chapkin, R.S., Huang, J.Z. and Cai, J.J., 2022. Patterns, 3(3), p.100434. (link)

• scInTime: A Computational Method Leveraging Single-Cell Trajectory and Gene Regulatory Networks to Identify Master Regulators of Cellular Differentiation.
  Xu, Q., Li, G., Osorio, D., Zhong, Y., Yang, Y., Lin, Y.T., Zhang, X. and Cai, J.J., 2022. Genes, 13(2), p.371. (link)

• scTenifoldNet: a machine learning workflow for constructing and comparing transcriptome-wide gene regulatory networks from single-cell data.
  Osorio, D., Zhong, Y., Li, G., Huang, J.Z. and Cai, J.J., 2020. Patterns, 1(9), p.100139. (link)

• Single-cell expression variability implies cell function.
  Osorio, D., Yu, X., Zhong, Y., Li, G., Serpedin, E., Huang, J.Z. and Cai, J.J., 2019. Cells, 9(1), p.14 (link)