Publications

Lingyu Li, Liangjie Sun, Shumin Li, Wai-Ki Ching, Zhi-Ping Liu (2026). Cell dynamics on energy landscape: Comparing attractor detection in Boolean network and diffusion-based models under in silico gene perturbations. In QUANT BIOL.

Lingyu Li, Weiqin Zhao, Qingpeng Zhang, Wai-Ki Ching, Zhi-Ping Liu (2026). CNet-Cox for interpretable network biomarker discovery and survival risk scoring in precise breast cancer prognosis. In npj Digit Med.

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Lingyu Li, Tianjie Wang, Zhuo Liang, Huajian Yu, Stephanie Ma, Lequan Yu, Yuanhua Huang (2026). FineST: Contrastive learning integrates histology and spatial transcriptomics for nuclei-resolved ligand-receptor analysis. In NAT COMMUN.

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Lingyu Li, Wai-Ki Ching, Zhi-Ping Liu (2026). Prognostic biomarker discovery via a connected network-constrained Cox proportional hazards model. In BRIEF BIOINFORM.

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Tianjie Wang, Lingyu Li, Yuanhua Huang (2026). SparseAEH: Scalable autoregressive expression histology discovery in spatial transcriptomics via sparse Gaussian kernels. In BioRxiv.

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Tong Wang, Lingyu Li, Zhi-Ping Liu (2025). getDNB: identifying dynamic network biomarkers from time-varying gene regulations utilizing graph embedding techniques. In BRIEF BIOINFORM.

Fatemeh Keikha, Lingyu Li, Wai-Ki Ching, Zhi-Ping Liu (2025). NetWalkRank: Cancer driver gene prioritization in multiplex gene regulatory networks by a random walk approach. In IEEE ACM T COMPUT BI.

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Lingyu Li, Zhi-Ping Liu (2023). Biomarker discovery from high-throughput data by connected network-constrained support vector machine. In EXPERT SYST APPL.

Lingyu Li, Liangjie Sun, Guangyi Chen, Chi-Wing Wong, Wai-Ki Ching, Zhi-Ping Liu (2023). LogBTF: gene regulatory network inference using Boolean threshold network model from single-cell gene expression data . In BIOINFORMATICS.

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Lingyu Li, Algabri, Yousif A, Zhi-Ping Liu (2023). Identifying diagnostic biomarkers of breast cancer based on gene expression data and ensemble feature selection. In CURR BIOINFORM.

Algabri, Yousif A, Lingyu Li, Zhi-Ping Liu (2022). scGENA: A single-cell gene coexpression network analysis framework for clustering cell types and revealing biological mechanisms. In Bioengineering.

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Lingyu Li, Wai-Ki Ching, Zhi-Ping Liu (2022). Robust biomarker screening from gene expression data by stable machine learning-recursive feature elimination methods. In COMPUT BIOL CHEM.

Lingyu Li, Zhi-Ping Liu (2022). A connected network-regularized logistic regression model for feature selection. In APPL INTELL.

Lingyu Li, Zhi-Ping Liu (2021). Detecting prognostic biomarkers of breast cancer by regularized Cox proportional hazards models. In J TRANSL MED.

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Lingyu Li, Zhi-Ping Liu (2021). Discovery of spontaneous preterm birth biomarkers based on machine learning. In Journal of Nanjing University(Natural Sciences).

Lingyu Li, Zhi-Ping Liu (2020). Biomarker discovery for predicting spontaneous preterm birth from gene expression data by regularized logistic regression. In COMPUT STRUCT BIOTEC.

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Lingyu Li, Ziwen Jiang, Zhe Yin (2020). Compact finite-difference method for 2D time-fractional convection–diffusion equation of groundwater pollution problems. In COMPUT APPL MATH.

Lingyu Li, Ziwen Jiang, Zhe Yin (2018). Fourth-order compact finite difference method for solving two-dimensional convection–diffusion equation. In ADV DIFFER EQU-NY.

Lingyu Li, Zhe Yin (2017). Numerical simulation of groundwater pollution problems based on convection diffusion equation. In AJCM.

Lingyu Li, Jinjun Fan (2016). Uniform convergence and application of function term's series. In Journal of Shandong Normal University (Natural Science).