Publications

You can also find my full publication list on my Google Scholar profile

Selected Publications

• STP: single-cell partition for subcellular spatially resolved transcriptomics.
  H Li, Q Hu, Z Qiu, Hui X, Y Hu, X Gao. Nature Communications, 2025.
• SANTO: a coarse-to-fine alignment and stitching method for spatial omics.
  H Li, Y Lin, W He, W Han, X Xu, C Xu, E Gao, H Zhao, X Gao. Nature Communications, 2024.
• A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics.
  H Li, J Zhou, Z Li, S Chen, X Liao, B Zhang, R Zhang, Y Wang, S Sun, X Gao. Nature Communications, 2023.
  Selected as Editors’ Highlight and “50 best papers in Biotechnology and Methods”
• SD2: Spatially resolved transcriptomics deconvolution through integration of spatial and dropout information.
  H Li, H Li, J Zhou, X Gao. Bioinformatics, 2022.
• Automatic and interpretable model for periodontitis diagnosis in panoramic radiographs.
  H Li, J Zhou, Y Zhou, J Chen, F Gao, Y Xu, X Gao. MICCAI, 2020.

Publications

• Large Language Models in Biomedicine and Healthcare.
  J Zhou, H Li, S Chen, Z Chen, Z Han, X Gao.
  npj Artificial Intelligence, 2025

• AggNet: Advancing Protein Aggregation Analysis Through Deep Learning and Protein Language Model.
  W He, X Xu, H Li, J Zhou, X Gao.
  Protein Science, 2024.

• ScholarChemQA: Unveiling the Power of Language Models in Chemical Research Question Answering.
  X Chen, T Wang, T Guo, K Guo, J Zhou, H Li, Z Song, X Gao, X Zhang.
  Communications Chemistry, 2024.

• An AI Agent for Fully Automated Multi-omic Analyses.
  J Zhou, B Zhang, X Chen, H Li, X Xu, S Chen, X Gao.
  Advanced Science, 2024.

• HELM-GPT: de novo macrocyclic peptide design using generative pre-trained transformer.
  X Xu, C Xu, W He, L Wei, H Li, J Zhou, R Zhang, Y Wang, Y Xiong, X Gao.
  Bioinformatics, 2024.

• KaryoXpert: An Accurate Chromosome Segmentation and Classification Framework for Karyotyping Analysis without Training with Manually Labeled Metaphase-Image Mask Annotations.
  S Chen, K Zhang, J Hu, N Li, A Xu, H Li, J Zhou, C Huang, Y Yu, X Gao.
  Computers in Biology and Medicine, 2024.

• PPML-Omics: a Privacy-Preserving Federated Machine Learning System Protects Patients’ Privacy from Omic Data.
  J Zhou, S Chen, Y Wu, H Li, B Zhang, L Zhou, Y Hu, Z Xiang, Z Li, N Chen, W Han, D Wang, X Gao.
  Science Advances*, 2023.

• Personalized and privacy-preserving federated heterogeneous medical image analysis with PPPML-HMI.
  J Zhou, L Zhou, D Wang, X Xu, H Li, Y Chu, W Han, X Gao.
  Computers in Biology and Medicine, 2023.

• Repetitive DNA sequence detection and its role in the human genome.
  X Liao, W Zhu, J Zhou, H Li, X Xu, B Zhang, X Gao.
  Communications Biology, 2023.

• Audit to Forget: A Unified Method to Revoke Patients’ Private Data in Intelligent Healthcare.
  J Zhou, H Li, X Liao, B Zhang, W He, Z Li, L Zhou, X Gao.
  Nature Communications, 2023.

• Annotating TSSs in Multiple Cell Types Based on DNA Sequence and RNA-seq Data via DeeReCT-TSS.
  J Zhou, B Zhang, H Li, L Zhou, Z Li, Y Long, W Han, M Wang, H Cui, W Chen, X Gao.
  Genomics, Proteomics & Bioinformatics, 2022.

• miR-596-3p suppresses brain metastasis of non-small cell lung cancer by modulating YAP1 and IL-8.
  C Li, H Zheng, J Xiong, Y Huang, H Li, H Jin, S Ai, Y Wang, T Su, G Sun, X Xiao, T Fu, Y Wang, X Gao, P Liang.
  Cell Death & Disease, 2022.

• An interpretable deep learning workflow for discovering subvisual abnormalities in CT scans of COVID-19 inpatients and survivors.
  L Zhou, X Meng, Y Huang, K Kang, J Zhou, Y Chu, H Li, D Xie, J Zhang, W Yang, N Bai, Y Zhao, M Zhao, G Wang, L Carin, X Xiao, K Yu, Z Qiu, X Gao.
  Nature Machine Intelligence, 2022.

• An Interpretable Computer-Aided Diagnosis Method for Periodontitis From Panoramic Radiographs.
  H Li, J Zhou, Y Zhou, Q Chen, Y She, F Gao, Y Xu, J Chen, X Gao.
  Frontiers in Physiology, 2021.

• A rapid, accurate and machine-agnostic segmentation and quantification method for CT-based COVID-19 diagnosis.
  L Zhou, Z Li, J Zhou, H Li, Y Chen, Y Huang, D Xie, L Zhao, M Fan, S Hashmi, F AbdelKareem, R Eiada, X Xiao, L Li, Z Qiu, X Gao.
  IEEE Transactions on Medical Imaging, 2020.

• Modern deep learning in bioinformatics.
  H Li, S Tian, Y Li, Q Fang, R Tian, Y Pan, C Huang, Y Xu, X Gao.
  Journal of Molecular Cell Biology, 2020.

• CaMeRe: a novel tool for inference of cancer metabolic reprogramming.
  H Li, J Zhou, H Sun, Z Qiu, X Gao, Y Xu.
  Frontiers in Oncology (Cancer Metabolism), 2020.

• Neural functions play different roles in Triple Negative Breast Cancer (TNBC) and non-TNBC.
  R Tan, H Li, Z Huang, Y Zhou, M Tao, X Gao, Y Xu.
  Scientific Reports, 2020.

Preprints

• PAST: A multimodal single-cell foundation model for histopathology and spatial transcriptomics in cancer.
  C Yang, H Li, Y Wu, Y Zhang, Y Jiao, Y Zhang, R Huang, Y Chang, Y Qi, X Guo, X Gao.

• Protein as a Second Language for LLMs.
  X Chen, Z Li, M Gao, Y Zhang, C Leong, H Li, J Chen.

• Deep Learning Enhanced Tandem Repeat Variation Identification via Multi-Modal Conversion of Nanopore Reads Alignment.
  X Liao, J Zhou, B Zhang, X Li, X Xu, H Li, X Gao.

• A Model for the Development of Alzheimer’s Disease.
  Z Huang, L Zhong, X Mu, J Xiao, Q Chen, Y Zhang, G Xiao, Y Qu, X Li, Y Cao, Z Wang, C Zuo, R Tan, F Xing, X Wu, H Li, L Xu, J Tang, X Chen, R Guan, Y Xu.

• Heart Region Anchoring: a Model-Agnostic Workflow to Improve Segmentation Robustness for Breast Cancer in DCE-MRI.
  L Zhou, Y Ding, J Guo, M Fan, J Zhou, H Li, Y Li, Y Huang, Y Zhao, Y Chu, K Wang, Q Fang, X Gao, H Zhang, L Li.