Zhang, Xuegong

A survey of best practices for RNA-seq data analysis

Conesa, A., Madrigal, P., Tarazona, S., Gomez-Cabrero, D., Cervera, A., McPherson, A., Szcześniak, M. W., Gaffney, D. J., Elo, L. L., Zhang, X., et al. (2016) · Genome Biology

Genomics and Phylogenetic StudiesSingle-cell and spatial transcriptomics

Cited by 2,794

Large Scale Foundation Model on Single-cell Transcriptomics

Hao, M., Gong, J., Zeng, X., Liu, C., Guo, Y., Cheng, X., Wang, T., Ma, J., Song, L., & Zhang, X. (2023) · Nature Methods

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 639

Large-scale foundation model on single-cell transcriptomics

Hao, M., Gong, J., Zeng, X., Liu, C., Guo, Y., Cheng, X., Wang, T., Ma, J., Zhang, X., & Song, L. (2024) · Nature Methods

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 628

ERNIE-RNA: an RNA language model with structure-enhanced representations

Yin, W., Zhang, Z., Zhang, S., He, L., Zhang, R., Jiang, R., Liu, G., Wang, J., Zhang, X., Qin, T., et al. (2025) · Nature Communications

RNA and protein synthesis mechanismsMachine Learning in Bioinformatics

Cited by 55

ERNIE-RNA: An RNA Language Model with Structure-enhanced Representations

Yin, W., Zhang, Z., He, L., Jiang, R., Zhang, S., Liu, G., Zhang, X., Qin, T., & Xie, Z. (2024) · Nature Communications

RNA and protein synthesis mechanismsMachine Learning in Bioinformatics

Cited by 55

CS-CO: A Hybrid Self-Supervised Visual Representation Learning Method for H&E-stained Histopathological Images

Yang, P., Yin, X., Lu, H., Hu, Z., Zhang, X., Jiang, R., & Lv, H. (2022) · Medical Image Analysis

AI in cancer detectionRadiomics and Machine Learning in Medical Imaging

Cited by 50

Generation of Synthetic Electronic Medical Record Text

Guan, J., Li, R., Yu, S., & Zhang, X. (2018) · 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Machine Learning in HealthcareArtificial Intelligence in Healthcare and Education

Cited by 49

Dynamic atlas of immune cells reveals multiple functional features of macrophages associated with progression of pulmonary fibrosis

Lv, J., Gao, H., Ma, J., Liu, J., Tian, Y., Yang, C., Li, M., Zhao, Y., Li, Z., Zhang, X., et al. (2023) · Frontiers in Immunology

Interstitial Lung Diseases and Idiopathic Pulmonary FibrosisTransplantation: Methods and Outcomes

Cited by 48

Benchmarking AI Models for In Silico Gene Perturbation of Cells

Li, C., Gao, H., She, Y., Bian, H., Chen, Q., Liu, K., Wei, L., & Zhang, X. (2024) · bioRxiv (Cold Spring Harbor Laboratory)

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 24

NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data

Ma, X., & Zhang, X. (2013) · BMC Bioinformatics

Genomics and Phylogenetic StudiesRNA Research and Splicing

Cited by 14