Method & analysis papers

  1. Shang, Lulu, Peijun Wu, and Xiang Zhou. “Statistical identification of cell type-specific spatially variable genes in spatial transcriptomics.” Nature Communications 16, no. 1 (2025): 1059.
  2. Shang, Lulu, and Xiang Zhou. “Spatially aware dimension reduction for spatial transcriptomics.” Nature communications 13, no. 1 (2022): 7203.
  3. Zhu, Jiaqiang, Lulu Shang, and Xiang Zhou. “SRTsim: spatial pattern preserving simulations for spatially resolved transcriptomics.” Genome biology 24, no. 1 (2023): 39.
  4. Shang, Lulu, Jennifer A. Smith, and Xiang Zhou. “Leveraging gene co-expression patterns to infer trait-relevant tissues in genome-wide association studies.” PLoS genetics 16, no. 4 (2020): e1008734.
  5. Shang, Lulu, Jennifer A. Smith, Wei Zhao, Minjung Kho, Stephen T. Turner, Thomas H. Mosley, Sharon LR Kardia†, and Xiang Zhou†. “Genetic architecture of gene expression in European and African Americans: an eQTL mapping study in GENOA.” The American Journal of Human Genetics 106, no. 4 (2020): 496-512.
  6. Shang, L., W. Zhao, Y. Z. Wang, Z. Li, J. J. Choi, M. Kho, T. H. Mosley, S. L. R. Kardia, J. A. Smith†, and X. Zhou†. meQTL Mapping in the GENOA Study Reveals Genetic Determinants of DNA Methylation in African Americans. Nat. Commun. 14, 2711. 2023.

Collaborative papers

  1. Ding, Jiayuan, Lingxiao Li, Qiaolin Lu, Julian Venegas, Yixin Wang, Lidan Wu, Wei Jin et al. “Spatialctd: A large-scale tumor microenvironment spatial transcriptomic dataset to evaluate cell type deconvolution for immuno-oncology.” Journal of Computational Biology 31, no. 9 (2024): 871-885.
  2. Chaar, Dima L., Zheng Li, Lulu Shang, Scott M. Ratliff, Thomas H. Mosley, Sharon LR Kardia, Wei Zhao, X. Zhou, and J. A. Smith. “Multi-ancestry transcriptome-wide association studies of cognitive function, white matter hyperintensity, and Alzheimer’s disease.” medRxiv (2024): 2024-01.
  3. Xi, Ellie, Tutu Hu, Chloe Yu, Lulu Shang, Xiang Zhou, and Yongsheng Bai. “Identification of Key Biomarkers Associated with Ductal Breast Cancer in Spatial Transcriptomics Data.” In 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 3840-3847. IEEE, 2023.
  4. Wen, Hongzhi, Wenzhuo Tang, Wei Jin, Jiayuan Ding, Renming Liu, Xinnan Dai, Feng Shi, Lulu Shang, Hui Liu, and Yuying Xie. “Single cells are spatial tokens: Transformers for spatial transcriptomic data imputation.” arXiv preprint arXiv:2302.03038 (2023).
  5. Wang, Yi Zhe, Wei Zhao, Farah Ammous, Yanyi Song, Jiacong Du, Lulu Shang, Scott M. Ratliff et al. “DNA methylation mediates the association between individual and neighborhood social disadvantage and cardiovascular risk factors.” Frontiers in cardiovascular medicine 9 (2022): 848768.
  6. Song, Melinda, Jiaqi Yu, Binze Li, Julian Dong, Jeslyn Gao, Lulu Shang, Xiang Zhou, and Yongsheng Bai. “Identification of functionally important miRNA targeted genes associated with child obesity trait in genome-wide association studies.” BMC genomics 23, no. Suppl 4 (2022): 360.
  7. Li, Zheng, Wei Zhao, Lulu Shang, Thomas H. Mosley, Sharon LR Kardia, Jennifer A. Smith, and Xiang Zhou. “METRO: Multi-ancestry transcriptome-wide association studies for powerful gene-trait association detection.” The American Journal of Human Genetics 109, no. 5 (2022): 783-801.
  8. Ammous, Farah, Wei Zhao, Scott M. Ratliff, Minjung Kho, Lulu Shang, Alana C. Jones, Ninad S. Chaudhary et al. “Epigenome-wide association study identifies DNA methylation sites associated with target organ damage in older African Americans.” Epigenetics 16, no. 8 (2021): 862-875.
  9. Wen, Jia, Munan Xie, Bryce Rowland, Jonathan D. Rosen, Quan Sun, Jiawen Chen, Amanda L. Tapia et al. “Transcriptome-wide association study of blood cell traits in african ancestry and hispanic/latino populations.” Genes 12, no. 7 (2021): 1049.
  10. Zhu, Huanhuan, Lulu Shang, and Xiang Zhou. “A review of statistical methods for identifying trait-relevant tissues and cell types.” Frontiers in Genetics 11 (2021): 587887.
  11. Li, Binze, Julian Dong, Jiaqi Yu, Yuqi Fan, Lulu Shang, Xiang Zhou, and Yongsheng Bai. “Pinpointing miRNA and genes enrichment over trait-relevant tissue network in Genome-Wide Association Studies.” BMC medical genomics 13 (2020): 1-13.
  12. Kho, Minjung, Wei Zhao, Scott M. Ratliff, Farah Ammous, Thomas H. Mosley, Lulu Shang, Sharon LR Kardia, Xiang Zhou, and Jennifer A. Smith. “Epigenetic loci for blood pressure are associated with hypertensive target organ damage in older African Americans from the genetic epidemiology network of Arteriopathy (GENOA) study.” BMC medical genomics 13 (2020): 1-10.
  13. Kho, Minjung, Jennifer A. Smith, Niek Verweij, Lulu Shang, Kathleen A. Ryan, Wei Zhao, Erin B. Ware et al. “Genome-wide association meta-analysis of individuals of european ancestry identifies suggestive loci for sodium intake, potassium intake, and their ratio measured from 24-hour or half-day urine samples.” The Journal of Nutrition 150, no. 10 (2020): 2635-2645.
  14. Ren, Jie, Lulu Shang, Qing Wang, and Jing Li. “Ranking cancer proteins by integrating PPI network and protein expression profiles.” BioMed research international 2019, no. 1 (2019): 3907195.