Qi Liu
Qi Liu

Professor, Bioinformatics & System Biology
Technical Director of VANGARD
Director of the Omics Coordinating Center at CQS

Dr. Liu’s research focuses on integrating multi-omics data to address fundamental biological questions. Her research interests include

  • Multiomics integration to study complex disease
  • Methodology development in high-dimensional data, such as single-cell and spatial omics data
  • Omics resource portal development

E-mail: qi.liu@vumc.org

Software and Resource Portal
A distribution-free and analytic method for power and sample size calculation in single-cell differential expression
aKNNO: single-cell and spatial transcriptomics clustering with an optimized adaptive k-nearest neighbor graph
EVPsort: An Atlas of Small ncRNA Profiling and Sorting in Extracellular Vesicles and Particles
scKWARN: Kernel-weighted-average robust normalization for single-cell RNA-seq data
Scalable and model-free detection of spatial patterns and colocalization
Dysregulated ligand-receptor interactions from single-cell transcriptomics
A pan-cancer immunogenomic atlas for immune checkpoint blockade immunotherapy
scMRMA: single cell multiresolution marker-based annotation
scRNABatchQC: multi-samples quality control for single cell RNA-seq data
HACER: an atlas of human active enhancers to interpret regulatory variants
Selected Publications
1.
Hsu, C. Y. , Liu, Q. , Shyr, Y. (2024). A distribution-free and analytic method for power and sample size calculation in single-cell differential expression. Bioinformatics.
PubMed PMC Code DOI Cite
2.
Li, J. , Simmons, A. J. , Hawkins, C. V. , Chiron, S. , Ramirez-Solano, M. A. , Tasneem, N. , Kaur, H. , Xu, Y. , Revetta, F. , Vega, P. N. , Bao, S. , Cui, C. , Tyree, R. N. , Raber, L. W. , Conner, A. N. , Pilat, J. M. , Jacobse, J. , McNamara, K. M. , Allaman, M. M. , Raffa, G. A. , Gobert, A. P. , Asim, M. , Goettel, J. A. , Choksi, Y. A. , Beaulieu, D. B. , Dalal, R. L. , Horst, S. N. , Pabla, B. S. , Huo, Y. , Landman, B. A. , Roland, J. T. , Scoville, E. A. , Schwartz, D. A. , Washington, M. K. , Shyr, Y. , Wilson, K. T. , Coburn, L. A. , Lau, K. S. , Liu, Q. (2024). Identification and multimodal characterization of a specialized epithelial cell type associated with Crohn's disease. Nat Commun.
PubMed PMC Code DOI Cite
3.
Li, J. , Shyr, Y. , Liu, Q. (2024). aKNNO: single-cell and spatial transcriptomics clustering with an optimized adaptive k-nearest neighbor graph. Genome Biol.
PubMed PMC Code DOI Cite
4.
Chen, H. C. , Wang, J. , Coffey, R. J. , Patton, J. G. , Weaver, A. M. , Shyr, Y. , Liu, Q. (2024). EVPsort: An Atlas of Small ncRNA Profiling and Sorting in Extracellular Vesicles and Particles. J Mol Biol.
PubMed PMC WebSite DOI Cite
5.
Hsu, C. Y. , Chang, C. J. , Liu, Q. , Shyr, Y. (2024). scKWARN: Kernel-weighted-average robust normalization for single-cell RNA-seq data. Bioinformatics.
PubMed PMC Code DOI Cite
6.
Yang, J. , Liu, Q. , Shyr, Y. (2023). A Large-Scale Meta-Analysis Reveals Positive Feedback between Macrophages and T Cells That Sensitizes Tumors to Immunotherapy. Cancer Res.
PubMed PMC WebSite DOI Cite
7.
Liu, Q. , Zhou, Y. , Cogan, J. D. , Mitchell, D. B. , Sheng, Q. , Zhao, S. , Bai, Y. , Ciombor, K. K. , Sabusap, C. M. , Malabanan, M. M. , Markin, C. R. , Douglas, K. , Ding, G. , Banovich, N. E. , Nickerson, D. A. , Blue, E. E. , Bamshad, M. J. , Brown, K. K. , Schwartz, D. A. , Phillips, J. A., 3rd , Martinez-Barricarte, R. , Salisbury, M. L. , Shyr, Y. , Loyd, J. E. , Kropski, J. A. , Blackwell, T. S. (2023). The Genetic Landscape of Familial Pulmonary Fibrosis. Am J Respir Crit Care Med.
PubMed PMC DOI Cite
8.
Liu, Q. , Hsu, C. Y. , Shyr, Y. (2022). Scalable and model-free detection of spatial patterns and colocalization. Genome Res.
PubMed PMC Code DOI Cite
9.
Liu, Q. , Hsu, C. Y. , Li, J. , Shyr, Y. (2022). Dysregulated ligand-receptor interactions from single-cell transcriptomics. Bioinformatics.
PubMed PMC Code DOI Cite
10.
Chu, S. K. , Zhao, S. , Shyr, Y. , Liu, Q. (2022). Comprehensive evaluation of noise reduction methods for single-cell RNA sequencing data. Brief Bioinform.
PubMed PMC DOI Cite
11.
Yang, J. , Zhao, S. , Wang, J. , Sheng, Q. , Liu, Q. , Shyr, Y. (2021). A pan-cancer immunogenomic atlas for immune checkpoint blockade immunotherapy. Cancer Res.
PubMed PMC WebSite DOI Cite
12.
Li, J. , Sheng, Q. , Shyr, Y. , Liu, Q. (2021). scMRMA: single cell multiresolution marker-based annotation. Nucleic Acids Res.
PubMed PMC Code DOI Cite
13.
Liu, Q. , Sheng, Q. , Ping, J. , Ramirez, M. A. , Lau, K. S. , Coffey, R. J. , Shyr, Y. (2019). scRNABatchQC: multi-samples quality control for single cell RNA-seq data. Bioinformatics.
PubMed PMC Code DOI Cite
14.
Liu, Q. , Herring, C. A. , Sheng, Q. , Ping, J. , Simmons, A. J. , Chen, B. , Banerjee, A. , Li, W. , Gu, G. , Coffey, R. J. , Shyr, Y. , Lau, K. S. (2018). Quantitative assessment of cell population diversity in single-cell landscapes. PLoS Biol.
PubMed PMC DOI Cite
15.
Wang, J. , Dai, X. , Berry, L. D. , Cogan, J. D. , Liu, Q. , Shyr, Y. (2018). HACER: an atlas of human active enhancers to interpret regulatory variants. Nucleic Acids Res.
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