Gang Li

Gang Li

UW Data Science Postdoctoral Science Fellow

Publications

You can also find my articles on my Google Scholar profile.

Work in progress

  1. Li, G.*, Eva K. Nichols*, Valentino E. Browning, Nicolas Longhi, Conor K. Camplisson, Beliveau, B., Noble, W. (2024+). Predicting cell cycle stage from 3D single-cell nuclear-stained images. [Code] [Presentation]
  2. Li, G., Kim, H., Pendyala, S., Zhang, R., Disteche, C., Vert, J., Deng, X., Fowler, D., Noble, W.(2024+, submitted). Pseudotime analysis and integration for time-series single-cell sequencing and imaging data. [Code] [Presentation]
  3. Li, G., Chengxiang Qiu, Xumeng Zhang, Kris G. Alavattam, Beth Martin, Josephine Lin, Riza M. Daza, Galina N. Filippova, Ran Zhang, Jay Shendure, Xinxian Deng, Disteche M. Christine, William S. Noble. (2024+). Allelic change surveyed by high throughput single-cell omics during mouse embryonic development.
  4. Li, G., Kim, H., Zhang, R., Pendyala, S., Papaxanthos, L., Deng, X., Disteche, C., Fowler, D., Vert, J., Noble, W.(2024+). Integrating imaging and sequencing data from visual cell sorting.
  5. Li, G.*, Jia, W.*, Chen, J., Sun, Q., Liu, W., Guan, W., Lai, B., He, X., Szatkiewicz, J., Sullivan, P. , Li, Y.(2024+, submitted). DeepGWAS to Enhance GWAS Signals for Neuropsychiatric Disorders via Deep Neural Network. [Code]
  6. Ran Zhang, Chengxiang Qiu, Gala Filippova, Gang Li, Jay Shendure, Jean-Philippe Vert, Xinxian Deng, Christine M. Disteche, and William Stafford Noble. (2024+) Multi-condition and multi-modal temporal profile inference during mouse embryonic development.
  7. Chenwei Tang, Quan Sun, Xinyue Zeng, Xiaoyu Yang, Fei Liu, Jinying Zhao, Gang Li, Yin Shen, Bixiang Liu, Jia Wen, Yun Li (2024+). Cell-type specific inference from bulk RNA-sequencing data by integrating single cell reference profiles via EPIC-unmix.

Note: * means co-first author.

Publications as leading author

  1. Li, G.*, Luan, C.*, Zentz, S., Zelt, R., Roach, J., Liu, J., Qian, L., Li, Y., Yang, Y. (2021). ExpressHeart: Web Portal to Visualize Transcriptome Profiles of Non-cardiomyocyte Cells. International Journal of Molecular Sciences, 2021; 22(16):8943. [Web]
  2. Li, G., Raffield, L., Logue, M., Miller, M.W., Santos, H.P., O’Shea, M., Fry, R. and Li,Y. (2020). CUE: CpG imPutation Ensemble for DNA Methylation Levels across Platforms. Epigenetics, 1-11. [Code]
  3. Li, G., Hannig, J. (2020). Deep Fiducial Inference. Stat. 2020; e308. [Code]
  4. Yang, Y.*, Li, G.*, Qian, H., Wilhelmsen, K., Shen, Y., Li., Y. (2020). SMNN: Batch Effect Correction for Single-cell RNA-seq data via Supervised Mutual Nearest Neighbor Detection. Briefings in Bioinformatics, Volume 22, Issue 3, May 2021, bbaa097, [Code]
  5. Li, G., Yang, Y., Van Buren, E., Li, Y. (2019). Dropout imputation and batch effectcorrection for single-cell RNA sequencing data. Journal of Bio-X Research, 2(4), 169-177.

Collaborative paper

  1. Tangqi Fang, Yifeng Liu, Addie Woicik, Minsi Lu, Anupama Jha, Xiao Wang, Gang Li, Borislav Hristov, Zixuan Liu, Hanwen Xu, William Noble, Sheng Wang. (2024 ISMB accepted). Enhancing Hi-C contact matrices for loop detection with Capricorn, a multi-view diffusion model. [Code]
  2. Gao W, Gu K, Ma L, Yang F, Deng L, Zhang Y, Miao MZ, Li W, Li G, Qian H, Zhang Z, Wang G, Yu H, Liu X. (2024). Interstitial Fluid Shear Stress Induces the Synthetic Phenotype Switching of VSMCs to Release Pro-calcified Extracellular Vesicles via EGFR-MAPK-KLF5 Pathway. Int J Biol Sci 2024; 20(7):2727-2747. doi:10.7150/ijbs.90725. https://www.ijbs.com/v20p2727.htm
  3. Y. Yang, T. Alves, M. Z. Miao, Y.C. Wu, G. Li, J. Lou, H. Hasturk, T.E. Van Dyke, A. Kantarci, D. Wu (2023). Single-Cell Transcriptomic Analysis of Dental Pulp and Periodontal Ligament Stem Cells. Journal of Dental Research. 2023;0(0). doi:10.1177/00220345231205283
  4. Michael Z. Miao, Qian Peter Su, Yang Cui, Edward M. Bahnson, Gang Li, Menglin Wang, Yuchen Yang, John A. Collins1, Di Wu, Susan Chubinskaya, Brian O. Diekman, Richard F. Loeser (2023). Redox-active endosomes mediate α5β1 integrin signaling and promote chondrocyte matrix metalloproteinase production in osteoarthritis. Sci. Signal.16,eadf8299(2023).DOI:10.1126/scisignal.adf8299
  5. Laetitia Meng-Papaxanthos, Ran Zhang, Li, G., Marco Cuturi, William Stafford Noble, Jean-Philippe Vert (2023). LSMMD-MA: scaling multimodal data integration for single-cell genomics data analysis. , Bioinformatics, Volume 39, Issue 7, July 2023, btad420, https://doi.org/10.1093/bioinformatics/btad420 [Code]
  6. Le Huang, Yuchen Yang, Gang Li, Minzhi Jiang, Jia Wen, Armen Abnousi, Jonathan D Rosen, Ming Hu, Yun Li. (2022). A systematic evaluation of Hi-C data enhancement methods for enhancing PLAC-seq and HiChIP data. Briefings in Bioinformatics, 2022;, bbac145, https://doi.org/10.1093/bib/bbac145
  7. Yu, W., Gu, Q., Wu, D., Zhang, W., Li, G., ..., Lu, E. (2022). Identification of potentially functional circRNAs and prediction of circRNA-miRNA-mRNA regulatory network in periodontitis: bridging the gap between bioinformatics and clinical needs. J Periodontal Res. 2022 Apr 6. doi: 10.1111/jre.12989. Epub ahead of print. PMID: 35388494.
  8. Ren, X., Wang, M., ..., Li, G., ..., Shen, Y. (2021). Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath. Science Advances. 2021 Sep;7(38):eabi4360. DOI: 10.1126/sciadv.abi4360. PMID: 34524848; PMCID: PMC8443183.
  9. Yang, Y., Li, G., Xie, Y., Wang, L., Liu, J., Qian, L., Li, Y. (2021). iSMNN: Batch Effect Correction for Single-cell RNA-seq data via Iterative Supervised Mu-tual Nearest Neighbor Refinement. Briefings in Bioinformatics, 2021;, bbab122 [Code]

Book Chapter

  1. Li, G., Zhang, G., Li, Y. (2022). DNA Methylation Imputation across Platforms. Epigenome-Wide Association Studies: Methods and Protocols. Springer, US, 2022. Methods in Molecular Biology \#2432.
  2. Wu, D., Karhade, D. S., Pillai, M., Jiang, M. Z., Huang, L., Li, G., ... & Divaris, K. (2021). Machine Learning and Deep Learning in Genetics and Genomics. In Machine Learning in Dentistry (pp. 163-181). Springer, Cham.

Dissertation