Gang Li

Gang Li

UW Data Science Postdoctoral Science Fellow

Publications

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

  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.

Note: * means co-first author.

Dissertation

Collaborative paper

  1. 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. Single-Cell Transcriptomic Analysis of Dental Pulp and Periodontal Ligament Stem Cells. Journal of Dental Research. 2023;0(0). doi:10.1177/00220345231205283
  2. 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
  3. 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]
  4. 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
  5. 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.
  6. 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.
  7. 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.

In Preparation

  1. 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]
  2. Li, G., Qiu, C., Alavattam, K., Deng, X., Disteche, C., Noble, W. (2024+). Allelic Change During Mouse Embroynic Development.
  3. Li, G., Valentino E. Browning, Nicolas Longhi, Eva K. Nichols, Fowler, D., Beliveau, B., Noble, W. (2024+). 3D cell cycle stage classification model for DAPI-stained image data.
  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. Jia, W.*, Li, G.*, 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. 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+, submitted). Enhancing Hi-C contact matrices for loop detection with Capricorn, a multi-view diffusion model. [Code]
  7. 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.
  8. J. Wen, Q. Sun, G. Li, X. Yang, J. Chen, Y. Shen, Y. Li. (2024+). Deconvolution of bulk RNA-seq reveals cell-type specificity mechanism in Alzheimer’s disease.