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. Le Huang, Yuchen Yang, Gang Li, Minzhi Jiang, Jia Wen, Armen Abnousi, Jonathan D Rosen, Ming Hu, Yun Li 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
  2. 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.
  3. 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.
  4. 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. 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.
  2. 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.

In Preparation

  1. Li, G., Kim, H., Pendyala, S., Papaxanthos, L., Fowler, D., Vert, J., Noble, W.(2022+). Integrating imaging and sequencing data from visual cell sorting.
  2. Li, G., Alavattam, K., Qiu, C., Deng, X., Disteche, C., Noble, W. (2022+). Allelic Change During Mouse Embroynic Development.
  3. Jia, W.*, Li, G.*, Szatkiewicz, J., Sullivan, P. , Li, Y.(2022). DeepGWAS to Enhance GWAS Signals for Neuropsychiatric Disorders via Deep Neural Network.
  4. Laetitia Meng-Papaxanthos, Ran Zhang, Li, G., Marco Cuturi, William Stafford Noble, Jean-Philippe Vert (2022+). LSMMD-MA: Scaling multimodal data integration for single-cell genomics data analysis. (Submitted) [Code]