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. J. Wen, Q. Sun, G. Li, X. Yang, J. Chen, Y. Shen, Y. Li. (2022). Deconvolution of bulk RNA-seq reveals cell-type specificity mechanism in Alzheimer’s disease.
  5. 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]