Publications

The full list of publications can be seen here.

Selected Publications:

Son, J., Ding, H., Farb, T. B., Efanov, A. M., Sun, J., Gore, J. L., ... & Califano, A. (2021). BACH2 inhibition reverses β cell failure in type 2 diabetes models. The Journal of clinical investigation, 131(24), e153876. Published with commentary by Dr. Yumi Imai.

Ding, H., Anastopoulos, I., Bailey, A. D., Stuart, J., & Paten, B. (2021). Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures. Nature communications, 12(1), 1-9.

Seninge, L., Anastopoulos, I., Ding, H., & Stuart, J. (2021). VEGA is an interpretable generative model for inferring biological network activity in single-cell transcriptomics. Nature communications, 12(1), 1-9.

Ding, H., Yang, Y., Xue, Y., Seninge, L., Gong, H., Safavi, R., ... & Stuart, J. M. (2021). Prioritizing transcriptional factors in gene regulatory networks with PageRank. Iscience, 24(1), 102017.

Ding, H., Bailey IV, A. D., Jain, M., Olsen, H., & Paten, B. (2020). Gaussian mixture model-based unsupervised nucleotide modification number detection using nanopore-sequencing readouts. Bioinformatics, 36(19), 4928-4934.

Ding, H., Blair, A., Yang, Y., & Stuart, J. M. (2019). Biological process activity transformation of single cell gene expression for cross-species alignment. Nature communications, 10(1), 1-6.

Ding, H., Douglass, E. F., Sonabend, A. M., Mela, A., Bose, S., Gonzalez, C., ... & Califano, A. (2018). Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm. Nature communications, 9(1), 1-10.

Ding, H., Wang, W., & Califano, A. (2018). iterClust: a statistical framework for iterative clustering analysis. Bioinformatics, 34(16), 2865-2866.