The full list of publications can be seen here.
Selected Publications:
Zhou, Y., Yang, Y., Guo, L., Qian, J., Ge, J., Sinner, D., Ding, H., Califano, A., & Cardoso, W. V. (2022). Airway basal cells show regionally distinct potential to undergo metaplastic differentiation. Elife, 11, e80083.
Son, J., Ding, H., Farb, T. B., Efanov, A. M., Sun, J., Gore, J. L., Syed, S. K., Lei, Z., Wang, Q., Accili, D., & 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., Califano. A., & 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., Canoll, P. D., Sims, P. A., Alvarez, M. J., & 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.