A full list of my publications is available on Google scholar.

Selected publications

* Equal contributions, † Corresponding authors

1. Ding, J., Adiconis, X., Simmons, S. K., Kowalczyk, M. S., Hession, C. C., Marjanovic, N. D., … & Regev, A., Levin, J.Z.^† (2020). Systematic comparative analysis of single cell RNA-sequencing methods. Nature Biotechnology, doi: https://doi.org/10.1038/s41587-020-0465-8 code

2. Ding, J.^†, & Regev, A.^† (2019). Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces. BioRxiv, 853457 doi: https://doi.org/10.1101/853457 code

3. Xu, H.^*†, Ding, J.*, Porter, C. B., Wallrapp, A., Tabaka, M., Ma, S., … & Regev, A.^†, Xavier, R.J.^† (2019). Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide α-CGRP Modulates Group 2 Innate Lymphoid Cell Responses. Immunity, 51(4), 696-708. code

4. Ding, J.^†, Condon, A, and Shah, S. P.^† (2018) Interpretable dimensionality reduction of single cell transcriptome data with deep generative models. Nature Communications, 9:2002. doi: https://doi.org/10.1038/s41467-018-04368-5 code

5. Ding, J.^†, Shah, S. P.^†, and Condon, A.^† (2016). densityCut: an efficient and versatile topological approach to clustering biological data. Bioinformatics, 32(17), 2567-2576. code

6. Ding, J., McConechy, M. K., Horlings, H. M., Ha, G., Chan, F., … & Shah, S. P. (2015). Systematic analysis of somatic mutations impacting gene expression in twelve tumour types. Nature Communications, 6:8554. doi: 10.1038/ncomms9554 code

7. Ding, J., & Shah, S. (2013). A robust hidden semi-Markov model with application to aCGH data processing. International journal of data mining and bioinformatics, 8(4), 427-442. code

8. Ding, J., Bashashati, A., Roth, A., Oloumi, A., Tse, K., Zeng, T., … & Shah, S. P. (2012). Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data. Bioinformatics, 28(2), 167- 175. code

9. McConechy, M. K.*, Ding, J.*, Cheang, M. C., Wiegand, K. C., Senz, J., Tone, A. A., … & Gilks, C.B. and Huntsman, D. G. (2012). Use of mutation profiles to refine the classification of endometrial carcinomas. The Journal of Pathology, 228(1), 20-30.

10. Bashashati, A.*, Haffari, G.*, Ding, J.*, Ha, G., Liu, K., Rosner, J., Huntsman, D., Caldas, C., Aparicio, S. and Shah, S.P. (2012). DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer. Genome Biology, 13:R124. doi: 10.1186/gb-2012-13-12-r124 code

11. Shah, S. P., Roth A.^§, Goya, R.^§, Oloumi, A.^§, Ha, G.^§, Zhao, Y.^§, Turashvili, G.^§, Ding, J.^§, Tse, K.^§, Haffari, G.^§, Bashashati, A.^§, … & Caldas, C., Marra, M.A., and Aparicio S. (2012). Primary triple negative breast cancers exhibit a continuous spectrum of clonal and mutational evolution. Nature, 486(7403), 395-399. (^§ Equal contributions)