A full list of our publications is available on Google scholar.
\(^{*}\) First authors; \(^{\dagger}\) corresponding authors; students and trainees; Ding, J.
Software tools are available on GitHub.
Guo, K. & Ding, J.\(^{\dagger}\) (2026). ProtoCloud: a Prototypical Self-explaining Model for Single-cell Analysis. https://www.biorxiv.org/content/10.64898/2026.02.06.704364v1.
Chen, S., Regev, A., Condon, A., & Ding, J.\(^{\dagger}\) (2025). CellUntangler: separating distinct biological signals in single-cell data with deep generative models. Cell Genomics, 1-24. https://www.cell.com/cell-genomics/fulltext/S2666-979X(25)00329-5.
Niu, J., Vasquez, C., & Ding, J.\(^{\dagger}\) (2025). Single-cell multiomics data integration and generation with scPairing. Cell Reports Methods, 5:101211, 1-25. https://www.cell.com/cell-reports-methods/fulltext/S2667-2375(25)00247-4.
Ma, M., Tu, W., Vasquez, C., & Ding, J.\(^{\dagger}\) (2025). Generating cognate epitope sequences of T-cell receptors with a generative transformer. https://www.biorxiv.org/content/10.1101/2025.01.13.632824v2.abstract.
Wenkel, F.\(^{\dagger, *}\), Tu, W.\(^*\), Masschelein, C., Shirzad, H., Eastwood, C., Whitfield, S.T., Bendidi, I., Russell, C., Hodgson, L., Mesbahi, Y.E., Ding, J., Fay, M.M., Earnshaw, B., Noutahi, E., Denton, A.K.\(^{\dagger}\) (2025). TxPert: Leveraging Biochemical Relationships for Out-of-Distribution Transcriptomic Perturbation Prediction.
Ding, J.\(^*\), Garber, J.J.\(^{*\dagger}\), Uchida, A., Lefkovith, A., Carter, G.T., Vimalathas, P., Canha, L., Dougan, M., Staller, K., Yarze, J., Delorey, T.M., Rozenblatt-Rosen, O., Ashenberg, O., Graham, D.B., Deguine, J., Regev, A.\(^{\dagger}\), Xavier, R.J.\(^{\dagger}\) (2024). An esophagus cell atlas reveals dynamic rewiring during active eosinophilic esophagitis and remission. Nature Communications, 15:3344, 1-18.
Benhar, I.\(^{\dagger*}\), Ding, J.\(^*\), Yan, W., Whitney, I. E., Jacobi, A., Sud, M., Burgin, G., Shekhar, K. Tran, N.M., Wang, C., He, Z., Sanes, J.R., & Regev, A.\(^{\dagger}\) (2023). Temporal single-cell atlas of non-neuronal retinal cells reveals dynamic, coordinated multicellular responses to central nervous system injury. Nature Immunology, 24, 700-713.
He, D.\(^{\dagger}\), Xu, H., Zhang, H., Tang, R., Lan, Y., Xing, R., Li, S., Christian, E., Hou, Y., Lorello, P., Caldarone, B., Ding, J., Nguyen, L., Dionne, D., Thakore, P., Schnell, A., Huh, J.R., Rozenblatt-Rosen, O., Regev, A.\(^{\dagger}\), & Kuchroo, V.K.\(^{\dagger}\) (2022). Disruption of the IL-33-ST2-AKT signaling axis impairs neurodevelopment by inhibiting microglial metabolic adaptation and phagocytic function. Immunity, 55(1), 159-173.
Ding, J.\(^{\dagger}\), & Regev, A.\(^{\dagger}\) (2021). Deep generative model
embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic
spaces. Nature Communications, 12:2554, 1-17. code
Ma, S., Zhang, B., LaFave, L.M., Earl, A.S., Chiang, Z., Hu, Y., Ding, J., Brack, A., Kartha, V.K., Tay, T., Law, T., Lareau, C., Hsu, Y.C., Regev, A.\(^{\dagger}\), & Buenrostro, J.D.\(^{\dagger}\) (2020). Chromatin potential identified by shared single-cell profiling of RNA and chromatin. Cell, 183(4), 1103-1116.
Ding, J., Adiconis, X., Simmons, S.K., Kowalczyk,
M.S., Hession, C.C., Marjanovic, N.D., Hughes, T.K., Wadsworth, M.H.,
Burks, T., Nguyen, L.T., Kwon, J.Y., Barak, B., Ge, W., Kedaigle, A.J.,
Carroll, S., Li, S., Hacohen, N., Rozenblatt-Rosen, O., Shalek, A.L.,
Villani, A.C., Regev, A., & Levin, J.Z.\(^{\dagger}\) (2020). Systematic comparison
of single-cell and single-nucleus RNA-sequencing methods. Nature
Biotechnology, 38(6), 737-746. code
Xu, H.\(^{*\dagger}\), Ding,
J.\(^{*}\), Porter, C.B.,
Wallrapp, A., Tabaka, M., Ma, S., Fu, S., Guo, X., Riesenfeld, S.J., Su,
C., Dionne, D., Nguyen, L.T., Lefkovith, A., Ashenberg, O., Burkett,
P.R., Shi, H.N., Rozenblatt-Rosen, O., Graham, D.B., Kuchroo, V.K,
Regev, A.\(^{\dagger}\), & Xavier,
R.J.\(^{\dagger}\) (2019).
Transcriptional atlas of intestinal immune cells reveals that
neuropeptide \(\alpha\)-CGRP modulates
group 2 innate lymphoid cell responses. Immunity, 51(4),
696-708. code
Aoki, T.\(^{*}\), Chong, L.C.\(^{*}\), Takata, K., Milne, K., Hav, M., Colombo, A., Chavez, E.A., Nissen, M., Wang, X., Miyata-Takata, T., Lam, V., Viganò, E., Woolcock, B.W., Telenius, A., Li, M.Y., Healy, S., Ghesquiere, C., Kos, D., Goodyear, T., Veldman, J., Zhang, A.W., Kim, J., Saberi, S., Ding, J., Farinha, P., Weng, A.P., Savage, K.J., Scott, D.W., Krystal, G., Nelson, B.H., Mottok, A., Merchant, A., Shah, S.P., & Steidl, C.\(^{\dagger}\) (2019). Single-cell transcriptome analysis reveals disease-defining T-cell subsets in the tumor microenvironment of classic Hodgkin lymphoma. Cancer Discovery, 10(3), 406-421.
Ding, J.\(^{\dagger}\), Condon, A, & Shah,
S.P.\(^{\dagger}\) (2018) Interpretable
dimensionality reduction of single cell transcriptome data with deep
generative models. Nature Communications 9:2002, 1-13. code
Ding, J.\(^{\dagger}\), Condon, A, & Shah,
S.P.\(^{\dagger}\) (2018) Interpretable
dimensionality reduction of single cell transcriptome data with deep
generative models. Nature Communications 9:2002, 1-13. code
Ding, J.\(^{\dagger}\), Shah, S. P.\(^{\dagger}\), & Condon, A.\(^{\dagger}\) (2016). densityCut: an
efficient and versatile topological approach to clustering biological
data. Bioinformatics, 32(17), 2567-2576. code
Ding, J., McConechy, M.K., Horlings, H.M., Ha, G.,
Chan, F.C., Funnell, T., Mullaly, S.C., Reimand, J., Bashashati, A.,
Bader, G.D., Huntsman, D., Aparicio, S., Condon, A., & Shah,
S.P.\(^\dagger\) (2015). Systematic
analysis of somatic mutations impacting gene expression in 12 tumor
types. Nature Communications, 6:8554, 1-13. code
Ding, J., & Shah, S.P.\(^{\dagger}\) (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
Ding, J., Bashashati, A., Roth, A., Oloumi, A., Tse,
K., Zeng, T., Haffari, G., Hirst, M., Marra, M.A., Condon, A., Aparicio,
S., & Shah, S.P.\(^{\dagger}\)
(2012). Feature-based classifiers for somatic mutation detection in
tumor-normal paired sequencing data. Bioinformatics, 28(2),
167-175. code
McConechy, M.K.*, Ding, J.*, Cheang, M.C., Wiegand, K.C., Senz, J., Tone, A.A., Yang, W., Prentice, L.M., Tse, K., Zeng, T., McDonald, H., Schmidt, A.P., Mutch, D.G., McAlpine, J.N., Hirst, M., Shah, S.P., Lee, C.H., Goodfellow, P.J., Gilks, C.B.\(^{\dagger}\), & Huntsman, D.G.\(^{\dagger}\) (2012). Use of mutation profiles to refine the classification of endometrial carcinomas. The Journal of Pathology, 228(1), 20-30.
Bashashati, A.*, Haffari, G.*, Ding, J.*, Ha, G., Liu, K., Rosner, J., Huntsman, D., Caldas, C., Aparicio, S., & Shah, S.P.\(^{\dagger}\) (2012). DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer. Genome Biology, 13:R124, 1-14.
Shah, S.P.\(^{\dagger}\), Roth A.\(^{\S}\), Goya, R.\(^{\S}\), Oloumi, A.\(^{\S}\), Ha, G.\(^{\S}\), Zhao, Y.\(^{\S}\), Turashvili, G.\(^{\S}\), Ding, J.\(^{\S}\), Tse, K.\(^{\S}\), Haffari, G.\(^{\S}\), Bashashati, A.\(^{\S}\), Prentice, L.M., ..., Caldas, C.\(^{\dagger}\), Marra, M.A.\(^{\dagger}\), & Aparicio, S.\(^{\dagger}\) (2012). Primary triple negative breast cancers exhibit a continuous spectrum of clonal and mutational evolution. Nature, 486(7403), 395-399. (\(^{\S}\) These authors contributed equally to this work.)