Ding, Jun - McGill University - Department of Medicine

个人简介

Jun received a PhD in Computer Science at University of Central Florida. He then completed a four-year postdoctoral fellowship in computational biology with Ziv Bar-Joseph (2012 Overton Prize winner) at Carnegie Mellon University. In 2021, he joined the Meakins-Christie Laboratories at McGill University as a tenure-track assistant professor.

研究领域

Our lab focuses on studying cell dynamics in various biological processes in many diseases (e.g., developmental disorder, pulmonary diseases, cancers). Decoding cell dynamics is essential for understanding the pathogenesis of diseases and finding novel therapeutics. The existence of enormous heterogeneity in those diseases makes it challenging to decipher the unknown. The advancing single-cell technologies that profile individual cell states provide unprecedented opportunities to tackle this problem, which could drive biological discoveries and medical innovations in various fields (such as developmental and cancer biology). However, the single-cell data presents numerous new challenges in developing computational models that bridge the biomedical data and potential discoveries. Our primary research is to develop machine learning approaches (particularly probabilistic graphical models) to jointly analyze, model, and visualize single-cell (and/or bulk) omics data (preferably longitudinal or spatial). Such computational models will be used to help us derive a deeper understanding of the cell dynamics in different biological systems, which will eventually benefit the public health with machine-learning driven new diagnostic and therapeutic strategies.

近期论文

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Li, D., Velazquez, J. J., Ding, J., Hislop, J., Ebrahimkhani, M. R., & Bar-Joseph, Z. (2022). TraSig: inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data. Genome biology, 23(1), 1-19. Hasanaj, E., Wang, J., Sarathi, A.,Ding, J., * & Bar-Joseph, Z. * (2022). Interactive single-cell data analysis using Cellar. Nature Communications, 13(1), 1-6. Bhattarai, S., Li, Q., Ding, J., Liang, F., Gusev, E., Lapohos, O., ... & Petrof, B. J. (2022). TLR4 is a regulator of trained immunity in a murine model of Duchenne muscular dystrophy. Nature communications, 13(1), 1-15. Ding, J., Sharon, N., & Bar-Joseph, Z. (2022). Temporal modelling using single-cell transcriptomics. Nature Reviews Genetics, 1-14. Aloufi, N., Haidar, Z., Ding, J., Nair, P., Benedetti, A., Eidelman, D. H., ... & Baglole, C. J. (2021). Role of human antigen R (HuR) in the regulation of pulmonary ACE2 expression. Cells, 11(1), 22. Jun Ding, Amir Alavi, Mo R Ebrahimkhani, Ziv Bar-Joseph. Computational tools for analyzing single-cell data in pluripotent cell differentiation studies .Cell Reports Methods. 2021 Ding J. A versatile model for single-cell data analysis. Nature Computational Science. 2021 July 22;1:460-461 Ding J, Hostallero DE, El Khili MR, Fonseca GJ, Milette S, Noorah N, Guay-Belzile M, Spicer J, Daneshtalab N, Sirois M, Tremblay K. A network-informed analysis of SARS-CoV-2 and hemophagocytic lymphohistiocytosis genes’ interactions points to Neutrophil extracellular traps as mediators of thrombosis in COVID-19.. PLoS Computational Biology. 2021 Mar 8;17(3):e1008810. Guerrina N, Traboulsi H, Souza A, Bossé Y, Thatcher TH, Robichaud A, Ding J, Li P, Simon L, Pareek S, Bourbeau J, Tan WC, Benedetti A, Obeidat M, Sin DD, Brandsma C, Nickle DC, Sime PJ, Phipps RP, Nair P, Zago M, Hamid Q, Smith BM, Eidelman DH, Baglole CJ. Aryl hydrocarbon receptor deficiency causes the development of chronic obstructive pulmonary disease through the integration of multiple pathogenic mechanisms.. FASEB journal: official publication of the Federation of American Societies for Experimental Biology, 2021, 35.3: e21376. Aloufi N, Traboulsi H, Ding J, Fonseca GJ, Nair P, Huang SK, Hussain SN, Eidelman DH, Baglole CJ. Angiotensin-converting enzyme 2 expression in COPD and IPF fibroblasts: the forgotten cell in COVID-19.. American Journal of Physiology-Lung Cellular and Molecular Physiology. 2021 Jan 1;320(1):L152-7. Li D, Ding J,Bar-Joseph Z. Identifying signaling genes in spatial single cell expression data. Bioinformatics, 2021; 37(7), 968-975. Ding J, Bar-Joseph Z. Analysis of time series regulatory networks. Current Opinion in Systems Biology. 2020 June; 21 Pages 16-24 Lin C, Ding J, Bar-Joseph Z. Inferring TF activation order in time series scRNA-Seq studies. PLoS computational biology. 2020 Feb 18;16(2):e1007644. Hurley K, Ding J (co-first), Villacorta-Martin C, Herriges MJ, Jacob A, Vedaie M, Alysandratos KD, Sun YL, Lin C, Werder RB, Huang J. , ..., Bar-Joseph Z, Kotton DN. Reconstructed single-cell fate trajectories define lineage plasticity windows during differentiation of human PSC-derived distal lung progenitors. Cell Stem Cell. 2020 Jan 30. McDonough JE, Ahangari F, ..., Ding J.,Maes K, Sadeleer LD, Vos R, Neyrinck A, Benos PV, Bar-Joseph Z, Tantin D, Hogg JC, Vanaudenaerde BM, Wuyts WA, Kaminski N. Transcriptional regulatory model of fibrosis progression in the human lung. JCI insight. 2019 Nov 14;4(22). Ding J, Ahangari F, Espinoza CR, Chhabra D, Nicola T, Yan X, Lal CV, Hagood JS, Kaminski N, Bar-Joseph Z, Ambalavanan N. Integrating multiomics longitudinal data to reconstruct networks underlying lung development. American Journal of Physiology-Lung Cellular and Molecular Physiology. 2019 Nov 1;317(5):L556-68. Liu H, Zhang CH, Ammanamanchi N, Suresh S, ..., Ding J, Bar-Joseph Z, Wu Y, Yechoor V, Moulik M, Johnson J, Weinberg J, Reyes-Mugica M, Steinhauser ML, Kuhn B. Control of cytokinesis by beta-adrenergic receptors indicates an approach for regulating cardiomyocyte endowment. Sci Transl Med., 2019; 11(513) Ding J, Lin C, Bar-Joseph Z. Cell lineage inference from SNP and scRNA-Seq data. Nucleic Acids Research, 2019 47(10), pp.e56-e56. Friedman C, Nguyen Q, Lukowski S, ..., Ding J, Wang Y, Hudson J, Ruohola-Baker H, Bar-Joseph Z, Tam P, Powell J, Palpant N. Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation. Cell Stem Cell. 2018; 23(4):586-598 Nguyen QH, Lukowski SW, Chiu HS, Friedman CE, Senabouth A, Crowhurst L, Bruxner TJ, Christ AN, Hudson J, Ding J, Bar-Joseph Z, Tam PP, Palpant NJ, Powell JE. Genetic networks modulating cell fate specification and contributing to cardiac disease risk in hiPSC-derived cardiomyocytes at single cell resolution. Human Genomics. 2018 Mar 9;12. Ding J, Aronow B, Kaminski N, Kitzmiller J, Whitsett J, Bar-Joseph Z. Reconstructing differentiation networks and their regulation from time series single cell expression data. Genome research. 2018 Jan 9:gr-225979.