null Jun Ding, PhD
computational biology • machine learning • cell dynamics • single-cell genomics
My research focuses on studying cell dynamics in various biological processes in many diseases (e.g., developmental disorders, 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 provide unprecedented opportunities to tackle this problem, leading to biological discoveries and medical innovations in various fields (such as developmental and cancer biology). However, single-cell data presents numerous new challenges in developing computational models that bridge biomedical data and potential discoveries.
My team’s primary research aim is to develop machine learning approaches to jointly analyze, model, and visualize single-cell (bulk) omics data. 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 public health with machine-learning driven new diagnostic and therapeutic strategies.
Hurley K, Ding J, Villacorta-Martin C, Herriges MJ, Jacob A, Vedaie M, Alysandratos KD, Sun YL, Lin C, Werder RB, Huang J, Wilson AA, Mithal A, Mostoslavsky G, Oglesby I, Caballero IS, Guttentag SH, Ahangari F, Kaminski N, Rodriguez-Fraticelli A, Camargo F, 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 Apr 2;26(4):593-608.e8. doi: 10.1016/j.stem.2019.12.009. Epub 2020 Jan 30. PMID: 32004478.
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. Am J Physiol Lung Cell Mol Physiol. 2019 Nov 1;317(5):L556-L568. doi: 10.1152/ajplung.00554.2018. Epub 2019 Aug 21. PMID: 31432713.
Ding J, Lin C, Bar-Joseph Z. Cell lineage inference from SNP and scRNA-Seq data. Nucleic Acids Res. 2019 Jun 4;47(10):e56. doi: 10.1093/nar/gkz146. PMID: 30820578.
Ding J, Aronow BJ, Kaminski N, Kitzmiller J, Whitsett JA, Bar-Joseph Z. Reconstructing differentiation networks and their regulation from time series single-cell expression data. Genome Res. 2018 Jan 9;28(3):383–95. doi: 10.1101/gr.225979.117. Epub ahead of print. PMID: 29317474.
Ding J, Li X, Hu H. TarPmiR: a new approach for microRNA target site prediction. Bioinformatics. 2016 Sep 15;32(18):2768-75. doi: 10.1093/bioinformatics/btw318. Epub 2016 May 20. PMID: 27207945.