Ding Lab
Bridge the biomedical data and discovery!

Publications

    2022


  • 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.

  • 2021


  • 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.

  • 2020


  • 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.
  • 2019



  • 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.

  • 2018


  • 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.

  • Ding J, Hagood JS, Ambalavanan N, Kaminski N, Bar-Joseph Z. iDREM: Interactive visualization of dynamic regulatory networks. PLoS computational biology. 2018 Mar 14;14(3):e1006019.

  • Before 2017


  • Ding J, Bar-Joseph Z. MethRaFo: MeDIP-seq methylation estimate using a Random Forest Regressor. Bioinformatics. 2017 Jul 13;33(21):3477-9.

  • Ding J, Li X, Hu H. CCmiR: a computational approach for competitive and cooperative microRNA binding prediction. Bioinformatics. 2017 Sep 25;34(2):198-206.

  • Roqueta-Rivera M, Esquejo RM, Phelan PE, Sandor K, Daniel B, Foufelle F, Ding J, Li X, Khorasanizadeh S, Osborne TF. SETDB2 links glucocorticoid to lipid metabolism through Insig2a regulation . Cell metabolism. 2016 Sep 13;24(3):474-84.

  • Ding J, Li X, Hu H. TarPmiR: a new approach for microRNA target site prediction. Bioinformatics. 2016 May 20;32(18):2768-75.

  • Ding J, Li X, Hu H. MicroRNA modules prefer to bind weak and unconventional target sites. Bioinformatics .2014; doi: 10.1093/bioinformatics/btu833.

  • Ding J, Dhillon V, Li X, Hu H. Systematic discovery of cofactor motifs from ChIP-seq data by SIOMICS. Methods . 2014; doi:10.1016/j.ymeth.2014.08.006

  • Ding J, Hu H, Li X. SIOMICS: a Novel Approach for Systematic Identification of Motifs in ChIP-seq Data. Nucleic Acids Research . 2014; 42(5): e35.

  • Ding J, Hu H, Li X. NIM, A novel computational method for predicting nuclear-encoded chloroplast proteins. Journal of Medical and Bioengineering. 2013; 2(2): 115-119.

  • Ding J, Cai X, Wang Y, Hu H, Li X. ChIPModule: Systematic discovery of transcription factors and their cofactors from ChIP-seq data. Pac Symp Biocomput. 2013.

  • Ding J, Li X, Hu H. Systematic discovery of cis-regulatory elements in Chlamydomonas reinhardtii genome using comparative genomics. Plant Physiology. 2012;160(2):613-23.

  • Ying Wang, Ding J, Daniell H, Hu H, Li X. Motif analysis unveils the possible co-regulation of chloroplast genes and nuclear genes encoding chloroplast proteins. Plant Molecular Biology . 2012;80(2):177-87.

  • Ding J, Hu H, Li X. Thousands of cis-regulatory sequences are shared by Arabidopsis and populus. Plant Physiology. 2012;158(1):145-55. Epub 2011 Nov 4.

  • Ding J, Liu Falin. Novel Tag Anti-Collision Algorithm with Adaptive Grouping. Wireless Sensor Network, 2009 1, 475-481