Single-cell transcriptomic analysis of cardiac differentiation from human PSCs reveals HOPX-dependent cardiomyocyte maturation CE Friedman, Q Nguyen, SW Lukowski, A Helfer, HS Chiu, J Miklas, ... Cell stem cell 23 (4), 586-598. e8, 2018 | 228 | 2018 |
TarPmiR: a new approach for microRNA target site prediction J Ding, X Li, H Hu Bioinformatics 32 (18), 2768-2775, 2016 | 170 | 2016 |
Transcriptional regulatory model of fibrosis progression in the human lung JE McDonough, F Ahangari, Q Li, S Jain, SE Verleden, J Herazo-Maya, ... JCI insight 4 (22), 2019 | 124 | 2019 |
Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors K Hurley, J Ding, C Villacorta-Martin, MJ Herriges, A Jacob, M Vedaie, ... Cell Stem Cell, 2020 | 121 | 2020 |
Control of cytokinesis by â-adrenergic receptors indicates an approach for regulating cardiomyocyte endowment H Liu, CH Zhang, N Ammanamanchi, S Suresh, C Lewarchik, K Rao, ... Science translational medicine 11 (513), eaaw6419, 2019 | 87 | 2019 |
Temporal modelling using single-cell transcriptomics J Ding, N Sharon, Z Bar-Joseph Nature Reviews Genetics 23 (6), 355-368, 2022 | 76 | 2022 |
SETDB2 links glucocorticoid to lipid metabolism through Insig2a regulation M Roqueta-Rivera, RM Esquejo, PE Phelan, K Sandor, B Daniel, ... Cell metabolism 24 (3), 474-484, 2016 | 60 | 2016 |
Reconstructing differentiation networks and their regulation from time series single-cell expression data J Ding, BJ Aronow, N Kaminski, J Kitzmiller, JA Whitsett, Z Bar-Joseph Genome research 28 (3), 383-395, 2018 | 40 | 2018 |
Identifying signaling genes in spatial single cell expression data D Li, J Ding, Z Bar-Joseph Bioinformatics, 2020 | 39 | 2020 |
MicroRNA modules prefer to bind weak and unconventional target sites J Ding, X Li, H Hu Bioinformatics 31 (9), 1366-1374, 2015 | 35 | 2015 |
Thousands of cis-regulatory sequence combinations are shared by Arabidopsis and poplar J Ding, H Hu, X Li Plant physiology 158 (1), pp.145-155., 2012 | 34 | 2012 |
TLR4 is a regulator of trained immunity in a murine model of Duchenne muscular dystrophy S Bhattarai, Q Li, J Ding, F Liang, E Gusev, O Lapohos, GJ Fonseca, ... Nature communications 13 (1), 879, 2022 | 33 | 2022 |
iDREM: Interactive visualization of dynamic regulatory networks J Ding, JS Hagood, N Ambalavanan, N Kaminski, Z Bar-Joseph PLoS computational biology 14 (3), e1006019, 2018 | 33 | 2018 |
SIOMICS: a novel approach for systematic identification of motifs in ChIP-seq data J Ding, H Hu, X Li Nucleic acids research 42 (5), e35-e35, 2014 | 33 | 2014 |
Systematic Prediction of cis-Regulatory Elements in the Chlamydomonas reinhardtii Genome Using Comparative Genomics J Ding, X Li, H Hu Plant physiology 160 (2), 613-623, 2012 | 32 | 2012 |
Cell lineage inference from SNP and scRNA-Seq data J Ding, C Lin, Z Bar-Joseph Nucleic Acids Research 47 (10), e56, 2019 | 30 | 2019 |
Chipmodule: systematic discovery of transcription factors and their cofactors from chip-seq data J Ding, X Cai, Y Wang, H Hu, X Li Biocomputing 2013, 320-331, 2013 | 26 | 2013 |
Systematic discovery of cofactor motifs from ChIP-seq data by SIOMICS J Ding, V Dhillon, X Li, H Hu Methods 79, 47-51, 2015 | 25 | 2015 |
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 J Ding, DE Hostallero, MR El Khili, GJ Fonseca, S Milette, N Noorah, ... PLoS Computational Biology 17 (3), e1008810, 2021 | 24 | 2021 |
Angiotensin-converting enzyme 2 expression in COPD and IPF fibroblasts: the forgotten cell in COVID-19 N Aloufi, H Traboulsi, J Ding, GJ Fonseca, P Nair, SK Huang, ... American Journal of Physiology-Lung Cellular and Molecular Physiology, 2021 | 22 | 2021 |