| 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 | 225 | 2018 |
| TarPmiR: a new approach for microRNA target site prediction J Ding, X Li, H Hu Bioinformatics 32 (18), 2768-2775, 2016 | 167 | 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 | 123 | 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 | 118 | 2020 |
| Control of cytokinesis by β-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 | 84 | 2019 |
| Temporal modelling using single-cell transcriptomics J Ding, N Sharon, Z Bar-Joseph Nature Reviews Genetics 23 (6), 355-368, 2022 | 72 | 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 | 59 | 2016 |
| Identifying signaling genes in spatial single cell expression data D Li, J Ding, Z Bar-Joseph Bioinformatics, 2020 | 39 | 2020 |
| 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 | 39 | 2018 |
| MicroRNA modules prefer to bind weak and unconventional target sites J Ding, X Li, H Hu Bioinformatics 31 (9), 1366-1374, 2015 | 34 | 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 |
| 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 |
| 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 | 32 | 2018 |
| 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 |
| 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 | 30 | 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 | 29 | 2022 |
| 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 |
Ziv Bar-JosephProfessor of Computational Biology and Machine Learning, School of Computer Science, Carnegie Mellon UniversityVerified email at andrew.cmu.edu
