scDART: integrating unmatched scRNA-seq and scATAC-seq data and learning cross-modality relationship simultaneously Z Zhang, C Yang, X Zhang Genome biology 23 (1), 139, 2022 | 45* | 2022 |
Inference of high-resolution trajectories in single-cell RNA-seq data by using RNA velocity Z Zhang, X Zhang Cell Reports Methods 1 (6), 2021 | 33* | 2021 |
VeloSim: Simulating single cell gene-expression and RNA velocity Z Zhang, X Zhang BioRxiv, 2021.01. 11.426277, 2021 | 12 | 2021 |
scMoMaT jointly performs single cell mosaic integration and multi-modal bio-marker detection Z Zhang, H Sun, R Mariappan, X Chen, X Chen, MS Jain, M Efremova, ... Nature Communications 14 (1), 384, 2023 | 10 | 2023 |
scMultiSim: simulation of multi-modality single cell data guided by cell-cell interactions and gene regulatory networks H Li, Z Zhang, M Squires, X Chen, X Zhang Research Square, 2022 | 8 | 2022 |
Inferring cell-specific gene regulatory networks from single cell gene expression data Z Zhang, J Han, L Song, X Zhang bioRxiv, 2022.03. 03.482887, 2022 | 5 | 2022 |
Maximum likelihood reconstruction of ancestral networks by integer linear programming V Rajan, Z Zhang, C Kingsford, X Zhang Bioinformatics 37 (8), 1083-1092, 2021 | 4 | 2021 |
scDisInFact: disentangled learning for integration and prediction of multi-batch multi-condition single-cell RNA-sequencing data Z Zhang, X Zhao, M Bindra, P Qiu, X Zhang Nature Communications 15 (1), 912, 2024 | 1 | 2024 |