| Statistics or biology: the zero-inflation controversy about scRNA-seq data R Jiang, T Sun, D Song, JJ Li Genome biology 23 (1), 31, 2022 | 224 | 2022 |
| scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured T Sun, D Song, WV Li, JJ Li Genome biology 22 (1), 163, 2021 | 103 | 2021 |
| scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics D Song, Q Wang, G Yan, T Liu, T Sun, JJ Li Nature Biotechnology 42 (2), 247-252, 2024 | 70 | 2024 |
| Explaining the ocean's richest biodiversity hotspot and global patterns of fish diversity EC Miller, KT Hayashi, D Song, JJ Wiens Proceedings of the Royal Society B 285 (1888), 20181314, 2018 | 70 | 2018 |
| PseudotimeDE: inference of differential gene expression along cell pseudotime with well-calibrated p-values from single-cell RNA sequencing data D Song, JJ Li Genome biology 22 (1), 124, 2021 | 69 | 2021 |
| Clipper: p-value-free FDR control on high-throughput data from two conditions X Ge, YE Chen, D Song, ML McDermott, K Woyshner, A Manousopoulou, ... Genome biology 22, 1-29, 2021 | 54 | 2021 |
| scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling D Song, K Li, Z Hemminger, R Wollman, JJ Li Bioinformatics 37 (Supplement_1), i358-i366, 2021 | 23 | 2021 |
| ClusterDE: a post-clustering differential expression (DE) method robust to false-positive inflation caused by double dipping D Song, K Li, X Ge, JJ Li Research Square, rs. 3. rs-3211191, 2023 | 17 | 2023 |
| Benchmarking computational methods to identify spatially variable genes and peaks Z Li, ZM Patel, D Song, G Yan, JJ Li, L Pinello Biorxiv, 2023 | 13 | 2023 |
| scSampler: fast diversity-preserving subsampling of large-scale single-cell transcriptomic data D Song, NM Xi, JJ Li, L Wang Bioinformatics 38 (11), 3126-3127, 2022 | 13 | 2022 |
| Increased novel single nucleotide polymorphisms in weedy rice populations associated with the change of farming styles: Implications in adaptive mutation and evolution DY Song, Z Wang, ZJ Song, CC Zhou, PH Xu, J Yang, J Yang, BR Lu Journal of Systematics and Evolution 55 (2), 149-157, 2017 | 12 | 2017 |
| Single-cell generalized trend model (scGTM): a flexible and interpretable model of gene expression trend along cell pseudotime EH Cui, D Song, WK Wong, JJ Li Bioinformatics 38 (16), 3927-3934, 2022 | 9 | 2022 |
| DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues KH Kock, PK Kimes, SS Gisselbrecht, S Inukai, SK Phanor, JT Anderson, ... Nature Communications 15 (1), 3110, 2024 | 3 | 2024 |
| Decoding heterogenous single-cell perturbation responses B Song, D Liu, W Dai, N McMyn, Q Wang, D Yang, A Krejci, A Vasilyev, ... bioRxiv, 2023 | 3 | 2023 |
| scReadSim: a single-cell RNA-seq and ATAC-seq read simulator G Yan, D Song, JJ Li Nature Communications 14 (1), 7482, 2023 | 3 | 2023 |
| Simulating single-cell gene expression count data with preserved gene correlations by scDesign2 T Sun, D Song, WV Li, JJ Li Journal of Computational Biology 29 (1), 23-26, 2022 | 3 | 2022 |
| Review of computational methods for estimating cell potency from single-cell RNA-seq data, with a detailed analysis of discrepancies between method description and code … Q Wang, Z Zhai, D Song, JJ Li arXiv preprint arXiv:2309.13518 10, 0 | 2 | |
| Learning single-cell spatial context through integrated spatial multiomics with CORAL S He, M Bieniosek, D Song, J Zhou, B Chidester, Z Wu, J Boen, P Sharma, ... bioRxiv, 2025.02. 01.636038, 2025 | | 2025 |
| Synthetic control removes spurious discoveries from double dipping in single-cell and spatial transcriptomics data analyses D Song, S Chen, C Lee, K Li, X Ge, JJ Li bioRxiv, 2023.07. 21.550107, 2024 | | 2024 |
| Spatial Single-Cell Mapping of Transcriptional Differences Across Genetic Backgrounds in Mouse Brains Z Hemminger, G Sanchez-Tam, H De Ocampo, A Wang, T Underwood, ... bioRxiv, 2024 | | 2024 |
Jingyi Jessica LiProfessor, Department of Statistics, University of California at Los Angeles (UCLA)Email verificata su stat.ucla.edu