Song D - Search Results

1

PseudotimeDE: inference of differential gene expression along cell pseudotime with well-calibrated p-values from single-cell RNA sequencing data.

Song D, Li JJ. Song D, et al. Genome Biol. 2021 Apr 29;22(1):124. doi: 10.1186/s13059-021-02341-y. Genome Biol. 2021. PMID: 33926517 Free PMC article.

2

scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured.

Sun T, Song D, Li WV, Li JJ. Sun T, et al. Among authors: song d. Genome Biol. 2021 May 25;22(1):163. doi: 10.1186/s13059-021-02367-2. Genome Biol. 2021. PMID: 34034771 Free PMC article.

3

Publisher Correction: scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured.

Sun T, Song D, Li WV, Li JJ. Sun T, et al. Among authors: song d. Genome Biol. 2021 Jun 9;22(1):177. doi: 10.1186/s13059-021-02394-z. Genome Biol. 2021. PMID: 34108038 Free PMC article. No abstract available.

4

scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling.

Song D, Li K, Hemminger Z, Wollman R, Li JJ. Song D, et al. Bioinformatics. 2021 Jul 12;37(Suppl_1):i358-i366. doi: 10.1093/bioinformatics/btab273. Bioinformatics. 2021. PMID: 34252925 Free PMC article.

5

Clipper: p-value-free FDR control on high-throughput data from two conditions.

Ge X, Chen YE, Song D, McDermott M, Woyshner K, Manousopoulou A, Wang N, Li W, Wang LD, Li JJ. Ge X, et al. Among authors: song d. Genome Biol. 2021 Oct 11;22(1):288. doi: 10.1186/s13059-021-02506-9. Genome Biol. 2021. PMID: 34635147 Free PMC article.

6

Simulating Single-Cell Gene Expression Count Data with Preserved Gene Correlations by scDesign2.

Sun T, Song D, Li WV, Li JJ. Sun T, et al. Among authors: song d. J Comput Biol. 2022 Jan;29(1):23-26. doi: 10.1089/cmb.2021.0440. Epub 2022 Jan 11. J Comput Biol. 2022. PMID: 35020490 Free PMC article.

7

Statistics or biology: the zero-inflation controversy about scRNA-seq data.

Jiang R, Sun T, Song D, Li JJ. Jiang R, et al. Among authors: song d. Genome Biol. 2022 Jan 21;23(1):31. doi: 10.1186/s13059-022-02601-5. Genome Biol. 2022. PMID: 35063006 Free PMC article. Review.

8

scSampler: fast diversity-preserving subsampling of large-scale single-cell transcriptomic data.

Song D, Xi NM, Li JJ, Wang L. Song D, et al. Bioinformatics. 2022 May 26;38(11):3126-3127. doi: 10.1093/bioinformatics/btac271. Bioinformatics. 2022. PMID: 35426898 Free PMC article.

9

Single-cell generalized trend model (scGTM): a flexible and interpretable model of gene expression trend along cell pseudotime.

Cui EH, Song D, Wong WK, Li JJ. Cui EH, et al. Among authors: song d. Bioinformatics. 2022 Aug 10;38(16):3927-3934. doi: 10.1093/bioinformatics/btac423. Bioinformatics. 2022. PMID: 35758616 Free PMC article.

10

Author Correction: scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured.

Sun T, Song D, Li WV, Li JJ. Sun T, et al. Among authors: song d. Genome Biol. 2023 Feb 22;24(1):32. doi: 10.1186/s13059-023-02884-2. Genome Biol. 2023. PMID: 36814256 Free PMC article. No abstract available.

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