Articles with public access mandates - Dongyuan SongLearn more
Available somewhere: 14
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
Mandates: US National Science Foundation, US National Institutes of Health
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
Mandates: US National Science Foundation, US National Institutes of Health
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
Mandates: US National Science Foundation
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
Mandates: US National Science Foundation, US National Institutes of Health
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
Mandates: Chan Zuckerberg Initiative
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
Mandates: US National Science Foundation, US National Institutes of Health, Alex's …
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
Mandates: US National Science Foundation, US National Institutes of Health
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, 2023
Mandates: US National Science Foundation, US National Institutes of Health, Chan …
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
Mandates: National Natural Science Foundation of China
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
Mandates: US National Science Foundation, US National Institutes of Health, Chan …
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
Mandates: US National Science Foundation, US National Institutes of Health
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
Mandates: US National Science Foundation, US National Institutes of Health
Decoding Heterogenous Single-cell Perturbation Responses
B Song, D Liu, W Dai, N McMyn, Q Wang, D Yang, A Krejci, A Vasilyev, ...
bioRxiv, 2023
Mandates: Howard Hughes Medical Institute, Chan Zuckerberg Initiative
scReadSim: a single-cell RNA-seq and ATAC-seq read simulator
G Yan, D Song, JJ Li
Nature Communications 14 (1), 7482, 2023
Mandates: Chan Zuckerberg Initiative
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