Dongyuan Song

Biochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

2in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 2 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

Papers

Driven by 27 papers. Top paper: “scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured”.

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

Genome biology(2021)10.1186/s13059-021-02367-2

N/A

2.7DataRank · unranked

127 citations

Dongyuan Song, Wei Vivian Li, Jingyi Jessica Li, Tianyi Sun

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

Genome biology(2022)10.1186/s13059-022-02601-5

N/A

0.972DataRank · unranked

650 citations

Tianyi Sun, Dongyuan Song, Jingyi Jessica Li, Ruochen Jiang

Decoding heterogeneous single-cell perturbation responses

Nature Cell Biology(2025)10.1038/s41556-025-01626-9

N/A

0.538DataRank · unranked

35 citations

Dingyu Liu, Weiwei Dai, Natalie F. McMyn, Qingyang Wang, Dapeng Yang +19 more

Benchmarking computational methods to identify spatially variable genes and peaks

10.1101/2023.12.02.569717

N/A

0.515DataRank · unranked

30 citations

Zain M.Patel, Dongyuan Song, Guanao Yan, Jingyi Jessica Li, Luca Pinello +1 more

Systematic benchmarking of computational methods to identify spatially variable genes

Genome biology(2025)10.1186/s13059-025-03731-2

N/A

0.425DataRank · unranked

14 citations

Z. Patel, Dongyuan Song, Sai Nirmayi Yasa, Robrecht Cannoodt, Guanao Yan +3 more

scReadSim: a single-cell RNA-seq and ATAC-seq read simulator

Nature Communications(2023)10.1038/s41467-023-43162-w

N/A

0.416DataRank · unranked

15 citations

Dongyuan Song, Jingyi Jessica Li, Guanao Yan

A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.09.20.508796

N/A

0.292DataRank · unranked

6 citations

Qingyang Wang, Guanao Yan, Tianyang Liu, Jingyi Jessica Li, Dongyuan Song

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

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.09.430550

N/A

0.165DataRank · unranked

2 citations

Kexin Li, Zachary Hemminger, Roy Wollman, Jingyi Jessica Li, Dongyuan Song

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

Bioinformatics(2022)10.1093/bioinformatics/btac423

N/A

0DataRank · unranked

7 citations

Dongyuan Song, Weng Kee Wong, Jingyi Jessica Li, Elvis Han Cui

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.19.390773

N/A

0DataRank · unranked

11 citations

Yiling Elaine Chen, Dongyuan Song, MeiLu McDermott, Kyla Woyshner, Antigoni Manousopoulou +5 more

Synthetic control removes spurious discoveries from double dipping in single-cell and spatial transcriptomics data analyses

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.21.550107

N/A

0DataRank · unranked

17 citations

Siqi Chen, Christy Lee, Kexin Li, Xinzhou Ge, Jingyi Jessica Li +1 more

ClusterDE: a post-clustering differential expression (DE) method robust to false-positive inflation caused by double dipping

Research Square(2023)10.21203/rs.3.rs-3211191/v1

N/A

0DataRank · unranked

6 citations

Dongyuan Song, Kexin Li, Xinzhou Ge, Jingyi Jessica Li

Decoding Heterogenous Single-cell Perturbation Responses

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.30.564796

N/A

0DataRank · unranked

5 citations

Dingyu Liu, Weiwei Dai, Natalie F. McMyn, Qingyang Wang, Dapeng Yang +19 more

DNA binding analysis of rare variants in homeodomains reveals novel homeodomain specificity-determining residues

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.16.545320

N/A

0DataRank · unranked

2 citations

Patrick K. Kimes, Stephen S. Gisselbrecht, Sachi Inukai, Sabrina K. Phanor, James T. Anderson +10 more

DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues

Nature Communications(2024)10.1038/s41467-024-47396-0

N/A

0DataRank · unranked

25 citations

Patrick K. Kimes, Stephen S. Gisselbrecht, Sachi Inukai, Sabrina K. Phanor, James T. Anderson +10 more

Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq

Nature Communications(2025)10.1038/s41467-025-60154-0

N/A

0DataRank · unranked

7 citations

Xuhang Li, Dongyuan Song, Onur Yukselen, Shivani Nanda, Alper Küçükural +4 more

Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.02.02.636107

N/A

0DataRank · unranked

4 citations

Xuhang Li, Dongyuan Song, Onur Yukselen, Shivani Nanda, Alper Küçükural +4 more

Comment on “Data Fission: Splitting a Single Data Point” Data Fission for Unsupervised Learning: A Discussion on Post-Clustering Inference and the Challenges of Debiasing

Journal of the American Statistical Association(2025)10.1080/01621459.2024.2412191

N/A

0DataRank · unranked

0 citations

Xinzhou Ge, Dongyuan Song, Jingyi Jessica Li, Changhu Wang

PseudotimeDE-fast: fast testing of differential gene expression along cell pseudotime

Bioinformatics(2025)10.1093/bioinformatics/btaf573

N/A

0DataRank · unranked

0 citations

Dongyuan Song, Lucy Xia, Jingyi Jessica Li, Yuheng Lai

scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics

Nature Biotechnology(2023)10.1038/s41587-023-01772-1

N/A

0DataRank · unranked

151 citations

Qingyang Wang, Guanao Yan, Tianyang Liu, Tianyi Sun, Jingyi Jessica Li +1 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.17.387795

N/A

0DataRank · unranked

10 citations

Dongyuan Song, Wei Vivian Li, Jingyi Jessica Li, Tianyi Sun

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.28.424633

N/A

0DataRank · unranked

9 citations

Tianyi Sun, Dongyuan Song, Jingyi Jessica Li, Ruochen Jiang

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.17.387779

N/A

0DataRank · unranked

7 citations

Jingyi Jessica Li, Dongyuan Song

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

Genome biology(2021)10.1186/s13059-021-02341-y

N/A

0DataRank · unranked

94 citations

Jingyi Jessica Li, Dongyuan Song

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

Genome biology(2021)10.1186/s13059-021-02506-9

N/A

0DataRank · unranked

55 citations

Yiling Elaine Chen, Dongyuan Song, MeiLu McDermott, Kyla Woyshner, Antigoni Manousopoulou +5 more

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

Bioinformatics(2021)10.1093/bioinformatics/btab273

N/A

0DataRank · unranked

31 citations

Kexin Li, Zachary Hemminger, Roy Wollman, Jingyi Jessica Li, Dongyuan Song

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

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.11.25.470059

N/A

0DataRank · unranked

0 citations

Dongyuan Song, Weng Kee Wong, Jingyi Jessica Li, Elvis Han Cui