Dongyuan Song

Dongyuan Song

Ph.D. candidate in Bioinformatics at UCLA

Publications

author*: equal distribution; author†: co-corresponding author

Under review

  1. Dongyuan Song*, Kexin Li*, Xinzhou Ge, Christy Li, and Jingyi Jessica Li. ClusterDE: a post-clustering differential expression (DE) method robust to false-positive inflation caused by double dipping. bioRxiv, 2024 link
  2. Qingyang Wang, Zhiqian Zhai, Dongyuan Song, and Jingyi Jessica Li. 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 implementation. Under review at Nature Communications, 2023
  3. Zhijian Li, Zain Patel, Dongyuan Song, Jingyi Jessica Li Guanao Yan, and Luca Pinello. Benchmarking the efficacy and scalability of computational methods for the identification of spatially variable genes and peaks. Under review at Nature Methods, 2023

Peer reviewed

  1. Kian Hong Kock, Patrick K Kimes, Stephen S Gisselbrecht, Sachi Inukai, Sabrina K Phanor, James L Anderson, Gayatri L Ramakrishnan, Colin H Lipper, Dongyuan Song, Jesse V Kurland, Julia M Rogers, Raehoon Jeong, Stephen C Blacklow, Rafael A Irizarry, and Martha L Bulyk. DNA binding analysis of rare variants in homeodomains reveals novel homeodomain specificity-determining residues. Accepted by Nature Communications, 2024 link
  2. Guanao Yan, Dongyuan Song, and Jingyi Jessica Li. scReadSim: a single-cell RNA-seq and ATAC-seq read simulator. Nature Communications, 2023
  3. Dongyuan Song, Qingyang Wang, Guanao Yan, Tianyang Liu, Tianyi Sun, and Jingyi Jessica Li. scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics. Nature Biotechnology, 2023
  4. Elvis Han Cui*, Dongyuan Song*†, Weng Kee Wong, and Jingyi Jessica Li. Single-cell generalized trend model (scGTM): a flexible and interpretable model of gene expression trend along cell pseudotime. Bioinformatics, 2022
  5. Dongyuan Song*, Nan Miles Xi*, Jingyi Jessica Li, and Lin Wang. scSampler: fast diversity-preserving subsampling of large-scale single-cell transcriptomic data. Bioinformatics, 2022
  6. Tianyi Sun, Dongyuan Song, Wei Vivian Li, and Jingyi Jessica Li. Simulating single-cell gene expression count data with preserved gene correlations by scDesign2. Journal of Computational Biology, 2022
  7. Ruochen Jiang, Tianyi Sun, Dongyuan Song, and Jingyi Jessica Li. Statistics or biology: the zero-inflation controversy about scRNA-seq data. Genome Biology, 2022
  8. Dongyuan Song*, Kexin Li*, Zachary Hemminger, Roy Wollman, and Jingyi Jessica Li. scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling. Bioinformatics, 2021
  9. Xinzhou Ge, Yiling Elaine Chen, Dongyuan Song, MeiLu McDermott, Kyla Woyshner, Antigoni Manousopoulou, Ning Wang, Wei Li, Leo D Wang, and Jingyi Jessica Li. Clipper: p-value-free FDR control on high-throughput data from two conditions. Genome Biology, 2021
  10. Tianyi Sun, Dongyuan Song, Wei Vivian Li, and Jingyi Jessica Li. scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured. Genome Biology, 2021
  11. Dongyuan Song and Jingyi Jessica Li. PseudotimeDE: inference of differential gene expression along cell pseudotime with well-calibrated p-values from single-cell RNA sequencing data. Genome Biology, 2021
  12. Elizabeth Christina Miller, Kenji T Hayashi, Dongyuan Song, and John J Wiens. Explaining the ocean’s richest biodiversity hotspot and global patterns of fish diversity. Proceedings of the Royal Society B, 2018
  13. Dongyuan Song*, Zhe Wang*, Zhuo-Jun Song, Cheng-Chuan Zhou, Peng-Hao Xu, Jie Yang, Ji Yang, and Bao-Rong Lu. Increased novel single nucleotide polymorphisms in weedy rice populations associated with the change of farming styles: Implications in adaptive mutation and evolution. Journal of Systematics and Evolution, 2017