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Nature Biotechnology|May 11, 2023
scDesign3 generates realistic in silico data for multimodal single-cell and spatial omicsDongyuan Song, Qingyang Wang, Guanao Yan, et al.Biorxiv : the Preprint Server for Biology|August 7, 2023
Synthetic control removes spurious discoveries from double dipping in single-cell and spatial transcriptomics data analysesDongyuan Song, Siqi Chen, Christy Lee, et al.Journal of Computational Biology : a Journal of Computational Molecular Cell Biology|November 2, 2018
Word and Sentence Embedding Tools to Measure Semantic Similarity of Gene Ontology Terms by Their DefinitionsDat Duong, Wasi Uddin Ahmad, Eleazar Eskin, et al.JACC. Case Reports|November 17, 2022
Narrow Complex Tachycardia With Intermittent 2:1 Atrioventricular RelationshipBernardo Acevedo-Mendez, Yuting Ye, Amit NoheriaProceedings of the National Academy of Sciences of the United States of America|December 3, 2011
Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimationJingyi Jessica Li, Ci-Ren Jiang, James B Brown, et al.Biorxiv : the Preprint Server for Biology|December 11, 2023
Benchmarking computational methods to identify spatially variable genes and peaksZhijian Li, Zain M Patel, Dongyuan Song, et al.Nucleic Acids Research|December 17, 2016
Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell statesYang Yang, Yu-Cheng T Yang, Jiapei Yuan, et al.Biorxiv : the Preprint Server for Biology|January 16, 2026
CIPHER: An end-to-end framework for designing optimized aggregated spatial transcriptomics experimentsZachery Hemminger, Haley De Ocampo, Fangming Xie, et al.Frontiers in Rehabilitation Sciences|October 10, 2022
Machine learning predicts improvement of functional outcomes in traumatic brain injury patients after inpatient rehabilitationIrene Say, Yiling Elaine Chen, Matthew Z Sun, et al.Bioinformatics (Oxford, England)|February 3, 2021
RAD: a web application to identify region associated differentially expressed genesYixin Guo, Ziwei Xue, Ruihong Yuan, et al.Pageof 21