Author

Dong-Yuan Song

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Open access Aug 2026

Leveraging long read RNA-seq to decipher neuronal regulation of alternative polyadenylation

Alternative polyadenylation (APA) is a pervasive co/post-transcriptional process affecting >70% of human genes which greatly enhances transcriptome diversity. Here we introduce APALORD (Alternative Polyadenylation Analysis of LOng-ReaDs), a computational framework for APA analysis of long-read (LR) RNA-seq data. For ge...

Zhiping Zhang, Heather R. Glatt-Deeley, Lehan Zou et al. · Nature Communications · 0 citations

Open access Sep 2026

Trustworthy super-resolution reconstruction across spatial omics modalities

Sequencing-based spatial omics platforms provide scalable and unbiased profiling of transcriptomic, epigenomic, and isoform-resolved signals, but their spatial resolution remains limited because each capture unit aggregates molecular information from multiple cells. Existing computational enhancement methods reconstruc...

Meng-Han Li, Xu-Tao Wang, Su-Sha-Guo-He-Jiang-Bo-Sun-Wei-Zhong-Chen-Xiang-Li Xu et al. · bioRxiv · 0 citations

Open access Sep 2026

spAlignDE unifies cross-sample and cross-modal spatial alignment with mismatch-aware differential expression

Comparative analysis of spatial omics requires aligning data across samples and modalities to a common coordinate system. Existing methods can be computationally intensive for large datasets, and cross-modal alignment is difficult when datasets lack comparable molecular features. In addition, residual alignment errors...

Su-Sha-Guo-He-Jiang-Bo-Sun-Wei-Zhong-Chen-Xiang-Li Xu, Yu Wang, Ling-Zhen Meng et al. · bioRxiv · 0 citations