Jiayu Wen

scPolyA provides a framework for analyzing alternative polyadenylation in single-cell and spatial transcriptomes, revealing APA patterns in cancer tissues.

RNAElectra is an RNA foundation model pretrained using replaced-token detection, showing strong performance across RNA regulatory tasks and supporting interpretability.

The paper analyzes RNAi pathway evolution in Drosophila, finding recurrent AGO2 expansion and testis-biased expression of RNAi factors, suggesting a role in sex chromosome conflicts.

NucEL improves genomic representation learning by using ELECTRA-style pre-training with single-nucleotide tokenization, achieving state-of-the-art performance on multiple tasks.

The paper shows that CX-5461, a ribosome biogenesis inhibitor, increases platelet counts in humans and enhances megakaryopoiesis in mice without affecting platelet function or inflammatory cytokines.

CS-Fold improves RNA secondary structure prediction by integrating compensatory mutations from phylogenetic trees into a deep learning framework, achieving a 5% higher F1 score on cross-family datasets.

The paper evaluates and optimizes sequence-based gene regulatory deep learning models using a DREAM Challenge dataset, showing improvements through architectural and training strategy refinements.

This study identifies Hamlet as a key regulator of epithelial tissue fusion in Drosophila reproductive system, revealing its role in gene regulation and tissue connectivity.

CRMnet is a deep learning model that predicts gene expression from regulatory sequences in yeast, achieving high accuracy and identifying transcription factor binding sites through model interpretation.

This study identifies PRDM16 as a co-repressor in the BMP pathway that suppresses neural stem cell proliferation by regulating SMAD complex genomic distribution and gene expression.

This study identifies H2A.B as a testis-specific factor that enhances ribosome biogenesis in Hodgkin Lymphoma by promoting rDNA transcription and ribosomal protein gene expression.

This study investigates the roles of ELAV/Hu RNA binding proteins in neuronal alternative splicing and polyadenylation, showing their overlapping functions in suppressing exons and polyadenylation sites.

This study investigates the in vivo functions of BEN-solo proteins in Drosophila embryos, showing they act as insulators to partition active chromatin and regulate gene activation.

This study shows PRDM16 promotes temporal progression of neural progenitors in the mouse neocortex by regulating gene expression and chromatin accessibility.