Haiyan Hu

misoTar: A novel approach for predicting miRNA and isomiR targets

misoTar predicts miRNA and isomiR targets using a deep learning framework trained on human interaction data, achieving high precision and recall.

Preferential IsomiR Enrichment in Extracellular Vesicles Improves Identification of Their Cellular Origins

The paper identifies isomiR enrichment in extracellular vesicles and develops a model to link EVs to their cellular origins using miRNA and isomiR features.

Recurrent enhancer-promoter interactions across samples

This study analyzes the recurrence of enhancer-promoter interactions across multiple Hi-C and HiChIP datasets, finding that most interactions are shared across samples and cell types.

Deep learning inference of miRNA expression from bulk and single-cell mRNA expression

The paper introduces two deep learning models to predict miRNA expression from bulk and single-cell mRNA data, showing improved accuracy over existing methods.

Novel features of miRNA and isomiR-mRNA interactions

The paper identifies 1,747 isomiRs and over 5 million microRNA/isomiR-mRNA interactions, finding that isomiRs bind mRNAs differently from their parent microRNAs.

A systematic study of HIF1A cofactors in hypoxic cancer cells

This study identifies 201 potential HIF1A cofactors in hypoxic cancer cells, with 30 validated and 21 matching known cofactors from public databases.

INSISTC: Incorporating Network Structure Information for Single-Cell Type Classification

INSISTC integrates gene regulatory network structure for single-cell type classification, improving accuracy and providing insights into cell-specific gene regulation.

Are known bacterial strains really present?

The paper investigates the reliability of known bacterial strains in shotgun metagenomic samples and finds they are often inconsistent and not supported by coverage data.

A Deep Learning Method for MiRNA/IsomiR Target Detection

DMISO improves miRNA/isomiR target prediction by incorporating deep learning and isomiR-mRNA interaction features, achieving high precision and recall.

A computational modeling of primary-microRNA expression

This study models pri-miRNA expression across 1829 cell types and tissues by associating them with mRNAs that reflect their expression patterns.

An intriguing characteristic of enhancer-promoter interactions

The paper identifies a new characteristic of enhancer-promoter interactions, showing enhancers form clusters that interact with specific gene sets.

Hundreds of motif pairs may facilitate enhancer-promoter interactions

The paper identifies hundreds of TF motif pairs that co-occur in enhancer-promoter pairs across seven human cell lines and show their biological relevance.