Michiel de Hoon

The paper shows enhancers are usually unidirectionally transcribed in a cell type but may appear bidirectional when aggregated across cell types, suggesting enhancer RNAs are functional.

The paper performs knockdown of 200 lncRNAs in human iPS cells, identifies 36 with growth inhibition, and finds molecular phenotypes in 29.3% of cases, with higher agreement in molecular than cell growth phenotypes across cell types.

The paper identifies widespread transcription initiation at microsatellites across species and develops deep learning models to predict STR-associated transcription and its impact on disease variants.

The paper identifies cis-interacting lncRNAs and their targets using RNA-chromatin and Hi-C data across 18 human cell types.

The paper presents FC-R2, an expanded transcriptome atlas of over 109,000 genes, including lncRNAs, and demonstrates its utility in analyzing gene expression across normal and diseased human samples.

RADICL-seq maps genome-wide RNA-chromatin interactions in intact nuclei, revealing general and cell type-specific patterns of transcript occupancy and the role of transcription in chromatin structure.

The paper investigates transcription initiation at polyT short tandem repeats (STRs) using CAGE data and develops a deep learning model to predict STR-associated transcription with high accuracy.