Yasuhiro Murakawa

The paper maps RNA-DNA interactions in 16 human cell types, showing cell-type-specific and dynamic networks that correlate with gene regulation and disease traits.

The paper identifies a post-transcriptional mechanism where ribosomal protein S12 regulates Xrp1 expression through alternative splicing, leading to cell death in unfit cells.

The paper develops a single-cell transcriptomic map of cynomolgus macaque hematopoietic stem cells and progenitors, revealing molecular differences from humans and a direct differentiation pathway to megakaryocyte lineages.

The paper introduces CAMBUS, a machine-learning framework to identify functionally important open chromatin regions by measuring sequence sensitivity, and finds these regions are enriched for evolutionary constraint and disease-related variants.

The paper develops a tool to genotype mobile element variants (MEVs) using short-read data and identifies population-specific MEs linked to disease and gene regulation.

This study presents de novo chromosome-scale genome assemblies for cynomolgus macaque and common marmoset using long-read and Hi-C data, achieving high contiguity and accuracy.

The paper develops MENTR, a machine learning framework to predict cell-type-specific ncRNA transcription from genome sequence, identifying causal variants and ncRNAs associated with complex traits.

This study shows that DUX4 regulates the oocyte-to-embryo transition in humans by activating enhancers and promoting genome reprogramming.

The paper develops NET-CAGE to detect nascent RNA 5-ends, identifies enhancer-promoter pairs, and reveals topological connections of cis-regulatory elements across cell types.

The paper shows that codon bias affects mRNA stability in humans through ILF2, with GC3 codons stabilizing and AT3 codons destabilizing mRNA.

The paper investigates how Wnt-responsive enhancers selectively activate alternative MYC promoters, showing their role in differential promoter usage and the influence of core promoter elements.