Akihide Yoshimi

Physiological mapping and prediction reveal stress-responsive translation initiation landscapes

This study introduces TISCA2 and IncepTIS to map and predict stress-responsive translation initiation sites, revealing tissue-specific patterns and enabling engineered mRNA 5' leaders.

NECTIN4 defines a subtype-dependent tumor state coupling enfortumab vedotin targetability to antitumor immunity in bladder cancer

The paper identifies NECTIN4 as a subtype-dependent determinant of tumor state and antitumor immunity in bladder cancer, linking its expression to response to enfortumab vedotin and checkpoint inhibitors.

A positional and combinatorial regulatory code for alternative splicing

This paper introduces SCALE-CLIP, a method to generate comparable RBP binding maps, and defines a positional and combinatorial regulatory code for alternative splicing.

Nocturnal intraocular pressure rise is regulated by norepinephrine via RHOB

This study identifies RHOB as a mediator of norepinephrine-induced intraocular pressure elevation in the trabecular meshwork, suggesting it as a potential therapeutic target for glaucoma.

Systematic identification of intron retention associated variants from massive publicly available transcriptome sequencing data

The paper identifies intron retention associated variants using transcriptome data alone, finding 27,937 variants and 3,077 putative disease-associated ones.

ProteomeGenerator: A framework for comprehensive proteomics based on de novo transcriptome assembly and high-accuracy peptide mass spectral matching

ProteomeGenerator enables sample-specific proteome discovery by integrating transcriptome sequencing and high-accuracy mass spectrometry, identifying non-canonical protein isoforms and improving proteogenomic analysis.