Yoshihide Hayashizaki

A Joint Promoterome-Proteome Atlas Highlights the Molecular Diversity of Human Skeletal Muscles

The paper creates a promoterome and proteome atlas of human skeletal muscles, revealing molecular diversity and identifying key transcription factors and genetic variants associated with muscle traits.

Fast and accurate short read alignment with hybrid hash-tree data structure

The paper introduces a hybrid hash-tree algorithm for short read alignment, achieving 4.4x speed improvement over bwa-mem while maintaining similar accuracy.

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.

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.

Evidence of transcription at polyT short tandem repeats

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.

Dynamics and Topology of Human Transcribed Cis-regulatory Elements

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.

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.

The paper identifies shared expression patterns of genetic variants across tissues and cell types, enabling fine mapping of disease-associated variants and revealing key cell types involved in disease pathogenesis.

Linking FANTOM5 CAGE Peaks To Annotations With CAGEscan

The paper enhances the FANTOM5 expression atlas by associating gene-orphan promoter regions with their transcripts using CAGEscan.

Single-cell transcriptomes of fluorescent, ubiquitination-based cell cycle indicator cells

The paper generates a single-cell RNA-seq dataset of HeLa cells labeled with Fucci reporters and provides an open workflow for data processing and quality control.

A role for YY1 in sex-biased transcription revealed through X-linked promoter activity and allelic binding analyses

The paper identifies YY1's role in X-linked gene escape from inactivation by analyzing promoter activity and allelic binding in human datasets.