Nozomu Yachie

This study shows Gp78 ubiquitin ligase regulates omegasome formation and mitochondrial protein degradation during mitophagy, independent of PINK1 and Parkin.

The paper introduces MILK, a framework for organizing single-cell genomic data into tree representations, enabling scalable analysis and preserving information across large datasets.

This paper introduces a cuffed guide RNA (cgRNA) that enables miRNA activity-dependent genome editing in human and mouse cells.

The paper introduces DemuxHMM, a recombination-aware demultiplexing method that improves scalability and performance for large-scale single-cell embryo profiling.

This paper identifies homology-induced data leakage in genome-trained sequence models and introduces hashFrag to improve evaluation and generalizability.

This paper introduces CloneSelect, a multi-kingdom genetic barcoding system that enables precise isolation of target clones using CRISPR base editing to trigger reporter gene expression.

INTERSTELLAR translates sequencing reads from any structure to any other, enabling analysis by existing tools for similar experiments.

This study develops a fluorescent assay to compare the activity of SpCas9 and SpCas9-NG variants, demonstrating its advantages over traditional methods.

The paper introduces GPS-seq, a theoretical framework for spatial transcriptomics that uses DNA barcodes to enable large-scale, optics-free imaging of tissue sections at single-cell resolution.

BFG-PCA is a high-throughput method for discovering binary protein interactions using DHFR-PCA, showing high sensitivity and specificity across human and yeast protein pairs.

This study uses base editing to systematically mutate over 17,000 sites across 1,500 genes in yeast, identifying 1,100 sites affecting fitness and providing guidelines for effective gRNA design.

beditor designs guide RNA libraries for CRISPR-mediated base editing across species and editors, using scores to select optimal guides for minimizing off-target effects and maximizing editing efficiency.

This paper develops a double selection strategy to improve CRISPR-Cas9 and base editing efficiency in yeast, enabling high-throughput mutagenesis screens.

The paper introduces SPADE, a software that detects periodic DNA and protein repeats in large genomic datasets with high-throughput and unsupervised methods, outperforming existing tools.