Koki Tsuyuzaki

TFActProfiler improves TF activity inference and perturbation prediction using pre-trained TF-mRNA interactions and RNA-seq data without additional training.

This study identifies neuropeptide signalling and perineurial barrier activation as mechanisms underlying persistent stress-induced behavioral changes in Drosophila.

scTensor identifies many-to-many cell-cell interactions from single-cell RNA-seq data by detecting triadic relationships not captured by conventional methods.

This study benchmarks PCA implementations for large-scale scRNA-seq, finding variations in speed, memory efficiency, and accuracy across algorithms and providing selection guidelines.

The paper introduces an NMF-based method to identify overlooked differentially expressed gene regions in single-cell RNA-seq data, finding novel transcripts related to neural stem/progenitor cell differentiation.

scTensor stacks ligand-receptor coexpression across cell-type pairs into a tensor and applies non-negative Tucker decomposition, recovering many-to-many cell-cell interactions that a label-permutation test missed in simulation.

CellFishing.jl efficiently searches large scRNA-seq datasets to find similar cells and identify notable genes with high accuracy and speed.