Author

Koki Tsuyuzaki

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Open access Sep 2026

A transcription factor regulatory atlas for activity inference and perturbation prediction

TFActProfiler is presented, a TF–mRNA resource and computational framework that learns signed, quantitative TF–mRNA regulatory coefficients by integrating heterogeneous prior evidence (ChIP-based, motif-based, and curated TF–mRNA annotations) with large-scale bulk and single-cell RNA-seq atlases.

Hikaru Sugimoto, Koki Tsuyuzaki, Zhao-Nan Zou et al. · Nucleic Acids Research · 0 citations

Review Open access Sep 2026

Ten quick tips for spatial transcriptomics analysis

Ten quick tips spanning the entire ST research workflow are presented: whether ST suits a given biological question, how to select a platform aligned with study objectives, how to understand and process ST data, and which software tools to employ for analysis and visualization.

Nagomi Kurogi, Koki Shimbara, Tatsuya Koreeda et al. · PLoS Computational Biology · 0 citations