Prediction of dinucleotide-specific RNA-binding sites in proteins. - Michael Fernández; Yutaro Kumagai; Daron M. Standley; Akinori Sarai; Kenji Mizuguchi; Shandar Ahmad (BMC Bioinform., 2011)

A Parzen window-based approach for the detection of locally enriched transcription factor binding sites. - Alexis Vandenbon; Yutaro Kumagai; Shunsuke Teraguchi; Karlou Mar Amada; Shizuo Akira; Daron M. Standley (BMC Bioinform., 2013)

Linking Transcriptional Changes over Time in Stimulated Dendritic Cells to Identify Gene Networks Activated during the Innate Immune Response. - Ashwini Patil; Yutaro Kumagai; Kuo-ching Liang; Yutaka Suzuki; Kenta Nakai (PLoS Comput. Biol., 2013)

Estimation of diffusion constants from single molecular measurement without explicit tracking. - Shunsuke Teraguchi; Yutaro Kumagai (BMC Syst. Biol., 2018)

BootCellNet, a resampling-based procedure, promotes unsupervised identification of cell populations via robust inference of gene regulatory networks. - Yutaro Kumagai (PLoS Comput. Biol., 2024)