Computational Systems Biology. - Sucheendra K. Palaniappan; Ayako Yachie-Kinoshita; Samik Ghosh (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)

Cell Modeling and Simulation. - Ayako Yachie-Kinoshita; Kazunari Kaizu (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)

Computational Systems Biology Applications. - Ayako Yachie-Kinoshita; Sucheendra K. Palaniappan; Samik Ghosh (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

IQCELL: A platform for predicting the effect of gene perturbations on developmental trajectories using single-cell RNA-seq data. - Tiam Heydari; Matthew A. Langley; Cynthia L. Fisher; Daniel Aguilar-Hidalgo; Shreya Shukla; Ayako Yachie-Kinoshita; Michael Hughes; Kelly M. McNagny; Peter W. Zandstra (PLoS Comput. Biol., 2022)