Gene Essentiality Prediction Using Topological Features From Metabolic Networks. - James Shiniti Nagai; Hério Sousa; Alexandre Hild Aono; Ana Carolina Lorena; Reginaldo Massanobu Kuroshu (BRACIS, 2018)

CrossTalkeR: analysis and visualization of ligand-receptorne tworks. - James Shiniti Nagai; Nils B. Leimkühler; Michael T. Schaub; Rebekka K. Schneider; Ivan G. Costa (Bioinform., 2021)

Optimal Transport Distances for Directed, Weighted Graphs: A Case Study With Cell-Cell Communication Networks. - James Shiniti Nagai; Ivan G. Costa; Michael T. Schaub (ICASSP, 2024)

Advances and challenges in cell-cell communication inference: a comprehensive review of tools, resources, and future directions. - Giulia Cesaro; James Shiniti Nagai; Nicolò Gnoato; Alice Chiodi; Gaia Tussardi; Vanessa Klöker; Carmelo Vittorio Musumarra; Ettore Mosca; Ivan G. Costa; Barbara Di Camillo; Enrica Calura; Giacomo Baruzzo (Briefings Bioinform., 2025)