VISIBIOweb: visualization and layout services for BioPAX pathway models. - Alptug Dilek; Mehmet E. Belviranli; Ugur Dogrusoz (Nucleic Acids Res., 2010)

CiSE: A Circular Spring Embedder Layout Algorithm. - Ugur Dogrusoz; Mehmet E. Belviranli; Alptug Dilek (IEEE Trans. Vis. Comput. Graph., 2013)

Chisio: A Compound Graph Editing and Layout Framework. - Cihan Küçükkeçeci; Ugur Dogrusoz; Esat Belviranli; Alptug Dilek (CoRR, 2017)