Computational interpretation of metabolomics measurements: steady-state metabolic network dynamics analysis. - Ali Cakmak 001; Xinjian Qi; A. Ercüment Çiçek; Gultekin Özsoyoglu (BCB, 2011)

PathCase-SB architecture and database design. - Ali Cakmak 001; Xinjian Qi; Sarp A. Coskun; Mitali Das; En Cheng; A. Ercüment Çiçek; Nicola Lai; Gultekin Özsoyoglu; Z. Meral Özsoyoglu (BMC Syst. Biol., 2011)

PathCase-SB: integrating data sources and providing tools for systems biology research. - Sarp A. Coskun; Xinjian Qi; Ali Cakmak 001; En Cheng; A. Ercüment Çiçek; Lei Yang; Rishiraj Jadeja; Ranjan K. Dash; Nicola Lai; Gultekin Özsoyoglu; Z. Meral Özsoyoglu (BMC Syst. Biol., 2012)

A New metabolomics Analysis Technique: steady-State metabolic Network Dynamics Analysis. - Ali Cakmak 001; Xinjian Qi; A. Ercüment Çiçek; Ilya Bederman; Leigh Henderson; Mitchell L. Drumm; Gultekin Özsoyoglu (J. Bioinform. Comput. Biol., 2012)

PathCase-MAW: An Online Metabolic Network Analysis Workbench. - A. Ercüment Çiçek; Xinjian Qi; Ali Cakmak 001; Stephen R. Johnson; Xu Han; Sami Alshalwi; Gultekin Özsoyoglu (BCB, 2013)

Locating basic bio-entities in genome-scale reconstructed metabolic networks. - Xinjian Qi; Gultekin Özsoyoglu (BIBM, 2013)

iPathCaseKEGG: An iPad interface for KEGG metabolic pathways. - Stephen R. Johnson; Xinjian Qi; A. Ercüment Çiçek; Gultekin Özsoyoglu (Health Inf. Sci. Syst., 2013)

An online system for metabolic network analysis. - Abdullah Ercument Cicek; Xinjian Qi; Ali Cakmak 001; Stephen R. Johnson; Xu Han; Sami Alshalwi; Zehra Meral Özsoyoglu; Gultekin Özsoyoglu (Database J. Biol. Databases Curation, 2014)

DORMAN: Database of Reconstructed MetAbolic Networks. - Furkan Ozden; Metin Can Siper; Necmi Acarsoy; Tugrulcan Elmas; Bryan Marty; Xinjian Qi; A. Ercüment Çiçek (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)