Global Optimization of Nonlinear Bilevel Programming Problems. - Zeynep H. Gümüs; Christodoulos A. Floudas (J. Glob. Optim., 2001)

Global optimization of mixed-integer bilevel programming problems. - Zeynep H. Gümüs; Christodoulos A. Floudas (Comput. Manag. Sci., 2005)

MINLP: Reactive Distillation Column Synthesis. - Amy Ciric; Zeynep H. Gümüs (Encyclopedia of Optimization, 2009)

Mixed Integer Nonlinear Bilevel Programming: Deterministic Global Optimization. - Zeynep H. Gümüs; Christodoulos A. Floudas (Encyclopedia of Optimization, 2009)

Bilevel Programming: Applications in Engineering. - Zeynep H. Gümüs; Kemal Sahin; Amy Ciric (Encyclopedia of Optimization, 2009)

Quantification and Analysis of Combination Drug Synergy in High-Throughput Transcriptome Studies. - Zeynep H. Gümüs; Fernando Siso-Nadal; Ada Gjrezi; Paul McDonagh; Iya Khalil; Paraskevi Giannakakou; Harel Weinstein (BIBE, 2010)

Developing Design Guidelines for Precision Oncology Reports. - Selim Kalayci; Çagatay Demiralp; Zeynep H. Gümüs (CoRR, 2018)

ImmuneRegulation: a web-based tool for identifying human immune regulatory elements. - Selim Kalayci; Myvizhi Esai Selvan; Irene Ramos; Chris Cotsapas; Eva Harris; Eun-Young Kim; Ruth R. Montgomery; Gregory A. Poland; Bali Pulendran; John S. Tsang; Robert J. Klein; Zeynep H. Gümüs (Nucleic Acids Res., 2019)

A Brave New World: Virtual Reality and Augmented Reality in Systems Biology. - Berk Turhan; Zeynep H. Gümüs (Frontiers Bioinform., 2022)

PhosNetVis: A web-based tool for fast kinase-substrate enrichment analysis and interactive 2D/3D network visualizations of phosphoproteomics data. - Osho Rawal; Berk Turhan; Irene Font Peradejordi; Shreya Chandrasekar; Selim Kalayci; Sacha Gnjatic; Jeffrey Johnson; Mehdi Bouhaddou; Zeynep H. Gümüs (Patterns, 2025)