Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects. - Jacqueline M. Dresch; Xiaozhou Liu; David N. Arnosti; Ahmet Ay (BMC Syst. Biol., 2010)

Multiple reference networks improve accuracy of signaling network construction. - Md Abdul Alim; Ahmet Ay; Md Mahmudul Hasan; My T. Thai; Tamer Kahveci (BCB, 2015)

Construction of signaling networks with incomplete RNAi data. - Qiyao Wang; Yuanfang Ren; Md Mahmudul Hasan; Ahmet Ay; Tamer Kahveci (BIBM, 2015)

Hierarchical decomposition of dynamically evolving regulatory networks. - Ahmet Ay; Dihong Gong; Tamer Kahveci (BMC Bioinform., 2015)

Identifying the topology of signaling networks from partial RNAi data. - Yuanfang Ren; Qiyao Wang; Md Mahmudul Hasan; Ahmet Ay; Tamer Kahveci (BMC Syst. Biol., 2016)

Differential transcriptional regulation by alternatively designed mechanisms: A mathematical modeling approach. - Necmettin Yildirim; Mehmet Emin Aktas; Seyma Nur Ozcan; Esra Akbas; Ahmet Ay (Silico Biol., 2017)

ANCA: Alignment-based Network Construction Algorithm. - Kevin Chow; Ahmet Ay; Rasha Elhesha; Tamer Kahveci (BCB, 2018)

Characterizing Building Blocks of Resource Constrained Biological Networks. - Yuanfang Ren; Ahmet Ay; Alin Dobra; Tamer Kahveci (BCB, 2018)

Shortest path counting in probabilistic biological networks. - Yuanfang Ren; Ahmet Ay; Tamer Kahveci (BMC Bioinform., 2018)

Identification of jointly correlated gene sets. - Yuanfang Ren; Ahmet Ay; Travis A. Gerke; Tamer Kahveci (J. Bioinform. Comput. Biol., 2018)

Construction of Signaling Pathways with RNAi Data and Multiple Reference Networks. - Md Abdul Alim; Ahmet Ay; Md Mahmudul Hasan; My T. Thai; Tamer Kahveci (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Finding Conserved Patterns in Multilayer Networks. - Yuanfang Ren; Aisharjya Sarkar; Ahmet Ay; Alin Dobra; Tamer Kahveci (BCB, 2019)

ANCA: Alignment-Based Network Construction Algorithm. - Kevin Chow; Aisharjya Sarkar; Rasha Elhesha; Pietro Cinaglia; Ahmet Ay; Tamer Kahveci (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Pattern Discovery in Multilayer Networks. - Yuanfang Ren; Aisharjya Sarkar; Pierangelo Veltri; Ahmet Ay; Alin Dobra; Tamer Kahveci (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Regulatory Effects of Cooperativity and Signal Profile on Adaptive Dynamics in Incoherent Feedforward Loop Networks. - Necmettin Yildirim; Thomas Brew; Ahmet Ay (Silico Biol., 2025)