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

Resolving observation conflicts in steady state metabolic network dynamics analysis. - 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)

Observation Conflict Resolution in steady-State metabolic Network Dynamics Analysis. - A. Ercüment Çiçek; Gultekin Özsoyoglu (J. Bioinform. Comput. Biol., 2012)

A Look-Ahead Approach to Secure Multiparty Protocols. - Mehmet Ercan Nergiz; A. Ercüment Çiçek; Thomas Pedersen; Yücel Saygin (IEEE Trans. Knowl. Data Eng., 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)

An online model composition tool for system biology models. - Sarp A. Coskun; A. Ercüment Çiçek; Nicola Lai; Ranjan K. Dash; Z. Meral Özsoyoglu; Gultekin Özsoyoglu (BMC Syst. Biol., 2013)

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

ADEMA: An Algorithm to Determine Expected Metabolite Level Alterations Using Mutual Information. - A. Ercüment Çiçek; Ilya Bederman; Leigh Henderson; Mitchell L. Drumm; Gultekin Özsoyoglu (PLoS Comput. Biol., 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)

MIRA: mutual information-based reporter algorithm for metabolic networks. - A. Ercüment Çiçek; Kathryn Roeder; Gultekin Özsoyoglu (Bioinform., 2014)

Ensuring location diversity in privacy-preserving spatio-temporal data publishing. - A. Ercüment Çiçek; Mehmet Ercan Nergiz; Yücel Saygin (VLDB J., 2014)

Privacy-Related Consequences of Turkish Citizen Database Leak. - Erin Avllazagaj; Erman Ayday; A. Ercüment Çiçek (CoRR, 2016)

ST-Steiner: a spatio-temporal gene discovery algorithm. - Utku Norman; A. Ercüment Çiçek (Bioinform., 2019)

Re-identification of individuals in genomic data-sharing beacons via allele inference. - Nora von Thenen; Erman Ayday; A. Ercüment Çiçek (Bioinform., 2019)

Potpourri: An Epistasis Test Prioritization Algorithm via Diverse SNP Selection. - Gizem Caylak; A. Ercüment Çiçek (RECOMB, 2020)

The effect of kinship in re-identification attacks against genomic data sharing beacons. - Kerem Ayoz; Miray Aysen; Erman Ayday; A. Ercüment Çiçek (Bioinform., 2020)

Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm. - Can Firtina; Jeremie S. Kim; Mohammed Alser; Damla Senol Cali; A. Ercüment Çiçek; Can Alkan; Onur Mutlu (Bioinform., 2020)

Machine learning assisted intraoperative assessment of brain tumor margins using HRMAS NMR spectroscopy. - Doruk Cakmakci; Emin Onur Karakaslar; Elisa Ruhland; Marie-Pierre Chenard; Francois Proust; Martial Piotto; Izzie-Jacques Namer; A. Ercüment Çiçek (PLoS Comput. Biol., 2020)

Predicting Carbon Spectrum in Heteronuclear Single Quantum Coherence Spectroscopy for Online Feedback During Surgery. - Emin Onur Karakaslar; Baris Coskun; Hassiba Outilaft; Izzie-Jacques Namer; A. Ercüment Çiçek (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

UnSplit: Data-Oblivious Model Inversion, Model Stealing, and Label Inference Attacks Against Split Learning. - Ege Erdogan; Alptekin Küpçü; A. Ercüment Çiçek (IACR Cryptol. ePrint Arch., 2021)

SplitGuard: Detecting and Mitigating Training-Hijacking Attacks in Split Learning. - Ege Erdogan; Alptekin Küpçü; A. Ercüment Çiçek (IACR Cryptol. ePrint Arch., 2021)

Potpourri: An Epistasis Test Prioritization Algorithm via Diverse SNP Selection. - Gizem Caylak; Öznur Tastan; A. Ercüment Çiçek (J. Comput. Biol., 2021)

A Tool for Detecting Complementary Single Nucleotide Polymorphism Pairs in Genome-Wide Association Studies for Epistasis Testing. - Gizem Caylak; Öznur Tastan; A. Ercüment Çiçek (J. Comput. Biol., 2021)

Genome Reconstruction Attacks Against Genomic Data-Sharing Beacons. - Kerem Ayoz; Erman Ayday; A. Ercüment Çiçek (Proc. Priv. Enhancing Technol., 2021)

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)

SPADIS: An Algorithm for Selecting Predictive and Diverse SNPs in GWAS. - Serhan Yilmaz; Öznur Tastan; A. Ercüment Çiçek (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Targeted metabolomics analyses for brain tumor margin assessment during surgery. - Doruk Cakmakci; Gun Kaynar; Caroline Bund; Martial Piotto; Francois Proust; Izzie-Jacques Namer; A. Ercüment Çiçek (Bioinform., 2022)

A unifying network modeling approach for codon optimization. - Oya Ekin Karasan; Alper Sen 002; Banu Tiryaki; A. Ercüment Çiçek (Bioinform., 2022)

Uncovering complementary sets of variants for predicting quantitative phenotypes. - Serhan Yilmaz; Mohamad Fakhouri; Mehmet Koyutürk; A. Ercüment Çiçek; Öznur Tastan (Bioinform., 2022)

DeepND: Deep multitask learning of gene risk for comorbid neurodevelopmental disorders. - Ilayda Beyreli; Oguzhan Karakahya; A. Ercüment Çiçek (Patterns, 2022)

MatchMaker: A Deep Learning Framework for Drug Synergy Prediction. - Halil Ibrahim Kuru; Öznur Tastan; A. Ercüment Çiçek (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Defense Mechanisms Against Training-Hijacking Attacks in Split Learning. - Ege Erdogan; Unat Teksen; Mehmet Salih Celiktenyildiz; Alptekin Küpçü; A. Ercüment Çiçek (CoRR, 2023)

DeepSide: A Deep Learning Approach for Drug Side Effect Prediction. - Onur Can Uner; Halil Ibrahim Kuru; Ramazan Gokberk Cinbis; Öznur Tastan; A. Ercüment Çiçek (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

PiDeeL: metabolic pathway-informed deep learning model for survival analysis and pathological classification of gliomas. - Gun Kaynar; Doruk Cakmakci; Caroline Bund; Julien Todeschi; Izzie-Jacques Namer; A. Ercüment Çiçek (Bioinform., 2023)

SplitOut: Out-of-the-Box Training-Hijacking Detection in Split Learning via Outlier Detection. - Ege Erdogan; Unat Teksen; Mehmet Salih Celiktenyildiz; Alptekin Küpçü; A. Ercüment Çiçek (CANS (2), 2024)