A. Ercüment Çiçek

49 papers B 1Journal 42Unranked 6
YearRankTypeTitle / Venue / Authors
2026 J jnl
One-hot news: drug synergy models shortcut molecular features.
Bioinform.
Emine Beyza Çandir, Halil Ibrahim Kuru, Magnus Rattray, A. Ercüment Çiçek, Öznur Tastan
2025 J jnl
Beacon Reconstruction Attack: Reconstruction of genomes in genomic data-sharing beacons using summary statistics.
Bioinform.
Kousar Saleem, A. Ercüment Çiçek, Sinem Sav
2025 J jnl
LYCEUM: learning to call copy number variants on low-coverage ancient genomes.
Bioinform.
Mehmet Alper Yilmaz, Ahmet Arda Ceylan, Gun Kaynar, A. Ercüment Çiçek
2025 J jnl
RNAtranslator: Modeling protein-conditional RNA design as sequence-to-sequence natural language translation.
PLoS Comput. Biol.
Sobhan Shukueian Tabrizi, Sina Barazandeh, Helyasadat Hashemi Aghdam, A. Ercüment Çiçek
2024 J jnl
From cell lines to cancer patients: personalized drug synergy prediction.
Bioinform.
Halil Ibrahim Kuru, A. Ercüment Çiçek, Öznur Tastan
2024 — conf
SplitOut: Out-of-the-Box Training-Hijacking Detection in Split Learning via Outlier Detection.
CANS (2)
Ege Erdogan, Unat Teksen, Mehmet Salih Celiktenyildiz, Alptekin Küpçü, A. Ercüment Çiçek
2023 J jnl
DeepSide: A Deep Learning Approach for Drug Side Effect Prediction.
IEEE ACM Trans. Comput. Biol. Bioinform.
Onur Can Uner, Halil Ibrahim Kuru, Ramazan Gokberk Cinbis, Öznur Tastan, A. Ercüment Çiçek
2023 J jnl
Defense Mechanisms Against Training-Hijacking Attacks in Split Learning.
CoRR
Ege Erdogan, Unat Teksen, Mehmet Salih Celiktenyildiz, Alptekin Küpçü, A. Ercüment Çiçek
2023 J jnl
PiDeeL: metabolic pathway-informed deep learning model for survival analysis and pathological classification of gliomas.
Bioinform.
Gun Kaynar, Doruk Cakmakci, Caroline Bund, Julien Todeschi, Izzie-Jacques Namer, A. Ercüment Çiçek
2022 J jnl
A unifying network modeling approach for codon optimization.
Bioinform.
Oya Ekin Karasan, Alper Sen, Banu Tiryaki, A. Ercüment Çiçek
2022 J jnl
DeepND: Deep multitask learning of gene risk for comorbid neurodevelopmental disorders.
Patterns
Ilayda Beyreli, Oguzhan Karakahya, A. Ercüment Çiçek
2022 J jnl
MatchMaker: A Deep Learning Framework for Drug Synergy Prediction.
IEEE ACM Trans. Comput. Biol. Bioinform.
Halil Ibrahim Kuru, Öznur Tastan, A. Ercüment Çiçek
2022 — conf
SplitGuard: Detecting and Mitigating Training-Hijacking Attacks in Split Learning.
WPES@CCS
Ege Erdogan, Alptekin Küpçü, A. Ercüment Çiçek
2022 J jnl
Targeted metabolomics analyses for brain tumor margin assessment during surgery.
Bioinform.
Doruk Cakmakci, Gun Kaynar, Caroline Bund, Martial Piotto, Francois Proust, Izzie-Jacques Namer, A. Ercüment Çiçek
2022 — conf
UnSplit: Data-Oblivious Model Inversion, Model Stealing, and Label Inference Attacks against Split Learning.
WPES@CCS
Ege Erdogan, Alptekin Küpçü, A. Ercüment Çiçek
2022 J jnl
Uncovering complementary sets of variants for predicting quantitative phenotypes.
Bioinform.
Serhan Yilmaz, Mohamad Fakhouri, Mehmet Koyutürk, A. Ercüment Çiçek, Öznur Tastan
2021 J jnl
A Tool for Detecting Complementary Single Nucleotide Polymorphism Pairs in Genome-Wide Association Studies for Epistasis Testing.
J. Comput. Biol.
Gizem Caylak, Öznur Tastan, A. Ercüment Çiçek
2021 J jnl
DORMAN: Database of Reconstructed MetAbolic Networks.
IEEE ACM Trans. Comput. Biol. Bioinform.
Furkan Ozden, Metin Can Siper, Necmi Acarsoy, Tugrulcan Elmas, Bryan Marty, Xinjian Qi, A. Ercüment Çiçek
2021 J jnl
Genome Reconstruction Attacks Against Genomic Data-Sharing Beacons.
Proc. Priv. Enhancing Technol.
Kerem Ayoz, Erman Ayday, A. Ercüment Çiçek
2021 J jnl
Potpourri: An Epistasis Test Prioritization Algorithm via Diverse SNP Selection.
J. Comput. Biol.
Gizem Caylak, Öznur Tastan, A. Ercüment Çiçek
2021 J jnl
SPADIS: An Algorithm for Selecting Predictive and Diverse SNPs in GWAS.
IEEE ACM Trans. Comput. Biol. Bioinform.
Serhan Yilmaz, Öznur Tastan, A. Ercüment Çiçek
2021 J jnl
SplitGuard: Detecting and Mitigating Training-Hijacking Attacks in Split Learning.
CoRR
Ege Erdogan, Alptekin Küpçü, A. Ercüment Çiçek
2021 J jnl
SplitGuard: Detecting and Mitigating Training-Hijacking Attacks in Split Learning.
IACR Cryptol. ePrint Arch.
Ege Erdogan, Alptekin Küpçü, A. Ercüment Çiçek
2021 J jnl
UnSplit: Data-Oblivious Model Inversion, Model Stealing, and Label Inference Attacks Against Split Learning.
CoRR
Ege Erdogan, Alptekin Küpçü, A. Ercüment Çiçek
2021 J jnl
UnSplit: Data-Oblivious Model Inversion, Model Stealing, and Label Inference Attacks Against Split Learning.
IACR Cryptol. ePrint Arch.
Ege Erdogan, Alptekin Küpçü, A. Ercüment Çiçek
2020 J jnl
Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm.
Bioinform.
Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercüment Çiçek, Can Alkan, Onur Mutlu
2020 J jnl
Genome Reconstruction Attacks Against Genomic Data-Sharing Beacons.
CoRR
Kerem Ayoz, Erman Ayday, A. Ercüment Çiçek
2020 J jnl
Machine learning assisted intraoperative assessment of brain tumor margins using HRMAS NMR spectroscopy.
PLoS Comput. Biol.
Doruk Cakmakci, Emin Onur Karakaslar, Elisa Ruhland, Marie-Pierre Chenard, Francois Proust, Martial Piotto, Izzie-Jacques Namer, A. Ercüment Çiçek
2020 B conf
Potpourri: An Epistasis Test Prioritization Algorithm via Diverse SNP Selection.
RECOMB
Gizem Caylak, A. Ercüment Çiçek
2020 J jnl
Predicting Carbon Spectrum in Heteronuclear Single Quantum Coherence Spectroscopy for Online Feedback During Surgery.
IEEE ACM Trans. Comput. Biol. Bioinform.
Emin Onur Karakaslar, Baris Coskun, Hassiba Outilaft, Izzie-Jacques Namer, A. Ercüment Çiçek
2020 J jnl
The effect of kinship in re-identification attacks against genomic data sharing beacons.
Bioinform.
Kerem Ayoz, Miray Aysen, Erman Ayday, A. Ercüment Çiçek
2019 J jnl
Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm.
CoRR
Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercüment Çiçek, Can Alkan, Onur Mutlu
2019 J jnl
Re-identification of individuals in genomic data-sharing beacons via allele inference.
Bioinform.
Nora von Thenen, Erman Ayday, A. Ercüment Çiçek
2019 J jnl
ST-Steiner: a spatio-temporal gene discovery algorithm.
Bioinform.
Utku Norman, A. Ercüment Çiçek
2016 J jnl
Privacy-Related Consequences of Turkish Citizen Database Leak.
CoRR
Erin Avllazagaj, Erman Ayday, A. Ercüment Çiçek
2015 J jnl
MIRA: mutual information-based reporter algorithm for metabolic networks.
Bioinform.
A. Ercüment Çiçek, Kathryn Roeder, Gultekin Özsoyoglu
2014 J jnl
Ensuring location diversity in privacy-preserving spatio-temporal data publishing.
VLDB J.
A. Ercüment Çiçek, Mehmet Ercan Nergiz, Yücel Saygin
2014 J jnl
MIRA: mutual information-based reporter algorithm for metabolic networks.
Bioinform.
A. Ercüment Çiçek, Kathryn Roeder, Gultekin Özsoyoglu
2013 J jnl
ADEMA: An Algorithm to Determine Expected Metabolite Level Alterations Using Mutual Information.
PLoS Comput. Biol.
A. Ercüment Çiçek, Ilya Bederman, Leigh Henderson, Mitchell L. Drumm, Gultekin Özsoyoglu
2013 J jnl
An online model composition tool for system biology models.
BMC Syst. Biol.
Sarp A. Coskun, A. Ercüment Çiçek, Nicola Lai, Ranjan K. Dash, Z. Meral Özsoyoglu, Gultekin Özsoyoglu
2013 — conf
PathCase-MAW: An Online Metabolic Network Analysis Workbench.
BCB
A. Ercüment Çiçek, Xinjian Qi, Ali Cakmak, Stephen R. Johnson, Xu Han, Sami Alshalwi, Gultekin Özsoyoglu
2013 J jnl
iPathCase
Health Inf. Sci. Syst.
Stephen R. Johnson, Xinjian Qi, A. Ercüment Çiçek, Gultekin Özsoyoglu
2012 J jnl
A Look-Ahead Approach to Secure Multiparty Protocols.
IEEE Trans. Knowl. Data Eng.
Mehmet Ercan Nergiz, A. Ercüment Çiçek, Thomas Pedersen, Yücel Saygin
2012 J jnl
A New metabolomics Analysis Technique: steady-State metabolic Network Dynamics Analysis.
J. Bioinform. Comput. Biol.
Ali Cakmak, Xinjian Qi, A. Ercüment Çiçek, Ilya Bederman, Leigh Henderson, Mitchell L. Drumm, Gultekin Özsoyoglu
2012 J jnl
Observation Conflict Resolution in steady-State metabolic Network Dynamics Analysis.
J. Bioinform. Comput. Biol.
A. Ercüment Çiçek, Gultekin Özsoyoglu
2012 J jnl
PathCase-SB: integrating data sources and providing tools for systems biology research.
BMC Syst. Biol.
Sarp A. Coskun, Xinjian Qi, Ali Cakmak, En Cheng, A. Ercüment Çiçek, Lei Yang, Rishiraj Jadeja, Ranjan K. Dash, Nicola Lai, Gultekin Özsoyoglu, Z. Meral Özsoyoglu
2011 — conf
Computational interpretation of metabolomics measurements: steady-state metabolic network dynamics analysis.
BCB
Ali Cakmak, Xinjian Qi, A. Ercüment Çiçek, Gultekin Özsoyoglu
2011 J jnl
PathCase-SB architecture and database design.
BMC Syst. Biol.
Ali Cakmak, Xinjian Qi, Sarp A. Coskun, Mitali Das, En Cheng, A. Ercüment Çiçek, Nicola Lai, Gultekin Özsoyoglu, Z. Meral Özsoyoglu
2011 — conf
Resolving observation conflicts in steady state metabolic network dynamics analysis.
BCB
A. Ercüment Çiçek, Gultekin Özsoyoglu