A. Ercüment Çiçek

Publication Activity (10 Years)

Years Active: 2011-2023
Publications (10 Years): 28

Top Topics

Sensitive Attributes

Top Venues

IEEE ACM Trans. Comput. Biol. Bioinform.

J. Comput. Biol.

Publications

Onur Can Uner, Halil Ibrahim Kuru, Ramazan Gokberk Cinbis, Oznur Tastan, A. Ercüment Çiçek
DeepSide: A Deep Learning Approach for Drug Side Effect Prediction. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (1) (2023)
Gun Kaynar, Doruk Cakmakci, Caroline Bund, Julien Todeschi, Izzie-Jacques Namer, A. Ercüment Çiçek
PiDeeL: metabolic pathway-informed deep learning model for survival analysis and pathological classification of gliomas. Bioinform. 39 (10) (2023)
Ege Erdogan, Unat Teksen, Mehmet Salih Celiktenyildiz, Alptekin Küpçü, A. Ercüment Çiçek
Defense Mechanisms Against Training-Hijacking Attacks in Split Learning. CoRR (2023)
Serhan Yilmaz, Mohamad Fakhouri, Mehmet Koyutürk, A. Ercüment Çiçek, Oznur Tastan
Uncovering complementary sets of variants for predicting quantitative phenotypes. Bioinform. 38 (4) (2022)
Doruk Cakmakci, Gun Kaynar, Caroline Bund, Martial Piotto, Francois Proust, Izzie-Jacques Namer, A. Ercüment Çiçek
Targeted metabolomics analyses for brain tumor margin assessment during surgery. Bioinform. 38 (12) (2022)
Ege Erdogan, Alptekin Küpçü, A. Ercüment Çiçek
SplitGuard: Detecting and Mitigating Training-Hijacking Attacks in Split Learning. WPES@CCS (2022)
Ege Erdogan, Alptekin Küpçü, A. Ercüment Çiçek
UnSplit: Data-Oblivious Model Inversion, Model Stealing, and Label Inference Attacks against Split Learning. WPES@CCS (2022)
Oya Ekin Karasan, Alper Sen, Banu Tiryaki, A. Ercüment Çiçek
A unifying network modeling approach for codon optimization. Bioinform. 38 (16) (2022)
Halil Ibrahim Kuru, Oznur Tastan, A. Ercüment Çiçek
MatchMaker: A Deep Learning Framework for Drug Synergy Prediction. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (4) (2022)
Ilayda Beyreli, Oguzhan Karakahya, A. Ercüment Çiçek
DeepND: Deep multitask learning of gene risk for comorbid neurodevelopmental disorders. Patterns 3 (7) (2022)
Ege Erdogan, Alptekin Küpçü, A. Ercüment Çiçek
SplitGuard: Detecting and Mitigating Training-Hijacking Attacks in Split Learning. CoRR (2021)
Ege Erdogan, Alptekin Küpçü, A. Ercüment Çiçek
SplitGuard: Detecting and Mitigating Training-Hijacking Attacks in Split Learning. IACR Cryptol. ePrint Arch. 2021 (2021)
Gizem Caylak, Oznur Tastan, A. Ercüment Çiçek
A Tool for Detecting Complementary Single Nucleotide Polymorphism Pairs in Genome-Wide Association Studies for Epistasis Testing. J. Comput. Biol. 28 (4) (2021)
Furkan Ozden, Metin Can Siper, Necmi Acarsoy, Tugrulcan Elmas, Bryan Marty, Xinjian Qi, A. Ercüment Çiçek
DORMAN: Database of Reconstructed MetAbolic Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (4) (2021)
Serhan Yilmaz, Oznur Tastan, A. Ercüment Çiçek
SPADIS: An Algorithm for Selecting Predictive and Diverse SNPs in GWAS. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (3) (2021)
Ege Erdogan, Alptekin Küpçü, A. Ercüment Çiçek
UnSplit: Data-Oblivious Model Inversion, Model Stealing, and Label Inference Attacks Against Split Learning. IACR Cryptol. ePrint Arch. 2021 (2021)
Ege Erdogan, Alptekin Küpçü, A. Ercüment Çiçek
UnSplit: Data-Oblivious Model Inversion, Model Stealing, and Label Inference Attacks Against Split Learning. CoRR (2021)
Kerem Ayoz, Erman Ayday, A. Ercüment Çiçek
Genome Reconstruction Attacks Against Genomic Data-Sharing Beacons. Proc. Priv. Enhancing Technol. 2021 (3) (2021)
Gizem Caylak, Oznur Tastan, A. Ercüment Çiçek
Potpourri: An Epistasis Test Prioritization Algorithm via Diverse SNP Selection. J. Comput. Biol. 28 (4) (2021)
E. Onur Karakaslar, Baris Coskun, Hassiba Outilaft, Izzie-Jacques Namer, A. Ercüment Çiçek
Predicting Carbon Spectrum in Heteronuclear Single Quantum Coherence Spectroscopy for Online Feedback During Surgery. IEEE ACM Trans. Comput. Biol. Bioinform. 17 (2) (2020)
Doruk Cakmakci, Emin Onur Karakaslar, Elisa Ruhland, Marie-Pierre Chenard, Francois Proust, Martial Piotto, Izzie Jacques Namer, A. Ercüment Çiçek
Machine learning assisted intraoperative assessment of brain tumor margins using HRMAS NMR spectroscopy. PLoS Comput. Biol. 16 (11) (2020)
Gizem Caylak, A. Ercüment Çiçek
Potpourri: An Epistasis Test Prioritization Algorithm via Diverse SNP Selection. RECOMB (2020)
Kerem Ayoz, Erman Ayday, A. Ercüment Çiçek
Genome Reconstruction Attacks Against Genomic Data-Sharing Beacons. CoRR (2020)
Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercüment Çiçek, Can Alkan, Onur Mutlu
Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm. Bioinform. 36 (12) (2020)
Utku Norman, A. Ercüment Çiçek
ST-Steiner: a spatio-temporal gene discovery algorithm. Bioinform. 35 (18) (2019)
Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercüment Çiçek, Can Alkan, Onur Mutlu
Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm. CoRR (2019)
Nora von Thenen, Erman Ayday, A. Ercüment Çiçek
Re-identification of individuals in genomic data-sharing beacons via allele inference. Bioinform. 35 (3) (2019)
Erin Avllazagaj, Erman Ayday, A. Ercüment Çiçek
Privacy-Related Consequences of Turkish Citizen Database Leak. CoRR (2016)
A. Ercüment Çiçek, Kathryn Roeder, Gultekin Özsoyoglu
MIRA: mutual information-based reporter algorithm for metabolic networks. Bioinform. 31 (7) (2015)
A. Ercüment Çiçek, Mehmet Ercan Nergiz, Yücel Saygin
Ensuring location diversity in privacy-preserving spatio-temporal data publishing. VLDB J. 23 (4) (2014)
A. Ercüment Çiçek, Kathryn Roeder, Gultekin Özsoyoglu
MIRA: mutual information-based reporter algorithm for metabolic networks. Bioinform. 30 (12) (2014)
Stephen R. Johnson, Xinjian Qi, A. Ercüment Çiçek, Gultekin Özsoyoglu
: An iPad interface for KEGG metabolic pathways. Health Inf. Sci. Syst. 1 (1) (2013)
Sarp A. Coskun, A. Ercüment Çiçek, Nicola Lai, Ranjan K. Dash, Z. Meral Özsoyoglu, Gultekin Özsoyoglu
An online model composition tool for system biology models. BMC Syst. Biol. 7 (2013)
A. Ercüment Çiçek, Ilya Bederman, Leigh Henderson, Mitchell L. Drumm, Gultekin Özsoyoglu
ADEMA: An Algorithm to Determine Expected Metabolite Level Alterations Using Mutual Information. PLoS Comput. Biol. 9 (1) (2013)
A. Ercüment Çiçek, Xinjian Qi, Ali Cakmak, Stephen R. Johnson, Xu Han, Sami Alshalwi, Gultekin Özsoyoglu
PathCase-MAW: An Online Metabolic Network Analysis Workbench. BCB (2013)
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
PathCase-SB: integrating data sources and providing tools for systems biology research. BMC Syst. Biol. 6 (2012)
Mehmet Ercan Nergiz, A. Ercüment Çiçek, Thomas Pedersen, Yücel Saygin
A Look-Ahead Approach to Secure Multiparty Protocols. IEEE Trans. Knowl. Data Eng. 24 (7) (2012)
A. Ercüment Çiçek, Gultekin Özsoyoglu
Observation Conflict Resolution in steady-State metabolic Network Dynamics Analysis. J. Bioinform. Comput. Biol. 10 (1) (2012)
Ali Cakmak, Xinjian Qi, A. Ercüment Çiçek, Ilya Bederman, Leigh Henderson, Mitchell L. Drumm, Gultekin Özsoyoglu
A New metabolomics Analysis Technique: steady-State metabolic Network Dynamics Analysis. J. Bioinform. Comput. Biol. 10 (1) (2012)
Ali Cakmak, Xinjian Qi, A. Ercüment Çiçek, Gultekin Özsoyoglu
Computational interpretation of metabolomics measurements: steady-state metabolic network dynamics analysis. BCB (2011)
Ali Cakmak, Xinjian Qi, Sarp A. Coskun, Mitali Das, En Cheng, A. Ercüment Çiçek, Nicola Lai, Gultekin Özsoyoglu, Z. Meral Özsoyoglu
PathCase-SB architecture and database design. BMC Syst. Biol. 5 (2011)
A. Ercüment Çiçek, Gultekin Özsoyoglu
Resolving observation conflicts in steady state metabolic network dynamics analysis. BCB (2011)