A. Ercüment Çiçek

According to our database, A. Ercüment Çiçek authored at least 36 papers between 2011 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

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., October, 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

Defense Mechanisms Against Training-Hijacking Attacks in Split Learning.

Ege Erdogan, Unat Teksen, Mehmet Salih Celiktenyildiz, Alptekin Küpçü, A. Ercüment Çiçek

CoRR, 2023

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

DeepND: Deep multitask learning of gene risk for comorbid neurodevelopmental disorders.

Ilayda Beyreli, Oguzhan Karakahya, A. Ercüment Çiçek

Patterns, 2022

Uncovering complementary sets of variants for predicting quantitative phenotypes.

Serhan Yilmaz, Mohamad Fakhouri, Mehmet Koyutürk, A. Ercüment Çiçek, Öznur Tastan

Bioinform., 2022

A unifying network modeling approach for codon optimization.

Oya Ekin Karasan, Alper Sen, Banu Tiryaki, A. Ercüment Çiçek

Bioinform., 2022

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

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

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

Genome Reconstruction Attacks Against Genomic Data-Sharing Beacons.

Kerem Ayoz, Erman Ayday, A. Ercüment Çiçek

Proc. Priv. Enhancing Technol., 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

Potpourri: An Epistasis Test Prioritization Algorithm via Diverse SNP Selection.

Gizem Caylak, Öznur Tastan, A. Ercüment Çiçek

J. Comput. Biol., 2021

SplitGuard: Detecting and Mitigating Training-Hijacking Attacks in Split Learning.

Ege Erdogan, Alptekin Küpçü, A. Ercüment Çiçek

IACR Cryptol. ePrint Arch., 2021

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

2020

Predicting Carbon Spectrum in Heteronuclear Single Quantum Coherence Spectroscopy for Online Feedback During Surgery.

E. Onur Karakaslar, Baris Coskun, Hassiba Outilaft, Izzie-Jacques Namer, A. Ercüment Çiçek

IEEE ACM Trans. Comput. Biol. 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

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

Potpourri: An Epistasis Test Prioritization Algorithm via Diverse SNP Selection.

Gizem Caylak, A. Ercüment Çiçek

Proceedings of the Research in Computational Molecular Biology, 2020

2019

Re-identification of individuals in genomic data-sharing beacons via allele inference.

Nora von Thenen, Erman Ayday, A. Ercüment Çiçek

Bioinform., 2019

ST-Steiner: a spatio-temporal gene discovery algorithm.

Utku Norman, A. Ercüment Çiçek

Bioinform., 2019

2016

Privacy-Related Consequences of Turkish Citizen Database Leak.

Erin Avllazagaj, Erman Ayday, A. Ercüment Çiçek

CoRR, 2016

2014

Ensuring location diversity in privacy-preserving spatio-temporal data publishing.

A. Ercüment Çiçek, Mehmet Ercan Nergiz, Yücel Saygin

VLDB J., 2014

MIRA: mutual information-based reporter algorithm for metabolic networks.

A. Ercüment Çiçek, Kathryn Roeder, Gultekin Özsoyoglu

Bioinform., 2014

An online system for metabolic network analysis.

Abdullah Ercument Cicek, Xinjian Qi, Ali Cakmak, Stephen R. Johnson, Xu Han, Sami Alshalwi, Zehra Meral Özsoyoglu, Gultekin Özsoyoglu

Database J. Biol. Databases Curation, 2014

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

iPathCase^KEGG: An iPad interface for KEGG metabolic pathways.

Stephen R. Johnson, Xinjian Qi, A. Ercüment Çiçek, Gultekin Özsoyoglu

Health Inf. Sci. Syst., 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

PathCase-MAW: An Online Metabolic Network Analysis Workbench.

A. Ercüment Çiçek, Xinjian Qi, Ali Cakmak, Stephen R. Johnson, Xu Han, Sami Alshalwi, Gultekin Özsoyoglu

Proceedings of the ACM Conference on Bioinformatics, 2013

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

Observation Conflict Resolution in steady-State metabolic Network Dynamics Analysis.

A. Ercüment Çiçek, Gultekin Özsoyoglu

J. Bioinform. Comput. Biol., 2012

A New metabolomics Analysis Technique: steady-State metabolic Network Dynamics Analysis.

Ali Cakmak, Xinjian Qi, A. Ercüment Çiçek, Ilya Bederman, Leigh Henderson, Mitchell L. Drumm, Gultekin Özsoyoglu

J. Bioinform. Comput. Biol., 2012

PathCase-SB: integrating data sources and providing tools for systems biology research.

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

BMC Syst. Biol., 2012

2011

PathCase-SB architecture and database design.

Ali Cakmak, Xinjian Qi, Sarp A. Coskun, Mitali Das, En Cheng, A. Ercüment Çiçek, Nicola Lai, Gultekin Özsoyoglu, Z. Meral Özsoyoglu

BMC Syst. Biol., 2011

Resolving observation conflicts in steady state metabolic network dynamics analysis.

A. Ercüment Çiçek, Gultekin Özsoyoglu

Proceedings of the ACM International Conference on Bioinformatics, 2011

Computational interpretation of metabolomics measurements: steady-state metabolic network dynamics analysis.

Ali Cakmak, Xinjian Qi, A. Ercüment Çiçek, Gultekin Özsoyoglu

Proceedings of the ACM International Conference on Bioinformatics, 2011