Publications

arXiv/bioRxiv/medRxiv

A Reinforcement Learning-based Approach for Dynamic Privacy Protection in Genomic Data Sharing Beacons

bioRxiv 2024

Poorghaffar-aghdam M, Shukueian-tabrizi S, Ayoz K, Ayday E, Sav S*, Cicek AE*

LYCEUM: Learning to call copy number variants on low coverage ancient genomes

bioRxiv 2024

Yilmaz MA, Ceylan AA, Kaynar G, Cicek AE

RNAGEN: A generative adversarial network-based model to generate synthetic RNA sequences to target proteins

bioRxiv 2023

Ozden F, Barazandeh S, Akboga D, Seker UOS*, Cicek AE*

UTRGAN: Learning to Generate 5’ UTR Sequences for Optimized Translation Efficiency and Gene Expression

bioRxiv 2023

Barazandeh S, Ozden F, Hincer A, Seker UOS*, Cicek AE*

JOURNAL PAPERS

SplitOut: Out-of-the-Box Training-Hijacking Detection in Split Learning via Outlier Detection

In the Proceedings of the 23rd International Conference on Cryptology And Network Security (CANS) 2024, accepted.

Erdogan E, Teksen U, Celiktenyildiz MS, Kupcu A*, Cicek AE*

From Cell-Lines to Cancer Patients: Personalized Drug Synergy Prediction

Bioinformatics 2024, 40(5), btae134,

Kuru HI, Cicek AE*, Tastan O*

Deep convolutional neural networks for PET super-resolution

In the Proceedings of the SPIE Medical Imaging 2024, 12926-113.

Ozaltan KC, Namer IJ, Cicek AE*, Aksoy S*

ECOLE: Learning to call copy number variants on whole exome sequencing data

Nature Communications 2023, 15, 132.

Mandiracioglu B*, Ozden F*, Kaynar G, Yilmaz MA, Alkan C, Cicek AE

DeepSide: A Deep Learning Framework for Side Effect Prediction

IEEE/ACM Transactions on Computational Biology and Bioinformatics 2023, 20(1), 330-339.

Selected Talk at ECML-PKDD PharML Workshop 2021

Uner C, Kuru HI, Cinbis G, Tastan O*, Cicek AE*

PiDeeL: Metabolic Pathway-Informed Deep Learning Model for Survival Analysis and Pathological Classification of Gliomas

Bioinformatics 2023, 39(11), btad684,

Kaynar G*, Cakmakci D*, Bund C, Todeschi J, Namer IJ, Cicek AE

Polishing Copy Number Variant Calls on Exome Sequencing Data via Deep Learning

Genome Research 2022, 32 (6), 1170-1182.

Highlight Talk at ISMB 2021 - 29th Annual International Conference on Intelligent Systems for Molecular Biology (HitSeq)

Ozden F, Alkan C*, Cicek AE*

A Unifying Network Modeling Approach for Codon Optimization

Bioinformatics 2022, 38, 16, 3935–3941.

Karasan O, Sen A, Tiryaki B, Cicek AE

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

Patterns 2022, 3, 100524.

Highlight Talk at ISMB 2021 - 29th Annual International Conference on Intelligent Systems for Molecular Biology (MLCSB)

Beyreli I, Karakahya O, Cicek AE

Targeted Metabolomics Analyses for Brain Tumor Margin Assessment During Surgery

Bioinformatics 2022, 38 (12), 3238–3244.

Cakmakci D*, Kaynar G*, Bund C, Piotto M, Proust F, Namer IJ, Cicek AE

Uncovering complementary sets of variants for the prediction of quantitative phenotypes

Bioinformatics 2022, 38(4), 908–917.

Yilmaz S, Fakhouri M, Koyuturk M, Cicek AE*, Tastan O*

UnSplit: Data-Oblivious Model Inversion, Model Stealing, and Label Inference Attacks Against Split Learning

WPES'22: Proceedings of the 21st Workshop on Privacy in the Electronic Society, 115–124.

Erdogan E, Kupcu A*, Cicek AE*

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

WPES'22: Proceedings of the 21st Workshop on Privacy in the Electronic Society, 125–137.

Erdogan E, Kupcu A*, Cicek AE*

MatchMaker: A Deep Learning Framework for Drug Synergy Prediction

IEEE/ACM Transactions on Computational Biology and Bioinformatics 2022, 19,4.

Highlight Talk at ISMB 2021 - 29th Annual International Conference on Intelligent Systems for Molecular Biology(MLCSB)

Kuru HI, Tastan O*, Cicek AE*

AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data

Genome Biology 2021, 22, 252.

Thibadeau A*, Eroglu A*, Lawlor N, Nehar-belaid D, Kursawe R, Marches R, Kuchel GA, Banchereau J, Stitzel ML, Cicek AE, Ucar D

Robust Inference of Kinase Activity using Functional Networks

Nature Communications 2021, 12, 1177.

Best Paper Award - RECOMB 2021 - 25th International Conference on Research in Computational Molecular Biology

Yilmaz S, Ayati M, Schlatzer D, Cicek AE, Chance M, Koyuturk M

Genome Reconstruction Attacks Against Genomic Data-Sharing Beacons

Proceedings on Privacy Enhancing Technologies (Po-PETS) 2021, (3):28–48

Ayoz K, Ayday E*, Cicek AE*

Genetic Circuits Combined with Machine Learning Provides Fast Responding Living Sensors

Biosensors and Bioelectronics 2021, 187, 113028.

Saltepe B, Bozkurt EU, Gungen M, Cicek AE*, Seker UOS*

Potpourri: An Epistasis Test Prioritization Algorithm via Diverse SNP Selection

Journal of Computational Biology 2021, 28(4), 365–377.

In Proceedings of RECOMB 2020 - 24th International Conference on Research in Computational Molecular Biology

Caylak G, Tastan O, Cicek AE

A tool for detecting complementary SNP pairs in GWAS for epistasis testing

Journal of Computational Biology 2021, 28(4), 378–380.

In Proceedings of RECOMB 2020 - 24th International Conference on Research in Computational Molecular Biology

Caylak G, Tastan O, Cicek AE

De novo missense variants disrupting protein-protein interactions affect risk for autism through gene co-expression and protein networks in neuronal cell types

Molecular Autism 2020, 11:76.

Chen S, Wang J, Cicek AE, Roeder K, Yu H, Devlin B

Machine Learning Assisted Intraoperative Assessment of Brain Tumor Margins Using HRMAS NMR Spectroscopy

PLoS Computational Biology 2020, 16(11): e1008184.

Selected talk in RECOMB-CCB 2020 - 24th International Conference on Research in Computational Molecular Biology Computational Cancer Biology Satellite Meeting

Cakmakci D, Karakaslar EO, Ruhland E, Chenard MP, Proust F, Piotto M, Namer IJ, Cicek AE

The Effect of Kinship in Re-identification Attacks Against Genomic Data Sharing Beacons

Bioinformatics 2020, 36(S2), i903–i910.

In Proceedings of ECCB 2020 - 19th European Conference of Computational Biology and also Selected Talk in GenoPri 2020 - Genome Privacy and Security Workshop

Ayoz K, Ayşen M, Ayday E, Cicek AE

Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm

Bioinformatics 2020, 36(12), 3669-3679.

Fırtına C, Kim JS, Alser M, Senol-cali D, Cicek AE, Alkan C, Mutlu O

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

IEEE/ACM Transactions on Computational Biology and Bioinformatics 2020, 17(2), 719-725.

Karakaslar EO, Coskun B, Outilaft H, Namer IJ, Cicek AE

Matrix metalloproteinase-11 promotes early mouse mammary gland tumor growth through metabolic reprogramming and increased IGF1/AKT/FoxO1 signalling pathway, enhanced ER stress and alteration in mitochondrial UPR

Cancers 2020, 12(9), 2357.

Tan B, Jaulin A, Bund C, Outilaft H, Wendling C, Chenard MP, Alpy F, Cicek AE, Namer IJ, Tomasetto C, Dali-youcef N

Revisiting the complex architecture of ALS in Turkey: Expanding genotypes, shared phenotypes, network analysis and a public variant database

Human Mutation 2020, 41, e7-e45.

Tunga C, ... ., Norman U, Karakahya O, .... ., Cicek AE, ... .

Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism

CELL 2020, 180 (3), 568-584.

Satterstrom FK, Kosmicki JA, .... ., Norman U, ... ., Cicek AE, Talkowski M, Cutler DJ, Devlin B, Sanders SJ, Roeder K, Daly M, Buxbaum JD

Whole-genome and RNA sequencing reveal variation and transcriptomic coordination in the developing human prefrontal cortex

Cell Reports 2020, 31 (1), 107489

Werling D, ... ., Cicek AE, .... .

Metabolomic profile of aggressive meningiomas by using high-resolution magic angle spinning nuclear magnetic resonance

Journal of Proteome Research, 2020, 19, 1, 292-299

Bender L, Somme F, Ruhland E, Cicek AE, Bund C, Namer IJ

DORMAN: Database Of Reconstructed MetAbolic Networks

IEEE/ACM Transactions on Computational Biology and Bioinformatics 2019, 18(4), 1474-1480.

System

Ozden F*, Siper MC*, Acarsoy N, Elmas T, Marty B, Qi X, Cicek AE

SPADIS: An Algorithm for Selecting Predictive and Diverse SNPs in GWAS

IEEE/ACM Transactions on Computational Biology and Bioinformatics 2019, 18, 1208-1216.

Selected talk at ISMB 2018 - 26th Annual International Conference on Intelligent Systems for Molecular Biology (3D Genome Session). Also read the GenomeWeb article on SPADIS

Yilmaz S, Tastan O*, Cicek AE*

Detailed modeling of positive selection significantly improves detection of cancer driver genes

Nature Communications 2019, 10.

Zhao S, Liu J, Nanga P, Liu Y, Cicek AE, Knoblauch N, He C, Stephens M, He X

ST-Steiner: A Spatio-Temporal Gene Discovery Algorithm

Bioinformatics 2019, 35(18):3433-3440.

Norman U, Cicek AE

What Does Reduced FDG Uptake Mean In High-Grade Gliomas?

Clinical Nuclear Medicine 2019, 44 (12), 936-942.

Bund C, Lhermitte B, Cicek AE, Ruhland E, Proust F, Namer IJ

Metabolomics of small intestine neuroendocrine tumors and related hepatic metastases

Metabolites 2019, 9(12), 300.

Imperiale A, Poncet G, Addeo P, Ruhland E, Roche C, Battini S, Cicek AE, Chenard MP, Hervieu V, Goichot B, Bachellier P, Walter T, Namer IJ

Metabolomic profiling highlights the metabolic bases of acute-on-chronic and post-hepatectomy liver failure

HPB 2019, 21(10), 1354-1361.

Faitot F, Ruhland E, Oncioui C, Besch C, Addeo P, Cicek AE, Bachellier P, Namer IJ

Re-identification of individuals in Genomic Data-Sharing Beacons via Allele Inference

Bioinformatics 2019, 35(3):365-371.

Highlight Talk at ISMB 2018 - 26th Annual International Conference on Intelligent Systems for Molecular Biology and selected talk at GenoPri 2017 - Genome in Privacy and Security Workshop

Thenen NV, Ayday E*, Cicek AE*

An integrated genomic and metabolomic approach for defining survival time in adult oligodendrogliomas patients

Metabolomics 2019, 15 (5), 69.

Bund C, Guergova-kuras M, Cicek AE, Moussalieh FM, Dali-youcef N, Piotto M, Schneider P, Heller R, Entz-werle N, Lhermitte B, Chenard MP, Schott R, Proust F, Noel G, Namer IJ

Hercules: a profile-HMM based error correction algorithm for long reads

Nucleic Acids Research 2018, 46(21):e125.

Highlight Talk at ISMB 2018 - 26th Annual International Conference on Intelligent Systems for Molecular Biology (HitSeq)

Fırtına C, Joseph ZB, Alkan C*, Cicek AE*

A Statistical Framework for Mapping Risk Genes from De Novo Mutations in Whole-Genome-Sequencing Studies

American Journal of Human Genetics 2018, 102(6):1031-1047.

Liu Y, Liang Y, Cicek AE, Li Z, Li J, Muhle RA, Krenzer M, Mei Y, Wang Y, Knoblauch N, Morrison J, He X

Landscape of Conditional eQTL in Dorsolateral Prefrontal Cortex and Co-localization with Schizophrenia GWAS

American Journal of Human Genetics 2018, 102(6):1169-1184.

Dobbyn A, ... ., Cicek AE, .... .

Metabolomic characterization of human hippocampus from drug resistant epilepsy with mesial temporal seizure

Epilepsia 2018, 59(3):607-616.

Detour J, Bund C, Behr C, Cebula H, Cicek AE, Valenti-hirsch M, Lannes B, Lhermitte B, Nehlig A, Kehrli P, Proust F, Hirsch F, Namer IJ

Metabolomics approaches in experimental allergic encephalomyelitis

Journal of Neuroimmunology 2018, 394:94-100.

Battini S, Bund C, Moussalieh FM, Cicek AE, Deseze J, Namer IJ

Metabolomics approach in pancreatic adenocarcinoma: tumor metabolism profiling predicts clinical outcome of patients

BMC Medicine 2017, 15:56, Featured article on BMC Medicine Vol 15.

Watch the video abstract prepared by BMC Medicine

Battini S, Faitot F, Imperiale A, Cicek AE, Heimburger C, Averous G, Bachellier P, Namer IJ

Characterization of the transcriptional and metabolic responses of pediatric high grade gliomas to mTOR-HIF-1α axis inhibition

Oncotarget 2017, doi: 10.18632/oncotarget.16500

Nguyen A, Mackay A, Moussalieh FM, Cicek AE, Coca A, Chenard MP, Weingartner N, Letouze E, Guerin E, Penreach E, Lasthaus C, Jannier S, Guenot D, Namer IJ, Jones C

k-Shell decomposition reveals structural properties of gene co-expression network for neurodevelopment

Cicek AE

Gene Expression Elucidates Functional Impact of Polygenic Risk for Schizophrenia

Nature Neuroscience 2016, 19(11):1442-1453

Fromer M, ... ., Cicek AE, .... .

High-Resolution Magic Angle Spinning 1H Nuclear Magnetic Resonance Spectroscopy Metabolomics of hyperfunctioning parathyroid glands

SURGERY 2016, 160(2): 384-94.

Described as "significant" by the editorial commentary.

Battini S, Imperiale A, Taieb D, Elbayed K, Cicek AE, Sebag F, Brunaud L, Namer IJ

De novo ChIP-seq analysis

Genome Biology 2015, 16:205.

He X, Cicek AE, Wang Y, Schulz M, Le H, Joseph ZB

Insights into autism spectrum disorder genomic architecture and biology from 71 risk loci

Neuron 2015, 87(6):1215–33.

Sanders SJ, ... ., Cicek AE, .... .

Metabolome profiling by HRMAS NMR spectroscopy of pheochromocytomas and paragangliomas detects SDH deficiency: clinical and pathophysiological implications

NEOPLASIA 2015. 17(1):55-65.

Imperiale A, Moussalieh FM, Roche P, Battini S, Cicek AE, Sebag F, Brunaud L, Barlier A, Elbayed K, Loundou A, Bachellier P, Goichot B, Stratakis CA, Pacak K, Namer IJ, Taieb D

Synaptic, transcriptional, and chromatin genes disrupted in autism

NATURE 2014. 515(7526):209-15

Derubeis S, ... ., Cicek AE, .... .

An Online System for Metabolic Network Analysis

DATABASE: The Journal of Biological Databases and Curation 2014, doi:10.1093/database/bau091

In proceedings of ACM International Conference on Bioinformatics, Computational Biology, and Biomedical Informatics (ACM BCB 2013), Sep 22 -25, Washington, DC

Cicek AE, Qi X, Cakmak A, Johnson SR, Han X, Alshalwi S, Ozsoyuoglu G

MIRA: Mutual Information-based Reporter Algorithm for Metabolic Networks

Bioinformatics 2014, 30 (12): i175-i184

In proceedings of ISMB 2014 - 22nd Annual International Conference on Intelligent Systems for Molecular Biology

Cicek AE, Roeder K, Ozsoyuoglu G

DAWN: A framework to identify autism genes and subnetworks using gene expression and genetics

Molecular Autism 2014, 5:22.

Liu L, Lei J, Sanders SJ, Wilsey JA, Kou Y, Cicek AE, Klei L, Lu C, He X, Li M, Muhle RA, Ma'ayan A, Noonan JP, Sestan N, Mcfadden K, State MW, Buxbaum JD, Devlin B, Roeder K

ADEMA: An Algorithm to Determine Expected Metabolite Level Alterations Using Mutual Information

PLoS Computational Biology 2013, 9(1): e1002859.

Cicek AE, Bederman I, Henderson L, Drumm M, Ozsoyuoglu G

Ensuring Location Diversity in Privacy Preserving Spatio-Temporal Data Publishing

VLDB Journal 2013, 23(4):609-625.

Cicek AE, Nergiz ME, Saygin Y

An Online Model Composition Tool for Systems Biology Models

BMC Systems Biology 2013, 7:88.

Coskun SA, Cicek AE, Lai N, Dash RK, Ozsoyuoglu ZM, Ozsoyuoglu G

iPathCase-KEGG: An iPad interface for KEGG metabolic pathways

Health Information Science and Systems 2013, 1:4.

Johnson SR, Qi X, Cicek AE, Ozsoyuoglu G

PathCase-SB: Integrating Data Sources and Providing Tools for Systems Biology Research

BMC Systems Biology 2012, 6:67.

Coskun SA, Qi X, Cakmak A, Cheng E, Cicek AE, Yang L, Dash RK, Lai N, Ozsoyuoglu G, Ozsoyuoglu ZM

A Look Ahead Approach to Secure Multi-Party Protocols

IEEE Transactions on Knowledge and Data Engineering (TKDE) 2012, 24(7):1170-85.

Nergiz ME, Cicek AE, Pedersen TB, Saygin Y

A New Metabolomics Analysis Technique: Steady State Metabolic Network Dynamics Analysis

Journal of Bioinformatics and Computational Biology 2012, 10:(1), 1240003

In proceedings of 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2011 (ACM BCB 2011), Aug 1 -3, Chicago, IL.

Cakmak A, Qi X, Cicek AE, Bederman I, Prasac L, Drumm M, Ozsoyuoglu G

Observation Conflict Resolution in Steady State Metabolic Network Dynamics Analysis

Journal of Bioinformatics and Computational Biology 2012, 10:(1), 1240004.

In proceedings of 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2011 (ACM BCB 2011), Aug 1 -3, Chicago, IL.

Cicek AE, Ozsoyuoglu G

PathCase-SB: Database-Enabled Tools for Regulatory Metabolic Networks

ACM SigBioinformatics Record 2012, 3(2):19-25

Qi X, Coskun SA, Cakmak A, Cheng E, Cicek AE, Das M, Yang L, Jadeya R, Syed S, Dash RK, Lai N, Ozsoyuoglu G, Ozsoyuoglu ZM

PathCase-SB Architecture and Database Design

BMC Systems Biology 2011, 5:188

Cakmak A, Qi X, Coskun SA, Das M, Cheng E, Cicek AE, Lai N, Ozsoyuoglu ZM, Ozsoyuoglu G

Operational Variable Job Scheduling with Eligibility Constraints

Journal of Technological and Economic Development of Economy, 2009, Vol. 15, N 2.

In proceedings of 20th International Euro Mini Conference (EUROPT-2008), Neringa, Lithuania.

Eliiyi DT, Korkmaz AG, Cicek AE

CONFERENCE PAPERS

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