Publications

JOURNAL PAPERS

Metabolomic characterization of human hippocampus from drug resistant epilepsy with mesial temporal seizure
Epilepsia 2018, in press.
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, Moussallieh FM, Cicek AE, De Sèze J, Namer IJ

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

BMC Medicine 2017, 15:56.
Battini S, Faitot F, Imperiale A, Cicek AE, Heimburger C, Averous G, Bachellier P, Namer IJ
Featured article on BMC Medicine Vol 15.
Watch the video abstract prepared by BMC Medicine 

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, Pencreach E, Lasthaus C, Jannier S, Guenot D, Namer IJ, Jones C

k-Shell decomposition reveals structural properties of gene co-expression network for neurodevelopment
Turkish Journal of Biology 2017, 41: 333-341.
Cicek AE

Gene Expression Elucidates Functional Impact of Polygenic Risk for Schizophrenia
Nature Neuroscience 2016, 19(11):1442-1453
Fromer M, Roussos P, Sieberts S, Johnson J,Kavanagh D, Perumal T, Ruderfer D, Oh EC, Topol A, Shah H, Klei L, Kramer R, Pinto D, Gumus ZH, Cicek AE, Dang KK, Browne A, Lu C, Xie L, Readhead B, Stahl EA, Parvizi M, Hamamsy T, Fullard JF, Wang Y, Mahajan MC, Derry JM, Dudley J, Hemby S, Logsdon B, Talbot K, Raj T, Bennett D, De Jager P, Zhu J, Zhang B, Sullivan PF, Chess A, Purcell SM, Shinobu L, Mangravite L, Toyoshiba H, Gur RE, Hahn C, Lewis D, Haroutunian V, Peters MA, Liska BK, Buxbaum J, Schadt EE, Hirai K,  Roeder K, Brennand K, Katsanis N, Dominici E, Devlin B, Sklar P.

High-Resolution Magic Angle Spinning 1H Nuclear Magnetic Resonance Spectroscopy Metabolomics of hyperfunctioning parathyroid glands
SURGERY 2016, 160(2): 384-94.
Battini S, Imperiale A, Taieb D, Elbayed K, Cicek AE, Sebag F, Brunaud L, Namer IJ
Described as "significant" by the editorial commentary.

De novo ChIP-seq analysis
Genome Biology 2015, 16:205.
He X*, Cicek AE*, Wang Y*, Schulz M, Le H, Bar-Joseph Z
(*) co-first authors

Insights into autism spectrum disorder genomic architecture and biology from 71 risk loci
Neuron 2015, 87(6):1215–33.
Sanders SJ, He X, Willsey J ,Ercan-Sencicek GA, Samocha KE, Cicek AE, Murtha MT, Bal VH, Bishop SH, Dong S, Goldberg AP, Jinlu C, Keaney III JF, Klei L, Mandell JD, de Luca DM, Poultney CS, Robinson EB, Smith L, Su MY, Teran NA, Walker MF, Werling DM, Beaudet AL, Cantor RM, Fombonne E, Geschwind DH, Grice DE, Lord C, Lowe JK, Mane SM, Martin DM, Morrow EM, Talkowski ME, Sutcliffe JS, Walsh CA, Yu TW, ASC Consortium, Ledbetter DH, Martin CL, Cook EH, Buxbaum JD, Daly MJ, Devlin B, Roeder K, State MW

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, Moussallieh 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, Taïeb D

Synaptic, transcriptional, and chromatin genes disrupted in autism
NATURE 2014. 515(7526):209-15
De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Cicek A.E., Kou Y, Liu L, Fromer M, Walker S, Singh T, Klei L, Kosmicki J, Shih-Chen F, Aleksic B,Biscaldi M, Bolton PF, Brownfeld JM, Cai J, Campbell NG, Carracedo A, Chahrour MH, Chiocchetti AG, Coon H, Crawford EL, Curran SR, Dawson G, Duketis E,Fernandez BA, Gallagher L, Geller E, Guter SJ, Hill RS, Ionita-Laza J, Jimenz Gonzalez P, Kilpinen H, Klauck SM, Kolevzon A, Lee I, Lei I, Lei J, Lehtimäki T, Lin CF, Ma'ayan A, Marshall CR, McInnes AL, Neale B, Owen MJ, Ozaki N, Parellada M, Parr JR, Purcell S, Puura K, Rajagopalan D, Rehnström K, Reichenberg A,Sabo A, Sachse M, Sanders SJ, Schafer C, Schulte-Rüther M, Skuse D, Stevens C, Szatmari P, Tammimies K, Valladares O, Voran A, Li-San W, Weiss LA,Willsey AJ, Yu TW, Yuen RK; DDD Study; Homozygosity Mapping Collaborative for Autism; UK10K Consortium, Cook EH, Freitag CM, Gill M, Hultman CM,Lehner T, Palotie A, Schellenberg GD, Sklar P, State MW, Sutcliffe JS, Walsh CA, Scherer SW, Zwick ME, Barett JC, Cutler DJ, Roeder K, Devlin B, Daly MJ,Buxbaum JD.
Highlighted in the news by CNN, Time, NBC, NPR.

An Online System for Metabolic Network Analysis
DATABASE: The Journal of Biological Databases and Curation 2014, doi:10.1093/database/bau091
Cicek AE, Qi X, Cakmak A, Johnson SR, Han X, Alshalwi S, Ozsoyoglu G, Ozsoyoglu M

MIRA: Mutual Information-based Reporter Algorithm for Metabolic Networks
Bioinformatics 2014, 30 (12): i175-i184
Cicek AE, Roeder K, Ozsoyoglu 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, Willsey 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, Ozsoyoglu G

Ensuring Location Diversity in Privacy Preserving Spatio-Temporal Data Publishing*
VLDB Journal 2013, 23(4):609-625.
Cicek AENergiz ME, Saygin Y

An Online Model Composition Tool for Systems Biology Models
BMC Systems Biology 2013, 7:88.
Coskun SA, Cicek AELai N, Dash RK, Ozsoyoglu ZM, Ozsoyoglu G

iPathCase-KEGG: An iPad interface for KEGG metabolic pathways
Health Information Science and Systems 2013, 1:4.
Johnson SR, Qi X, Cicek AEOzsoyoglu 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, Ozsoyoglu G, Ozsoyoglu ZM

A Look Ahead Approach to Secure Multi-Party Protocols
IEEE Transactions on Knowledge and Data Engineering (TKDE) 2012, 24(7):1170-85.
Nergiz M. E., Cicek A. E.Pedersen T. B., Saygin Y.

A New Metabolomics Analysis Technique: Steady State Metabolic Network Dynamics Analysis
Journal of Bioinformatics and Computational Biology 2012, 10:(1), 1240003
Cakmak A., Qi X., Cicek A.E., Bederman I., Prasac L. Drumm M., Ozsoyoglu G.

Observation Conflict Resolution in Steady State Metabolic Network Dynamics Analysis
Journal of Bioinformatics and Computational Biology 2012, 10:(1), 1240004.
Cicek AE, Ozsoyoglu 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, Jadeja R, Syed S, Dash RK, Lai N, Özsoyoğlu G, Özsoyoğlu 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, Ozsoyoglu ZM, Ozsoyoglu G

Operational Variable Job Scheduling with Eligibility Constraints
Journal of Technological and Economic Development of Economy, 2009, Vol. 15, N 2.
Eliiyi DT, Korkmaz AG, Cicek AE

CONFERENCE PAPERS

Inference Attacks Against Genomic Data-Sharing Beacons
Genome Privacy and Security (GenoPri 2017)
von Thenen N, Ayday E*, Cicek AE*

Privacy-Related Consequences of Turkish Citizen Database Leak
International Workshop on Inference and Privacy in a Hyperconnected World 2016 (INFER 2016)
Avllazagaj E, Ayday E*, Cicek AE*

MIRA: Mutual Information-based Reporter Algorithm for Metabolic Networks
22nd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2014).
Cicek AE, Roeder K, Ozsoyoglu G

PathCase-MAW:  An Online Metabolic Network Analysis Workbench 
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, Ozsoyoglu G

Computational Interpretation of Metabolomics Measurements: Steady-State Metabolic Network Dynamics Analysis 
Proceedings of  2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine  (ACM BCB 2011),  Aug 1 -3, Chicago, IL. (Short)
Cakmak A, Qi X, Cicek AE, Ozsoyoglu G

Resolving Observation Conflicts in Steady State Metabolic Network Dynamics Analysis 
Proceedings of  2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2011 (ACM BCB 2011),  Aug 1 -3, Chicago, IL. (Short)
Cicek AE, Ozsoyoglu G

Optimal Berth Allocation with Variable Job Scheduling
20th International Euro Mini Conference (EUROPT-2008) Selected Papers, pp. 358-363, Neringa, Lithuania.
Eliiyi DT, Korkmaz AG, Cicek AE

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