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Items: 33

1.

Metabolomic Profile of Aggressive Meningiomas by Using High-Resolution Magic Angle Spinning Nuclear Magnetic Resonance.

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

J Proteome Res. 2019 Nov 13. doi: 10.1021/acs.jproteome.9b00521. [Epub ahead of print]

PMID:
31679342
2.

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

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

Clin Nucl Med. 2019 Dec;44(12):936-942. doi: 10.1097/RLU.0000000000002765.

PMID:
31524681
3.

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

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

Nat Commun. 2019 Jul 30;10(1):3399. doi: 10.1038/s41467-019-11284-9.

4.

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

Bund C, Guergova-Kuras M, Cicek AE, Moussallieh FM, Dali-Youcef N, Piotto M, Schneider P, Heller R, Entz-Werle N, Lhermitte B, Chenard MP, Schott R, Proust F, Noël G, Namer IJ.

Metabolomics. 2019 Apr 29;15(5):69. doi: 10.1007/s11306-019-1522-5.

PMID:
31037432
5.

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

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

HPB (Oxford). 2019 Oct;21(10):1354-1361. doi: 10.1016/j.hpb.2019.02.008. Epub 2019 Mar 23.

PMID:
30914156
6.

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

Norman U, Cicek AE.

Bioinformatics. 2019 Sep 15;35(18):3433-3440. doi: 10.1093/bioinformatics/btz110.

PMID:
30759247
7.

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

Firtina C, Bar-Joseph Z, Alkan C, Cicek AE.

Nucleic Acids Res. 2018 Nov 30;46(21):e125. doi: 10.1093/nar/gky724.

8.

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

von Thenen N, Ayday E, Cicek AE.

Bioinformatics. 2019 Feb 1;35(3):365-371. doi: 10.1093/bioinformatics/bty643.

PMID:
30052749
9.

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

Liu Y, Liang Y, Cicek AE, Li Z, Li J, Muhle RA, Krenzer M, Mei Y, Wang Y, Knoblauch N, Morrison J, Zhao S, Jiang Y, Geller E, Ionita-Laza I, Wu J, Xia K, Noonan JP, Sun ZS, He X.

Am J Hum Genet. 2018 Jun 7;102(6):1031-1047. doi: 10.1016/j.ajhg.2018.03.023. Epub 2018 May 10.

10.

Metabolomics approaches in experimental allergic encephalomyelitis.

Battini S, Bund C, Moussallieh FM, Çiçek AE, De Sèze J, Namer IJ.

J Neuroimmunol. 2018 Jan 15;314:94-100. doi: 10.1016/j.jneuroim.2017.11.018. Epub 2017 Dec 2.

PMID:
29224959
11.

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

Nguyen A, Moussallieh FM, Mackay A, Cicek AE, Coca A, Chenard MP, Weingertner N, Lhermitte B, Letouzé E, Guérin E, Pencreach E, Jannier S, Guenot D, Namer IJ, Jones C, Entz-Werlé N.

Oncotarget. 2017 Mar 23;8(42):71597-71617. doi: 10.18632/oncotarget.16500. eCollection 2017 Sep 22.

12.

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

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

BMC Med. 2017 Mar 16;15(1):56. doi: 10.1186/s12916-017-0810-z.

13.

Gene expression elucidates functional impact of polygenic risk for schizophrenia.

Fromer M, Roussos P, Sieberts SK, Johnson JS, Kavanagh DH, Perumal TM, Ruderfer DM, Oh EC, Topol A, Shah HR, Klei LL, Kramer R, Pinto D, Gümüş ZH, Cicek AE, Dang KK, Browne A, Lu C, Xie L, Readhead B, Stahl EA, Xiao J, Parvizi M, Hamamsy T, Fullard JF, Wang YC, Mahajan MC, Derry JM, Dudley JT, Hemby SE, Logsdon BA, Talbot K, Raj T, Bennett DA, De Jager PL, Zhu J, Zhang B, Sullivan PF, Chess A, Purcell SM, Shinobu LA, Mangravite LM, Toyoshiba H, Gur RE, Hahn CG, Lewis DA, Haroutunian V, Peters MA, Lipska BK, Buxbaum JD, Schadt EE, Hirai K, Roeder K, Brennand KJ, Katsanis N, Domenici E, Devlin B, Sklar P.

Nat Neurosci. 2016 Nov;19(11):1442-1453. doi: 10.1038/nn.4399. Epub 2016 Sep 26.

14.

High-resolution magic angle spinning (1)H nuclear magnetic resonance spectroscopy metabolomics of hyperfunctioning parathyroid glands.

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

Surgery. 2016 Aug;160(2):384-94. doi: 10.1016/j.surg.2016.03.002. Epub 2016 Apr 20.

PMID:
27106795
15.

Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci.

Sanders SJ, He X, Willsey AJ, Ercan-Sencicek AG, Samocha KE, Cicek AE, Murtha MT, Bal VH, Bishop SL, Dong S, Goldberg AP, Jinlu C, Keaney JF 3rd, Klei L, Mandell JD, Moreno-De-Luca D, Poultney CS, Robinson EB, Smith L, Solli-Nowlan T, 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; Autism Sequencing Consortium, Ledbetter DH, Martin CL, Cook EH, Buxbaum JD, Daly MJ, Devlin B, Roeder K, State MW.

Neuron. 2015 Sep 23;87(6):1215-1233. doi: 10.1016/j.neuron.2015.09.016.

16.

De novo ChIP-seq analysis.

He X, Cicek AE, Wang Y, Schulz MH, Le HS, Bar-Joseph Z.

Genome Biol. 2015 Sep 23;16:205. doi: 10.1186/s13059-015-0756-4.

17.

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

Cicek AE, Roeder K, Ozsoyoglu G.

Bioinformatics. 2015 Apr 1;31(7):1160. doi: 10.1093/bioinformatics/btv081. Epub 2015 Mar 10. No abstract available.

18.

A multidisciplinary approach to expand the use of pediatric ECLS systems in Turkey.

Onan İS, Haydin S, Ündar A, Yalındağ-Öztürk MN, Demirkol D, Kalkan G, Ceyran H, Atay Y, Şaşmazel A, Karacı AR, Şevketoğlu E, Köroğlu T, Altın HF, Yazıcı P, Yıldızdaş D, Çicek AE, Ödemiş E, Akçevin A, Bakır İ.

Artif Organs. 2015 Jan;39(1):7-13. doi: 10.1111/aor.12374. No abstract available.

PMID:
25626574
19.

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

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.

Neoplasia. 2015 Jan;17(1):55-65. doi: 10.1016/j.neo.2014.10.010.

20.

Synaptic, transcriptional and chromatin genes disrupted in autism.

De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Cicek AE, 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.

Nature. 2014 Nov 13;515(7526):209-15. doi: 10.1038/nature13772. Epub 2014 Oct 29.

21.

An online system for metabolic network analysis.

Cicek AE, Qi X, Cakmak A, Johnson SR, Han X, Alshalwi S, Ozsoyoglu ZM, Ozsoyoglu G.

Database (Oxford). 2014 Sep 29;2014. pii: bau091. doi: 10.1093/database/bau091. Print 2014.

22.

Cost-effective usage of membrane oxygenators in extracorporeal membrane oxygenation in infants.

Özyüksel A, Ersoy C, Akçevin A, Türkoğlu H, Çiçek AE, Kahraman A, Kayhan B, Cantürk E.

Perfusion. 2015 Apr;30(3):239-42. doi: 10.1177/0267659114540025. Epub 2014 Jun 25.

PMID:
24965913
23.

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

Cicek AE, Roeder K, Ozsoyoglu G.

Bioinformatics. 2014 Jun 15;30(12):i175-84. doi: 10.1093/bioinformatics/btu290. Erratum in: Bioinformatics. 2015 Apr 1;31(7):1160.

24.

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

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

Mol Autism. 2014 Mar 6;5(1):22. doi: 10.1186/2040-2392-5-22.

25.

An online model composition tool for system biology models.

Coskun SA, Cicek AE, Lai N, Dash RK, Ozsoyoglu ZM, Ozsoyoglu G.

BMC Syst Biol. 2013 Sep 5;7:88. doi: 10.1186/1752-0509-7-88.

26.

ADEMA: an algorithm to determine expected metabolite level alterations using mutual information.

Cicek AE, Bederman I, Henderson L, Drumm ML, Ozsoyoglu G.

PLoS Comput Biol. 2013;9(1):e1002859. doi: 10.1371/journal.pcbi.1002859. Epub 2013 Jan 17.

27.

iPathCase(KEGG): An iPad interface for KEGG metabolic pathways.

Johnson SR, Qi X, Cicek AE, Ozsoyoglu G.

Health Inf Sci Syst. 2013 Jan 10;1:4. doi: 10.1186/2047-2501-1-4. eCollection 2013.

28.

Observation conflict resolution in steady-state metabolic network dynamics analysis.

Cicek AE, Ozsoyoglu G.

J Bioinform Comput Biol. 2012 Feb;10(1):1240004. doi: 10.1142/S0219720012400045.

PMID:
22809305
29.

A new metabolomics analysis technique: steady-state metabolic network dynamics analysis.

Cakmak A, Qi X, Cicek AE, Bederman I, Henderson L, Drumm M, Ozsoyoglu G.

J Bioinform Comput Biol. 2012 Feb;10(1):1240003. doi: 10.1142/S0219720012400033.

30.

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

Coskun SA, Qi X, Cakmak A, Cheng E, Cicek AE, Yang L, Jadeja R, Dash RK, Lai N, Ozsoyoglu G, Ozsoyoglu ZM.

BMC Syst Biol. 2012 Jun 14;6(1):67. doi: 10.1186/1752-0509-6-67.

31.

Istanbul symposium on neonatal and pediatric cardiopulmonary bypass procedures.

Ündar A, Alkan-Bozkaya T, Palanzo D, Ersayin-Kantas H, Chin C, Ödemiş E, Pekkan K, Ağirbaşli MA, Türköz A, Türköz R, Haydin S, Erek E, Yalçınbaş YK, Şaşmazel A, Karacı AR, Erkan H, Çicek AE, Bakır Í, Sarıoğlu T, Akçevin A, Aytaç A.

Artif Organs. 2012 May;36(5):463-6. doi: 10.1111/j.1525-1594.2012.01455.x. No abstract available.

PMID:
22568504
32.

Istanbul Symposiums on Pediatric Extracorporeal Life Support Systems.

Undar A, Haydin S, Yivli P, Weaver B, Pauliks L, Cicek AE, Erek E, Saşmazel A, Ağirbaşli MA, Alkan-Bozkaya T, Akçevin A, Bakir I.

Artif Organs. 2011 Nov;35(11):983-8. doi: 10.1111/j.1525-1594.2011.01368.x. No abstract available.

PMID:
22097976
33.

PathCase-SB architecture and database design.

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

BMC Syst Biol. 2011 Nov 9;5:188. doi: 10.1186/1752-0509-5-188.

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