Scientific Publications - 2019

IBG Affiliated: 43 ; * Current Adress IBG :1

Begüm Demirkurt, Gulcin Cakan-Akdogan, Yasar Akdogan. Preparation of albumin nanoparticles in water-in-ionic liquid microemulsions. Journal of Molecular Liquids. 2019 December; 295: 117713. doi:10.1016/j.molliq.2019.111713.

Soheil Akbari, Nur Arslan, Şerif Şentürk, Esra Erdal. Next-Generation Liver Medicine Using Organoid Models. Frontiers in Cell and Developmental Biology-Stem Cell Research. 2019 December; 7: 345. doi:10.3389/fcell.2019.00345.

Karakülah G, Arslan N, Yandım C, Suner A. TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model. PeerJ. 2019 December; 7: e8192. doi:10.7717/peerj.8192.

Yandım C, Karakülah G. Dysregulated expression of repetitive DNA in ER+/HER2- breast cancer. Cancer Genetics. 2019 November; 239: 36-45. doi:10.1016/j.cancergen.2019.09.002.

Azbazdar Y, Ozalp O, Sezgin E, Veerapathiran S, Duncan AL, Sansom MSP, Eggeling C, Wohland T, Karaca E, Ozhan G. More Favorable Palmitic Acid Over Palmitoleic Acid Modification of Wnt3 Ensures Its Localization and Activity in Plasma Membrane Domains. Frontiers in cell and developmental biology. 2019 November; 7: 281. doi:10.3389/fcell.2019.00281.

Arif E. Cetin, and Seda Nur Topkaya. Plasmonic Diffraction Field Pattern Imaging Could Resolve Ultra-Sensitive Bio-Information. ACS PHOTONICS. 2019 November; 6 (11): 2626-2635. doi:10.1021/acsphotonics.9b01076.

Düzgün MB, Theofilatos K, Georgakilas AG, Pavlopoulou A. A Bioinformatic Approach for the Identification of Molecular Determinants of Resistance/Sensitivity to Cancer Thermotherapy. Oxidative medicine and cellular longevity. 2019 November; 2019: 4606219. doi:10.1155/2019/4606219.

Delman M, Avcı ST, Akçok İ, Kanbur T, Erdal E, Çağır A. Antiproliferative activity of (R)-4'-methylklavuzon on hepatocellular carcinoma cells and EpCAM+/CD133+ cancer stem cells via SIRT1 and Exportin-1 (CRM1) inhibition. European Journal of Medicinal Chemistry. 2019 October; 180: 224-237. doi:10.1016/j.ejmech.2019.07.024.

Shukla, MS; Syed, SH; Boopathi, R; Ben Simon, E; Nahata, S; Ramos, L; Dalkara, D; Moskalenko, C; Travers, A; Angelov, D; Dimitrov, S; Hamiche, A; Bednar, J. Generation of Remosomes by the SWI/SNF Chromatin Remodeler Family. Scientific Reports. 2019 October; 9. doi:10.1038/s41598-019-50572-8.

Soheil Akbari, Gulben Gurhan Sevinc, Nevin Ersoy, Onur Başak, Kübra Kaplan, Kenan Sevinç, Erkin Özel, Berke Sengun, Eray Enustun, Burcu Özçimen,......... Robust, long-term culture of endoderm derived hepatic organoids (eHEPOs) for disease modeling. Stem Cell Reports. 2019 September. doi:10.1016/j.stemcr.2019.08.007.

Sag D, Ayyildiz ZO, Gunalp S, Wingender G. The Role of TRAIL/DRs in the Modulation of Immune Cells and Responses. Cancers. 2019 September; 11 (10): 1469. doi:10.3390/cancers11101469.

Onur Bulut, Anıl Tanburoğlu, Gülşah Bölük, Nurhak Demir, Erden Eren, Ufuk Vurgun, Şermin Genç, Görsev Yener. Examination of IL-1β level as an inflammasome marker in Alzheimer's disease. Neurological Sciences and Neurophysiology. 2019 September; 36 (3): 141-147. doi:10.5152/NSN.2019.10324.

Shome S, Parra RG, Fatima N, Monzon AM, Cuypers B, Moosa Y, Coimbra NDR, Assis J, Giner-Delgado C, Dönertaş HM, Cuesta-Astroz Y, Saarunya G, Allali I, Gupta S, Srivastava A, Kalsan M, Valdivia C, J Olguin-Orellana G, Papadimitriou S, Parisi D, Kristensen NP, Rib L, Guebila MB, Bauer E, Zaffaroni G, Bekkar A, Ashano E, Paladin L, Necci M, Moreyra NN, Rydén M, Villalobos-Solís J, Papadopoulos N, Rafael C, Karakulak T, Kaya Y, Gladbach Y, Dhanda SK, Šoštarić N, Alex A, DeBlasio D, Rahman F. Global network of computational biology communities: ISCB's Regional Student Groups breaking barriers. F1000Research. 2019 September; 8. doi:10.12688/f1000research.20408.1.

Tavsan, Z., Ayar Kayali H. Flavonoids showed anticancer effects on the ovarian cancer cells: Involvement of reactive oxygen species, apoptosis, cell cycle and invasion. Biomedicine & Pharmacotherapy. 2019 August; 116: 109004. doi:10.1016/j.biopha.2019.109004.

Seda Nur Topkaya and Arif E. Cetin. Investigation of Metal Ion Effect on Specific DNA Sequences and DNA Hybridization. Electroanalysis. 2019 August; 31: 1-8. doi:10.1002/elan.201900391.

Sengez B, Aygün I, Shehwana H, Toyran N, Tercan Avci S, Konu O, Stemmler MP, Alotaibi H. The Transcription Factor Elf3 Is Essential for a Successful Mesenchymal to Epithelial Transition. Cells. 2019 August; 8 (8). doi:10.3390/cells8080858.

Seda Nur Topkaya, and Arif E. Cetin. Determination of Electrochemical Interaction Between 2‐(1H‐benzimidazol‐2‐yl) Phenol and DNA Sequences. ELECTROANALYSIS. 2019 August; 31 (8): 1554-1561. doi:10.1002/elan.201900199.

Habibe Durmaz, Arif E Cetin, Yuyu Li, and Roberto Paiella. A Polarization Insensitive Wide-Band Perfect Absorber. ADVANCED ENGINEERING MATERIALS. 2019 August; 21 (8): 1900188. doi:10.1002/adem.201900188.

Dafsari HS, Sprute R, Wunderlich G, Daimagüler HS, Karaca E, Contreras A, Becker K, Schulze-Rhonhof M, Kiening K, Karakulak T, Kloss M, Horn A, Pauls A, Nürnberg P, Altmüller J, Thiele H, Assmann B, Koy A, Cirak S. Novel mutations in KMT2B offer pathophysiological insights into childhood-onset progressive dystonia. Journal of human genetics. 2019 August; 64 (8): 803-813. doi:10.1038/s10038-019-0625-1.

Nazlı Eda Kaleli, Murat Karadag, Sibel Kalyoncu. Phage display derived therapeutic antibodies have enriched aliphatic content: Insights for developability issues. Proteins: Structure, Function, and Bioinformatics. 2019 July; 87 (7): 607-618. doi:10.1002/prot.25685.

Kisa, Pelin Teke; Kose, Melis; Unal, Ozlem; Er, Esra; Hismi, Burcu Ozturk; Bulbul, Fatma Selda; Kose, Engin; Gunduz, Mehmet; Canda, Ebru; Kucukcongar, Aynur; Arslan, Nur. Clinical and molecular characteristics and time of diagnosis of patients with classical galactosemia in an unscreened population in Turkey. JOURNAL OF PEDIATRIC ENDOCRINOLOGY & METABOLISM. 2019 July; 32 (7): 675-681. doi:10.1515/jpem-2018-0457.

Pavlopoulou A, Karaca E, Balestrazzi A, Georgakilas AG. In Silico Phylogenetic and Structural Analyses of Plant Endogenous Danger Signaling Molecules upon Stress. Oxidative medicine and cellular longevity. 2019 July; 2019: 8683054. doi:10.1155/2019/8683054.

Türkdoğan D, Matthews E, Usluer S, Gündoğdu A, Uluç K, Mannikko R, Hanna MG, Sisodiya SM, Çağlayan HS. Possible role of SCN4A skeletal muscle mutation in apnea during seizure. Epilepsia open. 2019 July; 4 (3): 498-503. doi:10.1002/epi4.12347.

Karacicek B, Erac Y, Tosun M. Functional consequences of enhanced expression of STIM1 and Orai1 in Huh-7 hepatocellular carcinoma tumor-initiating cells. BMC cancer. 2019 July; 19 (1): 751. doi:10.1186/s12885-019-5947-z.

Arioz BI, Tastan B, Tarakcioglu E, Tufekci KU, Olcum M, Ersoy N, Bagriyanik A, Genc K, Genc S. Melatonin Attenuates LPS-Induced Acute Depressive-Like Behaviors and Microglial NLRP3 Inflammasome Activation Through the SIRT1/Nrf2 Pathway. Frontiers in immunology. 2019 July; 10: 1511. doi:10.3389/fimmu.2019.01511.

Yiş U., Hız S., Güneş S., Diniz G., Sönmezler E., Yılmaz E., Oktay Y. . Dihydropyridine receptor congenital myopathy in a consanguineous Turkish family. Journal of Neuromuscular Diseases. 2019 June; 6 (3): 377-384. doi:10.3233/JND-190383.

Arif E. Cetin, and Seda Nur Topkaya. Photonic Crystal and Plasmonic Nanohole Based Label-Free Biodetection. Biosensors & Bioelectronics. 2019 May; 132: 196-202. doi:10.1016/j.bios.2019.02.047.

Sen, Betul; Kalhan, Hatice Kubra; Demir, Volkan; Guler, Egemen Erdem; Kayali, Hulya Ayar; Subasi, Elif. Crystal structures, spectroscopic properties of new cobalt(II), nickel(II), zinc (II) and palladium(II) complexes derived from 2-acetyl-5-chloro thiophene thiosemicarbazone: Anticancer evaluation. MATERIALS SCIENCE & ENGINEERING C-MATERIALS FOR BIOLOGICAL APPLICATIONS. 2019 May; 98: 550-559. doi:10.1016/j.msec.2018.12.080.

Yandim, Cihangir; Karakulah, Gokhan. Expression dynamics of repetitive DNA in early human embryonic development. BMC GENOMICS. 2019 May; 20. doi:10.1186/s12864-019-5803-1.

Schulz H, Ruppert AK, Zara F, Madia F, Iacomino M, S Vari M, Balagura G, Minetti C, Striano P, Bianchi A, Marini C, Guerrini R, Weber YG, Becker F, Lerche H, Kapser C, Schankin CJ, Kunz WS, Møller RS, Oliver KL, Bellows ST, Mullen SA, Berkovic SF, Scheffer IE, Caglayan H, Ozbek U, Hoffmann P, Schramm S, Tsortouktzidis D, Becker AJ, Sander T. No evidence for a BRD2 promoter hypermethylation in blood leukocytes of Europeans with juvenile myoclonic epilepsy. Epilepsia. 2019 May; 60 (5): e31-e36. doi:10.1111/epi.14657.

Ege Ulgen, Ozge Can, Kaya Bilguvar, Yavuz Oktay, Cemaliye Akyerli, Ayça Danyeli, Cengiz Yakicier, Ugur Sezerman, Necmettin Pamir Koray Özduman. Whole Exome Sequencing-Based Analysis Identifies DNA Damage Repair Deficiency as a Major Contributor to Gliomagenesis in Adult Diffuse Gliomas. J Neurosurg. 2019 April: 1-12. doi:10.3171/2019.1.JNS182938.

Senem Demir, Cigdem Özen, Meltem Ceylan‐Ünlüsoy, Mehmet Öztürk, Oya Bozdağ‐Dündar. Novel Furochromone Derivatives: Synthesis and Anticancer Activity Studies. Journal of Heterocyclic Chemistry. 2019 April; 56 (4): 1341-1351. doi:10.1002/jhet.3508.

* Stimple SD, Kalyoncu S, Desai AA, Mogensen JE, Spang LT, Asgreen DJ, Staby A, Tessier PM. Sensitive detection of glucagon aggregation using amyloid fibril‐specific antibodies. Biotechnology and Bioengineering. 2019 April. doi:10.1002/bit.26994.

Arif E. Cetin. Effect of Left handed Materials in Surface Plasmon Excitation and Propagation Length. Turkish Journal of Physics. 2019 February; 43: 26-36. doi:10.3906/fiz-1804-9.

Dimitriou NM; Pavlopoulou A; Tremi I; Koukoulias V; Georgakilas AG. Prediction of Gold Nanoparticle and Microwave-Induced Hyperthermia Effects on Tumor Control via a Simulation Approach. Nanomaterials. 2019 February; 9 (2): E167. doi:10.3390/nano9020167.

Szmyd R, Niska-Blakie J, Diril MK, Renck Nunes P, Tzelepis K, Lacroix A, van Hul N, Deng LW, Matos J, Dreesen O, Bisteau X, Kaldis P.. Premature activation of Cdk1 leads to mitotic events in S phase and embryonic lethality. Oncogene. 2019 February; 38 (7): 998-1018. doi:10.1038/s41388-018-0464-0.

Kose E, Arslan N.. Vitamin/mineral and micronutrient status in patients with classical phenylketonuria. Clinical Nutrition. 2019 February; 38 (1): 197-203. doi:10.1016/j.clnu.2018.01.034.

Sharma AB, Dimitrov S, Hamiche A, Van Dyck E.. Centromeric and ectopic assembly of CENP-A chromatin in health and cancer: old marks and new tracks. Nucleic Acids Res. 2019 February; 47 (3): 1051–1069. doi:10.1093/nar/gky1298.

Merve Arslan, Dilara Karadag, Sibel Kalyoncu. Protein engineering approaches for antibody fragments: directed evolution and rational design approaches. Turkish Journal of Biology. 2019 February; 43 (1): 1-12. doi:10.3906/biy-1809-28.

Guzel, Orkide; Uysal, Utku; Arslan, Nur. Efficacy and tolerability of olive oil-based ketogenic diet in children with drug -resistant epilepsy: A single center experience from Turkey. EUROPEAN JOURNAL OF PAEDIATRIC NEUROLOGY. 2019 January; 23 (1): 143-151. doi:10.1016/j.ejpn.2018.11.007.

Okonechnikov K, Erkek S, Korbel JO, Pfister SM, Chavez L. InTAD: chromosome conformation guided analysis of enhancer target genes. BMC bioinformatics. 2019 January; 20 (1): 60. doi:10.1186/s12859-019-2655-2.

Erkek S, Johann PD, Finetti MA, Drosos Y, Chou HC, Zapatka M, Sturm D, Jones DTW, Korshunov A, Rhyzova M, Wolf S, Mallm JP, Beck K, Witt O, Kulozik AE, Frühwald MC, Northcott PA, Korbel JO, Lichter P, Eils R, Gajjar A, Roberts CWM, Williamson D, Hasselblatt M, Chavez L, Pfister SM, Kool M. Comprehensive Analysis of Chromatin States in Atypical Teratoid/Rhabdoid Tumor Identifies Diverging Roles for SWI/SNF and Polycomb in Gene Regulation. Cancer cell. 2019 January; 35 (1): 95-110.e8. doi:10.1016/j.ccell.2018.11.014.

Suner A, Carr BI, Akkiz H, Karakülah G, Üsküdar O, Yalçın K, Kuran S, Tokat Y, Yilmaz S, Özakyol A, Tokmak S, Ballı T, Yücesoy M, Bahçeci Hİ.... C-Reactive Protein and Platelet-Lymphocyte Ratio as Potential Tumor Markers in Low-Alpha-Fetoprotein Hepatocellular Carcinoma. Oncology. 2019 ; 96 (1): 25-32. doi:10.1159/000492473.

Kursun, Deniz; Kucuk, Can. Systematic analysis of the frequently amplified 2p15-p16.1 locus reveals PAPOLG as a potential proto-oncogene in follicular and transformed follicular lymphoma. TURKISH JOURNAL OF BIOLOGY. 2019 ; 43 (2). doi:10.3906/biy-1810-2.