Scientific Publications

Gökhan Karakülah and Athanasia Pavlopoulou In silico Phylogenetic Analysis of hAT Transposable Elements in Plants. Genes 2018 June 6; 9(6), 284: 1-13. doi: 10.3390/genes9060284

Brian I. Carr, Hikmet Akkiz, Oguz Uskudar, et al. C-reactive protein and hepatocellular carcinoma: analysis of its relationships to tumor factors. Clinical Practice (Therapy) 2018; 15(SI): 625-634. doi: 10.4172/clinical-practice.1000409

Hikmet Akkiz, Brian I. Carr, Sedef Kuran, et al. Macroscopic portal vein thrombosis in HCC patients. Canadian Journal of Gastroenterology and Hepatology 2018 June. doi: 10.1155/2018/3120185

Hande Server Çağlayan Lafora Disease: Molecular Etiology Epilepsi 2018; 24(1): 1-7. doi: 10.14744/epilepsi.2017.48278

AnnaRubio-Cosials, Eike C.Schulz, Lotte Lambertsen, et al. Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance. Cell 2018 March 22; 173(1): 208-220.

Tufekci KU, Vurgun U, Yigitaslan O, Keskinoglu P, Yaka E, Kutluk K, Genc S. Follow-up Analysis of Serum TNF-Related Apoptosis-Inducing Ligand Protein and mRNA Expression in Peripheral Blood Mononuclear Cells from Patients with Ischemic Stroke. Front Neurol. 2018 Mar 5; 9:102. doi: 10.3389/fneur.2018.00102.

Ilkcan Ercan, Kemal Ugur Tufekci, Ezgi Karaca, Sermin Genc, Kursad Genc. Peptide Derivatives of Erythropoietin in the Treatment of Neuroinflammation and Neurodegeneration. Advances in Protein Chemistry and Structural Biology 2018 Feb 28; 112: 309-357. doi: 10.1016/bs.apcsb.2018.01.007.

Rosalba D’Alessandro, Maria Grazia Refolo, Catia Lippolis, et al. Strong enhancement by IGF1-R antagonists of hepatocellular carcinoma cell migration inhibition by Sorafenib and/or vitamin K1. Cellular Oncology 2018 Feb 22; pp: 1-14. doi: 10.1007/s13402-018-0370-z

Shilpi Chandra, Gerhard Wingender, Jason A. Greenbaum et al. Development of asthma in inner-city children: Possible roles of MAIT cells and variation in the home environment. J Immunol 2018 Feb 05. doi: 10.4049/jimmunol.1701525

Brian I. Carr, Hikmet Akkiz, Oguz Uskudar, et al. HCC with low- and normal serum alpha-fetoprotein levels. Clinical Practice (Therapy) 2018; 15(1): 453-464.

Serhat Tozburun, Cedric Blatter, Meena Siddiqui, Eelco F. J. Meijer, and Benjamin J. Vakoc. Phase-stable Doppler OCT at 19 MHz using a stretched-pulse mode-locked laser. Biomedical Optics Express 2018; 9(3): 952-961. doi: 10.1364/BOE.9.000952.

Meena Siddiqui, Ahhyun S. Nam, Serhat Tozburun*, Norman Lippok, Cedric Blatter & Benjamin J. Vakoc. High-speed optical coherence tomography by circular interferometric ranging. Nature Photonics 2018 Jan 26; 12: 111–116. doi: 10.1038/s41566-017-0088-x.

Eren E, Tufekci KU, Isci KB, Tastan B, Genc K, Genc S. Sulforaphane Inhibits Lipopolysaccharide-Induced Inflammation, Cytotoxicity, Oxidative Stress, and miR-155 Expression and Switches to Mox Phenotype through Activating Extracellular Signal-Regulated Kinase 1/2-Nuclear Factor Erythroid 2-Related Factor 2/Antioxidant Response Element Pathway in Murine Microglial Cells. Front Immunol. 2018 Jan 23; 9:36. doi: 10.3389/fimmu.2018.00036.

Brian I. Carr, Hikmet Akkiz, Oguz Üsküdar et al. HCC with low- and normal serum alpha-fetoprotein levels. Clinical Practice (Therapy) 2018; 15(1): 453-464. doi: 10.4172/clinical-practice.1000393.

* Current address IBG.

Sag D, Özkan M, Kronenberg M, Wingender G. Improved Detection of Cytokines Produced by Invariant NKT Cells. Sci Rep 2017 Nov 30; 7(1):16607. doi: 10.1038/s41598-017-16832-1.

Cigdem Ozen, Meltem Ceylan Unlusoy, Nazanin Aliary, Mehmet Ozturk, Oya Bozdag Dundar. Thiazolidinedione or Rhodanine: A Study on Synthesis and Anticancer Activity Comparison of Novel Thiazole Derivatives. J Pharm Pharm Sci 2017 Nov; 20 (1): 415-427. doi:10.18433/J38P9R.

Gökhan Karakülah. RTFAdb: A database of computationally predicted associations between retrotransposons and transcription factors in the human and mouse genomes. Genomics 2017 Nov; 17. doi:10.1016/j.ygeno.2017.11.002.

Carr BI, Guerra V. Serum albumin levels in relation to tumor parameters in hepatocellular carcinoma patients. Int J Biol Markers 2017 Oct 31;32(4):e391-e396. doi:10.5301/ijbm.5000300.

Refolo MG, D'Alessandro R, Lippolis C, Carella N, Cavallini A, Messa C, Carr BI. IGF-1R tyrosine kinase inhibitors and Vitamin K1 enhance the antitumor effects of Regorafenib in HCC cell lines. Oncotarget 2017 Sep 30; 8(61):103465-103476. doi:10.18632/oncotarget.21403.

Onur Tokel, Ahmet Turnalı, Ghaith Makey, et al. In-chip microstructures and photonic devices fabricated by nonlinear laser lithography deep inside silicon. Nature Photonics 2017 Sep; 11: 639–645. doi:10.1038/s41566-017-0004-4.

Ozen C, Ceylan-Unlusoy M, Ozturk M, Bozdag-Dundar O. A novel chromonyl thiohydantoin with anti-proliferative action on primary hepatocellular carcinoma cells. Med Chem Res 2017 Sep; 1-8. doi:10.1007/s00044-017-2037-0.

Lina Zelinger, Gökhan Karakülah*, Vijender Chaitankar, Jung-Woong Kim, Hyun-Jin Yang, Matthew J. Brooks, Anand Swaroop. Regulation of Noncoding Transcriptome in Developing Photoreceptors by Rod Differentiation Factor NRL. Investigative Ophthalmology & Visual Science 2017 Sep; 58: 4422-4435. doi: 10.1167/iovs.17-21805.

Ozturk M, Batur T, Ekin U, Erdogan A, İscan E, Keles U, Oz O, Ozen C. Molecular Pathogenesis of Liver Cancer. J Gastrointest Cancer. 2017 Jul 17 (Review). doi: 10.1007/s12029-017-9957-2. [Epub ahead of print].

Carr BI, Guerra V. Serum albumin levels in relation to tumor parameters in hepatocellular carcinoma patients. Int J Biol Markers 2017 Aug 28. doi: 10.5301/ijbm.5000300.

Ors A, Papin C, Favier B, Roulland Y, Dalkara D, Ozturk M, Hamiche A, Dimitrov S, Padmanabhan K. Histone H3.3 regulates mitotic progression in mouse embryonic fibroblasts. Biochem Cell Biol 2017 Aug; 95(4):491-499. doi: 10.1139/bcb-2016-0190.

Yılmaz Y, Güneş A, Topel H, Atabey N. Signaling Pathways as Potential Therapeutic Targets in Hepatocarcinogenesis. J Gastrointest Cancer 2017 Aug 18. doi: 10.1007/s12029-017-9958-1.

Carr BI, Guerra V. Validation of a Liver Index and Its Significance for HCC Aggressiveness. J Gastrointest Cancer 2017 Jun 20. doi: 10.1007/s12029-017-9971-4.

Ezgi Karaca*, João P.G.L.M. Rodrigues, Andrea Graziadei, Alexandre M.J.J. Bonvin, Teresa Carlomagno. M3: an integrative framework for structure determination of molecular machines. Nature Methods 2017. doi: 10.1038 / nmeth.4392.

Alural B, Ayyildiz ZO, Tufekci KU, Genc S, Genc K. Erythropoietin Promotes Glioblastoma via miR-451 Suppression. Vitam Horm. 2017;105:249-271. doi: 10.1016/bs.vh.2017.03.002. Epub 2017 Apr 19. PubMed PMID: 28629521.

Gökhan Karakülah. Discovery and Annotation of Plant Endogenous Target Mimicry Sequences from Public Transcriptome Libraries: A Case Study of Prunus persica. Journal of Integrative Bioinformatics. 2017 (in press), doi: 10.1515/jib-2017-0009.

Sezgin E, Azbazdar Y, Ng XW, Teh C, Simons K, Weidinger G, Wohland T, Eggeling C, Ozhan G. Binding of canonical Wnt ligands to their receptor complexes occurs in ordered plasma membrane environments. FEBS J. 2017 Aug; 284(15): 2513-2526. doi: 10.1111/febs.14139.

Akyerli C., Yuksel S., Can O., Erson-Omay Z., Oktay Y.*, Cosgun E., Ulgen E., Erdemgil Y., San A., von Deimling A., Gunel M., Yakicier C., Pamir M.N., Ozduman K. Use of telomerase promoter mutations to mark specific molecular subsets with reciprocal clinical behavior in IDH mutant and IDH wild-type diffuse gliomas. Journal of Neurosurgery. 2017 Jun; 16:1-13. doi: 10.3171/2016.11.

Schneider F, Waithe D, Clausen MP, Galiani S, Koller T, Ozhan G, Eggeling C, Sezgin E. Diffusion of lipids and GPI-anchored proteins in actin-free plasma membrane vesicles measured by STED-FCS. Mol Biol Cell. 2017 Jun 1;28(11): 1507-1518. doi: 10.1091/mbc.E16-07-0536.

Oktay Y., Boylu C.A., Özduman K. Gliom Gelişiminde Genetik Yatkınlığın Rolü. Türk Nöroşirürji Dergisi. 2017 May; 27(2): 122-130.

Gökhan Karakülah, Aslı Suner. PlanTEnrichment: A tool for enrichment analysis of transposable elements in plants. Genomics. 2017 (in press), doi:10.1016/j.ygeno.2017.05.008.

Bağırsakçı E., Şahin E., Atabey N., Erdal E. & Carr B.I. Role of Albumin in growth inhibition in Hepatocellular Carcinoma. Oncology. 2017 May 10. doi:10.1159/000471807.

Gümürdü A., Yildiz R., Eren E., Karakülah G., Ünver T., Genç Ş. & Park Y. MicroRNA exocytosis by large dense-core vesicle fusion. Scientific Reports. 2017 Mar 30; 7:45661. doi:10.1038/srep45661.

Marino IR, Carr B.I. New Developments in Orthotopic Liver Transplant for Hepatocellular Carcinoma. Exp Clin Transplant. 2017 Mar;15(Suppl 2):1-6.

Alural B, Genc S, Haggarty S. Diagnostic and therapeutic potential of microRNAs in neuropsychiatric disorders: Past, present, and future. Prog Neuropsychopharmacol Biology Psychiatry. 2017 Feb; 6;73:87-103 doi: 10.1016/j.pnpbp.2016.03.010. Epub 2016 Apr 9. PubMed PMID: 27072377; PubMed Central PMCID: PMC5292013.

Pinato D., Sharma R., Allara E., Yen C., Arizumi T., Kubota K., Bettinger D., Jang J.W., Smirne C., Kim Y.W., Kudo M., Howell J., Ramaswami R., Burlone M.E., Guerra V., Thimme R., Ishizuka M., Stebbing J., Pirisi M. & Carr B.I. The ALBI grade provides objective hepatic reserve estimation across each BCLC stage of hepatocellular carcinoma. J. Hepatology, 2017 Feb; 66(2): 338-346. doi:http://dx.doi.org/10.1016/j.jhep.2016.09.008.

van Waalwijk van Doorn LJ, Gispert JD, Kuiperij HB, et al. Improved Cerebrospinal Fluid-Based Discrimination between Alzheimer's Disease Patients and Controls after Correction for Ventricular Volumes. J Alzheimers Dis. 2017 Jan 24; 56(2):543-555. doi: 10.3233/JAD-160668

Park CG, Park Y & Suh BC. The HOOK region of voltage-gated Ca2+ channel β subunits senses and transmits PIP2 signals to the gate. J Gen Physiol. 2017 Jan 13. doi:10.1085/jgp.201611677.

* Current address IBG.