Scientific Publications

iBG Affiliated Publications

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.

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].

Yuqing Zhu, Vahid Serpooshan, Sean Wu, Utkan Demirci, Pu Chen, Sinan Güven. Tissue Engineering of 3D Organotypic Microtissues by Acoustic Assembly. In: Methods in Molecular Biology. Humana Press 2017 Sep; 1-12. doi: 10.1007/7651_2017_68.

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.

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.

Arslan N, Guzel O, Kose E, Yılmaz U, Kuyum P, Aksoy B, Çalık T. Is ketogenic diet treatment hepatotoxic for children with intractable epilepsy? Seizure. 2016 Dec; 43: 32-38. doi:10.1016/j.seizure.2016.10.024.

Ebru Diler, Turgay Unver & Gökhan Karakülah. Differential Expression of Hyperhydricity Responsive Peach miRNAs. Journal of Integrative Bioinformatics. 2016 Dec; 13(5): 308. doi:10.2390/biecoll-jib-2016-308.

İşcan E, Güneş A, Korhan P, Yılmaz Y, Erdal E, Atabey N. The regulatory role of heparin on c-Met signaling in hepatocellular carcinoma cells. J Cell Commun Signal. 2016 Dec 14; 1-12. doi:10.1007/s12079-016-0368-0.

Gökhan Karakülah, Kuaybe Yücebilgili Kurtoğlu, Turgay Unver. PeTMbase: A Database of Plant Endogenous Target Mimics (eTMs). PLoS ONE. 2016 Dec 9; 11(12): e0167698. doi:10.1371/journal.pone.0167698.

Calibasi Kocal G, Güven S, Foygel K, Goldman A, Chen P, Sengupta S, Paulmurugan R, Baskin Y, Demirci U. Dynamic Microenvironment Induces Phenotypic Plasticity of Esophageal Cancer Cells Under Flow. Sci Rep. 2016 Dec 2; 6:38221. doi: 10.1038/srep38221.

Jung-Woong Kim, Hyun-Jin Yang, Matthew John Brooks, Lina Zelinger, Gökhan Karakülah*, Norimoto Gotoh, Alexis Boleda, Linn Gieser, Felipe Giuste, Dustin Thad Whitaker, Ashley Walton, Rafael Villasmil, Jennifer Joanna Barb, Peter Jonathan Munson, Koray Dogan Kaya, Vijender Chaitankar, Tiziana Cogliati, Anand Swaroop. NRL-Regulated Transcriptome Dynamics of Developing Rod Photoreceptors. Cell Reports. 2016 Nov 22; 17(9): 2460-2473. doi:http://dx.doi.org/10.1016/j.celrep.2016.10.074.

Arslan N, Kose E, Guzel O. The Effect of Ketogenic Diet on Serum Selenium Levels in Patients with Intractable Epilepsy. Biol Trace Elem Res. 2016 Nov 21. doi:10.1007/s12011-016-0897-7.

Erbayraktar Z, Alural B, Erbayraktar RS, Erkan EP. Cell division cycle 7-kinase inhibitor PHA-767491 hydrochloride suppresses glioblastoma growth and invasiveness. Cancer Cell Int. 2016 Nov 18;16:88. eCollection 2016. doi:10.1186/s12935-016-0364-8.

Muhammad Ayaz Mustufa, Cigdem Ozen, Imran Ali Hashmi, Afshan Aslam, Jameel Ahmed Baig, Gokhan Yildiz, Shoaib Muhammad, Imam Bakhsh Solangi, Naim ul Hasan Naqvi, Mehmet Ozturk and Firdous Imran Ali. Synthesis and bio-molecular study of (+)-N-Acetyl-α-amino acid dehydroabietylamine derivative for the selective therapy of hepatocellular carcinoma. BMC Cancer. 2016, Nov 14; 16: 883. doi:10.1186/s12885-016-2942-5.

Büyüköz M, Erdal E, Alsoy Altinkaya S. Nanofibrous gelatin scaffolds integrated with NGF-loaded alginate microspheres for brain tissue engineering. J Tissue Eng Regen Med. 2016 Nov 12. doi: 10.1002/term.2353.

Jeannot V, Busser B, Vanwonterghem L, Michallet S, Ferroudj S, Cokol M, Coll JL, Ozturk M, Hurbin A. Synergistic activity of vorinostat combined with gefitinib but not with sorafenib in mutant KRAS human non-small cell lung cancers and hepatocarcinoma. OncoTargets and Terapy. 2016, Nov 9; 9: 6843—6855. doi:10.2147/OTT.S117743.

Erkan D, Kayali HA. Replacement of Soybean Meal with Animal Origin Protein Meals Improved Ramoplanin A2 Production by Actinoplanes sp. ATCC 33076. Appl Biochem Biotechnol. 2016 Sep;180(2):306-21. doi:10.1007/s12010-016-2100-1.

Carr B.I., Guerra V., Giannini E.G. et al. A Liver Index and its Relations to Indices of HCC Aggressiveness. J. Integrative Oncology. 2016 Sept 5; 5:178. doi: 10.4172/2329-6771.1000178.

Hani Alotaibi, Nese Atabey, Kasım Diril, Esra Erdal, Mehmet Ozturk. Molecular Mechanisms of Hepatocellular Carcinoma, Chapter Hepatocellular Carcinoma Part of the series Current Clinical Oncology. Springer. 2016, Aug 27; 43-63. doi:10.1007/978-3-319-34214-6_3.

Alagoz Y., Gurkok T.,  Zhang B. & Unver T. Manipulating the Biosynthesis of Bioactive Compound Alkaloids for Next-Generation Metabolic Engineering in Opium Poppy Using CRISPR-Cas 9 Genome Editing Technology. Sci Rep. 2016 Aug 3; 6:30910. doi: 10.1038/srep30910.

Bakır Y., Eldem V., Zararsız G. & Unver T. Global Transcriptome Analysis Reveals Differences in Gene Expression Patterns Between Nonhyperhydric and Hyperhydric Peach Leaves. Plant Genome. 2016 Jul; 9(2). doi:10.3835/plantgenome2015.09.0080.

Marsano A, Medeiros da Cunha CM, Ghanaati S, Gueven S, Centola M, Tsaryk R, Barbeck M, Stuedle C, Barbero A, Helmrich U, Schaeren S, Kirkpatrick JC, Banfi A, Martin I. Spontaneous In Vivo Chondrogenesis of Bone Marrow-Derived Mesenchymal Progenitor Cells by Blocking Vascular Endothelial Growth Factor Signaling. Stem Cells Transl Med. 2016 Jul 26. doi: 10.5966/sctm.2015-0321.

Pavlopoulou A., Oktay Y., Vougas K., Louka M., Vorgias C.E., Georgakilas A.G. Determinants of resistance to chemotherapy and ionizing radiation in breast cancer stem cells. Cancer Letters, 2016, Jul 19; 380(2):485-493. doi: 10.1016/j.canlet.2016.07.018.

Carr B.I., Guerra V., Giannini E.O. et al. An HCC Aggressiveness Index and Blood GTP, Blirubin and Platelet Levels. J. Integrative Oncology. 2016 Jun 20; 5:172. doi: 10.4172/2329-6771.1000172.

Oktay Y., Ülgen E., Can Ö., Akyerli C.B., Yüksel Ş., Erdemgil Y., Durası I.M., Henegariu O.I., Nanni E.P., Selevsek N., Grossmann J., Erson-Omay E.Z., Bai H., Gupta M., Lee W., Turcan Ş., Özpınar A., Huse J.T., Sav M.A., Flanagan A., Günel M., Sezerman O.U., Yakıcıer M.C., Pamir M.N. & Özduman K. IDH-mutant glioma specific association of rs55705857 located at 8q24.21 involves MYC deregulation. Sci Rep. 2016 Jun 10; 6: 27569. doi: 10.1038/srep27569.

Yilmaz Y, Atabey N, Erdal E & Brian I. Carr. Platelets, Microenvironment and Hepatocellular Carcinoma. Biochemistry & Analytical Biochemistry, 2016 June 29; 5:281 (Review). doi:10.4172/2161-1009.1000281.

Antonio Mazzoccaa, Giovanni Ferrarob, Giovanni Misciagnac, Brian I. Carr. A systemic evolutionary approach to cancer: Hepatocarcinogenesis as a paradigm. Medical Hypotheses, 2016, Aug; 93: 132-137. doi:10.1016/j.mehy.2016.05.027.

Karakülah G, Karakuş M, Suner A, Demir S, Arserim SK, Töz S, Özbel Y. sandflyDST: a dynamic web-based decision support tool for the morphological identification of sandflies present in Anatolia and mainland Europe, and user study. Medical and Veterinary Entomology, 2016 June 24. doi:10.1111/mve.12182.

Can Küçük, Xiaozhou Hu, Qiang Gong, Bei Jiang, Adam Cornish, Philippe Gaulard, Timothy McKeithan, Wing C. Chan. Diagnostic and Biological Significance of KIR Expression Profile Determined by RNA-Seq in Natural Killer/T-Cell Lymphoma. The American Journal of Pathology, 2016 June; 186(6): 1435-1441. doi:10.1016/j.ajpath.2016.02.011.

Zeynep Firtina Karagonlar, Doğukan Koç, Eren Şahin, Sanem Tercan Avci, Mustafa Yilmaz, Neşe Atabey, Esra Erdal. Effect of adipocyte-secreted factors on EpCAM+/CD133+ hepatic stem cell population. Biochemical and Biophysical Research Communications, 2016 June 3; 474(3): 482-490. doi:10.1016/j.bbrc.2016.04.137.

Yakup Bakır, Vahap Eldem, Gökmen Zararsız, Turgay Unver. Global Transcriptome Analysis Reveals Significant Differences in Gene Expression Patterns Between The Non-Hyperhydric and Hyperhydric Leaves of Prunus persica. The Plant Genome, 2016, May; 9(2): 1-9.

Salimi R, Yener N, Safari R. Use and Evaluation of Newly Synthesized Fluorescence Probes to Detect Generated OH• Radicals in Fibroblast Cells. J Fluoresc. 2016 May; 26(3):919-24. doi: 10.1007/s10895-016-1780-9.

Firtina Karagonlar Z, Koc D, Iscan E, Erdal E, Atabey N. Elevated hepatocyte growth factor expression as an autocrine c‐Met activation mechanism in acquired resistance to sorafenib in hepatocellular carcinoma cells. Cancer Sci. 2016 Apr; 107(4):407-416 doi: 10.1111/cas.12891.

Carr BI & Guerra V. A Hepatocellular Carcinoma Aggressiveness Index and Its Relationship to Liver Enzyme Levels. Oncology 2016 Mar 15; 90(4). doi: 10.1159/000444394.

Gao LM, Zhao S, Liu WP, Zhang WY, Li GD, Küçük C, Hu XZ, Chan WC, Tang Y, Ding WS, Yan JQ, Yao WQ, Wang JC. Clinicopathologic Characterization of Aggressive Natural Killer Cell Leukemia Involving Different Tissue Sites. Am J Surg Pathol, 2016 Mar 11. doi: 10.1097/PAS.0000000000000634.

Carr BI & Guerra V. Low Alpha-Fetoprotein Levels Are Associated with Improved Survival in Hepatocellular Carcinoma Patients with Portal Vein Thrombosis. Digestive Diseases and Sciences, 2016 Feb 26; 61(3):937-947. doi: 10.1007/s10620-015-3922-3.

Ferroudj S, Yildiz G, Bouras M, Iscan E, Ekin U, Ozturk M. Role of fanconi anemia/BRCA pathway genes in hepatocellular carcinoma chemoresistance. Hepatol Res. 2016 Feb 16. doi: 10.1111/hepr.12675.

Carr BI & Guerra V. Hepatocellular Carcinoma Extrahepatic Metastasis in Relation to Tumor size and Alkaline Phosphatase Levels. Oncology 2016 Feb 12; 90(3):1-7. doi: 10.1159/000443480.

Durmaz I, Guven EB, Ersahin T, Ozturk M, Calis I, Cetin-Atalay R. Liver cancer cells are sensitive to Lanatoside C induced cell death independent of their PTEN status. Phytomedicine. 2016 Jan 15; 23(1):42-51. doi: 10.1016/j.phymed.2015.11.012.

Wingender G. From the deep sea to everywhere? Environmental antigens for iNKT cells. Arch Immunol Ther Exp, 2015 Dec 24 (Review). doi: 10.1007/s00005-015-0381-7.

Güzel O, Yılmaz U, Uysal U, Arslan N. The effect of olive oil-based ketogenic diet on serum lipid levels in epileptic children. Neurol Sci. 2015 Dec 23; 1-6. doi: 10.1007/s10072-015-2436-2.

Namkoong B, Guven S, Ramesan S, Liaudanskaya V, Abzhanov A, Demirci U. Recapitulating cranial osteogenesis with neural crest cells in 3-D microenvironments. Acta Biomaterialia, 2015 Dec 07. doi: 10.1016/j.actbio.2015.12.004.

Hanna RN, Cekic C, Sag D, Tacke R, Thomas GD, Nowyhed H, Herrley E, Rasquinha N, McArdle S, Wu R, Peluso E, Metzger D, Ichinose H, Shaked I, Chodaczek G, Biswas SK, Hedrick CC. Patrolling Monocytes Control Tumor Metastasis to the Lung. Science. 2015, Nov 20; 350(6263): 985-90.

Wingender G & Kronenberg M. Characterization of human T cell subsets via surface markers. Cytometry A, 2015, Oct 27; 87A; 1067-1069.

D’Alessandro R, Messa C, Refolo MG, Carr BI. Modulation of sensitivity and resistance to multikinase inhibitors by microenvironmental platelet factors in HCC. Expert Opinion on Pharmacotherapy. 2015 Oct 19; 16(18):1-8. doi: 10.1517/14656566.2015.1101065.

Wingender G, Sag D, Kronenberg M. NKT10 cells: a novel iNKT cell subset. Oncotarget. 2015 Sept 29; 6(29): 26552-26553 (Review). doi: 10.18632/oncotarget.5270.

Wingender G, Birkholz A, Sag D, Farber E, Chitale S, Howell AR, Kronenberg M. Selective conditions are required for the induction of iNKT cell hypo-responsiveness by antigenic stimulation. The Journal of Immunology. 2015 Sept 9; 195: 3838-3848. doi: 10.4049/jimmunol.1500203.

Lippolis C, Refolo MG, D’Alessandro R, Carella N, Messa C, Cavallini A, Carr BI. Resistance to multikinase inhibitor actions mediated by insulin like growth factor-1. Journal of Experimental & Clinical Cancer Research. 2015 Sept 2; 34(1):90. doi: 10.1186/s13046-015-0210-1.

Pančoška P, Skála L, Nešetřil J, Carr BI. Validation of the Concept of a Common Typical Time of Disease Duration for Hepatocellular Carcinoma Patients Using the Fisher Information Processing of Tumor Imaging Results Combined With Network Phenotyping Strategy Quantification of Individual Patient Clinical Profile Patterns. Seminars in Oncology. 2015 Aug; 42(4):672-678. doi: 10.1053/j.seminoncol.2015.05.004.

Gunes A, Iscan E, Topel H, Avci ST, Gumustekin M, Erdal E, Atabey N. Heparin treatment increases thioredoxin interacting protein expression in hepatocellular carcinoma cells. The International Journal of Biochemistry & Cell Biology. 2015 Aug; 65:169-181. doi: 10.1016/j.biocel.2015.05.025.

Hu X, Chan WC, Kücük C. Generation of a genetically engineered aggressive nk-cell leukemia cell line with stable IL2 expression. Acta Medica International. 2015 Jul; 2(2):78-84. doi: 10.5530/ami.2015.3.6.

Ozhan G and Weidinger G. Wnt/β-catenin signaling in heart regeneration. Cell Regen (Lond). 2015 Jul 8; 4(1):3. doi: 10.1186/s13619-015-0017-8

Alotaibi H, Basilicata MF, Shehwana H, Kosowan T, Schreck I, Braeutigam C, Konu O, Brabletz T, Stemmler MP. Enhancer cooperativity as a novel mechanism underlying the transcriptional regulation of E-cadherin during mesenchymal to epithelial transition. Biochimica et Biophysica Acta (BBA) – Gene Regulatory Mechanisms. 2015 June; 1849(6):731-742. doi: 10.1016/j.bbagrm.2015.01.005.

Alural B, Ozerdem A, Allmer J, Genc K, Genc S. Lithium protects against paraquat neurotoxicity by NRF2 activation and miR-34a inhibition in SH-SY5Y cells. Front Cell Neurosci. 2015 May 28; 9:209. doi: 10.3389/fncel.2015.00209.

Dilek Cevik, Gokhan Yıldız & Mehmet Ozturk. Common telomerase reverse transcriptase promoter mutations in hepatocellular carcinomas from different geographical locations. World J Gastroenterol. 2015 Jan 7; 21(1): 311–317. doi: 10.3748/wjg.v21.i1.311.

Alural B, Duran GA, Tufekci KU, Allmer J, Onkal Z, Tunali D, Genc K, Genc S. EPO Mediates Neurotrophic, Neuroprotective, Anti-Oxidant, and Anti-Apoptotic Effects via Downregulation of miR-451 and miR-885-5p in SH-SY5Y Neuron-Like Cells. Frontiers in Immunology. 2014 Sep 30; 5:475. doi: 10.3389/fimmu.2014.00475.

* Current address IBG.