Publications

Avci, M. E., Keskus, A. G., Targen, S., Isilak, M. E., Ozturk, M., Atalay, R. C., … Konu, O. (2018). Development of a novel zebrafish xenograft model in ache mutants using liver cancer cell lines. Scientific Reports, 8, 1570. doi.org/10.1038/s41598-018-19817-w

Tuncer, S., Keskus, A. G., Colakoglu, M., Cimen, I., Yener, C., Konu, O., Sreeparna, B. (2017). 15-Lipoxygenase-1 re-expression in colorectal cancer alters endothelial cell features through enhanced expression of TSP-1 and ICAM-1. Cellular Signaling, 39, 44-54. doi.org/10.1016/j.cellsig.2017.07.022

Demirkol, S., Gomceli, I., Isbilen, M., Dayanc, B. E., Tez, M., Bostanci, E. B., …, Konu, O., ..., Gure, A. O. (2017). A Combined ULBP2 and SEMA5A Expression Signature as a Prognostic and Predictive Biomarker for Colon Cancer. Journal of Cancer, 8(7), 1113–1122. doi.org/10.7150/jca.17872

E.T. Karoglu, D.O. Halim, B. Erkaya, F. Altaytas, A. Arslan-Ergul, O. Konu, M.M. Adams. (2017). Aging alters the molecular dynamics of synapses in a sexually dimorphic pattern in zebrafish (Danio rerio). Neurobiol. Aging, 54 (2017), pp. 10-21. doi.org/10.1016/j.neurobiolaging.2017.02.007

Mutlu, M., Saatci, Ö., Ansari, S. A., Yurdusev, E., Shehwana, H., Konu, Ö., … Şahin, Ö. (2016). miR-564 acts as a dual inhibitor of PI3K and MAPK signaling networks and inhibits proliferation and invasion in breast cancer. Scientific Reports, 6, 32541. doi.org/10.1038/srep32541

Sucularli, C., Shehwana, H., Kuscu, C., Dungul, D.C., Ozdag, H., & Konu, O. (2016). Functionally conserved effects of rapamycin exposure on zebrafish. Molecular Medicine Reports, 13, 4421-4430. doi.org/10.3892/mmr.2016.5059

Doldur-Balli, F., Ozel, M.N., Gulsuner, S., Tekinay, A.B., Ozcelik, T., Konu, O. and Adams, M.M., 2015. Characterization of a novel zebrafish (Danio rerio) gene, wdr81, associated with cerebellar ataxia, mental retardation and dysequilibrium syndrome (CAMRQ). BMC neuroscience, 16(1), p.1.doi: 10.1186/s12868-015-0229-4

Sayar, N., Karahan, G., Konu, O., Bozkurt, B., Bozdogan, O. and Yulug, I.G., 2015. Transgelin gene is frequently downregulated by promoter DNA hypermethylation in breast cancer. Clinical epigenetics, 7(1), pp.1-16. doi:10.1186/s13148-015-0138-5

Karahan, G., Sayar, N., GOzuM, G., BOzKuRT, B., Konu, O. and YuLuG, I.G., 2015. Relative expression of rRNA transcripts and 45S rDNA promoter methylation status are dysregulated in tumors in comparison with matched-normal tissues in breast cancer. Oncology reports, 33(6), pp.3131-3145. doi: 10.3892/or.2015.3940

Alotaibi, H., Basilicata, M.F., Shehwana, H., Kosowan, T., Schreck, I., Braeutigam, C., Konu, O., Brabletz, T. and Stemmler, M.P., 2015. 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, 1849(6), pp.731-742 doi:10.1016/j.bbagrm.2015.01.005

Pennakalathil, J., Jahja, E., Özdemir, E.S., Konu, O. and Tuncel, D., 2014. Red emitting, cucurbituril-capped, pH-responsive conjugated oligomer-based nanoparticles for drug delivery and cellular imaging. Biomacromolecules, 15(9), pp.3366-3374. doi: 10.1021/bm500839j

Ersahin, T., Carkacioglu, L., Can, T., Konu, O., Atalay, V. and Cetin-Atalay, R., 2014. Identification of Novel Reference Genes Based on MeSH Categories. PloS one, 9(3). doi:10.1371/journal.pone.0093341

Senses, K.M., Gonen, M., Barutcu, A.R., Kalaylioglu, Z., Isbilen, M., Konu, O., Chen, Y.T., Altorki, N.K. and Gure, A.O., 2013. Cancer-testis gene expression is associated with the methylenetetrahydrofolate reductase 677 C> T polymorphism in non-small cell lung carcinoma. BMC medical genetics, 14(1), p.97. doi: 10.1186/1471-2350-14-97

Gunel-Ozcan, A., Cagnan, I., Konu, O., Kaya, F.A., Kuskonmaz, B. and Uckan, D., 2013. Differential miRNA expression profile of bone marrow derived mesenchymal stem cells in fanconi anemia patients and healthy donors. Experimental Hematology, 8(41), p.S61. doi: 10.1016/j.exphem.2013.05.238

Yildiz G, Arslan-Ergul A, Bagislar S, Konu O, Yuzugullu H, Gursoy-Yuzugullu O, et al. (2013) Genome-Wide Transcriptional Reorganization Associated with Senescence-to-Immortality Switch during Human Hepatocellular Carcinogenesis. PLoS ONE 8(5): e64016. doi:10.1371/journal.pone.0064016

Dever, J.A., Fuiten, A.M., Konu, Ö. and Wilkinson, J.A., 2012. Cryptic torrent frogs of Myanmar: an examination of the Amolops marmoratus species complex with the resurrection of Amolops afghanus and the identification of a new species. Copeia, 2012(1), pp.57-76.

Kaya, K.D., Karakülah, G., Yakıcıer, C.M., Acar, A.C. and Konu, Ö., 2011. mESAdb: microRNA expression and sequence analysis database. Nucleic acids research, 39(suppl 1), pp.D170-D180. doi: 10.1093/nar/gkq1256

Carkacioglu, L., Atalay, R.C., Konu, O., Atalay, V. and Can, T., 2010. Bi-k-bi clustering: mining large scale gene expression data using two-level biclustering. International journal of data mining and bioinformatics4(6), pp.701-721. doi10.1504/IJDMB.2010.037548

Sucularli, C., Senturk, S., Ozturk, M. and Konu, O., 2011. Dose-and time-dependent expression patterns of zebrafish orthologs of selected E2F target genes in response to serum starvation/replenishment. Molecular biology reports, 38(6), pp.4111-4123. doi:10.1007/s11033-010-0531-2

Konu, O., Ozturk, A.R., Sayar, N. and Yulug, I.G., 2010. Meta-analysis of expression profiles of 5-aza-C treated cancer cells. New Biotechnology, 27, p.S82.

Acun, T., Terzioğlu-Kara, E., Konu, O., Ozturk, M. and Yakicier, M.C., 2010. Mdm2 Snp309 G allele displays high frequency and inverse correlation with somatic P53 mutations in hepatocellular carcinoma. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 684(1), pp.106-108. doi:10.1016/j.mrfmmm.2009.11.008

Gur-Dedeoglu, B., Konu, O., Bozkurt, B., Ergul, G., Seckin, S. and Yulug, I.G., 2009. Identification of endogenous reference genes for qRT-PCR analysis in normal matched breast tumor tissues. Oncology Research Featuring Preclinical and Clinical Cancer Therapeutics, 17(8), pp.353-365. doi: 10.3727/096504009788428460

Gur-Dedeoglu, B., Konu, O., Kir, S., Ozturk, A.R., Bozkurt, B., Ergul, G. and Yulug, I.G., 2008. A resampling-based meta-analysis for detection of differential gene expression in breast cancer. BMC cancer, 8(1), p.396. doi: 10.1186/1471-2407-8-396

Avci, M.E., Konu, O. and Yagci, T., 2008. Quantification of SLIT-ROBO transcripts in hepatocellular carcinoma reveals two groups of genes with coordinate expression. BMC cancer, 8(1), p.392.         doi: 10.1186/1471-2407-8-392

Wang, J., Gutala, R., Hwang, Y.Y., Kim, J.M., Konu, O., Ma, J.Z. and Li, M.D., 2008. Strain‐and region‐specific gene expression profiles in mouse brain in response to chronic nicotine treatment. Genes, Brain and Behavior, 7(1), pp.78-87. doi: 10.1111/j.1601-183X.2007.00328.x

Aydin, I.T., Tokcaer, Z., Dalgic, A., Konu, O. and Akcali, K.C., 2007. Cloning and expression profile of FLT3 gene during progenitor cell‐dependent liver regeneration. Journal of gastroenterology and hepatology, 22(12), pp.2181-2188. doi: 10.1111/j.1440-1746.2006.04731.x

Kaya, K.D., Karakulah, G., Yakicier, C. and Konu, O., 2007. MicroRNA sequence and expression database. BMC Systems Biology, 1(Suppl 1), p.P29. doi: 10.1186/1752-0509-1-S1-P29

Dalkic, E., Kuscu, C., Sucularli, C., Aydin, I.T., Akcali, K.C. and Konu, O., 2006. Alternatively spliced Robo2 isoforms in zebrafish and rat. Development genes and evolution, 216(9), pp.555-563.

Ilk, H.G., Ilk, Ö., Konu, Ö. and Özdağ, H., 2006, April. Investigation and Comparison of the Preprocessing Algorithms for Microarray Analysis for Robust Gene Expression Calculation and Performance Analysis of Technical Replicates. In Signal Processing and Communications Applications, 2006 IEEE 14th (pp. 1-4). IEEE. doi: 10.1109/SIU.2006.1659873

Gur, B., Bozkurt, B., Konu, O., Seckin, S. and Yulug, I.G., 2005. Real-time PCR-based expression profiling of BRCA1-induced genes in primary breast tumors. Breast Cancer Research, 7(Suppl 2), pp.1-2.

Kane, J.K., Hwang, Y., Konu, O., Loughlin, S.E., Leslie, F.M. and Li, M.D., 2005. Regulation of Homer and group I metabotropic glutamate receptors by nicotine. European Journal of Neuroscience, 21(5), pp.1145-1154. doi: 10.1111/j.1460-9568.2005.03945.x

Li, M.D., Kane, J.K. and Konu, O., 2005. Regulation by Nicotine of Food Intake and Body Weight: Implications for Obesity Treatment. Frontiers in Medicinal Chemistry-Online, 2(1), pp.273-297.   doi: 10.2174/1567204052931104

Kane, J.K., Konu, Ö., Ma, J.Z. and Li, M.D., 2004. Nicotine coregulates multiple pathways involved in protein modification/degradation in rat brain. Molecular brain research, 132(2), pp.181-191. doi:10.1016/j.molbrainres.2004.09.010

Konu, Ö., Xu, X., Ma, J.Z., Kane, J., Wang, J., Shi, S.J. and Li, M.D., 2004. Application of a customized pathway-focused microarray for gene expression profiling of cellular homeostasis upon exposure to nicotine in PC12 cells. Molecular brain research, 121(1), pp.102-113. doi:10.1016/j.molbrainres.2003.11.012

Li, M.D., Kane, J.K. and Konu, O., 2003. Nicotine, body weight and potential implications in the treatment of obesity. Current topics in medicinal chemistry, 3(8), pp.899-919.

doi: 10.2174/1568026033452203

Li, M.D., Konu, O., Kane, J.K. and Becker, K.G., 2002. Microarray technology and its application on nicotine research. Molecular neurobiology, 25(3), pp.265-285. doi: 10.1385/MN:25:3:265

Konu, Ö. and Li, M.D., 2002. Correlations between mRNA expression levels and GC contents of coding and untranslated regions of genes in rodents.Journal of molecular evolution54(1), pp.35-41.

doi: 10.1007/s00239-001-0015-z

Konu, Ö., Kane, J.K., Barrett, T., Vawter, M.P., Chang, R., Ma, J.Z., Donovan, D.M., Sharp, B., Becker, K.G. and Li, M.D., 2001. Region-specific transcriptional response to chronic nicotine in rat brain. Brain research, 909(1), pp.194-203. doi:10.1016/S0006-8993(01)02685-3

Grantham, Ö.K., Moorhead, D.L. and Willig, M.R., 1995. Foraging strategy of the giant rams-horn snail, Marisa cornuarietis: an interpretive model. Oikos, pp.333-342.

Grantham, Özlen K., Daryl L. Moorhead, and Michael R. Willig. "Feeding preference of an aquatic gastropod, Marisa cornuarietis: effects of pre-exposure." Journal of the North American Benthological Society (1993): 431-437.