CAP-RNAseq: an integrated pipeline for functional annotation and prioritization of co-expression clusters. Vural-Ozdeniz M, Calisir K, Acar R, Yavuz A, Ozgur MM, Dalgıc E, Konu O. Brief Bioinform. 2024 Jan 22;25(2):bbad536. doi: 10.1093/bib/bbad536. PMID: 38279653

Roadmap to DILI research in Europe. A proposal from COST action ProEuroDILINet. Lucena MI, Villanueva-Paz M, Alvarez-Alvarez I, Aithal GP, Björnsson ES, Cakan-Akdogan G, Cubero FJ, Esteves F, Falcon-Perez JM, Fromenty B, Garcia-Ruiz C, Grove JI, Konu O, Kranendonk M, Kullak-Ublick GA, Miranda JP, Remesal-Doblado A, Sancho-Bru P, Nelson L, Andrade RJ, Daly AK, Fernandez-Checa JC. Pharmacol Res. 2024 Feb;200:107046. doi: 10.1016/j.phrs.2023.107046. Epub 2023 Dec 28. PMID: 38159783

Long-Term Acetylcholinesterase Depletion Alters the Levels of Key Synaptic Proteins while Maintaining Neuronal Markers in the Aging Zebrafish (Danio rerio) Brain. Karoglu-Eravsar ET, Tuz-Sasik MU, Karaduman A, Keskus AG, Arslan-Ergul A, Konu O, Kafaligonul H, Adams MM. Gerontology. 2023;69(12):1424-1436. doi: 10.1159/000534343. Epub 2023 Oct 4. PMID: 37793352

Ozcelik, E., Kalayci, A., Celik, B., Avci, A., Akyol, H., Kilic, I. B., Guzel, T., Cetin, M., Tuzlakoglu-Ozturk, M., Caliskaner, Z. O., Tombaz, M., Yoleri, D., Konu, O., Kandilci, A. Doxorubicin induces prolonged DNA damage signal in cells overexpressing DEK isoform-2. 10.1371/journal.pone.0275476

Tombaz, M., Yanyatan, C., Keskus, A. G., Konu, O. (2022). Extraction and Prioritization of a Gene-Cancer-By-Survival Network Involved in Homeostasis of Intracellular Calcium Concentrations Using TCGA PANCAN Data. 10.1089/bioe.2022.0013

Cagnan, I., Keles, M., Keskus, A. G., Tombaz, M., Sahan O. B., Aerts-Kaya, F., Uckan-Cetinkaya, D. Konu, O. (2022). Global miRNA expression of bone marrow mesenchymal stem/stromal cells derived from Fanconi anemia patients. 10.1007/s13577-021-00626-9

Keskus, A. G., Tombaz, M., Arici, B. I., Dincaslan, F. B., Nabi, A., Shehwana, H., & Konu, O. (2022). Functional analysis of co-expression networks of zebrafish ace2 reveals enrichment of pathways associated with development and disease. Genome, 65(2), 57–74. 10.1139/gen-2021-0033

Targen, S., Konu, O. (2021). Zebrafish Xenotransplantation Models for Studying Gene Function and Drug Treatment in Hepatocellular Carcinoma 10.1007/s12029-021-00782-z

Ozhan, A., Tombaz, M., Konu, O. (2021). Discovery of Cancer-Specific and Independent Prognostic Gene Subsets of the Slit-Robo Family Using TCGA-PANCAN Datasets. 10.1089/omi.2021.0097

Ozhan, A., Tombaz, M., & Konu, O. (2021). SmulTCan: A Shiny application for multivariable survival analysis of TCGA data with gene sets. Computers in biology and medicine, 137, 104793. 10.1016/j.compbiomed.2021.104793

Vural-Ozdeniz, M., Akturk, A., Demirdizen, M., Leka, R., Acar, R., & Konu, O. (2021). CoVrimer: A tool for aligning SARS-CoV-2 primer sequences and selection of conserved/degenerate primers. Genomics, 113(5), 3174–3184. 10.1016/j.ygeno.2021.07.020

Fernandez-Checa, J. C., Bagnaninchi, P., Ye, H., Sancho-Bru, P., Falcon-Perez, J. M., Royo, F., Garcia-Ruiz, C., Konu, O., Miranda, J., Lunov, O., Dejneka, A., Elfick, A., McDonald, A., Sullivan, G. J., Aithal, G. P., Lucena, M. I., Andrade, R. J., Fromenty, B., Kranendonk, M., Cubero, F. J., … Nelson, L. J. (2021). Advanced preclinical models for evaluation of drug-induced liver injury – consensus statement by the European Drug-Induced Liver Injury Network [PRO-EURO-DILI-NET]. Journal of hepatology, 75(4), 935–959. 10.1016/j.jhep.2021.06.021

Gözen, D., Kahraman, D. C., Narci, K., Shehwana, H., Konu, Ö., & Çetin-Atalay, R. (2021). Transcriptome profiles associated with selenium-deficiency-dependent oxidative stress identify potential diagnostic and therapeutic targets in liver cancer cells. Turkish journal of biology = Turk biyoloji dergisi, 45(2), 149–161. 10.3906/biy-2009-56

Sierra-Ramos, C., Velazquez-Garcia, S., Keskus, A. G., Vastola-Mascolo, A., Rodríguez-Rodríguez, A. E., Luis-Lima, S., Hernández, G., Navarro-González, J. F., Porrini, E., Konu, O., & Alvarez de la Rosa, D. (2021). Increased SGK1 activity potentiates mineralocorticoid/NaCl-induced kidney injury. American journal of physiology. Renal physiology, 320(4), F628–F643. 10.1152/ajprenal.00505.2020

Shehwana, H., Keskus, A. G., Ozdemir, S. E., Acikgöz, A. A., Biyik-Sit, R., Cagnan, I., Gunes, D., Jahja, E., Cingir-Koker, S., Olmezer, G., Sucularli, C., & Konu, O. (2021). CHRNA5 belongs to the secondary estrogen signaling network exhibiting prognostic significance in breast cancer. Cellular oncology (Dordrecht), 44(2), 453–472. 10.1007/s13402-020-00581-x

Targen, S., Kaya, T., Avci, M. E., Gunes, D., Keskus, A. G., & Konu, O. (2020). ZenoFishDb v1.1: A Database for Xenotransplantation Studies in Zebrafish. Zebrafish, 17(5), 305–318. 10.1089/zeb.2020.1869

Karadayi, F. Z., Yaman, M., Kisla, M. M., Keskus, A. G., Konu, O., & Ates-Alagoz, Z. (2020). Design, synthesis and anticancer/antiestrogenic activities of novel indole-benzimidazoles. Bioorganic chemistry, 100, 103929. 10.1016/j.bioorg.2020.103929

Sengez, B., Aygün, I., Shehwana, H., Toyran, N., Tercan Avci, S., Konu, O., Stemmler, M. P., & Alotaibi, H. (2019). The Transcription Factor Elf3 Is Essential for a Successful Mesenchymal to Epithelial Transition. Cells, 8(8), 858. 10.3390/cells8080858

Dalgıç, E., Konu, O., Öz, Z. S., & Chan, C. (2019). Lower connectivity of tumor coexpression networks is not specific to cancer. In silico biology, 13(1-2), 41–53. 10.3233/ISB-190472

Shehwana, H., & Konu, O. (2019). Comparative Transcriptomics Between Zebrafish and Mammals: A Roadmap for Discovery of Conserved and Unique Signaling Pathways in Physiology and Disease. Frontiers in cell and developmental biology, 7, 5. 10.3389/fcell.2019.00005

Cagnan, I., Cosgun, E., Konu, O., Uckan, D., & Gunel-Ozcan, A. (2019). PKNOX2 expression and regulation in the bone marrow mesenchymal stem cells of Fanconi anemia patients and healthy donors. Molecular biology reports, 46(1), 669–678. 10.1007/s11033-018-4522-z

Cingir Koker, S., Jahja, E., Shehwana, H., Keskus, A. G., & Konu, O. (2018). Cholinergic Receptor Nicotinic Alpha 5 (CHRNA5) RNAi is associated with cell cycle inhibition, apoptosis, DNA damage response and drug sensitivity in breast cancer. PloS one, 13(12), e0208982. 10.1371/journal.pone.0208982

Avci, M. E., Keskus, A. G., Targen, S., Isilak, M. E., Ozturk, M., Atalay, R. C., Adams, M. M., & Konu, O. (2018). Development of a novel zebrafish xenograft model in ache mutants using liver cancer cell lines. Scientific reports, 8(1), 1570. 10.1038/s41598-018-19817-w

Tunçer, S., Keşküş, A. G., Çolakoğlu, M., Çimen, I., Yener, C., Konu, O., & Banerjee, S. (2017). 15-Lipoxygenase-1 re-expression in colorectal cancer alters endothelial cell features through enhanced expression of TSP-1 and ICAM-1. Cellular signalling, 39, 44–54. 10.1016/j.cellsig.2017.07.022

Demirkol, S., Gomceli, I., Isbilen, M., Dayanc, B. E., Tez, M., Bostanci, E. B., Turhan, N., Akoglu, M., Ozyerli, E., Durdu, S., Konu, O., Nissan, A., Gonen, M., & 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. 10.7150/jca.17872

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

Mutlu, M., Saatci, Ö., Ansari, S. A., Yurdusev, E., Shehwana, H., Konu, O., Raza, U., & 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. 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(5), 4421–4430. 10.3892/mmr.2016.5059

Sayar, N., Karahan, G., Konu, O., Bozkurt, B., Bozdogan, O., & Yulug, I. G. (2015). Transgelin gene is frequently downregulated by promoter DNA hypermethylation in breast cancer. Clinical epigenetics, 7, 104. 10.1186/s13148-015-0138-5

Karahan, G., Sayar, N., Gozum, G., Bozkurt, B., Konu, O., & 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), 3131–3145. 10.3892/or.2015.3940

Alotaibi, H., Basilicata, M. F., Shehwana, H., Kosowan, T., Schreck, I., Braeutigam, C., Konu, O., Brabletz, T., & 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, 1849(6), 731–742. 10.1016/j.bbagrm.2015.01.005

Doldur-Balli, F., Ozel, M. N., Gulsuner, S., Tekinay, A. B., Ozcelik, T., Konu, O., & 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), 96. 10.1186/s12868-015-0229-4

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

Ersahin, T., Carkacioglu, L., Can, T., Konu, O., Atalay, V., & Cetin-Atalay, R. (2014). Identification of novel reference genes based on MeSH categories. PloS one, 9(3), e93341. 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., & 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, 97. 10.1186/1471-2350-14-97

Yildiz, G., Arslan-Ergul, A., Bagislar, S., Konu, O., Yuzugullu, H., Gursoy-Yuzugullu, O., Ozturk, N., Ozen, C., Ozdag, H., Erdal, E., Karademir, S., Sagol, O., Mizrak, D., Bozkaya, H., Ilk, H. G., Ilk, O., Bilen, B., Cetin-Atalay, R., Akar, N., & Ozturk, M. (2013). Genome-wide transcriptional reorganization associated with senescence-to-immortality switch during human hepatocellular carcinogenesis. PloS one, 8(5), e64016. 10.1371/journal.pone.0064016

Kaya, K. D., Karakülah, G., Yakicier, C. M., Acar, A. C., & Konu, O. (2011). mESAdb: microRNA expression and sequence analysis database. Nucleic acids research, 39(Database issue), D170–D180. 10.1093/nar/gkq1256

Sucularli, C., Senturk, S., Ozturk, M., & 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), 4111–4123. 10.1007/s11033-010-0531-2

Carkacioğlu, L., Atalay, R. C., Konu, O., Atalay, V., & Can, T. (2010). Bi-k-bi clustering: mining large scale gene expression data using two-level biclustering. International journal of data mining and bioinformatics, 4(6), 701–721. 10.1504/ijdmb.2010.037548

Acun, T., Terzioğlu-Kara, E., Konu, O., Ozturk, M., & Yakicier, M. C. (2010). Mdm2 Snp309 G allele displays high frequency and inverse correlation with somatic P53 mutations in hepatocellular carcinoma. Mutation research, 684(1-2), 106–108. 10.1016/j.mrfmmm.2009.11.008

Gur-Dedeoglu, B., Konu, O., Bozkurt, B., Ergul, G., Seckin, S., & Yulug, I. G. (2009). Identification of endogenous reference genes for qRT-PCR analysis in normal matched breast tumor tissues. Oncology research, 17(8), 353–365. 10.3727/096504009788428460

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

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

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

Dalkic, E., Kuscu, C., Sucularli, C., Aydin, I. T., Akcali, K. C., & Konu, O. (2006). Alternatively spliced Robo2 isoforms in zebrafish and rat. Development genes and evolution, 216(9), 555–563. 10.1007/s00427-006-0070-y

Konu, O., Xu, X., Ma, J. Z., Kane, J., Wang, J., Shi, S. J., & 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. Brain research. Molecular brain research, 121(1-2), 102–113. 10.1016/j.molbrainres.2003.11.012

Kane, J. K., Konu, O., Ma, J. Z., & Li, M. D. (2004). Nicotine coregulates multiple pathways involved in protein modification/degradation in rat brain. Brain research. Molecular brain research, 132(2), 181–191. 10.1016/j.molbrainres.2004.09.010

Li, M. D., Kane, J. K., & Konu, O. (2003). Nicotine, body weight and potential implications in the treatment of obesity. Current topics in medicinal chemistry, 3(8), 899–919. 10.2174/1568026033452203

Konu, O., & Li, M. D. (2002). Correlations between mRNA expression levels and GC contents of coding and untranslated regions of genes in rodents. Journal of molecular evolution, 54(1), 35–41. 10.1007/s00239-001-0015-z