2017

 

• Turanli B, Gulfidan G, Arga KY. Transcriptomic-Guided Drug Repositioning Supported by a New Bioinformatics Search Tool: geneXpharma. OMICS: A Journal of Integrative Biology, accepted, 2017.
• Bereketoglu C, Arga KY, Eraslan S, Mertoglu B. Genome reprogramming in Saccharomyces cerevisiae upon nonylphenol exposure.  Physiological Genomics, accepted, 2017.
• Gov E, Kori M, Arga KY. Multi-omics analysis of tumor microenvironment proposed GATA2 and miRNA-124-3p as novel biomarkers in ovarian cancer. OMICS: A Journal of Integrative Biology, accepted, 2017.
• Gov E, Arga KY. Differential co-expression analysis reveals a novel prognostic gene module in ovarian cancer. Scientific  Reports, 7: 4996, 2017.
• Ayyildiz D, Arga KY. Hypothesis: Are there molecular signatures of Yoga practice in peripheral blood mononuclear cells?, OMICS: A Journal of Integrative Biology, 21(7): 426-428, 2017. 
• Gov E., Kori M, Arga KY. RNA based ovarian cancer research from ‘a gene to systems biomedicine’ perspective, Syst Biol Reprod Med., 2:1-20, 2017. doi: 10.1080/19396368.2017.1330368
• Ayyildiz D, Gov E, Arga KY. Ovarian cancer differential interactome and network entropy analysis reveal new candidate biomarkers, OMICS: A Journal of Integrative Biology, 21(5):285-294, 2017. doi: 10.1089/omi.2017.0010

 2016

 

• Ayyildiz D, Arga KY, Avci FG, Altinisik FE, Gurer C, Gulsoy Toplan G, Kazan D, Wozny K, Brügger B, Mertoglu B, Sarıyar Akbulut B. Transcriptomic analysis displays the effect of (-)-roemerine on the motility and nutrient uptake in Escherichia coli. Current Genomics, 1-14, 2016. DOI: 10.1007/s00294-016-0673-4

• Dayan İE, Arga KY, Ulgen K. Multi-omics approach to novel therapeutic targets for cancer and aging related diseases: Role of Sld7 in yeast aging network. OMICS: A Journal of Integrative Biology, 21(2):100-113. doi: 10.1089/omi.2016.0157.

• Karagoz K, Lehman H, Stairs D, Sinha R, Arga KY. Proteomic and metaolic signatures of esophageal squamous cell carcinoma. Current Cancer Drug Targets, 16: 721-736, 2016.

• Kori M, Aydın B, Unal S, Arga KY, Kazan D. Metabolic biomarkers and neurodegeneration: A pathway enrichment analysis of Alzheimer’s disease, Parkinson’s disease and Amyotrophic leteral sclerosis. OMICS: A Journal of Integrative Biology, 20(11): 645-661, 2016. Doi:10.1089/omi.2016.0106

• Bereketoglu C, Arga KY, Eraslan S, Mertoglu B. Analysis of transcriptional profiles of Saccharomyces cerevisiae exposed to bisphenol A. Current Genetics, 2016. Doi:10.1007/s00294-016-0633-z

• Kori M, Gov E, Arga KY. Molecular Signatures of Ovarian Diseases: Insights from Network Medicine Perspective. Systems Biology in Reproductive Medicine, 62(4):266-282, 2016. Doi:10.1080/19396368.2016.1197982 

• Karagoz K, Sevimoglu T, Arga KY. Integration of multiple biological features yield high condifence human protein interactome. J. Theoretical Biology, 403:85-96, 2016. Doi:10.1016/j.jtbi.2016.05.020

• Gov E, Arga KY. Integrative cooperation and hierarchical operation of microRNA and transcription factor crosstalk in human transcriptional regulatory network. IET Systems Biology, 10(6):219-228, 2016. Doi: 10.1049/iet-syb.2016.0001

• Sinha I, Karagoz K, Fogle R, Hollenbeak C, Zea A, Arga KY, Stanley A, Hawkes W, Sinha R. “Omics” of Selenium Biology: A Prospective Study of Plasma Proteome Network Before and After Selenized-Yeast Supplementation in Healthy Men. OMICS: A journal of Integrative Biology, 20(4):202-2013, 2016.

2015

• Sevimoglu T, Arga KY. Computational systems biology approach to elucidate the disease mechanism yields a proposal for psoriasis pathway and target genes. OMICS: A journal of Integrative Biology, accepted, 2015.

• Calimlioglu B, Karagoz K, Sevimoglu T, Kilic E, Gov E, Arga KY. Tissue-Specific Molecular Biomarker Signatures of Type 2 Diabetes: An Integrative Analysis of Transcriptomics and Protein–Protein Interaction Data. OMICS: A journal of Integrative Biology, in press, 2015.

• Diken E, Ozer T, Arikan M, Emrence Z, Toksoy Oner E, Ustek D, Arga KY. Genomic analysis reveals the biotechnological and industrial potential of levan producing halophilic extremophile, Halomonas smyrnensis AAD6T. SpringerPlus, 4(1), 2015.

• Karagoz K, Sinha R, Arga KY. Triple Negative Breast Cancer: A multi-omics network discovery strategy for candidate targets and driving pathways. OMICS: A journal of Integrative Biology, 19(2), 2015.

• Yasar Yildiz S, Radchenkova N, Arga KY, Kambourova M, Toksoy Oner E. Genomic analysis of Brevibacillus thermoruber 423 reveals its biotechnological and industrial potential. Applied Microbiol Biotechnol, 99(5),  2015.

2014

• Sarilmiser Kazak H, Ates O, Ozdemir G, Arga KY, Toksoy Oner E. Effective stimulating factors for microbial levan production by Halomonas smyrnensis AAD6T. Journal of Bioscience and Bioengineering, in press,  2014.

• Sevimoglu T, Arga KY. The role of protein interaction networks in systems biomedicine.Computational and Structural Biotechnology Journal, 11(18):22-27, 2014. doi:10.1016/j.csbj.2014.08.008

• Kasavi C, Eraslan S, Arga KY, Toksoy Oner E, Kirdar B. A System Based Network Approach to Ethanol Tolerance in Saccharomyces cerevisiae. BMC Systems Biology, 8:90, (2014). doi:10.1186/s12918-014-0090-6.

• Dilgimen AS, Arga KY, Erdmann VA, Wittmann-Liebold B, Denizci AA, Kazan D. Comparison of protein expression profiles of novel Halomonas smyrnensis AAD6T and Halomonas salina DSMZ 5928T. Natural Science, 6, 628-640, (2014). doi:10.4236/ns.2014.69062

• Gov E, Arga KY. Systems biology solutions to challenges in marine biotechnology. Frontiers in Marine Science, 1:14, (2014). doi:10.3389/fmars.2014.00014

• Gov E, Arga KY. Genetic mutations are characterized by increase in entropy at the transcriptional level. J. Biological Systems, 22(3):1-15, 2014. doi:10.1142/S0218339014500132

Earlier 2014

• Yasar Yildiz S., Margarita Kambourova, Arga KY, Ebru Toksoy Oner, Draft Genome Sequence of Exopolysaccharide-Producing Thermophilic Bacterium Brevibacillus thermoruber Strain 423. Genome announcements ASM, doi: 10.1128/genomeA. 00774-13 (2013).

• Ateş, Ö., Arga KY, Toksoy Öner, E., The stimulatory effect of mannitol on levan biosynthesis: lessons from metabolic systems analysis of Halomonas smyrnensis AAD6(T.) Biotechnology Progress 29(6):1386-97 (2013).

• Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttilä M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology, 26(10):1155-60, 2008.doi:10.1038/nbt1492

• Karagöz K, Arga KY. Assessment of high–confidence protein–protein interactome in yeast. J. Computational Biology and Chemistry, 45:1-8, 2013. doi:10.1016/j.compbiolchem.2013.03.002

• Ateş Ö, Arga KY, Toksoy Öner E. The stimulatory effect of mannitol on levan biosynthesis: lessons from metabolic systems analysis of Halomonas smyrnensis AAD6. Biotechnology Progress, 2013. doi:10.1002/btpr.1823

• Sogutcu E, Emrence Z, Arikan M, Cakiris A, Abaci N, Oner ET, Ustek D, Arga KY. Draft Genome of Halomonas smyrnensis AAD6T . Journal of Bacteriology, 194 (20), 5690-5691, (2012). doi:10.1128/JB.00559-12

• Ateş, Ö., Toksoy Öner, E., Arga KY, “Genome-scale Reconstruction of Metabolic Network for a Halophilic Extremophile, Chromohalobacter salexigens DSM 3043” BMC Systems Biology, 5:12 (2011).

• Ates Ö, Toksoy Öner E, Arga KY. Genome-scale reconstruction of metabolic network for a halophilic extremophile, Chromohalobacter salexigens DSM 3043. BMC Systems Biology, 5:12, 2011.doi:10.1186/1752-0509-5-12

• Vanderschuren H, Heinzmann D, Faso C, Stupak M, Arga KY, Hoerzer H, Laizet Y, Leduchowska P, Silva N, Simkova K. A cross-sectional study of biotechnology awareness and teaching in European high schools. New Biotechnology, 27(6):822-828, 2010.doi:10.1016/j.nbt.2010.01.338

• Tekir SD, Arga KY, Ülgen KÖ. Drug targets for tumorigenesis: Insights from structural analysis of EGFR signaling network, Journal of Biomedical Informatics, 42:228-236, (2009), doi:10.1016/j.jbi.2008.08.008

• Arga KY, Önsan ZI, Kırdar B, Ülgen KÖ, Nielsen J. Understanding signaling in yeast: insights from network analysis. Biotechnology & Bioengineering, 97(5):1246-1258. 2007.doi:10.1002/bit.21317

• Çakır T, Arga KY, Altıntas MM, Ülgen KÖ. Flux analysis of the recombinant Saccharomyces cerevisiae YPB-G utilizing starch for optimum ethanol production. Process Biochemistry, 39:2097-2108, 2004.

• Arga KY, Çakır T, Pir P, Özer N, Altıntas MM, Ülgen KÖ. Transfer function approach in structured modeling of recombinant yeast utilizing starch. Process Biochemistry, 39:1237-1248. 2004.