BIOSYSTEMS ENGINEERING RESEARCH GROUP 

 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

1993 - 2010

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

2015

¨  Utku Deniz, Kutlu O. Ulgen, and Elif Ozkirimli, 2015, "Identification of Tpx inhibitors against pathogen-host interactions", Computational Biology and Chemistry 58 (2015) 126–138.

¨   Borklu-Yucel E., Eraslan S., Ulgen K., 2015, "Transcriptional remodeling in response to transfer upon carbon-limited or metformin-supplemented media in S. cerevisiaeand its effect on chronological life span" Appl Microbiol Biotechnol., DOI 10.1007/s00253-015-6728-5.

2014

¨  Kasavi C., Eraslan S., Arga K.Y., Toksoy Oner E., Kirdar B., 2014, "A system based network approach to ethanol tolerance in Saccharomyces cerevisiae", BMC Systems Biology, doi:10.1186/s12918-014-0090-6.

¨  Finore I., Di Donato P., Poli A., Kirdar B., Kasavi C., Toksoy Oner E., Nicolaus B., Lama L., 2014, "Use of Agro Waste Biomass for α-Amylase Production by Anoxybacillus amylolyticus: Purification and Properties.", Journal of Microbial & Biochemical Technology, 6:6, 320-326. doi:10.4172/1948-5948.1000162.

¨   Sertbas M., Ulgen K., Cakir T., 2014, "Systematic analysis of transcription-level effects of neurodegenerative diseases on human brain metabolism by a newly reconstructed brain-specific metabolic network", FEBS Open Bio, Vol. 4, 542–553.

¨   Dikicioglu D., Oc S., Rash B.M., Dunn W.B., Pir P., Kell D.B., Kirdar B., Oliver S.G., 2014, "Yeast cells with impaired drug resistance accumulate glycerol and glucose", Molecular Biosystems, doi:10.1039/c2mb25512j.

¨  Borklu-Yucel E., Eraslan S., Ulgen K., 2014, "The Impacts of Medium Acidity on Chronological Life Span of Saccharomyces cerevisiae: Lipids, Signaling Cascades, Mitochondrial and Vacuolar Functions", FEBS Journal, doi:10.1111/febs.12705.

2013

¨  Ozbuyukkaya G., Ozkirimli Olmez E., Ozergin Ulgen K., 2013, "Discovery of YopE inhibitors by pharmacophore-based virtual screening and docking", ISRN Bioinformatics, doi: http://dx.doi.org/10.1155/2013/640518.

¨  Gursoy Yılmaz O., Ozkirimli Olmez E., Ulgen K.O., 2013, "Targeting the Akt1 allosteric site to identify novel scaffolds through virtual screening", Computational Biology and Chemistry, http://dx.doi.org/10.1016/j.compbiolchem.2013.10.005.

¨  Cankorur-Cetinkaya A., Eraslan S., Kirdar B., 2013, "Transcriptional Remodelling in Response to Changing Copper Levels in Wilson and Menkes Disease Model of Saccharomyces cerevisiae", Molecular Biosystems, doi:10.1039/C3MB70276F.

¨  Borklu-Yucel E., Ulgen K., "Assesment of Crosstalks between Snf1 Kinase Complex and Sphingolipid Metabolism in S. cerevisiae via Systems Biology Approaches", Molecular Biosystems, doi:10.1039/C3MB70248K.

¨  Rende D., Baysal N., Kirdar B., 2013, "Complex Disease Interventions from a Network Model for Type 2 Diabetes", PlosOne, 8:6, e65854.

¨  Durmus Tekir S., Çakır T., Ardıç E., Sayılırbaş A.S., Konuk G., Konuk M., Sarıyer H., Uğurlu A., Karadeniz İ., Özgür A., Sevilgen F.E., Ulgen K.O., 2013, "PHISTO: Pathogen-Host Interaction Search Tool", Bioinformatics, doi: 10.1093/bioinformatics/btt137.

¨  Ozbuyukkaya G., Ozkirimli Olmez E., Ozergin Ulgen K., 2013, "Aminopurine derivatives as putative SopE inhibitors", Journal of Enzyme Inhibition and Medical Chemistry, DOI: http://dx.doi.org/10.3109/14756366.2012.759217.

¨  Durmus Tekir S., Ulgen K.O., 2013, "Systems biology of pathogen-host interaction: Networks of protein-protein interaction within pathogens and pathogen-human interactions in the post-genomic era", Biotechnology Journal, Special issue: Biotech Methods and Advances.

2012

¨  Kasavi C., Finore I., Lama L., Nicolaus B., Oliver S.G., Toksoy Oner E., Kirdar B., 2012, "Evaluation of industrial Saccharomyces cerevisiae strains for ethanol production from biomass", Biomass and Bioenergy, 45, 230-8, doi: 10.1016/j.biombioe.2012.06.013.

¨  Cankorur-Cetinkaya A., Dereli E., Eraslan S., Karabekmez E., Dikicioglu D., Kirdar B., 2012, "A Novel Strategy for Selection and Validation of Reference Genes in Dynamic Multidimensional Experimental Design in Yeast", PLoS ONE 7(6): e38351 doi:10.1371/journal.pone.0038351.

¨  Dikicioglu D., Dunn W.B., Kell D.B., Kirdar B., Oliver S.G., 2012, "Short- and Long-Term Dynamic Responses of the Metabolic Network and Gene Expression in Yeast to a Transient Change in the Nutrient Environment", Mol Biosyst 8(6):1760-74.

¨  Durmus Tekir S., Cakir T., Ulgen K.O., 2012 "Infection Strategies of Bacterial and Viral Pathogens through Pathogen-Human Protein-Protein Interactions", Frontiers in Microbial Immunology, Reserch topic: Systems Biology of Microbial Infection, Vol 3, 46.

¨  Nalbantoğlu B., Durmuş Tekir S., Ülgen K., 2012, "Wnt Signaling Network in Homo Sapiens", Cell Metabolism - Cell Homeostasis and Stress Response. Edited by Paula Bubulya. Rijeka: Intech, ISBN: 978-953-307-978-3.

2011

¨  Borklu Yucel E., Ulgen K.O., 2011, "A Network-Based Approach on Elucidating the Multı-Faceted Nature of Chronological Ageing in S. cerevisiae", PLoS ONE, 6(12):e29284, doi: 10.1371/journal.pone.0029284.

¨  Dikicioglu D., Karabekmez E., Rash B., Pir P., Kirdar B., Oliver S.G., 2011, "How yeast re-programmes its transcriptional profile in response to different nutrient impulses", BMC Systems Biology, 5:148, doi: 10.1186/1752-0519-5-148.

¨  Eren Toku A., Durmuş Tekir S., Kavun Özbayraktar F.B., Ülgen K., 2011, "Reconstruction and Crosstalk of Protein-Protein Interaction Networks of Wnt and Hedgehog Signaling in Drosophila Melanogaster", Computational Biology and Chemistry, Vol. 35(5), 282-292.

¨  Rende D., Baysal N., Kırdar B., (2011), "A Novel Integrative Network Approach to Understand the Interplay between Cardiovascular Disease and Other Complex Disorders", Molecular Biosystems, Vol. 7 (7), 2205-2219, doi:10.1039/c1mb05064h.

¨  Acuner Özbabacan S.E., Durmuş Tekir S., Ülgen K.Ö., 2011, "Crucial components in toll-like receptor signalling network as key regulators for immunological disorders", International Journal of Physical Sciences, Vol. 6 (8), 2016-2026.

¨  Finore I., Kasavi C., Poli A., Romano I., Toksoy Oner E., Kirdar B., Dipasquale L., Nicolaus B., Lama L., 2011, “Purification, biochemical characterization and gene sequencing of a thermostable raw starch digesting α-amylase from Geobacillus thermoleovorans subsp. stromboliensis subsp. nov.”, World J Microbiol Biotechnol, Vol. 27, 2425-2433, doi:10.1007/s11274-011-0715-5.

¨  Kavun Özbayraktar F.B. and Ülgen K.Ö., 2011, "Stoichiometric Network Reconstruction and Analysis of Yeast Sphingolipid Metabolism Incorporating Different States of Hydroxylation", Biosystems, Vol. 104 (1), 63-75.