BIOSYSTEMS ENGINEERING RESEARCH GROUP 

 
KUTLU ÜLGEN-Publications
  1. 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.

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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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, Special Issue: Systems Biology of Microbial Infection, Vol. 3, 46.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. Durmuş Tekir S., Ümit P., Eren A., Ülgen K.Ö., (2010), "Reconstruction of insulin signaling protein-protein interaction network in Homo sapiens", Journal of Biomedicine and Biotechnology, doi:10.1155/2010/690925.

  18. Kavun Özbayraktar F.B. and Ülgen K.Ö., (2010), Drug Target Identification in Sphingolipid Metabolism by Computational Systems Biology Tools: Metabolic Control Analysis and Metabolic Pathway Analysis, Journal of Biomedical Informatics, Vol. 43,537-549.

  19. Kavun Özbayraktar, F.B,Ülgen, K., (2009) Molecular facets of sphingolipids: Potential drug targets, Biotechnology Journal,Vol. 4 (7), 1028-1041 (Review).

  20. S. Durmuş, K.Y.Arga, K. Ülgen (2009) Drug targets for tumorigenesis: Insights from structural analysis of EGFR signaling network, Journal of Biomedical Informatics, 30, 327-338.

  21. Esra YÜCEL, Ayça CANKORUR, Elif DERELİ, Feras ALAZİ, İlkay ASLANDAG, Betül KAVUN, Saliha D. TEKIR, K. Yalcin ARGA, Kutlu Ö. ÜLGEN, (2008) Deciphering the Cross-talk between Sphingolipid Mechanism and Signaling Pathways in Baker’s Yeast, Sigma: Journal of Engineering and Natural Sciences, 26(3): 162-174.

  22. D. Dikicioğlu, Pınar Pir, Z. İlsen Önsan, Kutlu Ö. Ülgen, Betül Kırdar, Stephen G. Oliver, (2008) Integration of Metabolic Modelling and Phenotypic Data in Evaluation and Improvement of Ethanol Production Using Respiration-Deficient Mutants of S. cerevisiae, Applied and Environmental Microbiology, 74 (18): 5809-5816.

  23. Pınar Pir, Betül Kırdar, Andrew Hayes, Z. İlsen Önsan, Kutlu Ö. Ülgen, Stephen G. Oliver, (2008) Exometabolic and transcriptional response in relation to phenotype and gene copy number in respiration-related deletion mutants of S. cerevisiae, Yeast, 25: 661-672.

  24. Mehmet M. Altintas, Kutlu O. Ulgen, Darryl Palmer-Toy, Vivian E. Shih, Dhinakar S. Kompala, Jochen Reiser (2008) Emerging Roles for Metabolic Engineering - Understanding Primitive and Complex Metabolic Models and Their Relevance to Healthy and Diseased Kidney Podocytes, Current Chemical Biology, 2(1): 68-82.

  25. Tunahan Cakir, Selma Alsan, Hale Saybasili, Ata Akin and Kutlu O Ulgen (2007) Reconstruction and flux analysis of coupling between metabolic pathways of astrocytes and neurons: application to cerebral hypoxia, Theoretical Biology and Medical Modelling, 4:48.

  26. Tunahan Çakır, Zeynep İlsen Önsan, Betül Kırdar, Kutlu Özergin Ülgen, Jens Nielsen (2007) Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae, BMC Systems Biology, DOI: 10.1186/1752-0509-1-18.

  27. K. Y. Arga, Zeynep İlsen Önsan, Betül Kırdar, Kutlu Özergin Ülgen, Jens Nielsen (2007) Understanding Signaling in Yeast: Insights from Network Analysis, Biotechnology and Bioengineering, 97(5), 1246-1258.

  28. Tunahan Çakır, Kiran Raosaheb Patil, Zeynep İlsen Önsan, Kutlu Özergin Ülgen, Betül Kırdar, Jens Nielsen (2006) Integration of metabolome data with metabolic networks reveals reporter reactions, Molecular Systems Biology, DOI: 10.1038/msb4100085.

  29. S. Durmuş, T. Çakır, K. Ülgen (2006) Analysis of enzymopathies in the human red blood cells by constraint based stoichiometric modeling approaches, Computational Biology and Chemistry, 30, 327-338.

  30. Pınar Pir, Betül Kırdar, Andrew Hayes, Z. İlsen Önsan, Kutlu Ö. Ülgen, Stephen G. Oliver, (2006) Integrative Investigation of Metabolic and Transcriptomic Data, BMC Bioinformatics, 7:203.

  31. Pınar Pir, Kutlu Ö. Ülgen, Andrew Hayes, Z. İlsen Önsan, Betül Kırdar, Stephen G. Oliver, (2006) Annotation of Unknown Yeast ORFs by Correlation Analysis of Microarray Data and Extensive Literature Searches, Yeast, 23, 553-571.

  32. S. Tiveci, A.Akın, T. Çakır, H. Saybaşılı, K. Ülgen (2005) Modelling of calcium dynamics in brain energy metabolism and Alzheimer’s disease’, Computational Biology and Chemistry, 29, 151-162.

  33. Nigar Kantarci, Fahir Borak, Kutlu O. Ulgen (2005) A Study on Hydrodynamics and Heat Transfer in a Bubble Column Reactors with Yeast and Bacterial Cell Suspensions, The Canadian Journal of Chemical Engineering, 83, 764-773.

  34. Nigar Kantarci, Fahir Borak, Kutlu O. Ulgen (2005) Bubble Column Reactors: Review, Process Biochemistry, 40, 2263-2283.

  35. T. Cakir, C.S. Tacer, K. Ö. Ülgen (2004) “Metabolic Pathway Analysis of Enzymedeficient Human Red Blood Cells”, BioSystems, 86(3), 251-260.

  36. T. Cakir, B. Kırdar, K. Ö. Ülgen (2004) “Metabolic Pathway Analysis of Yeast Strenghtens the Bridge between Transcriptomics and Metabolic Networks”, Biotechnology and Bioengineering, 86(3), 251-260.

  37. T. Cakir, K Y Arga, M.M. Altintas, K. Ö. Ülgen (2004) “Flux analysis of recombinant Saccharomyces cerevisiae YPB-G utilizing starch for optimal ethanol production”, Process Biochemistry, 39, 2097-2108.

  38. K Y Arga, T. Cakir, Pinar Pir, Nevra Özer, M.M. Altintas, K. Ö.Ülgen (2004) “Transfer function approach in structured modeling of recombinant yeast utilizing starch”, Process Biochemistry, 39, 1237-1248.

  39. M.M. Altintas, K. Ülgen, B. Kırdar, Z.İ.Önsan, S. Oliver, (2003) “Optimal substrate feeding policy for fed-batch cultures of Recombinant S. cerevisiae, YPG expressing bi-functional fusion protein displaying amylolytic activities”, Enzyme and Microbial Technology, 33, 262-269.

  40. E. Toksoy-Öner, B. Kırdar, Z.İ.Önsan, K. Ülgen (2003) " Modeling of the induced expression for high-level production of a foreign protein by recombinant E. coli under the control of T7 phage promoter ", Process Biochemistry, 39, 315-323.

  41. M.Düzenli, K. Ö. Ülgen (2002) ‘Modelling of TaqI endonuclease Purification by HPLC’, Turkish Journal of Chemistry, 26(6), 877-887.

  42. M.M. Altıntaş, B. Kırdar, Z.İ. Önsan, K. Ö. Ülgen, S. G. Oliver (2002) ‘Improvement of ethanol production from starch by recombinant yeast through manipulation of environmental factors’, Enzyme and Microbial Technology, 31, 640-647.

  43. M.M. Altıntaş, B. Kırdar, Z.İ. Önsan, K. Ö. Ülgen (2002) ‘Cybernetic Modelling of Growth and Ethanol Production in a Recombinant S.cerevisiae Strain Secreting a Bifunctional Fusion Protein’, Process Biochemistry, 37(11), 1439-1445.

  44. K.Ö. Ülgen, B. Saygılı, Z.İ. Önsan, B. Kırdar (2002) Bioconversion of Starch into Ethanol by a Recombinant S.cerevisiae Strain YPB-AB, Process Biochemistry, 37(10), 1157-1168.

  45. S. Özyurt, B.Kırdar, K. Ö. Ülgen (2002) ‘Recovery of Antithrombin III From Milk By Expanded Bed Chromatography’ , Journal of Chromatography A., 944, 203-210.

  46. M.M. Altıntaş, B. Kırdar, Z.İ. Önsan, K. Ö. Ülgen (2001) ‘Plasmid Stability in a Recombinant S.cerevisiae Strain Secreting A Bifunctional Fusion Protein’, Journal of Chemical Technology and Biotechnology, 76(6), 612-618.

  47. E. Güzeltunç, K. Ö. Ülgen (2001) ‘Recovery of Actinorhodin from Fermentation Broth’, Journal of Chromatography A., 914, 67-76.

  48. C.Tamerler, K. Ülgen, B. Kırdar, Z.İ. Önsan, (2001) ‘A Structured Model for Intracellular EcoRI Endonuclease Production by Recombinant E.coli 294’, Process Biochemistry, 36, 621-627.

  49. A.Avcı, M.C.Camurdan and K. Ö. Ülgen (2000) “Quantitative Description of Protein Adsorption by Frontal Analysis”, Process Biochemistry, 36(1), 141-148.

  50. M.Düzenli, K. Ö. Ülgen (2000) ‘Optimisation of Mobile Phase Conditions for the Purification of TaqI endonuclease’, Chromatographia, 52 (6), 377-380.

  51. B.Özbek, K. Ö. Ülgen (2000) “The Stability of Enzymes after Sonication”, Process Biochemistry, 35 (9), 1037-1043.

  52. M. M. Altıntaş, K. Ülgen (1999) ‘Growth of Thermus aquaticus and its TaqI Endonuclease Production’ , Acta Biotechnologica, 19, 45-56.

  53. M. M. Altıntaş, N. Özer, K. Ö. Ülgen (1998) ‘Purification of TaqI Endonuclease from Thermus Aquaticus’ , Journal of Chromatography A., 828, 373-381.

  54. K. Ö. Ülgen, F. Mavituna (1998) “Oxygen Transfer and Uptake in  Streptomyces coelicolor A3(2) Culture in a Batch Bioreactor”, Journal of Chemical Technology and Biotechnology, 73, 243-250.

  55. G. Birol, P. Doruker, B. Kırdar, Z.I.Önsan and K.Ülgen (1998) “Mathematical Description of Ethanol Fermentation by Immobilized Saccharomyces cerevisiae”, Process Biochemistry, 33(7), 763-771.

  56. M. M. Habbaba and K.Ülgen (1997) “Analysis of Protein Adsorption to Ion Exchangers in a Finite Bath”, Journal of Chemical Technology and Biotechnology, 69 (4), 405-414.

  57. S.Yılmaz, B. Beleli, M. Fesli, K. Ülgen (1997) “ A study on the Effect of Operating Parameters on Protein Purification by Ion Exchange Column Chromatography”, Institution of Chemical Engineers Research Event 97, p 841-844, Nottingham-U.K.

  58. G. Birol and K.Ülgen (1995) “A Study on the Effect of Inoculum On Yeast Cell Growth and Ethanol Production”, Doğa - Turkish Journal of Chemistry 19 (4), 250-257.

  59. 43.  M. Elibol. K. Ülgen, K. Kamaruddin, F. Mavituna(1995) “Effect of Inoculum Type on Actinorhodin Production by Streptomyces coelicolor A3(2)”, Biotechnology Letters 17 (6), 579-582.

  60. K. Özergin and F. Mavituna (1994) “Production of Actinorhodin by Immobilised and Freely Suspended Streptomyces coelicolor A3(2)” ECB6 Proceedings of the 6th European Congress on Biotechnology (eds. L. Alberghina, L. Frontali, P. Sensi), Progress in Biotechnology Series -9, Elsevier Science B.V., pp. 497-500.

  61. K. Özergin-Ülgen and F. Mavituna (1994) “Comparison of the Activity of Immobilised and Freely Suspended Streptomyces coelicolor A3(2)”, Applied Microbiology and Biotechnology  41, 197-202.

  62. K. Özergin-Ülgen and F. Mavituna (1993) “Actinorhodin Production by Streptomyces coelicolor A3(2): Kinetic Parameters Related to Growth, Substrate Uptake and Production”, Applied Microbiology and Biotechnology 40, 457-462.

  63. K. Özergin, Y.Khoury, Z.İ. Önsan, B. Kırdar (1993) “ The Effect of Immobilisation on Yeast Cell Growth and Ethanol Production”, Doğa - Turkish Journal of Chemistry 17 (2), 154-159.