Kutlu ÜLGEN

Prof.
E-mail: 

ulgenk@bogazici.edu.tr

Address: 
Department of Chemical Engineering, Boğaziçi University, Bebek 34342, Istanbul-TURKEY
Phone: 
+90 (212) 359 6869
Web: 

http://ulgen.che.bogazici.edu.tr

Education: 

PhD: Chemical Engineering, University of Manchester, England, 1992 
MS: Chemical Engineering, Bogazici University, Turkey, 1989 
BS: Chemical Engineering, Bogazici University, Turkey, 1987

Experience: 

2012-Dec 2015: Associate Dean, Faculty of Engineering, Bogazici University 
2009 - 2011: Head, Department of Chemical Engineering, Bogazici University 
2002 - present: Professor, Department of Chemical Engineering, Bogazici University 
1996 - 2002: Associate Professor, Department of Chemical Engineering, Bogazici University 
1994 - 1996: Assistant Professor, Department of Chemical Engineering, Bogazici University 
1992 - 1994: Instructor, Department of Chemical Engineering, Bogazici University 
1989 - 1991: Teaching Assistant, Department of Chemical Engineering, UMIST, Manchester-U.K.

Research Interests: 
  • Reconstruction of signaling networks in yeast, worm and human using systems biology approaches
  • Metabolic pathway engineering
  • Computational physiology
  • Protein purification
Selected Papers: 
  • Elif Gencturk, Muge Kasim, Berna Morova, Alper Kiraz, and Kutlu O. Ulgen (2022) Understanding the Link between Inflammasome and Apoptosis through the Response of THP‐1 Cells against Drugs Using Droplet- Based Microfluidics https://doi.org/10.1021/acsomega.1c06569
  • Gencturk E., Mutlu S., Ulgen K.O. (2022) Fabrication Protocol for Thermoplastic Microfluidic Devices: Nanoliter Volume Bioreactors for Cell Culturing. In: . Methods in Molecular Biology. Springer, New York, NY. https://doi.org/10.1007/7651_2021_397
    Print ISSN 1064-3745, Electronic ISSN1940-6029
  • B Atas, CS Aksoy, FG Avci, NA Sayar, K Ulgen, E Ozkirimli, BS Akbulut, 2022, Current Microbiology 79 (5), 1-8
  • Muge Kasim, Elif Gencturk, and Kutlu O. Ulgen Real-Time Single-Cell Monitoring of Drug Effects Using Droplet-Based Microfluidic Technology: A Proof-of-Concept Study OMICS A Journal of Integrative Biology Volume 25, Number 10, 25(10):641-651. 2021 a Mary Ann Liebert, Inc. DOI: 10.1089/omi.2021.0128 Epub 2021 Sep 28
  • Elif Esvap, Kutlu O Ulgen, Advances in Genome-Scale Metabolic Modeling toward Microbial Community Analysis of the Human Microbiome, ACS Synthetic Biology, 2021 10 (9), 2121-2137. DOI: 10.1021/acssynbio.1c00140
  • Merve Yuce, Elif Ozkirimli, Berna Sariyar Akbulut Kutlu Ulgen, Live Cell Imaging of Peptide Uptake Using a Microfluidic Platform 2021 , International Journal of Peptide Research and Therapeutics,  volume 27, pages2003–2013 (2021). DOI 10.1007/s10989-021-10228-6
  • Ozlem Ozbek, Kutlu O. Ulgen, and Nazar Ileri Ercan, The Toxicity of Polystyrene-Based Nanoparticles in Saccharomyces cerevisiae Is Associated with Nanoparticle Charge and Uptake Mechanism, Chemical Research in Toxicology 2021, © 2021 American Chemical Society
    https://doi.org/10.1021/acs.chemrestox.0c00468

  • M Sertbas, KO Ulgen (2020). Genome-Scale Metabolic Modeling for Unraveling Molecular Mechanisms of High Threat Pathogens. Frontiers in Cell and Developmental Biology, 8.

  • E Gencturk, E Yurdakul, AY Celik, S Mutlu, KO Ulgen (2020). Cell trapping microfluidic chip made of Cyclo olefin polymer enabling two concurrent cell biology experiments with long term durability. Biomedical microdevices, 22(1), 1-12.
  • E Gencturk, KO Ulgen, S Mutlu (2020). Thermoplastic microfluidic bioreactors with integrated electrodes to study tumor treating fields on yeast cells. Biomicrofluidics, 14(3), 034104.
  • MG Durmaz, A Dilmac, B Camli, E Gencturk, ZCC Ozdil, AE Pusane, AD Yalcinkaya, KO Ulgen, T Tugcu, (2020). Preliminary Studies on Flow Assisted Propagation of Fluorescent Microbeads in Microfluidic Channels for Molecular Communication Systems. In International Conference on Bio-inspired Information and Communication Technologies (pp. 294-302). Springer, Cham.
  • Ege Ertekin, Elif Gencturk, Muge Kasim, and Kutlu O. Ulgen (2020) A Drug Repurposing and Protein-Protein Interaction Network Study of Ribosomopathies Using Yeast as a Model System OMICS A journal of Integrative Biology, 2019 online, 2020 print Volume 24, 2020
  • ZB Yagci, E Esvap, HA Ozkara, KO Ulgen, E Ozkirimli (2019) Inflammatory response and its relation to sphingolipid metabolism proteins: Chaperones as potential indirect anti-inflammatory agents. Advances in Protein Chemistry and Structural Biology 114 (1), 153-220 ISSN 1876-1623
  • P Yılmaz, EÖ Er, S Bakırdere, K Ülgen, B Özbek (2019) Application of supercritical gel drying method on fabrication of mechanically improved and biologically safe three-component scaffold composed of graphene oxide/chitosan/hydroxyapatite and characterization studies, Journal of Materials Research and Technology, Volume 8, Issue 6, Pages 5201-5216
  • E Gencturk, E Yurdakul, AY Celik, S Mutlu, KO Ulgen (2019) Application of Thermoplastic Microbioreactor to the Single Cell Study of Budding Yeast to Decipher the Effect of 5-Hydroxymethylfurfural on Growth, International Journal of Chemical and Molecular Engineering 13 (6), 280-287
  • IE Odabasi, E Gencturk, S Puza, S Mutlu, KO Ulgen (2018) A low cost PS based microfluidic platform to investigate cell cycle towards developing a therapeutic strategy for cancer  Biomedical microdevices 20 (3), 57 
  • M Sertbas, KO Ulgen (2018) Unlocking Human Brain Metabolism by Genome-Scale and Multiomics Metabolic Models: Relevance for Neurology Research, Health, and Disease  Omics: a journal of integrative biology 22 (7), 455-467
  • O Bayraktar, E Ozkirimli, KO Ulgen (2018) In silico identification of novel orthosteric inhibitors of Sphingosine Kinase 1 (SK1)  Current Protein and Peptide Science 19 (5), 430-444 
  • Elif Gencturk, Senol Mutlu and Kutlu O. Ulgen (2017) Advances in Microfluidic Devices Made from Thermoplastics used in Cell Biology and Analyses, Biomicrofluidics, Biomicrofluidics Vol.11, Issue 5. DOI: 10.1063/1.4998604
  • Buge Yilmazer, Begum Yagci, Emre Bakar, Burcu Ozden, Elif Ozkirimli, Kutlu O. Ulgen (2017) Investigation of novel pharmacological chaperones for Gaucher disease, Journal of Molecular Graphics and Modelling, 76, 364-378 doi: https://doi.org/10.1016/j.jmgm.2017.07.014
  • Sercan Altundemir, Kerem Uguz, Kutlu Ulgen (2017) A review on wax printed microfluidic paper-based devices for international health, Biomicrofluidics, 11 (4), http://dx.doi.org/10.1063/1.4991504
  • Sevde Puza, Elif Gencturk, Irem Ezgi Odabasi, Emre Iseri, Senol Mutlu, Kutlu O. Ulgen (2017) Fabrication of cyclo olefin polymer microfluidic devices for trapping and culturing of yeast cells, Biomedical Microdevices 19 (2), 40 doi:10.1007/s10544-017-0182-3
  • Özge Bayraktar, Elif Ozkirimli, Kutlu O. Ulgen (2017) Sphingosine kinase 1 (SK1) allosteric inhibitors that target the dimerization site, Computational Biology and Chemistry, doi: https://doi.org/10.1016/j.compbiolchem.2017.05.006
  • İrem Ezgi Dayan, Kazim Yalcin Arga, Kutlu O. Ulgen (2017) 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
  • Saliha Durmuş, Kutlu O. Ulgen (2017) Comparative interactomics for virus-human protein-protein interactions: DNA viruses versus RNA viruses, FEBS Open Bio 7 (1), 96-107 December 2016 / DOI: 10.1002/2211-5463.12167
  • Özge Bayraktar, Elif Ozkirimli, Kutlu O. Ulgen (2016) In Silico Identification of Novel Orthosteric Inhibitors of Sphingosine Kinase 1 (SK1), Current protein & peptide science
  • Utku Deniz, Elif Ozkirimli, Kutlu O. Ulgen(2016) A systematic methodology for large scale compound screening: A case study on the discovery of novel S1PL inhibitors, Journal of Molecular Graphics and Modelling (2016) 63, 110-124 doi:10.1016/j.jmgm.2015.11.004
  • Emre Iseri, Kutlu O. Ulgen, Cetin Yilmaz, and Senol Mutlu (2016) Fabrication of steel displacement amplifiers integrated to microfluidic channels." In Micro Electro Mechanical Systems (MEMS), 2016 IEEE 29th International Conference on, pp. 493-496. IEEE, doi: 10.1109/MEMSYS.2016.7421669
  • Pinar Eribol, Kerem Uguz, Kutlu O. Ulgen (2016) Screening Applications In Drug Discovery Based On Microfluidic Technology, Biomicrofluidics, 10, 011502 (2016); doi: 10.1063/1.4940886
  • Esra Borklu-Yucel & Serpil Eraslan & Kutlu O. Ulgen 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 (2015) DOI 10.1007/s00253-015-6728-5
  • Utku Deniz, Kutlu O. Ulgen, Elif Ozkirimli Identification of potential Tpx inhibitors against pathogen-host interactions Computational biology and chemistry, Volume58, (2015) 126–138 http://dx.doi.org/10.1016/j.compbiolchem.2015.05.005
  • Esra Borklu Yucel, Serpil Eraslan, Kutlu O. Ulgen, 2014 The Impacts of Medium Acidity on Chronological Life Span of Saccharomyces cerevisiae: Lipids, Signaling Cascades, Mitochondrial and Vacuolar Functions, FEBS Journal
  • (Impact Factor: 4.25). 01/2014; DOI:10.1111/febs.12705.
  • Oya Gursoy Yilmaz, Elif Ozkirimli Olmez, Kutlu O Ulgen, 2014/2/28 Targeting the Akt1 allosteric site to identify novel scaffolds through virtual screening, Computational biology and chemistry,
  • Volume48, 1-13. http://dx.doi.org/10.1016 /j.compbiolchem.2013.10.005
  • Mustafa Sertbas, Kutlu Ülgen, Tunahan Çakır 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 4 (2014) 542–553. http://dx.doi.org/10.1016/j.fob.2014.05.006
  • 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.
  • Borklu Yucel E., Ulgen K.O., (2011), "A Network-Based Approach on Elucidating the Multi-Faceted Nature of Chronological Ageing in S. cerevisiae", PLoS ONE, 6(12):e29284, doi: 10.1371/journal.pone.0029284.
  • 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.
  • 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.
  • 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.
  • Cakir T., Patil K. R., Onsan Z. I., Ulgen K. O., Kirdar B., Nielsen J., (2006), “Integration of metabolome data with metabolic networks reveals reporter reactions”, Mol Sys Biol, Vol. 2
  • Pir P., Kirdar B., Hayes A., Onsan Z. I., Ulgen K. O. , Oliver S. G., (2006), “Integrative investigation of metabolic and transcriptomic data”, BMC Bioinformatics, Vol. 7
  • Kantarci N., Borak F., Ulgen K. O., (2005), “Bubble column reactors”, Process Biochemistry, Vol. 40 (7), 2263-2283
  • Cakir T., Kirdar B., Ulgen K. O., (2004), “Metabolic pathway analysis of yeast strengthens the bridge between transcriptornics and metabolic networks”, Biotech and Bioeng, Vol. 86 (3), 251-260
Research Laboratory: 
Biosystems Engineering Research Group*