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Kutlu O. Ulgen - Professor of Chemical Engineering, Bogazici University
Elif Gencturk, Muge Kasim, Berna Morova, Alper Kiraz, and Kutlu O. Ulgen () Understanding the Link between Inflammasome and Apoptosis through the Response of THP‐1 Cells against Drugs Using Droplet- Based Microfluidics funduszeue.info
Gencturk E., Mutlu S., Ulgen K.O. () Fabrication Protocol for Thermoplastic Microfluidic Devices: Nanoliter Volume Bioreactors for Cell Culturing. In: . Methods in Molecular Biology. Springer, New York, NY. funduszeue.info Print ISSN , Electronic ISSN
B Atas, CS Aksoy, FG Avci, NA Sayar, K Ulgen, E Ozkirimli, BS Akbulut, , Carvacrol Enhances the Antimicrobial Potency of Berberine in Bacillus subtilis Current Microbiology 79 (5),
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) a Mary Ann Liebert, Inc. DOI: /omi Epub Sep 28
Elif Esvap, Kutlu O Ulgen, Advances in Genome-Scale Metabolic Modeling toward Microbial Community Analysis of the Human Microbiome, ACS Synthetic Biology, 10 (9), DOI: /acssynbio.1c
Merve Yuce, Elif Ozkirimli, Berna Sariyar Akbulut Kutlu Ulgen, Live Cell Imaging of Peptide Uptake Using a Microfluidic Platform , International Journal of Peptide Research and Therapeutics, volume 27, pages– (). DOI /s
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 , © American Chemical Society funduszeue.info
M Sertbas, KO Ulgen (). 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 (). Cell trapping microfluidic chip made of Cyclo olefin polymer enabling two concurrent cell biology experiments with long term durability. Biomedical microdevices, 22(1),
E Gencturk, KO Ulgen, S Mutlu (). Thermoplastic microfluidic bioreactors with integrated electrodes to study tumor treating fields on yeast cells. Biomicrofluidics, 14(3),
MG Durmaz, A Dilmac, B Camli, E Gencturk, ZCC Ozdil, AE Pusane, AD Yalcinkaya, KO Ulgen, T Tugcu, (). 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. ). Springer, Cham.
Ege Ertekin, Elif Gencturk, Muge Kasim, and Kutlu O. Ulgen () A Drug Repurposing and Protein-Protein Interaction Network Study of Ribosomopathies Using Yeast as a Model System OMICS A journal of Integrative Biology, online, print Volume 24,
ZB Yagci, E Esvap, HA Ozkara, KO Ulgen, E Ozkirimli () Inflammatory response and its relation to sphingolipid metabolism proteins: Chaperones as potential indirect anti-inflammatory agents. Advances in Protein Chemistry and Structural Biology (1), ISSN
P Yılmaz, EÖ Er, S Bakırdere, K Ülgen, B Özbek () 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
E Gencturk, E Yurdakul, AY Celik, S Mutlu, KO Ulgen () 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),
IE Odabasi, E Gencturk, S Puza, S Mutlu, KO Ulgen () 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 () 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),
O Bayraktar, E Ozkirimli, KO Ulgen () In silico identification of novel orthosteric inhibitors of Sphingosine Kinase 1 (SK1) Current Protein and Peptide Science 19 (5),
Elif Gencturk, Senol Mutlu and Kutlu O. Ulgen () Advances in Microfluidic Devices Made from Thermoplastics used in Cell Biology and Analyses, Biomicrofluidics, Biomicrofluidics Vol, Issue 5. DOI: /
Buge Yilmazer, Begum Yagci, Emre Bakar, Burcu Ozden, Elif Ozkirimli, Kutlu O. Ulgen () Investigation of novel pharmacological chaperones for Gaucher disease, Journal of Molecular Graphics and Modelling, 76, doi: funduszeue.info
Sercan Altundemir, Kerem Uguz, Kutlu Ulgen () A review on wax printed microfluidic paper-based devices for international health, Biomicrofluidics, 11 (4), funduszeue.info
Sevde Puza, Elif Gencturk, Irem Ezgi Odabasi, Emre Iseri, Senol Mutlu, Kutlu O. Ulgen () Fabrication of cyclo olefin polymer microfluidic devices for trapping and culturing of yeast cells, Biomedical Microdevices 19 (2), 40 doi/s
Özge Bayraktar, Elif Ozkirimli, Kutlu O. Ulgen () Sphingosine kinase 1 (SK1) allosteric inhibitors that target the dimerization site, Computational Biology and Chemistry, doi: funduszeue.info
İrem Ezgi Dayan, Kazim Yalcin Arga, Kutlu O. Ulgen () 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), doi: /omi
Saliha Durmuş, Kutlu O. Ulgen () Comparative interactomics for virus-human protein-protein interactions: DNA viruses versus RNA viruses, FEBS Open Bio 7 (1), December / DOI: /
Özge Bayraktar, Elif Ozkirimli, Kutlu O. Ulgen () In Silico Identification of Novel Orthosteric Inhibitors of Sphingosine Kinase 1 (SK1), Current protein & peptide science
Utku Deniz, Elif Ozkirimli, Kutlu O. Ulgen() A systematic methodology for large scale compound screening: A case study on the discovery of novel S1PL inhibitors, Journal of Molecular Graphics and Modelling () 63, doi/funduszeue.info
Emre Iseri, Kutlu O. Ulgen, Cetin Yilmaz, and Senol Mutlu () Fabrication of steel displacement amplifiers integrated to microfluidic channels." In Micro Electro Mechanical Systems (MEMS), IEEE 29th International Conference on, pp. IEEE, doi: /MEMSYS
Pinar Eribol, Kerem Uguz, Kutlu O. Ulgen () Screening Applications In Drug Discovery Based On Microfluidic Technology, Biomicrofluidics, 10, (); doi: /
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 () DOI /s
Utku Deniz, Kutlu O. Ulgen, Elif Ozkirimli Identification of potential Tpx inhibitors against pathogen-host interactions Computational biology and chemistry, Volume58, () – funduszeue.info
Esra Borklu Yucel, Serpil Eraslan, Kutlu O. Ulgen, The Impacts of Medium Acidity on Chronological Life Span of Saccharomyces cerevisiae: Lipids, Signaling Cascades, Mitochondrial and Vacuolar Functions, FEBS Journal
(Impact Factor: ). 01/; DOI/febs
Oya Gursoy Yilmaz, Elif Ozkirimli Olmez, Kutlu O Ulgen, /2/28 Targeting the Akt1 allosteric site to identify novel scaffolds through virtual screening, Computational biology and chemistry,
Volume48, funduszeue.info /funduszeue.infoolchem
Mustafa Sertbas, Kutlu Ülgen, Tunahan Çakır 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 () – funduszeue.info
Saliha Durmuş Tekir, Kutlu Ö. Ülgen, Patojen-Konak Etkileşimlerinin Sistem Biyolojisi, in Book entitled ‘ENFEKSİYON PATOGENEZİ ve BAĞIŞIKLIK’, Book Chapter 18/
Saliha Durmuş Tekir, Kutlu Ö. Ülgen, () “Systems biology of pathogen-host interaction: Networks of protein-protein interaction within pathogens and pathogen-human interactions in the post-genomic era”, Biotechnology Journal: Methods and Advances,
DOI /biot
Ozbuyukkaya G., Ozkirimli Olmez E., Ozergin Ulgen K., , "Aminopurine derivatives as putative SopE inhibitors", Journal of Enzyme Inhibition and Medical Chemistry,
DOI: funduszeue.info
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., , "PHISTO: Pathogen-Host Interaction Search Tool", Bioinformatics,
Doi: /bioinformatics/btt
Borklu Yucel E, Ulgen KO () Assessment of crosstalks between Snf1 kinase complex and sphingolipid metabolism in S. cerevisiae via systems biology approaches. Mol. BioSyst., ,
DOI: /C3MBK.
Ozbuyukkaya G., Ozkirimli Olmez E., Ozergin Ulgen K., , " Discovery of YopE inhibitors by pharmacophore-based virtual screening and docking", ISRN Bioinformatics,
DOI: funduszeue.info
Nalbantoğlu B., Durmuş Tekir S., Ülgen K., () Wnt Signaling Network in Homo Sapiens, Cell Metabolism - Cell Homeostasis and Stress Response. Edited by Paula Bubulya. Rijeka: Intech, ISBN:
Durmus Tekir S., Cakir T., Ulgen K.O., () "Infection Strategies of Bacterial and Viral Pathogens through Pathogen-Human Protein-Protein Interactions", Frontiers in Microbial Immunology, Research topic: Systems Biology of Microbial Infection, Vol. 3,
Özbayraktar Kavun, F. B., Ülgen, K., () Stoichiometric network reconstruction and analysis of yeast sphingolipid metabolism incorporating different states of hydroxylation, BioSystems, Vol. (1), , doi/funduszeue.infotems
Acuner Özbabacan S.E., Durmuş Tekir S., Ülgen K.Ö., () Crucial components in toll-like receptor signalling network as key regulators for immunological disorders, International Journal of Physical Sciences, Vol. 6 (8),
Eren Toku A., Durmuş Tekir S., Kavun Özbayraktar F.B., Ülgen K., () Reconstruction and Crosstalk of Protein-Protein Interaction Networks of Wnt and Hedgehog Signaling in Drosophila Melanogaster, Computational Biology and Chemistry, Vol. 35(5),
Borklu Yucel E, Ulgen KO () A Network-Based Approach on Elucidating the Multi-Faceted Nature of Chronological Aging in S. cerevisiae. PLoS ONE 6(12): e doi/funduszeue.info
Özbayraktar Kavun, F. B., Ülgen, K., () Drug target identification in sphingolipid metabolism by computational systems biology tools: Metabolic control analysis and metabolic pathway analysis, Journal of Biomedical Informatics, 43 () –
S. Durmuş, P. Umit, A. Eren, K. Ülgen () Reconstruction of Protein-Protein Interaction Network of Insulin Signaling in H. Sapiens, Journal of Biomedicine and Biotechnology, doi//
S. Durmuş, funduszeue.info, K. Ülgen () Drug targets for tumorigenesis: Insights from structural analysis of EGFR signaling network, Journal of Biomedical Informatics, 42 (2),
Kavun, F. B., Ülgen, K., () Molecular facets of sphingolipids: Potential drug targets, Biotechnology Journal, 4(7),
Mehmet M. Altintas, Kutlu O. Ulgen, Darryl Palmer-Toy, Vivian E. Shih, Dhinakar S. Kompala, Jochen Reiser () 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):
Pınar Pir, Betül Kırdar, Andrew Hayes, Z. İlsen Önsan, Kutlu Ö. Ülgen, Stephen G. Oliver, () Exometabolic and transcriptional response in relation to phenotype and gene copy number in respiration-related deletion mutants of S. cerevisiae, Yeast,
D. Dikicioğlu, Pınar Pir, Z. İlsen Önsan, Kutlu Ö. Ülgen, Betül Kırdar, Stephen G. Oliver, () 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):
Esra YÜCEL, Ayça CANKORUR, Elif DERELİ, Feras ALAZİ1, İlkay ASLANDAG, BetüL KAVUN, Saliha D. TEKIR, K. Yalcin ARGA, Kutlu Ö. ÜLGEN, () Deciphering The Cross-Talk Between Sphingolipid Mechanism And Signaling Pathways In Baker’s Yeast, Sigma: Journal Of Engineering And Natural Sciences, 26(3):
K. Y. Arga, Zeynep İlsen Önsan, Betül Kırdar, Kutlu Özergin Ülgen, Jens Nielsen () Understanding Signaling in Yeast: Insights from Network Analysis, Biotechnology and Bioengineering, 97(5),
Tunahan Çakır, Zeynep İlsen Önsan, Betül Kırdar, Kutlu Özergin Ülgen, Jens Nielsen () Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae, BMC Systems Biology, DOI: /
Tunahan Cakir, Selma Alsan, Hale Saybasili, Ata Akin and Kutlu O Ulgen () Reconstruction and flux analysis of coupling between metabolic pathways of astrocytes and neurons: application to cerebral hypoxia, Theoretical Biology and Medical Modelling,
Pınar Pir, Kutlu Ö. Ülgen, Andrew Hayes, Z. İlsen Önsan, Betül Kırdar, Stephen G. Oliver, () Annotation of Unknown Yeast ORFs by Correlation Analysis of Microarray Data and Extensive Literature Searches, Yeast, 23,
Pınar Pir, Betül Kırdar, Andrew Hayes, Z. İlsen Önsan, Kutlu Ö. Ülgen, Stephen G. Oliver, () Integrative Investigation of Metabolic and Transcriptomic Data, BMC Bioinformatics,
S. Durmuş, T. Çakır, K. Ülgen () Analysis of enzymopathies in the human red blood cells by constraint based stoichiometric modeling approaches, Computational Biology and Chemistry, 30,
Tunahan Çakır, Kiran Raosaheb Patil, Zeynep İlsen Önsan, Kutlu Özergin Ülgen, Betül Kırdar, Jens Nielsen () Integration of metabolome data with metabolic networks reveals reporter reactions, Molecular Systems Biology, DOI: /msb
Nigar Kantarci, Fahir Borak, Kutlu O. Ulgen () Bubble Column Reactors: Review, Process Biochemistry, 40,
Nigar Kantarci, Fahir Borak, Kutlu O. Ulgen () 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,
S. Tiveci, funduszeue.infoın, T. Çakır, H. Saybaşılı, K. Ülgen () Modelling of calcium dynamics in brain energy metabolism and Alzheimer’s disease’, Computational Biology and Chemistry, 29,
K Y Arga, T. Cakir, Pinar Pir, Nevra Özer, M.M. Altintas, K. Ö.Ülgen () “Transfer function approach in structured modeling of recombinant yeast utilizing starch” Process Biochemistry, 39,
T. Cakir, K Y Arga, M.M. Altintas, K. Ö. Ülgen () “Flux analysis of recombinant Saccharomyces cerevisiae YPB-G utilizing starch for optimal ethanol production” Process Biochemistry, 39,
T. Cakir, B. Kırdar, K. Ö. Ülgen () “Metabolic Pathway Analysis of Yeast Strenghtens the Bridge between Transcriptomics and Metabolic Networks”, Biotechnology and Bioengineering, 86(3),
T. Cakir, C.S. Tacer, K. Ö. Ülgen () “Metabolic Pathway Analysis of Enzyme-deficient Human Red Blood Cells”, BioSystems, 86(3),
E. Toksoy-Öner, B. Kırdar, Z.İ.Önsan, K. Ülgen () " 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,
M.M. Altintas, K. Ülgen, B. Kırdar, Z.İ.Önsan, S. Oliver, () “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,
S. Özyurt, B.Kırdar, K. Ö. Ülgen () ‘Recovery of Antithrombin III From Milk By Expanded Bed Chromatography’ , Journal of Chromatography A., ,
K.Ö. Ülgen, B. Saygılı, Z.İ. Önsan, B. Kırdar () Bioconversion of Starch into Ethanol by a Recombinant funduszeue.infosiae Strain YPB-AB, Process Biochemistry, 37(10),
M.M. Altıntaş, B. Kırdar, Z.İ. Önsan, K. Ö. Ülgen () ‘Cybernetic Modelling of Growth and Ethanol Production in a Recombinant funduszeue.infosiae Strain Secreting a Bifunctional Fusion Protein’, Process Biochemistry, 37(11),
M.M. Altıntaş, B. Kırdar, Z.İ. Önsan, K. Ö. Ülgen, S. G. Oliver () ‘Improvement of ethanol production from starch by recombinant yeast through manipulation of environmental factors’, Enzyme and Microbial Technology, 31,
M.Düzenli, K. Ö. Ülgen () ‘Modelling of TaqI endonuclease Purification by HPLC’, Turkish Journal of Chemistry, 26(6),
funduszeue.infoer, K. Ülgen, B. Kırdar, Z.İ. Önsan, () ‘A Structured Model for Intracellular EcoRI Endonuclease Production by Recombinant funduszeue.info ’, Process Biochemistry, 36,
E. Güzeltunç, K. Ö. Ülgen () ‘Recovery of Actinorhodin from Fermentation Broth’, Journal of Chromatography A., ,
M.M. Altıntaş, B. Kırdar, Z.İ. Önsan, K. Ö. Ülgen () ‘Plasmid Stability in a Recombinant funduszeue.infosiae Strain Secreting A Bifunctional Fusion Protein’, Journal of Chemical Technology and Biotechnology, 76(6),
B.Özbek, K. Ö. Ülgen () “The Stability of Enzymes after Sonication”, Process Biochemistry, 35 (9),
M.Düzenli, K. Ö. Ülgen () ‘Optimisation of Mobile Phase Conditions for the Purification of TaqI endonuclease’, Chromatographia, 52 (6),
funduszeue.infoı, funduszeue.infoan and K. Ö. Ülgen () “Quantitative Description of Protein Adsorption by Frontal Analysis” Process Biochemistry, 36(1),
M. M. Altıntaş, K. Ülgen () ‘Growth of Thermus aquaticus and its TaqI Endonuclease Production’, Acta Biotechnologica, 19,
G. Birol, P. Doruker, B. Kırdar, Z.I.Önsan and K.Ülgen () “Mathematical Description of Ethanol Fermentation by Immobilized Saccharomyces cerevisiae” Process Biochemistry, 33(7),
K. Ö. Ülgen, F. Mavituna () “Oxygen Transfer and Uptake in Streptomyces coelicolor A3(2) Culture in a Batch Bioreactor” Journal of Chemical Technology and Biotechnology, 73,
M. M. Altıntaş, N. Özer, K. Ö. Ülgen () ‘Purification of TaqI Endonuclease from Thermus Aquaticus’ , Journal of Chromatography A., ,
S.Yılmaz, B. Beleli, M. Fesli, K. Ülgen () “ A study on the Effect of Operating Parameters on Protein Purification by Ion Exchange Column Chromatography”, Institution of Chemical Engineers Research Event 97, p , Nottingham-U.K.
M. M. Habbaba and K.Ülgen () “Analysis of Protein Adsorption to Ion Exchangers in a Finite Bath” Journal of Chemical Technology and Biotechnology, 69 (4),
M. Elibol. K. Ülgen, K. Kamaruddin, F. Mavituna() “Effect of Inoculum Type on Actinorhodin Production by Streptomyces coelicolor A3(2)” Biotechnology Letters 17 (6),
G. Birol and K.Ülgen () “A Study on the Effect of Inoculum On Yeast Cell Growth and Ethanol Production” Doğa - Turkish Journal of Chemistry 19 (4),
K. Özergin-Ülgen and F. Mavituna () “Comparison of the Activity of Immobilised and Freely Suspended Streptomyces coelicolor A3(2)” Applied Microbiology and Biotechnology 41,
K. Özergin and F. Mavituna () “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.
K. Özergin, funduszeue.info, Z.İ. Önsan, B. Kırdar () “ The Effect of Immobilisation on Yeast Cell Growth and Ethanol Production” Doğa - Turkish Journal ofChemistry 17 (2),
K. Özergin-Ülgen and F. Mavituna () “Actinorhodin Production by Streptomyces coelicolor A3(2): Kinetic Parameters Related to Growth, Substrate Uptake and Production” Applied Microbiology and Biotechnology 40,