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Systems Biology



Systems Biology and Human Metabolism

Systems Biology and Systems Medicine arethe new branches of science, investigating cell as a whole with the help of biological data and computational methods rather than focusing solely on individual cellular components and providing solutions to biomedical problems. Transcriptomics, proteomics and metabolomics, high-throughput measurement of the messenger RNA, proteins and metabolites respectively, constitute the basis of the systems biology and enable scientists to understand the complexities occurring in cells simultaneously. One of the important research area in systems biology is human metabolism, which covers all the chemical reactions existing in the human body. Our aim is to investigate metabolic changes occurring in human tissues due to perturbations by employing the Systems Biology and Systems Medicine approaches.

PhD and Master thesis will be offered to graduate students who have strong computational background and interest in genome scale modeling/quantitative methods.

Culturing of Yeast Cells in 1.5 nL Microbioreactors

Miniaturization of devices and systems has gained significant attention in recent years. This popularity of the microfluidics especially increased in chemical, biological and medical fields. The microfluidic chips, also called as Lab-on-a-Chip technologies, exhibit clear advantages when compared to their conventional (macroscale) counterparts, such as low-cost fabrication and improved efficiency with respect to sample size, response time, analytical performance and process control. The major goal of this project is to create a microfluidic system (Lab-on-a-Chip platform, LOC) to perform biological experiments with yeast cells combined with subsequent image analysis. This LOC platform is used to measure time resolved changes in cell physiology in response to stress. The culturing of yeast cells in these nano-scale bioreactors provides multiple benefits: (i) low cost fabrication at BU-MEMS Lab-Clean Room, (ii) high throughput system: simultaneous working of 16 microbioreactors, (iii) more data at a shorter time period due to the dynamics of microfluidic systems.

Collaboration: Assoc. Prof. Şenol Mutlu (Department of Electrical and Electronics Engineering, Bogazici University)


Principle Investigator

Dr. Kutlu Ulgen

Professor of Chemical Engineering

Research Interests: Drug discovery, Microchemostat, Systems Biology

Kutlu O. Ulgen is Professor of Chemical Engineering at Boğaziçi University. She holds a PhD in Chemical Engineering from the University of Manchester (UMIST, UK) where she studied antibiotic production by Streptomyces coelicolor at different bioreactor operating strategies. Since 1992, she has been a faculty member in the Department of Chemical Engineering at Boğaziçi University. Dr. Ulgen has served as department head (2009-2011) and Associate Dean of Faculty of Engineering (2012-2015). Her current research focuses on Pharmacophore Modelling and Virtual Screening for Identification of new Inhibitors/activators-pharmacological chaperons for the treatment of infectious and genetic diseases as well as cancer. She has also been working on systems biology (computational and experimental), computational reconstruction and analysis of signaling networks (protein-protein and domain-domain interactions) and rational design by metabolic engineering approaches. She has supervised the theses of 85 MS and PhD students and published more than 90 journal articles and a book chapter on the topics of biomolecular engineering and systems biology.

She is a member of the Association of the Sphingolipid Club.


Elif Gençtürk (PhD 2021) Co-supervised with Dr. Senol Mutlu

İrem Özbek (MSc 2022)
Sena Erimli (MSc 2022)
Şafak Kılıç (MSc 2021)
Handan Çetin (MSc 2021)
Yiğit Demirtaş (MSc 2021)
Gamze Ege Kahya (MSc 2020) Co-supervised with Dr. Arzucan Ozgur
Esra Börklü Yücel (PhD 2013)
Saliha Durmuş Tekir (PhD 2013)
F.Betul Kavun (PhD 2011)
Senem Tiveci (PhD 2011)
Kazım Yalçın Arga (PhD 2007)
Tunahan Çakır (PhD 2006)
Pınar Pir (PhD 2005) Co-supervised with Prof. Z.İlsen Önsan
Mehmet Mete Altıntaş (PhD 2001)

Merve Yüce (MSc 2019) Co-supervised with Dr. Elif Özkırımlı
Özlem Özbek (MSc 2019) Co-supervised with Dr. Nazar İleri Ercan
Müge Kasım (MSc 2019)
Selma Başıbüyük (MSc 2019)
Pelin Yılmaz (MSc 2018) Co-supervised with Prof. Belma Özbek
Begüm Yağcı (MSc 2018) Co-supervised with Dr. Elif Özkırımlı
Elif Esvap (MSc 2018) Co-supervised with Dr. Elif Özkırımlı
Ekin Yurdakul (MSc 2018) Co-supervised with Dr. Şenol Mutlu
Ayse Eren (MSc 2017) Co-supervised with Dr. Elif Özkırımlı
İrem Ezgi Dayan (MSc 2017)
Sevde Üçpınar (MSc 2016) Co-supervised with Dr. Şenol Mutlu
Elif Gençtürk (MSc 2015) Co-supervised with Dr. Şenol Mutlu
Utku Deniz (MSc 2014) Co-supervised with Dr. Elif Özkırımlı
Büşra Gürses (MSc 2014)
Mustafa Serbaş (MSc 2013) Co-supervised with Dr. Tunahan Çakır
Oya Gürsoy Yılmaz (MSc 2013) Co-supervised with Dr. Elif Özkırımlı
Gizem Özbüyükkaya (MSc 2012)Co-supervised with Dr. Elif Özkırımlı
Gözde Taşkın(-) Co-supervised with Dr. Elif Özkırımlı
Seval Aladağ (MSc 2012) Co-supervised with Dr. Elif Özkırımlı
Bahar Nalbantoğlu (MSc 2011)
Kübra Büyükyanbolu (MSc 2010)
Aysun Eren (MSc 2010)
Yasemen Güngörmez (MSc 2010)
Pelin Ümit (MSc 2009)
Feras Alazi (MSc 2009)
Banu Yavuztürk(MSc 2009)
Çiğdem Filiz (MSc 2009)
İlkay Arslandağ (-)
Enes Oruç (MSc 2008)
Ece Acuner (MSc 2008)
Selin Taşdöğen (MSc 2007)
Esra Börklü(MSc 2007)
Can Çavlı (MSc 2007)
Saliha Durmuş (MSc 2007)
Erdem Aygök (MSc 2007)
Selma Alsan (MSc 2005)
Hatice Kınış (MSc 2005)Co-supervised with Prof. Z.İlsen Önsan
Senem Tiveci (MSc 2004)
Serhan Tacer (MSc 2004)
Azra Köne (MSc 2004)
Cüneyt Katıel(MSc 2004)
Nigar Kantarcı(MSc 2003)
Fatma Günel (MSc 2002)
Neslihan Günel (MSc 2002)
Sinem Özyurt (MSc 2001)Co-supervised with Prof. Betül Kırdar
Erdem Çelik (MSc 2001)
Erdem Güzeltunç (MSc 2000)
Nevra Özer (MSc 1999)
Fedai Akdeniz (MSc 1999)
Mehmet Gürcan Düzenli (MSc 1999)
Nedret Ümit (MSc 1999)
Semra Yılmaz (MSc 1997)
Alp Kırmaz (MSc 1997) Co-supervised with Prof. Mehmet Çamurdan
Mehmet Mete Altıntaş (MSc 1996)


Google Scholar

Kutlu O. Ulgen - Professor of Chemical Engineering, Bogazici University

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

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. Print ISSN 1064-3745, Electronic ISSN1940-6029

B Atas, CS Aksoy, FG Avci, NA Sayar, K Ulgen, E Ozkirimli, BS Akbulut, 2022, Carvacrol Enhances the Antimicrobial Potency of Berberine in Bacillus subtilis 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

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:

Sercan Altundemir, Kerem Uguz, Kutlu Ulgen (2017) A review on wax printed microfluidic paper-based devices for international health, Biomicrofluidics, 11 (4),

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:

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

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. /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.

Saliha Durmuş Tekir, Kutlu Ö. Ülgen, Patojen-Konak Etkileşimlerinin Sistem Biyolojisi, in Book entitled ‘ENFEKSİYON PATOGENEZİ ve BAĞIŞIKLIK’, Book Chapter 18/114

Saliha Durmuş Tekir, Kutlu Ö. Ülgen, (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: Methods and Advances,
DOI 10.1002/biot.201200110

Ozbuyukkaya G., Ozkirimli Olmez E., Ozergin Ulgen K., 2013, "Aminopurine derivatives as putative SopE inhibitors", Journal of Enzyme Inhibition and Medical Chemistry,

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.

Borklu Yucel E, Ulgen KO (2013) Assessment of crosstalks between Snf1 kinase complex and sphingolipid metabolism in S. cerevisiae via systems biology approaches. Mol. BioSyst., 2013,
DOI: 10.1039/C3MB70248K.

Ozbuyukkaya G., Ozkirimli Olmez E., Ozergin Ulgen K., 2013, " Discovery of YopE inhibitors by pharmacophore-based virtual screening and docking", ISRN Bioinformatics,

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.

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, Research topic: Systems Biology of Microbial Infection, Vol. 3, 46.

Özbayraktar Kavun, F. B., Ülgen, K., (2011) Stoichiometric network reconstruction and analysis of yeast sphingolipid metabolism incorporating different states of hydroxylation, BioSystems, Vol. 104 (1), 63-75, doi:10.1016/j.biosystems.2011.01.001.

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.

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.

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

Özbayraktar Kavun, F. B., Ülgen, K., (2010) Drug target identification in sphingolipid metabolism by computational systems biology tools: Metabolic control analysis and metabolic pathway analysis, Journal of Biomedical Informatics, 43 (2010) 537–549.

S. Durmuş, P. Umit, A. Eren, K. Ülgen (2010) Reconstruction of Protein-Protein Interaction Network of Insulin Signaling in H. Sapiens, Journal of Biomedicine and Biotechnology, doi:10.1155/2010/690925.

S. Durmuş, K.Y.Arga, K. Ülgen (2009) Drug targets for tumorigenesis: Insights from structural analysis of EGFR signaling network, Journal of Biomedical Informatics, 42 (2), 228-236.

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

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.

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.

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.

Esra YÜCEL, Ayça CANKORUR, Elif DERELİ, Feras ALAZİ1, 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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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

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.

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

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.

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

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

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

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

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.

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.

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

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.

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.

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.

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.

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.

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.

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

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.

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