¨ Canelas  A. B., Harrison N., Fazio A., Zhang J., Pitkänen J.P., van den Brink J., Bakker B.M., Bogner L., Bouwman J., Castrillo J.I., Cankorur A., Chumnanpuen P., Daran-Lapujade P., Dikicioglu D., van Eunen K., Ewald J.C., Heijnen J.J., Kirdar B., Mattila I., Mensonides F.I.C., Niebel A., Penttilä M., Pronk J.T., Reuss M., Salusjärvi L., Sauer U., Sherman D., Siemann-Herzberg M., Westerhoff H., de Winde J., Petranovic D., Oliver S.G., Workman C.T., Zamboni, Nielsen J., (2010), Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains, Nature Communications, Doi: 10.1038/ncomms1150.

¨  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.

¨ 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.


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

¨ Huang H., Ozkirimli E., Post C.B., (2009), Comparison of Three Perturbation Molecular Dynamics Methods for Modeling Conformational Transitions”, Journal of Chemical Theory and Computation, Volume: 5, Issue: 5, p. 1304-1314.   

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


¨ Ozkirimli E, Yadav SS, Miller WT, et al. (2008), An electrostatic network and long-range regulation of Src kinases, Protein Science, Vol. 17 (11), 1871-1880.

¨ Herrgċrd, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M.,     Blüthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novère, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasi, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kırdar, B., Penttilä, M., Klipp, E., Palsson, B. Ĝ., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J. & Kell, D. B., (2008), A consensus yeast metabolic network obtained from a community approach to systems biology,  Nature Biotechnol., 26, 1155-1160.

¨ Dikicioğlu D, Pınar Pir, Z. İlsen Onsan, Kutlu O. Ulgen, Betul Kirdar,  Stephen G. Oliver, (2008), Integration of metabolic modeling and phenotypic data in evaluation and improvement of ethanol production using respiration defiant mutants of  S. Cerevisiae, Applied and Environmental Microbiology, 74 (18), 5809-5816.

¨ Pir P, Betul Kirdar, Andrew Hayes, Z. İlsen Onsan, Kutlu O. Ulgen, 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.

¨ 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.


¨ Oh H, Ozkirimli E, Shah K, et al., (2007), Generation of an analog-sensitive syk tyrosine kinase for the study of signaling dynamics from the B cell antigen receptor, Journal of Biological Chemistry, Vol. 282 (46), 33760-33768.

¨ 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. 

¨ Çakir T., Kirdar B., Onsan Z.İ., Ulgen O.K., Nielsen J., (2007), Effect of carbon source perturbations on regulation of metabolic fluxes in S. Cerevisiae, BMC Systems Biology, 1:18.

¨ Cakir T., Efe Ç., Dikicioğlu D., Hortaçsu A., B. Kirdar, Oliver GO. (2007), Flux balance analysis of a genome scale yeast model constrained by exometabolomic data allows metabolic system identification and strain genotype prediction, Biotechnology Progress, 23, 320-326.

¨ K. Yalcin Arga, Z. İlsen Onsan, Betul Kırdar,  Kutlu O. Ulgen, Jens Nielsen (2007), Understanding signalling in yeast : Insights from network analysis, Biotechnology and Bioengineering; 97(5), 1246-1258. 

¨ Misirli Z.,Toksoy Öner, E.,B. Kirdar (2007), Real imaging and size values of  Saccharomyces cerevisiae cells with comparable contrast tuning to two ESEM-modes, Scanning, 29, 11-19.

¨ Taymaz H., Eraslan E.,Toksoy Öner, E., Alkan T., Agırbaslı M., B. Kirdar (2007), Sequence variations within the genes related to hemostatic imbalance and their impact on coronary artery disease in Turkish population, Thrombosis Research, 119, 55-62. 


¨ Ozkirimli E, Post CB, (2006), Src kinase activation: A switched electrostatic network, Protein Science, Vol.15 (5), 1051-1062.

¨ Nikerel, İ.E., Toksoy Öner, E., Yıldırım, R.,B. Kirdar (2006), Optimization of Medium Composition for Biomass Production of Recombinant Escherichia coli Cells Using Response Surface Methodology, Biochemical Engineering Journal, 32, 1-6.

¨ Çakır T, Kiran Raosaheb Patil, Z. İlsen Onsan, Kutlu O. Ulgen, Betul Kirdar, Jens Nielsen (2006), Integration of mtabolome data with metabolic networks reveals reporter reactions, Molecular Systems Biology, doi:10.1038/msb4100085.

¨ Pir P, Kutlu O. Ulgen, Andrew Hayes, Z. İlsen Onsan, Betul Kirdar, Stephen G. Oliver (2006), Annotation of Unknown Yeast ORFs by Correlation Analysis of Microarray Data and Extensive Literature Searches, Yeast, 23, 553-571. 

¨ Pir P, Kutlu O. Ulgen, Andrew Hayes, Z. Ilsen Onsan, Betul Kirdar, Stephen G. Oliver(2006), Integrative Investigation of Metabolic and Transcriptomic Data, BMC Bioinformatics, 7:203, doi: 10.1186/1471-2105-7-203. 

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


¨ 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.

¨ Toksoy E. Oliver S.G., Kırdar B., (2005), Production of   ethanol from starch by respiration-deficient recombinant Saccaromyces cerevisiae, Applied and Environmental Microbiology   71 (10), 6443-6445.

¨ Akarsubaşı T.A., İnce O., Orhon D.,Oz N.A., Kırdar B.,İnce B. Curtis P.C., Head I.M. (2005), Effect of wastewater composition on archael population diversity, Water Research 39, 1576-1584.

¨ Nikerel I E, Toksoy E. Kırdar B, Yıldırım R., (2005) Optimizing medium composition for TaqI endonyclease production by recombinant E.coli cells using response surface methodology, Process Biochemistry 40, 1633-1639.


¨ K. Y. Arga, T. Çakır, P. Pir, N. Özer, M. M. Altıntaş, K. Ö. Ülgen (2004), Transfer function approach in structured modeling of recombinant yeast utilizing starch' Process Biochemistry, 39, 1237-1248.

¨ T. Çakır, K. Y. Arga, M. M. Altıntaş, K. Ö. Ülgen, (2004), Flux analysis of the recombinant Saccharomyces cerevisiae YPB-G utilizing starch for optimal ethanol production, Process Biochemistry, Vol: 39, Issue:12,  2097-2108.

¨ T. Çakır, B. Kırdar, K. Ö. Ülgen (2004), Metabolic pathway analysis of yeast strengthens the bridge between transcriptomics and metabolic networks, Biotechnology&Bioengineering, 86, 251-260.

¨ T. Çakır, C.S. Tacer, K. Ö. Ülgen (2004), Metabolic pathway analysis of enzyme-deficient human red blood cells, Biosystems, 78, 49-67.


¨ G. Birol, I. Birol, B. Kırdar and Z. I. Önsan, (2003), Investigating the Fermentation Dynamics Structure of Recombinant Saccharomyces cerevisiae, YPB-G, Computers and Chemical Engineering, 27, 45-54.

¨ M.M. Altıntaş, K. Ö. Ülgen, B. Kırdar, Z.İ. Önsan, S.G. Oliver (2003), Optimal substrate feeding policy for fed-batch cultures of S. cerevisiae expressing bifunctional fusion protein displaying amylolytic activities, Enzyme and Microbial Technology, 33, 262-269.

¨ 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.


¨ G. Birol, Z. İ. Önsan, B. Kırdar (2002), Simple Structured Model for Biomass and Extracellular Enzyme Production with Recombinant Saccharomyces cerevisiae YPB-G, Journal of Industrial Microbiology and Biotechnology, 29, 111-116.

¨ S. Özyurt, B.Kırdar, K. Ülgen (2002), Recovery of Antithrombin III from milk by expanded bed chromatography, Journal of Chromatography A., 944, 203-210.

¨ K. 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, S. Oliver, K. Ö. Ülgen (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', Doğa - Turkish Journal of Chemistry, 26(6), 877-887.

¨ E. Toksoy, Z.İ. Önsan, B. Kırdar (2002), High-level production of TaqI restriction endonuclease by three different expression systems in Escherchia coli cells using the T7 phage promoters', Applied Microbiology and Biotechnology, 59, 239-245.

¨ Toksoy E., Önsan Z.I.., Kırdar B., (2002), Expression of a thermostable restiriction endonuclease in recombinant Escherichia coli cells and optimisation of fermentation conditions, World Journal of Microbiology and Biotechnology, 18, 23-27.

¨ S. Savas, S.Eraslan, S. Kantarcı, B.Karaman, D. Acarsöz, T. Tükel, O. Çogulu, F. Özkınay, S.Başaran, K.Aydınlı, M. Yüksel-Apak, B.Kırdar, (2002), Prenatal prediction of childhood onset of Spinal Muscular Atrophy(SMA) in Turkish families", Prenatal Diagnosis, 22 (8), 703-709.


¨ M.M. Altıntaş, B. Kırdar, Z.İ. Önsan, K. 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.

¨ E. Güzeltunç, K. Ülgen, (2001), ‘Recovery of Actinorhodin from fermentation broth’, Journal of Chromatography A.,  914, 67-76.

¨ C.Tamerler, B. Kırdar, Z.İ. Önsan, K. Ülgen, (2001), ‘A Structural Model for intracellular EcoRI endonuclease production by recombinant E.coli 294’ , Process Biochemistry, 36, 7, 621-627.  

¨ Yildir, C., Önsan Z.I.., Kırdar B., (2001),"Comparison of the recovery of EcoRI endonuclease from two genetically modified strains of E.coli", Doga-Turkish Journal of Chemistry, 25, 63-71.

¨ Onay T., Topaloglu Ö., Zielinski J. ,Gökgöz N., Kayserili H., Çokugras H., Söylemez Y., Akçakaya N., Apak M., Tsui L.-C., Kırdar B., (2001), "Cystic fibrosis mutations and associated haplotypes in Turkish CF patients", Human Biology, 73, 2, 191-203.

¨ Toksoy E., Önsan Z.I.., Kırdar B., (2001), "Effect of the co-expression of methyltransferase activity on extracellular production of TaqI restriction endonuclease in recombinant E.coli cells", Process Biochemistry, 37, 527-534. 


¨ Avci, A., M. C. Camurdan, K. Ülgen, (2000), "Analysis of Protein Adsorption to Ion Exchangers", Process Biochemistry, 36, 1, 141-148.

¨ Birol, G., Z. I. Önsan, B. Kirdar, (2000), "Studies on Fermentation with Recombinant Yeast Cells: Plasmid Stability and Kinetics of Biomass Growth and Protein Production", Journal of Chemical Technology and Biotechnology, 75, 729-737.

¨ Dork, K., Jr. M. Macek, F. Mekus, et al., (2000), "A novel 21 kilobase deletion, CFTRdele2,3(21kB), in the CFTR Gene: A Cystic Fibrosis Mutation of Slavic Origin Common in Central and East Europe", Human Genetics, 106, 3, 259-268.

¨ Düzenli, M. and K. Ülgen, (2000), “Modelling of TaqI endonuclease by HPLC", Chromatographia, 52, 6, 377-380.

¨ Özbek, B. and K. Ülgen, (2000), "Studies on the Stabilities of Enzymes after Disruption by a Sonifier", Process Biochemistry, 35, 9, 1037-1043.

¨ Savas, S., N. Gökgöz, H. Kayserili, F. Özkinay, M. Yüksel-Apak, B. Kirdar, (2000),  "Screening of Deletions in SMN, NAIP and BTF2p44 Genes in Turkish Muscular Atrophy Patients", Human Heredity, 50, 162-165.

¨ Savas, S., Kırdar B., Keats J. B.B, (2000), "Tecniques and technologies for detection of genomic abnormalities", Archive of Oncology, 8, 4, 171-176.


¨ Altintas, M. M., K. Ülgen (1999), Growth and Production by Thermus aquaticus, Acta Biotechnologica, 19, 45-56.

¨ Eraslan, S., H. Kayserili, M. Yüksel-Apak, B. Kirdar, (1999), Identification of Point Mutations in Turkish DMD/BMD Families using SSCA, European Journal of Human Genetics, 7 (7), 765-771.

¨ Onay, T., H. Kayserili, M. Yüksel-Apak, B. Kirdar (1999), Analysis of Infertile Brothers with Congential Bilateral Absence of Vas Deference for Mutations in the CFTR Gene, Clinical Genetics, 55, 63-64.

¨ Toksoy, E., P. H. Özdinler, Z. I. Önsan, B. Kırdar, (1999), High Level Secretion of TaqI Restriction Endonuclease by Recombinant Escherichia coli, Biotechnology Techniques, 13, 803-808.


¨ Altintas, M. M., N. Özer, K. Ülgen, (1998), Purification of TaqI endonuclease from Thermus aquaticus, Journal of Chromatography A., 828 (1-2), 373-381.

¨ Birol, G., Z. I. Önsan, B. Kirdar, S. Oliver, (1998), Ethanol Production and Fermentation Characteristics of Recombinant Saccharomyces cerevisiae Strains Grown on Starch, Enzyme & Microbial Technology, 22, 672-677.

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

¨ Brega, A., R. Scacchi, B. Kirdar, G. Poloso, R. M. Corbo, (1998), A Study of Fifteen Polymorphisms in a Sample of the Turkish Population, Human Biology, 70 (4), 715-728.

¨ Eraslan, S., N. Gökgöz, B. Kirdar (1998), Identification of Deletion Carriers in DMD/BMD Families Using a DIG-labeled Quantitative PCR, Molecular Diagnosis, 2 (4), 251-258.

¨ Onay, T., O. Topaloglu, J. Zielinski, N. Gökgöz, H. Kayserili, H. Çokugras, Y. Söylemez, N. Akçakaya, M. Apak, L. C. Tsui, B. Kirdar, (1998), Analysis of the CFTR Gene in the Turkish Cystic Fibrosis Patients: Identification of Three New Mutations (3172delAC, P1013L, M1028I), Human Genetics, 102, 224-230.

¨ Ülgen, K., 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.

¨ Yildir, C., Z. I. Önsan, B. Kirdar, (1998), Optimization of Starting Time and Period of Induction and Inducer Concentration in the Production of the Restriction Enzyme EcoRI from Recombinant E.coli 294, Turkish Journal of Chemistry, 22, 221-226.


¨ Çelik, A., S. Eraslan, N. Gökgöz, H. Ilgin, S. Basaran, I. Bökesoy, H. Kayserili, M. Yüksel-Apak, B. Kirdar, (1997), Identification of the Parental Origin of Polysomy in Two 49,XXXXY Cases, Clinical Genetics, 51 (6), 426-429.

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


¨ Birol, G., K.Ülgen, (1995), A Study on the Effect of Inoculum on Yeast Cell Growth And Ethanol Production, Turkish Journal Of Chemistry, 19 (4), 250-257.

¨ Çaglayan, H., Y. Gökmen, B. Kirdar, (1995), Polymorphisms Associated with the Factor VIII and IX Genes in the Turkish Population, Hemophilia, 1, 184-189.

¨ Çaglayan, H., Y. Gökmen, G. Aktuglu, C. Altay, B. Kirdar, (1995), Carrier Detection and Prenatal Diagnosis in Turkish Families, Turkish Medical Journal, 25, 172-182.

¨ Doruker, P., Z. I. Önsan, B. Kirdar, (1995), Ethanol Fermentation by Growing S. cerevisiae Cells Immobilized in Small Ca-Alginate Beads, Turkish Journal of Chemistry, 19, 37-42.

¨ Elibol, M., 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.

¨ Kayserili, H., D. Polat, N. Gökgöz, S. Basaran, B. Karaman, B. Kirdar, A. Tolun, K. Aydinli, A. Yüksel, S. Apak, M. Apak-Yüksel, (1995), Duchenne Kas Distrofisi (DMD) icin Riskli Ailelerde Tasiyiciligin Belirlenmesi ve Prenatal Tani: 132 Aile ve 35 Gebeligin Sonuçlari, Istanbul Cocuk Klinigi Dergisi, 30, 200-206.


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

¨ Özergin-Ülgen, K., 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, 497-500.


¨ Basak, A. N., A. Özer, N. Akar, B. Kirdar, (1993), A Novel 13 bp Deletion in the 3' UTR of the beta-globin Gene Causes beta-thalassemia in a Turkish patient, Hemoglobin, 17 (6), 551-555.

¨ Gökgöz, N., F. Kuseyri, H. Topaloglu, M. Yüksel-Apak, B. Kirdar, (1993), "Screening of Deletions and RFLP Analysis in Turkish DMD Families by PCR", Clinical Genetics, 43, 261-266.

¨ Özergin-Ülgen, K., Y. Khoury, Z. I. Önsan, B. Kirdar, (1993), "The Effect of Immobilization on Yeast Cell Growth and Ethanol Production", Turkish Journal of Chemistry, 17, 154-159.

¨ Özergin-Ülgen, K., 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.