BIOSYSTEMS ENGINEERING RESEARCH GROUP 

 
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BETÜL KIRDAR-Publications

 

  1. Kasavi C., Eraslan S., Arga K.Y., Toksoy Oner E., Kirdar B., 2014, "A System Based Network Approach to Ethanol Tolerance in Saccharomyces cerevisiae", BMC Systems Biology, 8:90, doi:10.1186/s12918-014-0090-6.

  2. Finore I., Di Donato P., Poli A., Kirdar B., Kasavi C., Toksoy Oner E., Nicolaus B., Lama L., 2014, "Use of Agro Waste Biomass for alpha-Amylase Production by Anoxybacillus amylolyticus: Purification and Properties", Journal of Microbial & Biochemical Technology, 6:6, 320-326, doi:10.4172/1948-5948.1000162.

  3. Dikicioglu D., Oc S., Rash B.M., Dunn W.B., Pir P., Kell D.B., Kirdar B., Oliver S.G., 2014, "Yeast cells with impaired drug resistance accumulate glycerol and glucose", Molecular Biosystems, doi:10.1039/c2mb25512j.

  4. Cankorur-Cetinkaya A., Eraslan S., Kirdar B., 2013, "Transcriptional Remodelling in Response to Changing Copper Levels in Wilson and Menkes Disease Model of Saccharomyces cerevisiae", Molecular Biosystems, doi:10.1039/C3MB70276F.

  5. Rende D., Baysal N., Kirdar B., 2013, "Complex Disease Interventions from a Network Model for Type 2 Diabetes", PlosOne, 8:6, e65854.

  6. Kasavi C., Finore I., Lama L., Nicolaus B., Oliver S.G., Toksoy Oner E., Kirdar B., 2012, "Evaluation of industrial Saccharomyces cerevisiae strains for ethanol production from biomass", Biomass and Bioenergy, 45, 230-8, doi: 10.1016/j.biombioe.2012.06.013.

  7. Cankorur-Cetinkaya A., Dereli E., Eraslan S., Karabekmez E., Dikicioglu D., Kirdar B., (2012), "A Novel Strategy for Selection and Validation of Reference Genes in Dynamic Multidimensional Experimental Design in Yeast", PLoS ONE 7(6): e38351 doi:10.1371/journal.pone.0038351.

  8. Dikicioglu D., Dunn W.B., Kell D.B., Kirdar B., Oliver S.G., (2012), "Short- and Long-Term Dynamic Responses of the Metabolic Network and Gene Expression in Yeast to a Transient Change in the Nutrient Environment", Mol Biosyst 8(6):1760-74.

  9. Dikicioglu D., Karabekmez E., Rash B., Pir P., Kirdar B., Oliver S.G., (2011), "How yeast re-programmes its transcriptional profile in response to different nutrient impulses", BMC Systems Biology 5:148, doi: 10.1186/1752-0519-5-148.

  10. Rende D., Baysal N., Kırdar B., (2011), "A Novel Integrative Network Approach to Understand the Interplay between Cardiovascular Disease and Other Complex Disorders", Molecular Biosystems, Vol. 7 (7), 2205-2219, doi:10.1039/c1mb05064h.

  11. Finore I., Kasavi C., Poli A., Romano I., Toksoy Oner E., Kirdar B., Dipasquale L., Nicolaus B., Lama L., (2011), “Purification, biochemical characterization and gene sequencing of a thermostable raw starch digesting α-amylase from Geobacillus thermoleovorans subsp. stromboliensis subsp. nov.”, World J Microbiol Biotechnol, doi:10.1007/s11274-011-0715-5.

  12. 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.

  13. 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., Spasić, 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.; A consensus yeast metabolic network obtained from a community approach to systems biology, Nature Biotechnol. 26, 1155-1160, 2008.

  14. M. Erdem Günay, I. Emrah Nikerel, Ebru Toksoy Oner,Betul Kirdar, Ramazan Yildirim; Simultaneous modeling of enzyme production and biomass growth in recombinant Escherichia coli using artificial neural networks, Biochemical Engineering Journal 42, 329-335, 2008

  15. Duygu Dikicioğlu, Pınar Pir, Z. İlsen Onsan, Kutlu O. Ulgen,Betul Kirdar,   Stephen G. Oliver; 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, 2008.

  16. Pınar Pir, Betul Kirdar, Andrew Hayes, Z. İlsen Onsan, Kutlu O. Ulgen, Stephen G. Oliver; Exometabolic and transcriptional response in relation to phenotype and gene copy number in respiration-related deletion mutants of S. cerevisiae, Yeast, 25:661-672, 2008.

  17. Çakir T., Kirdar B., Onsan Zİ., Ulgen OK.,  Nielsen J.;Effect of carbon source perturbations on regulation of metabolic fluxes in S. cerevisiae , BMC Systems Biology, 1:18, 2007.

  18. Çakir T., Efe Ç., Dikicioğlu D., Hortaçsu A., B. Kirdar, Oliver GO.: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, 2007.

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

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

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

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

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

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

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

  26. Akarsubaşı T.A., İnce O.,Oz N.A.,Kırdar B.,İnce B.; Evaluation of performance, acetoclastic methanogenic activity and archeal composition of full scale UASB reactors treating alcohol distillery wastewaters, Process Biochemistry 41,28-35, 2006.

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

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

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

  30. Cakir T, B. Kırdar,  Ülgen K : Metabolic pathway analysis of yeast strengthens the bridge between transcriptomics and metabolic networks, Biotechnology and Bioengineering 86(3), 251-260, 2004.

  31. Sariyar B., Ozkan P, B. Kırdar, Hortacsu A :  Expression of glucose isomerase as a fusion protein in E.coli, Enzyme and Microbial Technology  35, 105-112, 2004.

  32. M.M. Altıntaş, B. Kırdar, Z.İ. Önsan, S.G.Oliver, K. Ülgen : Optimal substrate feeding policy for fed-batch cultures of the recombinant Saccharomyces cerevisiae YPB-G , Enzyme and Microbial Technology 33, 262-269, 2003.

  33. Toksoy E., Kırdar B., Önsan Z.İ., Ülgen K.: Modelling 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(3), 315-323, 2003.

  34. Birol G., Birol I., B.Kırdar, Z.İ. Önsan:Investigating the fermentation dynamic structure of  recombinant yeast YPB-G, Computers and Chemical Engineering 27, 45-54, 2003.

  35. Birol G., Z.İ. Önsan, B.Kırdar: A simple structured model for biomass and extracellular enzyme production with recombinant Saccharomyces cerevisiae YPB-G, Journal of  Industrial Microbiology&Biotechnology 29, 111-116, 2002.

  36. M.M. Altıntaş, B. Kırdar, Z.İ. Önsan, K. Ülgen and S.G.Oliver : Improvement of ethanol production from starch by recombinant yeast through manipulation of environmenatal factors, Enzyme and Microbial Technology 31, 640-647, 2002.

  37. Toksoy E.,Önsan Z.İ.,Kırdar B: High level production of Taq restriction endonuclease by three different expression system in Escherichia coli cells using T7 phage promoter, Applied Microbiology and Biotechnology 59, 239-245, 2002.

  38. M.M. Altıntaş, B. Kırdar, Z.İ. Önsan, K. Ülgen: Cybernetic modeling  of growth and ethanol production in a recombinant S.cerevisiae strain secreting a bifunctional protein, Process Biochemistry, 37, 1439-1445, 2002.

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

  40. Ülgen K., Saygılı B., Önsan Z.İ.,Kırdar B.; Bioconversion of starch into ethanol by a recombinant  Saccaromyces cerevisiae strain YPG-AB, Process Biochemistry 37, 1157-1168, 2002.

  41. Toksoy E.,Önsan Z.İ.,Kırdar B.: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, 2002.

  42. Ozyurt S., Kırdar B., Ulgen K.: Recovery of antithrombin III from milk by expanded bed chromatography, Journal of Chromatography A ,944,203-210, 2002.

  43. Toksoy E.,Önsan Z.İ.,Kırdar B.: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, 2001.

  44. Altıntaş M.,Kırdar B.,Önsan Z.İ.,Ülgen  K.: Plasmid stability in a recombinant S. cerevisiae strain secreting a bifunctional fusion protein, Journal of Chemical Technology and Biotechnology 76(6),612-618, 2001.

  45. Tamerler C., Ülgen K., Kırdar B.,Önsan Z.İ.: A structured model for intracellular production of EcoRI by recombinant E.coli Process Biochemistry 36,621-627, 2001.

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

  47. Yıldır C., Önsan Z.İ., Kırdar B. : Comparison of the recovery of EcoRI    endonuclease from two genetically modified strains of E.coli, Doğa-Turkish Journal of Chemistry 25,63-71, 2001.

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

  49. Birol G., Önsan Z.İ., Kırdar B.: Studies on the fermentation of recombinant yeast cells: Stability and kinetics of biomass and protein production, Journal of Chemical Technology and Biotechnology 75,729-737, 2000.

  50. Dork K., Macek Jr M., Mekus F., Tümmler B., Sakmaryova I., Krebsova A., Vavrova V., Zemkova D., Macek Sr.M., Koudova M., Ginter E., Petrova N. V., Ivaschenko T., Baranov B., Witt M., Pogorzelski A., Bal J., Zekanowski C., Stuhrmann M., Bauer I., Thamm B., Wagner K., Nechiporenko M., Livshits L., Komel R., Vouk K., Ravnic-Glavac M., Kocheva S., Efremov G.D., Kucinkas V., Teder M., Krumina A., Kusic J., Radojkovic D., Sangiuolo F., Jordanova A., Sertic J., Richter D., Rukavina A.S., Kadasi L., Malone G., Cuppens H., Carles S., Claustres M., Verlingue C., Ferec C., Bjorck E., Strandvik B., Onay T., Kırdar B., Cardoso H., Montgomery M., Nakielna B., Hughes D., Casals T., Estivill X., Aznarez I., Tzountzouris J., Tsui L-C., Zielenski J.: 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, 2000.

  51. Savaş S., Gökgöz N, Kayserili H, Ozkınay F., Yüksel-Apak M., Kırdar B., Screening of deletions in SMN,NAIP and BTF2p44  genes in Turkish muscular atrophy  patients, Human Heredity  50 , 162-165, 2000.

  52. Toksoy E., Özdinler P.H., Önsan Z.İ., Kırdar B.: High level secretion  of TaqI restriction endonuclease by recombinant E.coli, Biotechnology Techniques 13, 803-808, 1999.

  53. Eraslan S.,Kayserili H.Yüksel-Apak M.,Kırdar B.: Identification of point   mutaitons in Turkish DMD/BMD families using SSCA European Journal of Human Genetics 7(7),765-771, 1999.

  54.  Onay T.,Kayserili H.,Yüksel Apak M.,Kırdar B.: Analysis of infertile brothers with congenital bilateral absence of vas deference for mutations in the CFTR gene, Clinical Genetics 55,63-64, 1999.

  55. Brega A.,Scacchi R.,Kırdar B.Peloso G.,Corbo R.M.:A study of fifteen polymorphisms in a sample of the Turkish population, Human Biology  70(4), 715-728, 1998.

  56. Birol G.,Doruker P.,Kırdar B.,Önsan Z.İ.,Ülgen K.:Mathematical description of ethanol fermentation by immobilised Saccharomyces cerevisiae, Process Biochemistry 33(7),763-771, 1998.

  57. Onay T., Topaloğlu Ö, Zielinski J., Gökgöz N., Kayserili H., Çokuğraş H., Söylemez Y., Akçakaya N., Apak M., Tsui L.-C., Kırdar B.: Analysis of the CFTR gene in the Turkish cystic fibrosis patients:Identification of three new mutations (3172delAC,P1013L,M1028I), Human Genetics  102,224-  230, 1998.

  58. Birol G.,Önsan Z.İ.,Kırdar B. and Oliver S.G.: Investigation of fermentation characteristics of recombinant S. cerevisae on starch, Enzyme and Microbiol Technology  22,672-677, 1998.

  59. Eraslan S.,Gökgöz N.,Kırdar B.: Identification of deletion carriers in DMD/BMD families using a DIG-labeled quantitative PCR, Molecular Diagnosis 2(4),251-258,1998

  60. Yılır C.,Önsan Z.İ.,Kırdar B.: Optimization of the starting time and period of induction and inducer conditions in the recovery of the restriction enzyme EcoRI from recombinant E.coli 294, Turkish Journal of Chemistry  22(3),221-226, 1998.

  61. Çelik A.,Eraslan S.,Gökgöz N., Ilgın H., Başaran S.,Bökesoy I.,Kayserili H.,Yüksel-Apak M.,Kırdar B.:Identification of the parental origin of polysomy in two 49,XXXXY cases, Clinical Genetics 51(6),426-429, 1997.

  62. Kayserili H.,Polat D.,Gökgöz N.,Başaran S.,Karaman B.,Kırdar B.,Tolun A.,Aydınlı K,Yüksel A.,Apak.S.,Apak-Yüksel M.: Duchenne kas distrofisi (DMD) için riskli ailelerde taşıyıcılığın belirlenmesi ve prenatal tanı:132 aile ve 35 gebeliğin sonuçları, İstanbul Çocuk Kliniği Dergisi 30, 200-206, 1995.

  63. Çağlayan H.,Gökmen Y.Aktuğlu G.,Altay Ç.,Kırdar B.; Carrier detection and prenatal diagnosis in Turkish families, Doğa, Turkish Medical Journal,25,172-182,1995.

  64. Çağlayan H. Gökmen Y.,Kırdar B.,Polymorphisms associated with the factor VIII and IX genes in the Turkish populati, Hemophilia 1,184-189,1995.

  65. Doruker,P.Önsan Z.İ.,Kırdar B.;Ethanol fermentation by growing S.cerevisiae cells immobilizied in small Ca-alginate beads. Turkish Journal of Chemistry (DOĞA), 19,37-42,1995.

  66. Ülgen, K., Khoury Y., Önsan Z.İ., Kırdar B.: The effect of Immobilization on yeast cell growth and ethanol production. Turkish  Journal of Chemistry  (DOĞA) 17 (2), 154-159, 1993.

  67. Başak, A.N., Özer, A., Akar, N., Kırdar, B.: A novel 13 bp deletion in the 3'UTR of the b-globin gene causes b-thalassemia in a Turkish patient, Hemoglobin 17(6), 551-555, 1993.

  68. Gökgöz, N., Kuseyri,F., Topaloğlu, H. Yüksel-Apak M., Kırdar B.: Screening of Deletions and RFLP Analysis in Turkish DMD Families by PCR Clinical Genetics 43, 261-266, 1993.

  69. Başak, A.N., Özer, A., Özçelik, H., Gürgey, A., Kırdar., B.: A novel frameshift mutation: Deletion of C in codons 74/75 of the b-Globin gene causes b-Thalassemia in a Turkish patient, Hemoglobin 16, 309-312, 1992.

  70. Başak, A.N., Özçelik, H., Özer, A., Tolun, A., Aksoy, M., Ridolfi, F., Ulukutlu, L., Akar, N., Gürgey, A., Kırdar, B.:The molecular basis of b-thalassemia in Turke, Human Genetics, 89, 315-318, 1992.

  71. Gökgöz,N., Topçu, M., Kuseyri, F, Renda,Y., Apak, S., Yüksel-Apak, M., Kırdar, B.: Screering of deletions in Turkish Duchenne/Becker muscular dystrophy patients by using two separate multiplex gene amplification systems. Doğa, Turkish Medical Journal,, 16(2), 113-123, (1992).

  72. Eğilmez, N., Gökmen, L., Bahçecioğlu, H., Kırdar, B. :Human factor VIII HindIII RFLP: Genotypic distribution and use for carrier detection of hemophilia A in the Turkish population. Doğa,Turkish Medical Journal 16(2), 105-1112, 1992.

  73. Başak, A.N., Özçelik, H., Özer, A., Tolun, A., Kırdar, B.: b-Thalassemia in Turkey: A systematic molecular  characterization of point mutations by gene amplification and dot-blot hybridization. Doğa, Turkish Medical Journal, 15, 426-434, 1991.

  74. Kırdar, B., Dalay, N., Bermek, E.: Binding of protein uH2A  and H2A to DNA. Cell Biophysics 14, 43-51, 1989.

  75. Dalay, N., Kırdar, B., Bermek, E.:  Effect of cycloheximide on nuclear uH2A content. Experiantia 40, 1398-1400, 1984.

  76. Dalay N., Özkaynak, E., Kırdar, B., Çarin, M., Bermek, E.: Isolation of protein uH2A  using a one step preparative gel electrophoresis. Preparative Biochemistry 14 (2), 181-192,1984.

  77. Kırdar, B., Dalay, N., Özkaynak, E., Bermek E.: Sıçan karaciğer kromatininin kesimlendirilmesi ve alt fraksiyonlarının nitelikleri. Doğa Bilim Dergisi 7(3), 270-278, 1983.

  78. Gökçe, S., Kan, B., Kırdar, B., Bermek,E.:High salt effect on RNA synthesis in Krebs   Ascites Tumor cells. Experiantia 38, 666, 1982.