Betul Kirdar

Summary

Country: Turkey

Publications

  1. doi request reprint A novel topological centrality measure capturing biologically important proteins
    Muhammed Erkan Karabekmez
    Bogazici University, Department of Chemical Engineering, Istanbul, Turkey
    Mol Biosyst 12:666-73. 2016
  2. doi request reprint An integrative analysis of transcriptomic response of ethanol tolerant strains to ethanol in Saccharomyces cerevisiae
    Ceyda Kasavi
    Department of Chemical Engineering, Bogazici University, Istanbul, Turkey
    Mol Biosyst 12:464-76. 2016
  3. pmc A system based network approach to ethanol tolerance in Saccharomyces cerevisiae
    Ceyda Kasavi
    Department of Chemical Engineering, Bogazici University, Istanbul, Turkey
    BMC Syst Biol 8:90. 2014
  4. doi request reprint Transcriptional remodelling in response to changing copper levels in the Wilson and Menkes disease model of Saccharomyces cerevisiae
    Ayca Cankorur-Cetinkaya
    Department of Chemical Engineering, Bogazici University, Bebek, Istanbul, Turkey
    Mol Biosyst 9:2889-908. 2013
  5. pmc Integration of metabolome data with metabolic networks reveals reporter reactions
    Tunahan Cakir
    Department of Chemical Engineering, Bogazici University, Bebek, Istanbul, Turkey
    Mol Syst Biol 2:50. 2006
  6. ncbi request reprint Metabolic pathway analysis of yeast strengthens the bridge between transcriptomics and metabolic networks
    Tunahan Cakir
    Department of Chemical Engineering, Bogazici University, 34342 Bebek Istanbul, Turkey
    Biotechnol Bioeng 86:251-60. 2004
  7. pmc A novel strategy for selection and validation of reference genes in dynamic multidimensional experimental design in yeast
    Ayca Cankorur-Cetinkaya
    Department of Chemical Engineering, Bogazici University, Bebek, Istanbul, Turkey
    PLoS ONE 7:e38351. 2012
  8. ncbi request reprint Annotation of unknown yeast ORFs by correlation analysis of microarray data and extensive literature searches
    Pinar Pir
    Department of Chemical Engineering, Bogazici University, Bebek 34342, Istanbul, Turkey
    Yeast 23:553-71. 2006
  9. doi request reprint Exometabolic and transcriptional response in relation to phenotype and gene copy number in respiration-related deletion mutants of S. cerevisiae
    Pinar Pir
    Department of Chemical Engineering, Bogazici University, Bebek, 34342 Istanbul, Turkey
    Yeast 25:661-72. 2008
  10. pmc Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae
    Tunahan Cakir
    Bogazici University, Department of Chemical Engineering, 34342, Bebek, Istanbul, Turkey
    BMC Syst Biol 1:18. 2007

Collaborators

Detail Information

Publications21

  1. doi request reprint A novel topological centrality measure capturing biologically important proteins
    Muhammed Erkan Karabekmez
    Bogazici University, Department of Chemical Engineering, Istanbul, Turkey
    Mol Biosyst 12:666-73. 2016
    ....
  2. doi request reprint An integrative analysis of transcriptomic response of ethanol tolerant strains to ethanol in Saccharomyces cerevisiae
    Ceyda Kasavi
    Department of Chemical Engineering, Bogazici University, Istanbul, Turkey
    Mol Biosyst 12:464-76. 2016
    ..Transcription factors around which most important changes occur were determined and active subnetworks in response to ethanol and functional clusters were identified in all strains. ..
  3. pmc A system based network approach to ethanol tolerance in Saccharomyces cerevisiae
    Ceyda Kasavi
    Department of Chemical Engineering, Bogazici University, Istanbul, Turkey
    BMC Syst Biol 8:90. 2014
    ....
  4. doi request reprint Transcriptional remodelling in response to changing copper levels in the Wilson and Menkes disease model of Saccharomyces cerevisiae
    Ayca Cankorur-Cetinkaya
    Department of Chemical Engineering, Bogazici University, Bebek, Istanbul, Turkey
    Mol Biosyst 9:2889-908. 2013
    ..The observation of the improvement in the respiratory capacity of CCC2 deleted cells by supplementation with pyridoxine as well as with nicotinic acid may shed light on novel therapeutic interventions for Wilson and Menkes diseases. ..
  5. pmc Integration of metabolome data with metabolic networks reveals reporter reactions
    Tunahan Cakir
    Department of Chemical Engineering, Bogazici University, Bebek, Istanbul, Turkey
    Mol Syst Biol 2:50. 2006
    ..Hereby, the reported approach represents an attempt to map different layers of regulation within metabolic networks through combination of metabolome and transcriptome data...
  6. ncbi request reprint Metabolic pathway analysis of yeast strengthens the bridge between transcriptomics and metabolic networks
    Tunahan Cakir
    Department of Chemical Engineering, Bogazici University, 34342 Bebek Istanbul, Turkey
    Biotechnol Bioeng 86:251-60. 2004
    ..Control-effective flux distribution was found to be promising in in silico predictions by incorporating functionality and regulation into the metabolic network structure...
  7. pmc A novel strategy for selection and validation of reference genes in dynamic multidimensional experimental design in yeast
    Ayca Cankorur-Cetinkaya
    Department of Chemical Engineering, Bogazici University, Bebek, Istanbul, Turkey
    PLoS ONE 7:e38351. 2012
    ....
  8. ncbi request reprint Annotation of unknown yeast ORFs by correlation analysis of microarray data and extensive literature searches
    Pinar Pir
    Department of Chemical Engineering, Bogazici University, Bebek 34342, Istanbul, Turkey
    Yeast 23:553-71. 2006
    ....
  9. doi request reprint Exometabolic and transcriptional response in relation to phenotype and gene copy number in respiration-related deletion mutants of S. cerevisiae
    Pinar Pir
    Department of Chemical Engineering, Bogazici University, Bebek, 34342 Istanbul, Turkey
    Yeast 25:661-72. 2008
    ..Thus, Hap4p targets genes that are required for respiration and for fitness in nutrient-limited conditions. This suggests that Hap4p may enable cells to adapt to nutrient limitation as well as diauxy...
  10. pmc Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae
    Tunahan Cakir
    Bogazici University, Department of Chemical Engineering, 34342, Bebek, Istanbul, Turkey
    BMC Syst Biol 1:18. 2007
    ..The CEF analysis is based on a simple stoichiometric model that includes reactions of the central carbon metabolism and the amino acid metabolism...
  11. doi request reprint Short- and long-term dynamic responses of the metabolic network and gene expression in yeast to a transient change in the nutrient environment
    Duygu Dikicioglu
    Department of Chemical Engineering, Bogazici University, Istanbul, Turkey
    Mol Biosyst 8:1760-74. 2012
    ..Our study highlighted the role of inosine accumulation and recycling in energy homeostasis and indicated possible bottlenecks in the process...
  12. ncbi request reprint Understanding signaling in yeast: Insights from network analysis
    K Yalçin Arga
    Department of Chemical Engineering, Bogazici University, 34342 Istanbul, Turkey
    Biotechnol Bioeng 97:1246-58. 2007
    ....
  13. ncbi request reprint Flux balance analysis of a genome-scale yeast model constrained by exometabolomic data allows metabolic system identification of genetically different strains
    Tunahan Cakir
    Department of Chemical Engineering, Bogazici University, 34342 Bebek, Istanbul, Turkey
    Biotechnol Prog 23:320-6. 2007
    ..The FBA approach thereby enables identification of responsive pathways and so permits the elucidation of the genetic characteristics of strains in terms of expressed metabolite profiles...
  14. pmc How yeast re-programmes its transcriptional profile in response to different nutrient impulses
    Duygu Dikicioglu
    Department of Chemical Engineering, Bogazici University, Bebek 34342, Istanbul, Turkey
    BMC Syst Biol 5:148. 2011
    ..cerevisiae in response to the sudden and transient removal of either carbon or nitrogen limitation has been studied by following both the short- and long-term changes in yeast's transcriptomic profiles...
  15. pmc Integrative investigation of metabolic and transcriptomic data
    Pinar Pir
    Department of Chemical Engineering, Bogazici University, Bebek 34342, Istanbul, Turkey
    BMC Bioinformatics 7:203. 2006
    ..At the same time, existing methods are being modified to serve the objectives of systems biology and permit the interpretation of the huge datasets currently being generated by high-throughput methods...
  16. pmc Transcriptomic response of yeast cells to ATX1 deletion under different copper levels
    Ayca Cankorur-Cetinkaya
    Department of Chemical Engineering, Faculty of Engineering, Bogazici University, 34342, Istanbul, Turkey
    BMC Genomics 17:489. 2016
    ..Atx1p plays an important role in the intracellular copper transport as a copper chaperone transferring copper from the transporters to Ccc2p for its subsequent insertion into Fet3p, which is required for high affinity iron transport...
  17. ncbi request reprint Real imaging and size values of Saccharomyces cerevisiae cells with comparable contrast tuning to two environmental scanning electron microscopy modes
    Zulal Misirli
    Department of Chemical Engineering, Bogazici University, Istanbul, Turkey
    Scanning 29:11-9. 2007
    ....
  18. ncbi request reprint Sequence variations within the genes related to hemostatic imbalance and their impact on coronary artery disease in Turkish population
    Hilal Taymaz
    Department of Chemical Engineering, Bogazici University, 34342 Bebek Istanbul, Turkey
    Thromb Res 119:55-62. 2007
    ....
  19. pmc Production of ethanol from starch by respiration-deficient recombinant Saccharomyces cerevisiae
    Ebru Toksoy Oner
    Marmara University, Faculty of Engineering, Department of Chemical Engineering, Goztepe 34722 Istanbul, Turkey
    Appl Environ Microbiol 71:6443-5. 2005
    ..In a comparison of ethanol fermentation performances with the parental respiration-sufficient WTPB-G strain, the NPB-G strain showed an increase of ca. 48% in both ethanol yield and ethanol productivity...
  20. pmc Genome-Wide Transcriptional Response of Saccharomyces cerevisiae to Stress-Induced Perturbations
    Hilal Taymaz-Nikerel
    Department of Chemical Engineering, Bogazici University, Istanbul, Turkey
    Front Bioeng Biotechnol 4:17. 2016
    ..It is aimed to conclude on common regulatory phenomena that allow yeast to organize its transcriptomic response after any perturbation under different external conditions. ..
  21. ncbi request reprint Recovery of antithrombin III from milk by expanded bed chromatography
    Sinem Ozyurt
    Department of Chemical Engineering, Bogazici University, Bebek, Istanbul, Turkey
    J Chromatogr A 944:203-10. 2002
    ..5 cm. However, antithrombin III was concentrated to a higher degree by using the column with an internal diameter of 1 cm...