Hilal TAYMAZ NİKEREL

Assoc. Prof.
E-mail: 

hilal.taymaz@bogazici.edu.tr

Education: 

PhD: 2010, Department of Biotechnology, Delft University of Technology, The Netherlands.
MS: 2003, Department of Chemical Engineering, Bogazici University, Turkey.
BS: 2001, Department of Chemical Engineering, Bogazici University, Turkey.

Experience: 

• 2024-Present, Associate Professor, Department of Chemical Engineering, Bogazici University, Turkey.
• 2023-2024, Associate Professor, Department of Genetics and Bioengineering, Istanbul Bilgi University, Turkey.
• 2017-2023, Assistant Professor, Department of Genetics and Bioengineering, Istanbul Bilgi University, Turkey.
• 2016-2017, Part-Time Instructor, Department of Genetics and Bioengineering, Istanbul Bilgi University, Turkey.
• 2014-2016, Postdoctoral Researcher, Department of Chemical Engineering, Bogazici University, Turkey.
• 2010-2012, Postdoctoral Researcher, Medical Genomics/Centre for Integrative Bioinformatics, VU University Amsterdam, Netherlands.
• 2005-2010, Doctoral Researcher, Department of Biotechnology, Delft University of Technology, Netherlands.
• 2001-2005, Research and Teaching Assistant, Department of Chemical Engineering, Bogazici University, Turkey.

 

Research Interests: 

Analysis of biological networks via systems biology approaches
Bioprocess engineering
Dynamic response of microbial systems to various perturbations
Microbial production of relevant organic acids/enzymes

Selected Papers: 

Journal Articles

  • Lara AR, Kunert F, Vandenbroucke V, Taymaz-Nikerel H, Martínez LM, Sigala JC, Delvigne F, Gosset G, Büchs J. 2024. Transport-controlled growth decoupling for self-induced protein expression with a glycerol-repressible genetic circuit. Biotechnology and Bioengineering 121(6): 1789-1802.

  • de la Cruz M, Kunert F, Taymaz-Nikerel H, Sigala JC, Gosset G, Büchs J, Lara AR. 2024. Increasing the pentose phosphate pathway flux to improve plasmid DNA production in engineered E. coli. Microorganisms 12(1): 150.

  • Taymaz-Nikerel H. 2022. Doxorubicin-induced transcriptome meets interactome: identification of new drug targets. Turkish Journal of Biology 46(2): 137-144.

  • Taymaz-Nikerel H, Lara AR. 2022. Vitreoscilla Haemoglobin: a tool to reduce overflow metabolism. Microorganisms 10(1): 43.

  • Taymaz-Nikerel H. 2021. Integration of fluxome and transcriptome data in Saccharomyces cerevisiae offers unique features of doxorubicin and imatinib. Molecular Omics 17(5): 783-789.

  • Cakir A, Tuncer M, Taymaz-Nikerel H, Ulucan O. 2021. Side effect prediction based on drug- induced gene expression profiles and random forest with iterative feature selection. The Pharmacogenomics Journal 21(6): 673-681.

  • Karabekmez ME, Taymaz-Nikerel H, Eraslan S, Kirdar B. 2021. Time-dependent re- organization of biological processes by the analysis of dynamic transcriptional response of yeast cells to doxorubicin. Molecular Omics 17(4): 572-582.

  • Taymaz-Nikerel H, Eraslan S, Kirdar B. 2020. Insights into the mechanism of anti-cancer drug imatinib revealed through multi-omic analyses in yeast. OMICS: A Journal of Integrative Biology 24(11): 667-678.

  • Taymaz-Nikerel H, Karabekmez ME, Eraslan S, Kirdar B. 2018. Doxorubicin induces an extensive transcriptional and metabolic rewiring in yeast cells. Scientific Reports 8: 13672.

  • Taymaz-Nikerel H, Lara AR. 2016. Editorial: Quantitative Systems Biology for Engineering Organisms and Pathways. Frontiers in Bioengineering and Biotechnology 4:22.

  • Taymaz-Nikerel H, De Mey M, Baart GJ, Maertens J, Foulquie-Moreno MR, Charlier D, Heijnen JJ, van Gulik WM. 2016. Comparative fluxome and metabolome analysis for overproduction of succinate in Escherichia coli. Biotechnology and Bioengineering 113(4): 817-829.

  • Taymaz-Nikerel H, Cankorur-Cetinkaya A, Kirdar B. 2016. Genome wide transcriptional response of Saccharomyces cerevisiae to stress-induced perturbations. Frontiers in Bioengineering and Biotechnology 4:17.

  • Wunderlich M, Taymaz-Nikerel H, Gosset G, Ramirez OT, Lara AR. 2014. Effect of growth rate on plasmid DNA production and metabolic performance of engineered Escherichia coli strains. Journal of Bioscience and Bioengineering, 117(3): 336-342.

  • Taymaz-Nikerel H, De Mey M, Baart G, Maertens J, Heijnen JJ, van Gulik WM. 2013. Changes in substrate availability in Escherichia coli lead to rapid metabolite, flux and growth rate responses. Metabolic Engineering 16: 115-129.

  • Taymaz-Nikerel H, van Gulik WM, Heijnen JJ. 2011. Escherichia coli responds with a rapid and large change in growth rate upon a shift from glucose-limited to glucose-excess conditions. Metabolic Engineering 13: 307-318.

  • Taymaz-Nikerel H, Espah Borujeni A, Verheijen PJT, Heijnen JJ, van Gulik WM. 2010. Genome-derived minimal metabolic models for Escherichia coli MG1655 with estimated in- vivo respiratory ATP stoichiometry. Biotechnology and Bioengineering 107: 369-381.

  • De Mey M§, Taymaz-Nikerel H§, Baart G, Waegeman H, Maertens J, Heijnen JJ, van Gulik WM. 2010. Catching prompt metabolite dynamics in Escherichia coli with the BioScope at oxygen rich conditions. Metabolic Engineering 12: 477-487. (§ Equal contribution)

  • Lara AR§, Taymaz-Nikerel H§, Mashego M, van Gulik WM, Heijnen JJ, Ramírez OT, van Winden WA. 2009. Fast dynamic response of the fermentative metabolism of Escherichia coli to aerobic and anaerobic glucose pulses. Biotechnology and Bioengineering 104: 1153-1161. (§ Equal contribution)

  • Taymaz-Nikerel H, De Mey M, Ras C, ten Pierick A, Seifar RM, van Dam J, Heijnen JJ, van Gulik WM. 2009. Development and application of a differential method for reliable metabolome analysis in Escherichia coli. Analytical Biochemistry 386: 9-19.

  • Taymaz H, Eraslan S, Toksoy Oner E, Alkan T, Agirbasli M, Kirdar B. 2007. Sequence variations within the genes realated to hemostatic imbalance and their impact on coronary artery disease in Turkish population. Thrombosis Research 119: 55-62.