1. Hilal Taymaz Nikerel
Assoc. Prof.

Hilal Taymaz Nikerel

hilal.nikerel@bilgi.edu.tr

+90 212 311 7063

Santralistanbul / EN1-107

Academic Experience

  • 2023-Present, 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. 

Education

  • PhD, 2010, Department of Biotechnology, Delft University of Technology, Netherlands. 
  • MSc, 2003, Department of Chemical Engineering, Bogazici University, Turkey. 
  • BSc, 2001, Department of Chemical Engineering, Bogazici University, Turkey.

Courses

  • BIOE 212 Bioengineering Lab. III
  • BIOE 333 Transfer Phenomena in Living Systems
  • BIOE 356 Bioprocess Engineering
  • BIOE 401 Bioengineering Design

Areas of Interest

  • (Integrative) Systems Biology
  • Metabolic Engineering
  • Regulation of Metabolic Networks

Rewards and Achievements

  • TUBITAK BIDEB 2232- Scholarship for Returning to Turkey After Doctorate Degree, Turkey, 2014-2016.

Other Information

Projects

  • Investigation of the effectiveness of CO2 fixation pathways through thermodynamic feasibility analysis of E. coli metabolic model under dynamic conditions, 2021-2024, Funded by TUBITAK ARDEB 1001 (Project No. 221M108), Role: Principal Investigator.
  • Development of Escherihia coli kinetic model for sustainable production from renewable resources, 2021-2023, Funded by Istanbul Bilgi University Research Fund,  Role: Principal Investigator.
  • Analysis of the common effects of doxorubicin on different disease types by integrative genome-wide approaches, 2019-2021, Funded by Istanbul Bilgi University Research Fund,  Role: Principal Investigator.
  • Investigation of intracellular effects of chemotherapeutic drugs using systems biology approaches and genome-wide models, 2014-2016, Funded by TUBITAK BIDEB 2232 (Project No. 114C062), Role: Principal Investigator.
  • Computational modeling approaches and fluxomics, 2010-2012, Funded by NCSB (Netherlands Consortium for Systems Biology) - NBIC (Netherlands Bioinformatics Centre), Role: Postdoctoral Researcher.


Publications

  • 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 1-14.
  • 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 Hemoglobin: a tool to reduce overflow metabolism. Microorganisms 10(1): 43.
  • 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.
  • 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.
  • Karabekmez ME, Taymaz-Nikerel H, Eraslan S, Kirdar B. 2021. Time-dependent re-organization of biological processes by the analysis of the 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§, Jamalzadeh E§, Espah Borujeni A, van Gulik WM, Heijnen JJ. 2013. A thermodynamic analysis of dicarboxylic acid production in microorganisms (§ Equal contribution). In Biothermodynamics: The role of Thermodynamics in Biochemical Engineering, editors: von Stockar U, van der Wielen L, EPFL-Press. (ISBN: 1466582162, 9781466582163)
  • van Gulik WM, Canelas AB, Taymaz-Nikerel H, Douma RD, de Jonge LP, Heijnen JJ. 2012. Fast sampling of the cellular metabolome. In Methods in Molecular Biology. Microbial Systems Biology: Methods and Protocols, Navid, A (ed). Vol. 881, Part 4, 279-306. Springer, New York, USA. (ISBN: 978-1-61779-826-9)  
  • 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.

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