|
Emrah Nikerel Assistant Professor Yeditepe University, Department of Genetics and Bioengineering |
Last Updated: 20-10-2014
 |
Education: B.Sc in ChE, Bogazici University, June 2001 M.Sc in (Bio)ChE, Bogazici University, June 2003 PhD in Biotechnology, Delft University of Technology, November 2009 Contact information:
|
Research Activities
Currently, I am an assistant professor at the Department of Genetics and Bioengineering in Yeditepe University. I work on systems biology and bioinformatics approaches, to understand microbial metabolism. In particular, I focus on the analysis of weak acid stress on yeast cells using hybrid (in time scale) models. Below are my broader research topics
Published papers/book chapters (in case you wish to get a copy of the articles, please send an email)
|
Alkaya U., Nikerel E., ' Integration of transcriptome and fluxome data reveals insights in understanding the effect of weak acid stress in Saccharomyces cerevisiae, International Conference on Applied Informatics for Health and Life Sciences, Kusadasi-TURKIYE 19-22 October 2014 Cakir T. ve Nikerel E.,
Biyolojik Aglarin Modellenmesi, Biyomedikal Muhendisliginin Temelleri, ISBN: 978-605-133-943-6, September 2014.
Berkhout J.,
Bosdriesz E., Nikerel E.,
Molenaar D., de Ridder D., Teusink B., Bruggeman F., 'How Biochemical
Constraints of Cellular Growth Shape Evolutionary Adaptations in
Metabolism', Genetics, 2013, 194(2), 505-512, Available
online Nikerel E.,
Verheijen P., van Gulik W., Heijnen J., 'Model-Based Design
of Superior Cell Factory: An Illustrative Example of Penicillium chrysogenum',
in
Systems Metabolic Engineering (Eds.S.Y. Lee, C. Witmann), Springer, 2012, pp 221-270, Available
online Nikerel
E., Berkhout J., Hu F., Teusink B.,
Reinders M., de Ridder D., 'Understanding
Regulation of Metabolism through Feasibility Analysis',
PLoS ONE, 2012, 7, e39396 Available
online Nikerel E.,
van Winden W.A, Verheijen
P.J.T.,
Heijnen J.J, 'Construction
of kinetic models for metabolic reaction networks: Lessons learned in
analysing short-term stimulus response data',
Mathematical and Computer Modelling of Dynamical Systems, 2011, 17(3),
243-260, Available
online Nikerel E.,
van Winden W.A, Verheijen
P.J.T., Heijnen J.J, 'Model
reduction and a priori kinetic parameter identifiability analysis using
metabolome time series for metabolic reaction networks with linlog
kinetics',
Metabolic Engineering, 2009, 11(1), 20-30 Available
online Gunay M.E., Nikerel E.,
Toksoy
E., Kirdar B., Yıldırım R., 'Simultaneous
modeling of enzyme production and biomass growth in recombinant
Escherichia coli using artificial neural networks',
Biochemical Engineering Journal, 2008, 42(3), 329-335 Available
online Nikerel E.,
Ates O, Toksoy E., 'Effect
of bioprocess conditions
on growth and alkaline protease production by halotolerant Bacillus
licheniformis BA17',Applied Biochemistry and Microbiology,
2008, 44(5), 487-492 Available
online Nikerel
I.E., van Winden W.A, van Gulik W.M,
Heijnen J.J, 'Linear-logarithmic
kinetics; a framework for modelling kinetics of metabolic reaction
networks', Simulation News Europe, 2007, 17(1)19-26 Issue
available
online Nikerel
I.E., van Winden W.A, van Gulik W.M,
Heijnen J.J, 'A
method for estimation of elasticities in metabolic networks using
steady state and dynamic metabolomics data and linlog kinetics',
BMC Bioinformatics, 2006, 7:540 Available
online
Nikerel
I.E. , Toksoy E., Kirdar B.,
Yildirim R., 'Optimization
of medium composition for biomass production of recombinant Escherichia
coli cells using response surface methodology',
Biochemical Engineering Journal, November
2006, Vol(32), pp 1-6, Available online Nikerel E.,
Toksoy E., Kirdar
B., Yildirim R., 'Optimizing medium composition
for TaqI endonuclease production by recombinant Escherichia coli cells
using response surface methodology', Process
Biochemistry, April 2005, Vol40(5),pp 1633-1639 available online. |