Scientific Career

I’m an evolutionary biologist, interested in mutations and their phenotypic consequences in humans. I use bioinformatic tools and available data sets. Hence my job is mainly in front of the computer.

After the PhD:

Since last year, I am a research associate in the University of Lausanne in the Department of Computational Biology, with three PIs: Ana Marques, Christophe Dessimoz and Sven Bergmann. My project is on gene regulation evolution in humans through long noncoding RNAs. These are RNAs are not translated. They are also conserved and expressed at a lower rate compared to protein coding ones. Nevertheless their highly tissue-specific expression and link to gene regulation make them important to understand phenotypic variation and disease.

Before here, I made a postdoc with Michael Kruetzen on orangutan genomics in the Anthropology Department of the University of Zurich, funded by Forschungskredit Postdoc fellowship.  Orangutans are the least studied great ape species, yet they present possibly the greatest phenotypic variation in terms of brain size and cognitive skills. They are also exposed to highly varying environmental conditions making them ideal to understand genomic signature of phenotypic variation and adaptation. I studied both single nucleotide variants and short tandem repeat variants to trace this signature.  Those two papers are soon to be out. Meanwhile, you can find our latest paper on a new and highly endangered orangutan species here. I also worked on selective pressures on marine mammals, which should be published soon, as well.

Master and PhD :F1.medium

I carried out a fast track master studies integrated with a PhD in Andreas Wagner’s lab. I could finish both my masters and PhD in four years with four publications.

Initially, I have worked on metabolism evolution (a project given to me by Andreas) and codon usage bias evolution (a follow up project to I was doing in my undergrad thesis). After publishing those, I developed a project to investigate the role of highly polymorphic tandem repeat elements in DNA on gene expression divergence. I chose primates as my model system, as I was most excited about great ape evolution. I gave couple of talks. The one in the ESEB 2013 (watch my talk here), in Lisbon gave rise to a fruitful collaboration with Tomas Marques Bonet’s lab in Spain. This paper came out in Genome Research, as the cover story. I also worked on cancer genomes to study the abundance of tandem repeat variation in tumors compared to normal tissues: here is the paper.

Bachelor and Internships:

I studied Genetics and Bioengineering in Yeditepe University in Istanbul, Turkey. Although the department was more into wet lab experiments, I found modelling and data analysis through computational biology and bioinformatics lot more interesting and decided to revive an old project of my professors Isil Aksan Kurnaz (actually a neurobiologist) and Levent Kurnaz (actually a physicist) on the evolution of alternative genetic codes. We have become good collaborators and published two papers, (see my Publications), before I graduated.

I did two internships, one at my own university in the Chemical Engineering Departmenton modeling of biochemical pathways and the other in Bogazici University, Istanbul, Polymer Res. Center on prediction of protein-protein interaction sites. Both of them took around one year.

In my last year (summer 2009), I visited Wagner lab for three months, where I started my bachelor graduation project on codon robustness. This project turned out to be bigger than expected. We have finally published it in J Mol Evol, in 2013.