Short Tandem Repeats: Variation, Evolution and Cancer
I decided to work on short tandem repeats while I was doing my PhD. No-one in my lab knew about them but we were anyways a highly diverse lab, interested in how evolution creates phenotypic variation. Hence, Andreas (Wagner) was highly supportive of me to go my own independent way.
So 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. We showed how short tandem repeat polymorphism in primates associate with greater gene expression divergence. Our findings were published in the journal of Genome Research, as the cover story. It was also mentioned in Nature Genetics news.
Next, with my master student we published the first findings for the possible role of short tandem repeats in carcinogenesis. I have also co-supervised a master student project with Joshua Payne from ETH to look for the evolution of short tandem repeats in transcription factor binding sites.
In another master student project in collaboration with Michael Kruetzen, we found possibly adaptive short tandem repeat variations in orang-utan populations. Those results will be soon published. Currently, I collaborate with Maria Rodriguez from IBM and Maria Anisimova from ZHAW to work on short tandem repeat changes in tumors. We have a few grad students working on different aspects of the projects. I also continuously work on research proposals to retrieve more funding.
Adaptation of orang-utans to changing environments
For my post-doc, I acquired a funding to work on orang-utan genomics. 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.
Undergrad: Evolution of Genetic Codes, modelling of biochemical pathways, protein interaction site prediction
Although my undergrad department was more into wet lab, 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 Department on 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.
Masters and PhD: Metabolism Evolution, Codon Usage Bias Evolution
I have also worked on metabolism evolution (a project given to me by Andreas) and codon usage bias evolution (an extended work on my undergrad thesis). Both of them are published.
Current: gene regulation evolution through long noncoding RNAs
My project in the University of Lausanne is on gene regulation evolution in humans through long noncoding RNAs. These RNAs are not translated, less conserved and less expressed 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.