User:Tugce

Hello, my name is Tugce (pronounced as 2che). I am from Istanbul. You can find more details on me in my personal website [1].

Short Bio on Research

I obtained my PhD in Andreas Wagner's lab [2] in University of Zurich, where I have worked on several layers of gene regulation, from protein interactions to metabolic networks. This was also the time, when I met DNA tandem repeats. I studied, how these extremely unstable elements can confer gene expression divergence both in the context of gene regulation evolution in primates and in carcinogenesis. I continued working on them during my post-doc, as well.

Later, I got the Forschungskredit Postdoc grant to work on orangutan genomes in the Anthropology Department of the University of Zurich [3]. I have involved in various genomics project during that time.

Recently, I moved to UNIL to work with Christophe Dessimoz [4], Ana Marques [5] and Sven Bergmann on another highly variable element that works in gene regulation, this time in RNA level: long non-coding RNAs.

Peer-reviewed Publications

Chech out my wiki page for the most up-to-date version: [6]

[6] Bilgin Sonay T, Carvalho T, Robinson MD, Krutzen M, Lorente-Galdos B, Comas D, Highnam D, Sharp A, Marques Bonet T, Wagner A. Tandem repeat variation in human and great ape populations and its impact on gene expression divegence, 2015, Genome Research, 25:1591-1599, in cover [7]

Nature Reviews Genetics, Research Highlights in Brief, Human Evolution, 16, 3 November 2015

[5] Bilgin Sonay T, Koletou M, Wagner A. A survey of tandem repeat instability and gene expression changes in 35 colorectal tumors, 2015, BMC Genomics, 16:702 [8]

[4] Bilgin T, Kurnaz I., Wagner, A. 2012, Selection shapes the robustness of ligand-binding amino acids, J Mol Evol [9]

[3] Bilgin T, Wagner, A. 2011, Design constraints on a synthetic metabolism, PloS ONE 7(6):e39903 [10]

[2] Kurnaz, ML, Bilgin, T, and Aksan Kurnaz, I. 2009, Certain non-Standard coding tables appear to be more robust to error than the standard code, J Mol Evol, 70:13-28 [11]

[1] Kurnaz, ML, Bilgin, T, and Aksan Kurnaz, I. 2008, A statistical analysis of the robustness of alternate genetic coding tables, Int. J. Molec. Sci. 9(5): 679 – 697 [12]

Teaching

Since childood, I wanted to be a teacher and after taking an intense course in biology teaching, it became a desire for me. Beside the teaching I do in the university, I participate in workshops, where I can lead small projects or organize myself.

I have so far supervised three master thesis projects, one of which was succesfully published and the more recent two others are getting close.

I have taught in S3++ Summer School of Science for high school in Croatia [13] and in Quantitative Evolutionary Biology Summer School in Izmir [14]. Besides, since two years with colleagues, we organize Evolutionary Genomics Winterschool [15].

Talks

I like expressing myself. I love painting, writing fiction and non-fiction [16]. And I also like talking. So why not talking about science? I have given many talks in many prestigious conferences and congresses. Here is a list of some of them:

2017 Invited Speaker, Tandem repeats and phenotypic evolution, AKEK, ODTU, Ankara

2016 Tandem repeats in promoters confer expression divergence, EPD30, Lausanne

2016 Codon models reveal the adaptive history of orangutans, PhyloSIB, Zurich

2015 Tandem repeat instability in colorectal cancer, SMBE, Austria

2013 Tandem repeats enhance expression divergence in primates, ESEB, Portugal

2013 Invited Speaker, Tandem repeats in promoters enhance expression divergence in primates, CBRG Colloquium, ETH Zurich

2013 Unstable tandem repeats in primate promoters enhance expression divergence, SIB Days, Biel

2008 A statistical analysis of the robustness of alternate genetic coding tables, National Molecular Biology and Genetics Student Congress, Istanbul

Next one is again in ESEB this time in Netherlands.

Ongoing Projects and Collaborators

2017- lncRNA and gene expression evolution, Christophe Dessimoz, Ana Marques, Sven Bergmann

2017- Population genomics study on Walser indiduals, Simon Aeschbacher, Natasha Arora, Michael Kruetzen, Laurent Excoffier

2016- Tandem repeat variation in wild orangutan populations, Alina Voicu

2016- Tandem repeat instability at transcription factor binding sites, Stephany Orjuela, Joshua Payne

2016- Tracing adaptive evolution in marine mammal genomes, Michael Kruetzen

2015- Tracing adaptive evolution in orangutan genomes, Michael Kruetzen, Maria Anisimova, Maja Greminger, Alexander Nater