Research:

Although I am still curious about diverse natural phenomena and dedicated to their scientific understanding (and teaching), most of my own research revolves around a fundamental phenomenon of life: gene regulation, i.e. how amount and timing of gene expression (RNA and protein: functional molecules of the organism itself) are adjusted. I am especially interested in mathematical and biophysical understanding of regulatory mechanisms and factors determining the characteristics of gene regulation in developmental and evolutionary time scales. In order to achieve this ambitious aim, I try to position myself at the intersection of i- mathematical & biophysical modelling, ii- quantitative experimentation and iii- computational data analysis.

In my PhD, I studied the evolution of transcriptional regulatory sequences with Nick Barton and Gasper Tkacik at IST Austria. I tried to set a mathematical population genetic framework for the evolution of TF binding sites with the help of biophysical models. I also collaborated with experimentalists to understand the binding site evolution of bacterial RNA polymerase.

In my postdoctoral research experience in Kovar lab in Children’s Cancer Research Institute (CCRI) in Vienna, I did research about Ewing sarcoma disease, a bone and soft tissue cancer dominantly seen in childhood and adolescence. We aimed at a deep molecular understanding of this disease by focusing on the epigenetic reprogramming by EWS-FLI1 which is the defining fusion mutation and the master regulator of this disease leading the cells into a cancerous gene regulatory state.

Publications:

9- Saravana P. Selvanathan, Garrett T. Graham, Murat Tuğrul, Eleni M. Tomazou, Heinrich Kovar, Alexander R. Grego, Tabari M. Baker, Mark Simpson, Mona Batish, Brian Crompton, Kimberly Stegmaier, Aykut Üren, Jeffrey A. Toretsky, (2017) “EWS-FLI1 modulated alternative splicing of ARID1A reveals novel oncogenic function through the BAF complex”, in review (Nature comm.)

8- Murat Tuğrul. (2016) PhD Thesis: “Evolution of Transcriptional Regulatory Sequences

7- Murat Tuğrul, Tiago Paixao, Nick Barton and Gasper Tkacik. (2015) “Dynamics of Transcription Factor Binding Site Evolution”, Plos Genetics, 11(11): e1005639. arXiv:1506.05162

6- Stephanie Keller-Schmidt, Murat Tuğrul, Victor M. Eguiluz, Emilio Hernandez- Garcia, and Konstantin Klemm. (2015) “Anomalous scaling in an age-dependent branching model,” Physical Review E, v.91, 2, p. 022803, arXiv:1012.3298.

5- Murat Tuğrul & Alkan Kabakçıoğlu. (2010) “Anomalies in the transcriptional regulatory network of Saccharomyces Cerevisiae”, J. Theoretical Biology 263, pp. 328–336, arXiv:0904.1515.

4- Emilio Hernandez-Garcia, Murat Tuğrul, E. Alejendro Herrada, Victor M. Eguiluz and Konstantin Klemm. (2010) “Simple Models for Phylogenetic Trees”, Int. J. Bifurcation and Chaos 20-3, pp. 805-881, arXiv:0810.3877.

3- Murat Tuğrul & Alkan Kabakçıoğlu. (2010) “Robustness of Transcriptional Reg- ulation in Yeast-like Model Boolean Networks”, Int. J. Bifurcation and Chaos 20-3, pp.929–935, arXiv:0902.4147.

2- Murat Tuğrul. (2009) MSc thesis: “Simple Branching Models for Macroevolution”, available at http://ifisc.uib-csic.es/publications

1- Murat Tuğrul.(2007) MSc thesis: “The Structure and Dynamics of Gene Regulation Networks”, available at http://arxiv.org/abs/0802.1989

 

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