I am a postdoctoral researcher at IMADA, The University of Southern Denmark since June/2022!.

I was a PhD student at Friedrich-Schiller University Jena, Germany. My PhD research topic was the development of open-source chemical graph generators, an application of algorithmic group theory. In the field, MOLGEN was the fast and efficient structure generator but a commercial tool. In my PhD, I developed two chemical graph generators. The first one is maygen [1] and the second one is surge[2]. Chemical graph theory and its applications in chemistry were also reviewed[3,4]. maygen is based on orderly generation method and developed for the CDK. While working on it, I also tried integer partitioning based chemical graph generator, called PartGen; however, this trials trigger the great algorithm surge. After noticing that all the functions I need are already provided in nauty package [5], we worked on the nauty based structure generator, surge, the fastest chemical graph generator and outperforms the de facto gold standard in the field, molgen, in order of magnitudes!

The applications of chemical graph generators are not restricted to only chemistry. In astrobiology and the generation of new amino acid libraries, these generators can be used. The application of in astrobiology is just published this year [6]. My interest in graph algorithms started in my bachelor. I took topology, geometry, group theory and graph theory courses in my last year; moreover, worked on the symmetry groups especially wallpaper groups and the symmetry groups of Archimedian and Platonic Solids at Mimar Sinan Fine Arts University, Mathematics department. However, I was interested in the implementation of these theorems to understand nature better. The symmetry of the creation amazed me and I would love to learn this beautiful artwork as much as I can. However, just the pure mathematics knowledge was not enough and there was something missed: The education in computer sciences. A day, I was watching a dancer, I started thinking about the correlation between the music and the brain. That thoughts brought me to a new research area: computational neuroscience. I took my master degree from the Computational Science and Engineering Department of Boğaziçi University. My master thesis is Development of a Data Collection and Analysis Tool for Protein-Ligand Interactions. Besides the development of the tool, I also worked on the protein-protein interaction network analysis of sphingolipid and insulin metabolisms playing crucial role in the treatment of neural diseases such as Alzheimer & epilepsy. The source code of my thesis is given in this repository. This was the first step into software development.After my master, I combined both knowledge from math and computer sciences; and worked on chemical graph generators in my PhD. I presented my algorithms in Cambridge Cheminformatics Meeting in November 2021.

All these methods I have learned and worked on so far are general data science and mathematical algorithms; moreover, these methods can be implemented on any kind of datasets or real world problems. For more details about me, please look at my CV. Here, you can find all my Github repositories.

Besides sciences, I love fine arts, such as movies, music, and dance. I am the producer of the short documentary called Mountain of Servants about Assyrian minority in south-eastern Turkiye, directed by Daniel Lombroso. I also like the combination of modern and traditional ethnic art. I have two good examples: One of my favorite artists is Hikmet Barutçugil, inspired by the beauty of symmetry in nature and has this great artwork, his book called Symmetry. Some of its images are given here. The other one is Gülnihal Gül Mamat, mainly working on modern kufic caligraphy. She is also the designer of MAYGEN logo

References

[1] Yirik, M.A., Sorokina, M. & Steinbeck, C. MAYGEN: an open-source chemical structure generator for constitutional isomers based on the orderly generation principle. J Cheminform 13, 48 (2021). https://doi.org/10.1186/s13321-021-00529-9

[2] McKay, B.D., Yirik, M.A. & Steinbeck, C. Surge: a fast open-source chemical graph generator. J Cheminform 14, 24 (2022). https://doi.org/10.1186/s13321-022-00604-9

[3] Yirik MA, Steinbeck C (2021) Chemical graph generators. PLoS Comput Biol 17(1): e1008504. https://doi.org/10.1371/journal.pcbi.1008504

[4] Preprint/Chemical Graph Theory. (2022, May 1). Wikiversity. Retrieved 09:52, May 1, 2022 from https://en.wikiversity.org/w/index.php?title=Preprint/Chemical_Graph_Theory&oldid=2391985.

[5] McKay, B.D. and Piperno, A., Practical Graph Isomorphism, II, Journal of Symbolic Computation, 60 (2014), pp. 94-112, https://doi.org/10.1016/j.jsc.2013.09.003

[6] Mayer-Bacon, C., Yirik, M. A. Curation of Computational Chemical Libraries Demonstrated with alpha-Amino Acids. J. Vis. Exp. (182), e63632, doi:10.3791/63632 (2022).