Today, I have invited Konstantin Okonechnikov, who received his PhD in Germany, to the “Defenses around the world” series. Konstantin is currently a bioinformatics PostDoc in the Pediatric Neurooncology division at German Cancer Research Center. He is also quite interested in blogging and has a personal blog about bioinformatics. You can learn more about his research on his Google Scholar page.
Bioinformatics is an astonishing and developing science that it is becoming really important in molecular biology and medicine due to amazing novel technologies like Next Generation Sequencing, where a lot of data analysis is required to understand the functionality of genome, transcriptome and proteome. After finishing my bioinformatics Master in Novosibirsk State University in Russia I decided to search for a PhD position in this area as well. I performed several visits to research institutes in Europe, and decided to do my PhD in the Max Planck Institute (MPI) for Infection Biology in Berlin. Since this institute is focused on research only and has no direct connection to education, an additional important step for me was also to find a university. My choice was Freie Universität Berlin. After registering there as a “Doktorand” I started my PhD in 2011.
As far as I know universities in Germany have slightly various requirements for finishing the PhD. My first step was to write a PhD thesis. This task was started in 2015. In general, the thesis materials were based on one published manuscript and one work in progress along with detailed introduction. Creating this first introductory chapter was a really interesting task since it was an effective short combination of all research aspects in the area. Basically, it consists only of 20 pages, but includes summarized information from more than 50 manuscripts in the area. Further chapters were based on performed work and there was also a final discussion chapter describing possible novel directions.
An important step closer to finishing the thesis was to find the reviewers for the assessment. The main assessor was my official supervisor Prof. Knut Reinert. However, I also had to find an external assessor and this was an interesting task, similar to searching for a possible reviewer of a manuscript. I was super glad to get a positive confirmation for external assessment from Prof. Steven Salzberg (a well-known and highly cited scientist in the bioinformatics area). Finally, during my work in Max Planck Institute I also had my direct supervisor in research Dr. Fernando Garcia-Alcalde, and he was also allowed to be an assessor.
The assessment time was about 2 months after submitting the thesis. During this period the next requirement for me was to find a committee and select the defense day. Basically, there was a list of Profs from Freie University, and I was writing them e-mails asking about the participation, possible defense time etc. Finally, everything was established and the defense date was adjusted! Also, one day before the defense I was allowed to read the assessment and prepare for possible remarks from the committee.
In my case the defense was consisting of two parts. The first part was a basic overview of the research area starting from theory (~20 min). Next step was a detailed focus on a certain problem (~10 min). During both steps there were questions from the committee. One really nice permission was “openness” i.e. everyone interested was allowed to be present during the defense and also ask questions. Therefore, my friends and MPI colleagues were also there. In the beginning of the defense I was a bit nervous, but already after getting the first questions from the committee I forgot about this and was really excited to discuss my research topic. In the end my final mark was “Magna Cum Laude” and the thesis is officially available online for everyone.
Of course, already a year before my defense I started to think about a future PostDoc position. I guess this can be an additional big story. The PhD is an amazing period of life that has many interesting and exciting moments, but after the defense nothing stops and being a PhD opens a giant majority of possible ways to continue the adventure.