A PhD in genomics – lessons learned

This is it! With finishing my PhD I have become an “adult” member of the scientific Graduierungcommunity. I grew out of a bachelor in biochemistry on transfection methods in neuronal cell lines, a research semester in Canberra with focus on B-cell immunology and master into a  PhD in epilepsy genomics. I was involved in the EPICURE IGE copy number projects and recently my work changed to the analysis of rare variants in RE and IGE in the EUROepinomics framework. During this time I was involved in the identification of variants in RBFOX genes and GRIN2A as well as other risk factors which are currently in review. I share my experience and thoughts and hope they help others who are about to or have just started their thesis. The aspects reflect my personal view and some are specific for graduation in disease genomics.

Select your project with care. I was “lucky” because working on my genomics projects was easy for me. Previously, on biochemistry or immunology projects during my master studies I also worked long hours but it never felt as easy as it does today. Different environments during lab courses or internships may help you figure out what factors are particularly relevant for you and there’s probably nothing wrong with a bit of trial and error.

You and your mentor. I have seen my supervisors only every other month but we had several phone calls each week. Good communication between you and your supervisor is essential for a successful PhD but the time in face-to-face meeting are no measure of the communication level. I learned much from experienced PhD students and postdocs in our institute in the beginning. In addition, in the first and second year of my PhD project I applied for international courses and workshops (EMBO, Wellcome Trust) to get additional expertise, which was lacking at my institute. During this time your supervisor should be supportive in a way that allows you to develop the skill set to successfully generate results. In the final year, the contact with my supervisors was more direct as my work routine changed from data generation to interpretation, trying to make sense of the big picture. At this point an experienced supervisor with the big picture in mind is a necessity.

Is your PhD project your project? This question sounds redundant but not in genome science. We often work within large collaborative efforts consisting of data analysis teams of several members including PIs and postdocs. Make sure that you can spin off several small projects from the big study. For these particular projects you have to become the expert and take responsibility. Feeling responsible can also feel very good: When we published my first paper on RBFOX1 deletions in IGE, we got a letter from a patient’s mother. She was thankful that we were working on this topic, wrote us about her family life and encouraged us to go on with our research. I guess for a physician this is not special but for me it was! This letter keeps me still motivate because I knew that I was responsible for this project.

Should you take breaks? In the last few years I have not taken real holidays but I wonder if I should have taken more often breaks. I stayed one or two days longer during conferences and worked in coffee shops to spend my lunch breaks on sightseeing and took few weekends off. However, if my projects would have developed in a different, less fortunate way, this time would have been frustrating. One of my supervisors once said that we as scientists are not sprinters – we are marathon runners. I guess he is right. In order to work efficiently in the long run we have to take breaks.

Graduation

Taken from http://flickr.com/photos/smemon/with/5061210124/, licensed under creative commons (by-at)

Plan your research. What do you want to achieve this week, this month or even this year? What are the general requirements for a publication in your target journal? It might be the case that your university requires several first authorships for a PhD, which might be a problem in consortium projects. Look for results, which are publishable at medium to low impact, most likely these results are not interesting to publish for your supervisor. Try to convince your mentor that you need these studies as a back-up and that this will help you to develop good writing skills. Supervisors have a different perspective than graduate students on this.

Take responsibility. Be open minded, especially if you are new in the field, but don’t perform analyses that you do not agree with or you do not know the reason for. Ask why! Otherwise you are not able to learn. In the end you have to present the data and if people ask critical questions you do not want to answer with “because my supervisor said so”.

You should read. I can highly recommend reading a lot. Without you can only take responsibility for your work. In the first years you will most likely read more new publications and reviews directly related to you topic. When you start writing progress reports or publication you will start reading the relevant literature in your field. Don’t try to reinvent the wheel! It is also important to read beyond your direct line of work. Publications on schizophrenia or autism genetics can be useful for epilepsy genetics, particularly when it comes to study design or data analysis. There is always another fields a step ahead.

Start writing early. I hate to say it but the more you write the better you get. This is particularly true for non-native speakers like me. I can read and understand a broad range of words but when it comes to writing my vocabulary is limited. I have written my master thesis in English, followed by progress reports, first publications and at the end my PhD thesis. I think that I have really improved. Nevertheless, I am still far away from being good. As you might have noticed, my latest training method is blogging on a weekly basis for the Channelopathist. Blogging takes time but I am sure it will pay off. I really encourage young students to start writing; you don’t want your precious publications to be rejected because of writing style.

5 thoughts on “A PhD in genomics – lessons learned

  1. Pingback: The surprising truth about your motivation in epilepsy genetics – 2014 update | Beyond the Ion Channel

  2. Pingback: Papers of the week – next-level mutation classifiers and 3′UTR variants in Dravet Syndrome | Beyond the Ion Channel

  3. Pingback: 9 things you didn’t know about bioinformatics | Beyond the Ion Channel

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