Meet Ioannis: Ioannis started his PhD at the University of Leeds in 2017 studying the molecular mechanisms of long non-coding RNA (lncRNA) function in X chromosome inactivation across mammalian gestation evolution (see more here). He is now working as an Editor for two scientific journals published by FEBS Press, Molecular Oncology and FEBS Open Bio. We asked him about his career and any advice that he has for current students …
About Ioannis’ PhD
“In 2017 I was accepted for a PhD at the University of Leeds to undertake a project on dissecting the molecular mechanisms of long non-coding RNA (lncRNA) function in X chromosome inactivation across mammalian gestation evolution. LncRNAs are >200-nucleotide transcripts that do not encode proteins, but interact with proteins to regulate gene expression. The XIST lncRNA mediates dosage compensation via X chromosome inactivation (XCI) of a single X chromosome in females. Maintaining gene dosage across sexes is vital for placental mammal prenatal development, failure of which is embryonic lethal. I aimed to dissect XIST’s interactors in placental mammals with different implantation strategies such as human, mouse, cow and pig.
Using a combination of biochemical and cell culture technique, I analysed the expression of XIST and putative protein partners in endometrial tissues/cells from those species. I also showed a subset of protein partners identified in the mouse and humans previously bind human XIST but interactions could not be robustly assessed in cow. Additionally, I demonstrated for the first time that the bovine version of one of those proteins, originally identified as partners of mouse XIST, also interact with a region of the XIST RNA in cow. Proteomic analyses indicated that similar proteins bind bovine XIST regions as seen in human and mouse. Most notably, I observed that bovine XIST regions could be bound by human proteins from lysates, highlighting a cross-species specificity. Selective pressure variation analyses identified residues under positive selection in a subset of these proteins, but could not explain their differential binding to human and bovine XIST.
Altogether, the XIST interactome was characterised for the first time in endometrial-derived bovine cells, revealing cow-specific and conserved interactors across placental mammals. Bovine XIST interactors from human cells reported may contribute to our understanding of lncRNA-protein partner co-evolution.”
Q. What are you doing now?
Currently I am working as an Editor for two scientific journals published by FEBS Press, Molecular Oncology and FEBS Open Bio. Mainly, I evaluate new manuscripts submitted for peer review, identify reviewers, coordinate the peer review process and provide feedback to authors in terms of writing their manuscript to fit the journals’ styles. I also promote the visibility of the journals through writing blog posts, authoring interview pieces with Editorial Board members, handling the social media accounts, designing promotional material and attending conferences, where I commission review articles or expert opinions on trending topics (such as Commentaries).
In parallel, I am carrying out an ASAPbio Fellowship which aims to enhance the understanding of the scientific community about preprints and how they can benefit research. There are several projects running at the same time in the ASAPbio Community, but the two I am involved with are about replacing published articles with preprints as a requirement for PhD degree awards in countries outside the UK and categorising preprints in order to identify alternative uses of preprints (e.g. hypotheses / protocols).
Q. When did you start thinking about your career?
Prior to commencing a PhD, I reflected on where I would want to be in my life and what job I wanted to be doing in the future. Having a PhD opens a lot of doors to professions which are otherwise unattainable. Conversely, there are jobs which do not require a PhD that pay well and one can gain a lot of promotions in the four years of a PhD. I had an idea that I would still want to be involved in research somehow, although at the time I did not have a clear idea in my mind. After the second year of my PhD I started thinking more about what skills would be useful for as many jobs possible and thus I focused on developing or enhancing skills that would be the most transferrable to a lot of jobs. The White Rose DTP PIPs was particularly helpful in making me think hard about what career I would like to follow in the future and allowed me to test the waters of one of the ideas I had. In summary, I thought about my career both before my PhD and during, especially around the time when I was deciding where to carry out my PIPS internship.
Q. What do you most enjoy about your career?
Remaining abreast of the latest scientific advances and pursuing the dissemination of this knowledge to experts and laypeople via issuing news articles, social media posts or communicating through other emerging media was an exciting prospect for me. A stimulating aspect of working across Molecular Oncology, FEBS Open Bio as well as the ASAPbio Community is the commitment of the teams to make scientific research open access and more broadly, the not-for-profit nature of FEBS Press and associated FEBS initiatives. I am passionate about making science more accessible in a time when scientific publishing is transforming. Moreover, the emphasis of the FEBS mission to promote early-career scientist training, scientific collaboration and influence science policy has appealed to me more in recent years as these values align with mine.
Q. How did your PhD and the White Rose DTP prepare you for what you are doing now?
During my time at the University of Leeds, I was involved with the White Rose DTP Communications team which allowed me to author blog posts which enhanced my writing and the generation of leads for new blog topics. Additionally, during my 3-month editorial internship at FEBS Press, I wrote four article highlights for the FEBS Network, one of which featured custom-made graphical artwork which I commissioned from a friend. Writing was a key skill required to become a successful Editor and one that will need continuous improvement. But don’t worry, there will be plenty of opportunities to do that (both during the PhD and afterwards)!
As part of the White Rose DTP Communications team, I also interviewed PhD students and highlighted their experience and achievements which was a transferrable skill that I developed further now that I am interviewing Editorial Board members of the journals.
Participating in journal club during my PhD, I learned how to critically read and review manuscripts, identifying their strengths and weaknesses. This is another key skill that Editors need since it’s practically used in the day-to-day tasks. Attending departmental seminars on a diverse range of topics was another activity that helped me become more familiar with other research areas of biology, outside of my PhD focus. Again, this is highly relevant to being a great Editor since you will be exposed to different areas of biology through assessing manuscripts, attending conferences and thinking how different fields of biology come together.
Lastly, during my PhD I took the initiative to co-organise one-day RNA-themed symposia sponsored by the RNA Society to strengthen relationships across the local RNA community bringing researchers from three different universities together. Networking and working as part of a team are also great skills for an Editor given how much one needs to keep up with the literature and different fields, which is facilitated by maintaining contacts with academics and other Editors.
For more information on my internship, please visit the blog post I wrote for my PIPS Case Study for the White Rose DTP Communications team.
Q. What advice would you give to current students who are thinking about and planning their graduate careers?
It’s important to think about one’s career as early as possible and know where one sees themselves in the next five but also in the next ten years. As such identifying training opportunities that match the job you want to do is a crucial process before and during the PhD. However, each person works in their own time zone and matures at a different pace compared to others. Inevitably some people will not know where to begin or what they want to do post-PhD. My advice to this group of people would be to take risks and try new things. Testing new waters until you find something you like. This could be via signing up for organising a seminar at your or another department, becoming a student representative or a member of a committee, take initiative in co-organising a one-day symposium with your PI or with other students, use social media to become part of conversations, reach out to other scientists for advice or internship opportunities in areas you feel you may like. The PIPS internship is a great initiative to narrow down some of the ideas you may have. Worst case scenario you can at least exclude jobs that you definitely do not want to get into.
During your PIPs (and your PhD as well), it’s important to network and meet people every opportunity you get. Science is hard and you will need allies at every step of the way, even after the PhD. You never know who can introduce you to your future employer. Despite this opportunistic angle, having a network of peers for support is key in having a successful but also a mentally healthy trajectory in science. Along the same note, don’t forget to do things for you in your free time, whether this is a hobby, a coffee outside or cooking a nice meal.
Dr Tsagakis highlighted some opportunities offered by FEBS and ASAPbio
If you would like to take advantage of the opportunities offered by the FEBS or the ASAPbio Community to improve your skills or be part of a diverse scientific community, you should definitely check out their webpages and feel free to give me a shout if you need any guidance.
- Apply for funding
- Apply for travel grants
- Attend meetings with peers
- Enhance your writing
- Get experience in reviewing manuscripts
- Find out more about preprints
- Join the preprint Community
Get in contact with Ioannis through his twitter, @tsagakis_bio.
Key links from Ioannis
Links to organisation and Journals
Links to some of Ioannis’ blogs
- Heterogeneity and metabolic adaptations of tumour associated macrophages in the tumour microenvironment
- Lymph node T cells break a sweat early during breast cancer metastasis
- Dissecting the molecular profile of a rare gynaecological cancer
Ioannis’ non-peer reviewed publications
- Maniyar, S. and Tsagakis, I. (2023), Breaking barriers in breast cancer therapy. Mol Oncol. https://doi.org/10.1002/1878-0261.13532
- Tsagakis, I., & Rayner, S. (2023). An open chat with…Simon Rayner. FEBS open bio, 13(2), 214–216. https://doi.org/10.1002/2211-5463.13543
- Tsagakis, I., & Wlodawer, A. (2022). An open chat with…Alexander Wlodawer. FEBS open bio, 12(9), 1564–1566. https://doi.org/10.1002/2211-5463.13462
- Blaszczak, W., Ahmed, A., Leithner, K., Schubert, A., Leech, M., Bonder, C., & Tsagakis, I. (2022). Outlook of women in science: an interview with our authors. Molecular oncology, 16(5), 1047–1056. https://doi.org/10.1002/1878-0261.13189
- Tsagakis, I. and Papatriantafyllou, M. (2020), Safeguarding cancer research funding by European charities amidst the COVID‐19 pandemic. Mol. Oncol., 14: 2987-2993. [DOI: https://doi.org/10.1002/1878-0261.12839]