In this month’s newsletter, we would like to introduce PhD graduate, Susie Grigson from College of Science and Engineering.
Susie’s recently submitted thesis, “Advancing Microbial Protein Function Prediction” received outstanding results from the examiners.
We asked Susie to share what her research was about and what she has been doing since and advice to new students.
Tell us about your research
I completed my PhD in bioinformatics, which sits at the intersection of biology and computer science. My thesis, Advancing Microbial Function Prediction, focused on one of the biggest challenges in microbiology today: even though we’ve read the DNA of millions of microbes, we still don’t know what many of their genes actually do.
I used artificial intelligence to help predict the jobs of these unknown genes — basically teaching computers to recognise patterns that humans can’t easily see. Understanding these hidden functions helps us learn how microbes survive, interact, and sometimes cause disease. It also supports things like developing new antibiotics or improving phage therapy, which uses naturally occurring viruses that infect bacteria to treat infections, especially when antibiotics stop working. These viruses are everywhere in the environment, from the ocean to soil to our own gut, and studying them helps us understand the ecosystems that shape our world.
What have you been doing since you completed?
Since finishing my PhD, I’ve moved to the USA and started a postdoc at the Lawrence Berkeley National Laboratory. It’s been a massive change! I’m now working as part of the NIH Human Virome Program, which aims to better understand the huge collection of viruses that live in and on our bodies. My role focuses on developing new AI-based methods to study these viruses, especially the ones that infect bacteria, called bacteriophages or “phages.” Most of these viruses are still uncharacterised, so I work on predicting what they might be doing and who their bacterial hosts are.
What was been one of the most enjoyable parts of the journey?
One of the highlights of my PhD was the opportunity to travel and connect with people from all over the world. I was lucky enough to attend a range of international conferences, which not only broadened my scientific perspective but also introduced me to an amazing community of researchers. I also spent several months in Germany. Getting to live in a new country, experience a different research environment, and immerse myself in a new culture was incredibly rewarding.
What advice would you give to those who are about to undertake a PhD?
My biggest piece of advice is to build a strong support network. A PhD can be incredibly rewarding, but it also has its tough moments, and having people around you makes all the difference. I was very lucky to have supportive labmates and friends outside of work who kept me grounded and encouraged me through the highs and lows.
It’s also important to maintain hobbies and a life outside of your research. Your PhD is a big part of your life, but it shouldn’t be your whole life. For me, picking up running, baking, going to music festivals and concerts and weekend trips helped me stay balanced and gave me something to look forward to outside the office. Whatever your interests are, make time for them, they’ll help you recharge and keep perspective along the way.
Have you published anything?
My literature review, published in Microbiology and Molecular Biology Reviews, provides an overview of current approaches for predicting gene and protein functions in bacteria and viruses.
(https://journals.asm.org/doi/10.1128/mmbr.00022-25)
I’ve also developed viral annotation software called Phynteny, which is freely available on GitHub:
https://github.com/susiegriggo/Phynteny_transformer/tree/main
A preprint describing the method is available here:
https://www.biorxiv.org/content/10.1101/2025.07.28.667340v1