This year has been a big one. Somewhat glad it is coming to an end, and while it has been
challenging at times, our lab and extended science family of collaborators has achieved a
lot. I have found an important part of keeping myself on track (a constant battle!) is to
reflect regularly. So here are my reflections on 2022.
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We passed the two-year milestone of the lab. Which also means I am just over half way of the first four years of my fellowship. Starting a lab in September 2020 during a global pandemic has not been easy and many plans have not worked out the way I thought they would. But from a “glass-half-full” perspective, I think we have done reasonably well.
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Our success is definitely a team effort, and I am incredibly grateful to a number of people, including Dave Bartley and Alison Morrison at Moredun Research Institute for their invaluable role in and support of our Haemonchus contortus work, Roz Laing (U. Glasgow) and Guillaume Salle (INRAE) for the many insightful discussions and collaborative work together, Matt Berriman and James Cotton who both are now at U.Glasgow for all things genomics, Jose Munoz at ISGLOBAL for bringing me into the STOP Consortium and enabling our STH genomics work, Jan Slapeta for helping us access Dirofilaria immitis data, and Tim Littlewood (NHM) and Cinzia Cantacessi (U.Cambridge) in their shared mentorship of Marina. This list is not exhaustive, there are people missing here. But it is clear team science is the way to go.
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I have had the privilege of supporting some close colleagues in their own journey towards establishing their scientific independence this year. It has been great to be able to share my experiences in getting my own UKRI fellowship, and play a small role in helping them achieve their goals. Sharing experiences of being a “new PI” and setting up a lab for the first time does make it easier.
- It has been a busy year for publications.
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In particular, there were two major papers published to note, one the completion of a multi-year large collaborative effort to map drug resistance variation in Haemonchus contortus in Cell Reports from the BUG Consortium, and the other the first major piece of work during my fellowship and started and completed during lockdown on the population genetics of ancient and modern Trichuris trichiura in Nature Communications. Both set solid foundations for a number of new avenues of research in the lab.
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I published my first, sole-author paper in Trends in Parasitology on the need to improve helminth genomes over time. This is increasingly becoming a theme of our research – to generate really high-quality resources and continue to add to them for our AND the community’s benefit – and so there will be more coming from us in this space soon.
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There were also a variety of papers published as part of several different collaborative groups. I enjoy the challenge of working on different problems, but I also think it reflects I am lucky to have the opportunity to work with many people who inspire and motivate me.
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Two grants were submitted, and a third written ready for submission in early 2023. All very collaborative efforts. If successful, these will bring new people to the group, and consolidate new collaborative relationships built over the year and toward exciting new projects pushing helminth genomics in a variety of different ways.
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Sarah Buddenborg joined the lab as a senior Postdoctoral Fellow, bringing with her invaluable new skills and experience to the lab. She has made an immediate impact, both properly setting up the wet lab space and getting on with optimising single-cell genomic techniques, and is set up now for an exciting 2023.
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Our extended team of mentored scientists are also making great progress on various projects. Among a variety of great achievements:
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Jenni McIntyre (PDF at U.Glasgow) has all but finished a chromosomal assembly of Teladorsagia circumcincta, with a manuscript draft started for 2023. This is a huge achievement, on a project I have literally been working for years. Very excited to share this one next year.
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Javier Gandasegui (PDF at ISGLOBAL, Spain) drafted a manuscript of Dirofilaria immitis population genomics, published a piece on Strongyloides in Lancet Infectious Diseases, and facilitated the sequencing of 170 soil-transmitted helminth genomes. Lots of big plans ahead with the STOP Consortium in 2023 and beyond.
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Marina Papaiakovou (PhD candidate at U. Cambridge) started the second year of her PhD with the publication of a review in Parasites and Vectors and recently, acceptance of manuscript #2 in International Journal for Parasitology now in press, amassed a huge collection of STH samples from around the world for the next phase of her genome skimming work, and has a great foundation in bioinformatics and work to support the rest of her PhD.
- PhD student Julia Rivero (Universidad de Sevilla) was the first of a number of visiting scientists with planned stays with us. Over three months, she quickly picked up bioinformatics from scratch and got busy comparing genomic data from Trichuris trichiura that infect humans and some non-human primates. Some really neat questions regarding host specificity and zoonotic transmission are starting to be addressed, and I am looking forward to seeing where these go.
Reflection is important as it helps me remember to celebrate the successes, which sometimes can be forgotten in the seemingly neverending cycle of science and life as a scientist. I feel very fortunate to work at Sanger, collaborate broadly with inspiring people, and have a great group of “young people” who I have the privilege of mentoring towards their aspirations, whatever they may be. However, it is also important to refect on when plans went astray. It has been a very successful year, however, adjusting to the “new normal” and a dealing with (and adapting to) a variety of personal and professional challenges that could not have been foreseen, it has also been one of the most challenging years of my career. I know I have missed deadlines, been slow to respond or missed emails, undoubtedly let people down, among other things. I know I have some work to do to be a better person, scientist, and leader in 2023 and beyond, and look forward to the challenge.
Wishing everyone a safe and merry holiday season. Cheers to kicking science goals in 2023!
Steve