We speak to some of our Alumni on how EI has influenced and helped hone their skills for new roles in bioscience; from future leader fellowships to global technology enterprises, we find out where they are now.
We speak to some of our Alumni on how EI has influenced and helped hone their skills for new roles in bioscience; from future leader fellowships to global technology enterprises, we find out where they are now.
I am currently working as a postdoctoral researcher for IBM Research UK in the Machine Learning Applications team at the STFC Hartree Centre, based at the Daresbury Scitech Laboratory site near Warrington. Here, I apply machine learning to the analysis of genomics datasets to solve industry-led problems in agriculture and healthcare.
While working within EI, I gained additional training in bioinformatics and HPC, it was partly this familiarity with HPC systems, genomics data analysis and my growing publication record that secured my employment with IBM Research.
However, with wanting to make the move from bioinformatics into artificial intelligence and machine learning applications, it was also important that I recognised the need to develop my skills in these areas and that I showed a desire to undertake further training.
While working within EI, I gained additional training in bioinformatics and HPC, (which helped) secure my employment with IBM Research.
My HPC training from EI inspired me to work in an industry more focused on the application and development of HPC. IBM was an ideal employer since it is pioneering the future of AI, blockchain and quantum computing.
My role involves research on multiple projects at one time, so my main challenges involve balancing my workload to enable me to progress with all aspects in a timely manner. This is slightly different from my postdoc, where I was more focused on a single main project. However, I do enjoy the variety of training and analyses that come as part of my new position.
In terms of career achievements, I get a huge sense of pride from receiving invitations to present my work at conferences and also from my highest impact publications. For example, one of my publications that was published in Genome Biology this year originated from a sideline project that aimed to investigate if SNP arrays could be used to define chromosome crossovers in wheat without the need for further sequencing.
Not only were we able to use SNP arrays in this way, but we were able to identify a gene linked to chromosome crossover and gene conversion. What was a sideline project, became an exciting explorative research project.
At EI, Laura was lead author on a landmark paper published in Genome Research, which links crop evolution and phenotypic change to agricultural conditions.
As an ongoing collaboration with EI, I’m currently involved in research activity with the Anthony Hall Group.
Here, I am applying machine learning to the analysis of wheat transcriptomic datasets to identify rhythmic patterns of gene expression. For those considering getting into my field, I’d recommend to never be afraid to change direction and always continue training.
I was initially trained in biology with little to no computational background. I have steadily gained more and more computational training throughout and since my PhD and now have become a computational biologist working in artificial intelligence.
Changing specialisms is difficult and may involve taking a step down the ladder at some point, but ultimately you will become a more desirable employee with a wider skillset.
...never be afraid to change direction and always continue training. I was initially trained in biology with little to no computational background.
After leaving EI, I did a short post-doc then won a BBSRC Future Leader Fellowship to study the evolution and adaptation of aphid crop pests at the John Innes Centre. This fellowship gives me impendent funding to develop a research area and transition from postdoc to PI. To do this, I am supported by a host lab at the John Innes Centre, led by Saskia Hogenhout.
Working at EI made a massive difference to my career. I gained skills in comparative genomics, genome assembly and genome annotation which have been central to my current project. While at EI, I also gained funding from an EI development grant. This money enabled me to generate key preliminary data that made my fellowship application competitive.
Working at EI made a massive difference to my career. I gained skills in comparative genomics, genome assembly and genome annotation which have been central to my current project.
My fellowship project aims to understand how generalist aphid crop pests are able to colonise a diverse range of host plant species whereas the majority of aphids are highly specialised.
To do this, I am using comparative genomics to identify generalism-associated genes; comparing the genomes of multiple closely specialists and generalists from three different aphid genera. These candidate genes are then tested experimentally by knocking-down their expression and measuring the effect on the ability of generalist aphids to move between different host plant species.
I am using genome assembly, annotation and comparative analysis approaches that I learnt while at EI to create a large genomic resource to study aphid evolution.
So far, my proudest achievement is winning my own money to test the ideas that I have developed. I have also really enjoyed working with Saskia Hogenhout and her lab at JIC, this has enabled me to combine evolutionary analysis with functional approaches which has been really exciting.
In terms of working with EI now, I have an ongoing collaboration with David Swarbreck at EI who is an expert in genome annotation and has supported my fellowship application.
Focus on the important biological questions you want to answer rather than specific techniques. Bioinformatics and lab work are all just tools to answer scientific questions, so spend time constructing testable hypotheses and developing research questions. Also, take the lead in writing papers and other articles whenever possible.
Focus on the important biological questions you want to answer rather than specific techniques.
Year in Industry Student
After I completed my Year in Industry at EI, I finished my final year of university and then started a position working for Illumina. Illumina produces next-generation-sequencing instruments such as the NovaSeq, HiSeq, NextSeq, MiSeq, MiniSeq and iSeq as well as many array-based solutions.
I work for Illumina within the consumables development team. The team designs and tests the reagents used on our sequencing platforms. Day-to-day, I work on instrument recipes as well as various reagents, helping to improve their activity, robustness and reliability. I work very collaboratively with various other development teams at Illumina in order to create world-class products.
My work at the EI certainly helped me achieve my position at Illumina. During my industry placement, I had great exposure to the next-generation-sequencing process, from sample preparation to sequencing and bioinformatic analysis.
Troubleshooting is something that I regularly encounter in my job, while it is one of the hardest aspects of the role, it is also one of the most rewarding. Integration of various systems together is a challenging task, but something I love working on. My proudest achievement was the release of the NovaSeq, which I developed several reagents and workflows for.
While I'm not personally collaborating with the EI currently, I always feel like I could in the future. It certainly introduced me to several connections in the next-generation-sequencing field, which I am very grateful for.
Get some experience with next-generation-sequencing or product development! Both are beasts in their own right. The east and south-east of England are full of fantastic opportunities for research and biotechnology.
Get some experience with next-generation-sequencing or product development! Both are beasts in their own right.
I was a Year in Industry student at EI so immediately after finishing, I went back to York to complete my undergraduate degree in Biochemistry. After this, I worked as a research technician in a Drosophila lab at the Gurdon Institute which is part of the University of Cambridge.
This required me to perform injections into Drosophila embryos and Drosophila genetics in order to make ligand-tagged fly stocks with the aim of looking at cell polarity proteins using super-resolution microscopy. This involved a lot of fly pushing, as well as molecular biology and microscopy.
My work at EI definitely helped me with this role. Although the project was completely different, the skills I learnt at EI helped me to settle into the lab more quickly. For example, I already knew the simple things I needed in the lab, such as pipetting, PCR, running gels, as well as being used to weekly lab meetings and being able to manage my time well.
My work at EI definitely helped me with this role. Although the project was completely different, the skills I learnt at EI helped me to settle into the lab more quickly.
I am currently a PhD student in the USA at the University of Rochester, New York looking at using cell culture techniques to look at epithelial cells. As a lab we are interested in how cell division and adhesion are coupled to influence tissue shape. Maintaining tissue homeostasis is important for function; by studying how tissues grow and initially develop, we can start to elucidate what goes awry in disease situations.
Working at EI helped me decide I wanted to pursue my PhD and enabled me to get my initial job. The fact that I already had experience working in a lab and developed basic lab skills from working at EI definitely worked in my favour. If I’d have had no experience, I do not think I would have gotten the job.
I think the hardest thing for me is when experiments don’t work; sometimes things don’t work for no apparent reason. For example, I recently had a molecular cloning project; half of the reactions worked, and half didn’t, even though it was the same reaction I was trying to do. It’s super frustrating but when it does work, it makes it even more satisfying!
Working at EI helped me decide I wanted to pursue my PhD and enabled me to get my initial job. The fact that I already had experience working in a lab and developed basic lab skills from working at EI definitely worked in my favour.
I think my proudest achievement is moving to the states to do my PhD. The programme is a lot longer here and I take classes and teach, but overall, I think it was the best thing for me to do. I have never had to teach before, but I’ve actually really enjoyed it, both in the lab and in a classroom setting. Not only have I had a different educational experience, I have also gotten to live in a different country and travel around America.
I’ve no plans, as such to collaborate with EI – we do not do much DNA sequencing these days, at least not on the scale EI would be able to help with! But, if in the future the opportunity arose, I would not rule it out.
After I have completed my PhD, I think I would like to do a postdoc here in the USA, but we will have to wait and see!
I took a role at a small private company called Food Forensics based on the Norwich Research Park. They wanted someone to develop a Next Generation Sequencing pipeline for speciation for food. I was able to source the necessary equipment, develop the protocols and write the SOP’s to eventually gain UKAS accreditation for them.
EI definitely helped get this role. I was at the Institute (formerly TGAC) from the beginning in 2009. I was the first person to make an Illumina library and run the sequencer back then, the GAII. Having been exposed to NGS sequencing for almost eight years, I was perfectly placed to set the pipelines up for Food Forensics.
My experience at EI enabled me to implement an efficient high-quality service very quickly.
After ten months at Food Forensics, an opportunity to return to the public sector taking the sequencing role at QIB was too attractive to turn down. They had the sequencing hardware in place but needed someone to set up and run their in-house core sequencing facility. We mainly focus on microbial sequencing whether it be on the human microbiome or microbes in the food chain, all linked to improving human health.
My experience at EI enabled me to implement an efficient high-quality service very quickly. I was able to use my previous core sequencing experience to cover all aspects including project managing, high throughput library construction, running the instruments and basic bioinformatics.
The biggest challenge is not having enough time in the day! I’m essentially running all aspects of the sequencing facility, so some days are a juggling act but it's very rewarding. Proudest achievements would have to be helping to give a ‘Sequencing and Bioinformatics’ workshop in Gambia to groups from West Africa in December 2018 (hosted jointly by MRC Gambia and MRC CLIMB) and of course heading sequencing at QIB!
EI has a lot of expertise and specialist equipment that QIB doesn’t have so I am in continual communication with EI on PacBio and Illumina NovaSeq access in particular. We also have several Group Leaders here at QIB that have a foot in both Institutes so there will continue to be a healthy collaborative relationship between us and EI.
For those trying to get into my field, I’d say you’re too late! No, seriously, I was fortunate to be part of the beginnings of NGS at TGAC and so to be there from the start has provided me with a lot of experience. Getting your foot in the door is critical so either work experience or even if you are a PhD student that needs to generate sequencing data, observing a high throughput core sequencing facility would be a useful starting point.
