Ph.D., University of Canterbury

Nicole Wheeler: I really enjoy the flexibility in work hours that comes from working on a computational project

Interviewed by Nowreen Priyanka

Interviewer’s note:  Thanks Nicole for sharing your story and experiences as a doctoral student at the University of Canterbury. The University of Canterbury is New Zealand’s second-oldest university.  Located in Christchurch, this university offers world-class research, inspirational teaching, and a vibrant campus environment.

Nicole Wheeler

Nicole Wheeler

Doctoral Candidate

University of Canterbury, New Zealand

I am in my third year of a Ph.D. studying bioinformatics at the University of Canterbury in New Zealand. As a bioinformatician, I analyze and interpret genome sequence data. I am interested in studying how bacteria develop the ability to cause disease, and what makes newly emerging disease agents so dangerous. To do this I aim to develop new approaches to studying the genomes of these organisms. I am using intelligent computing approaches to seek out patterns in complex data that lead to new insights into unresolved questions.

Why the University of Canterbury

I initially chose to do my undergraduate degree in biochemistry at the University of Canterbury, because I wanted to keep my career options open, and biochemistry opened up into a range of different jobs, while other universities in my area offered more specialized degrees that would limit my options.

I chose to stay in New Zealand for my undergraduate to be close to my family and spend some time exploring this beautiful country. When it came time to decide where to do my Ph.D., I had planned to study abroad, but fell in love with a project I was working on here and decided to stay and finish it.

My research area and its importance

For my thesis, I’m developing software that predicts whether a genetic mutation will affect the functioning of a gene. I’m using the software to study the evolution of disease-causing bacteria, and discover what sorts of mutations allow them to become really dangerous. I’m then using this information to look for recurring patterns in the adaptation of different bacteria to the same lifestyle in order to understand disease-causing bacteria better. I also hope to be able to use the information to build predictive software that can identify a newly evolved bacterial threat, based on these key signs of adaptation.

My primary focus in applying my software to research questions is the agents behind bloodstream infections, particularly Salmonella. In developing countries, invasive variants of Salmonella are a huge threat to public health, particularly because patients present with vague symptoms and if the infection is detected late, the prognosis can be very poor, but if caught early it is treatable. Having a better understanding of the biology of invasive Salmonella variants can help us design effective treatments for infection, and having a robust test for these agents of disease could improve outcomes for those infected, and improve public health strategies to control the spread of these infectious agents.

The focus of my thesis is on disease-causing bacteria, but the software I’m developing can be applied to many fields of research, such as public health (identifying genetic mutations that are likely to cause disease), agriculture (identifying genetic variants in breeding stock that is likely to influence key traits), conservation (identifying which individuals are best to pair together to maintain genetic diversity and minimize the threat of mutational meltdown), and many others.

We are a broadly focussed Biology department, so there’s a chance to learn about research and approaches to problems from really diverse fields and to collaborate on some really interesting and unexpected projects.

New Zealand is a beautiful country, with friendly people and is a pleasure to live in.

Funding and/or scholarships as a Graduate Student

I’m a domestic student. I received some scholarships in my undergraduate to complete a number of research projects over the summer break periods. I started a Master’s degree, and as I approached the end of my thesis, the project was going well so my supervisor offered me a scholarship to stay on and continue the work as a Ph.D. student.

Availability of teaching or research assistantship within the Department

I work as a teaching assistant, generally helping out for one or two classes per year. This is an optional commitment of about 2 hours per week. On top of this, I work as a tutor for some of the students.

What I like most about being here

I enjoy the breadth of research that goes on in our department – we are a broadly focussed Biology department, so there’s a chance to learn about research and approaches to problems from really diverse fields and to collaborate on some really interesting and unexpected projects.

One downside is that we lack critical mass in my area of specialty, so if I need specific advice relating to my thesis I often have to turn to the literature or get in touch with academics from other institutions. This has actually been beneficial though. It has taught me to be more independent and has fostered some really good relationships with people from other universities, which can often lead to new collaborations and ideas.

I also enjoy studying at Canterbury because of the variety of travel opportunities around New Zealand, and the field stations that we can visit. We have yearly retreats to a nearby field station that is near a waterfall where seal pups spend a few months growing up before they swim out to the ocean. New Zealand is a beautiful country, with friendly people and is a pleasure to live in.

Finding a supervisor and settling

I had a lot of options in choosing my thesis supervisor, but in the end, research experience from my undergraduate years lead me to choose a project outside of my immediate field.

I got a scholarship to do a short research project over the summer during my undergraduate and decided to work with Paul Gardner, a new lecturer at the university working in bioinformatics. The discipline had not yet been introduced as a taught course at my university, so it was a chance to try something really new. I found the project really stimulating, and kept thinking about it as I continued with my degree. I did a number of other short projects with my university and another more medically focussed university in New Zealand and this gave me an idea of what different fields of research were like.

In choosing a supervisor for my Master’s thesis, I talked to a number of people about different projects, and one of the projects I talked about with Paul stood out as the most exciting to me. In addition to this, Paul offered me the most freedom in what I’d be doing – some of the other projects were already clearly defined and just waiting for someone to come along and do the work. I wanted to develop my own questions and approaches, so I decided to go with Paul. Paul likes to keep regular contact with each of his students, so the group has stayed reasonably small, which I liked. It certainly helped me to break into a new field, knowing I’d have the support I needed.

I really enjoy the flexibility in work hours that comes from working on a computational project.

Life as a graduate student

I enjoy grad student life. It can be hard budget-wise if you’re not careful, but I’ve always been quite sensible with money so I find my scholarship supports me quite well. I’m looking forward to getting a job and being a bit more financially comfortable, but there are other perks of this lifestyle that make it worthwhile. I really enjoy the flexibility in work hours that comes from working on a computational project. I can work from home or while traveling, and if I need a break I can take one without much fuss. Also, if I have an idea in the middle of the night, I can just grab my laptop and get to work. The freedom to work on a project without any fixed requirements for other teaching and administrative work is something I really appreciate. It allows a level of focus that you don’t get in some other academic positions.

I think during graduate school it’s important to get any practical experience you can – the realities of research are very different from learning about a field in lectures. It’s also a good idea to get an understanding of the relative pace, competitiveness, and funding opportunities of different specialties. Taking on projects slightly outside your field of study can also open up unexpected areas of interest like it did for me and bioinformatics.

Challenges or struggles

Coming into postgraduate work I really had no idea how much public speaking was involved in a typical scientist’s work life. I find especially with my work, where I thrive on collaborations with other universities, giving a really interesting and engaging talk at a conference can make a huge difference in terms of the people you meet and the opportunities you encounter. When I started my postgraduate studies I was absolutely terrified of speaking in front of other people, particularly other academics, and would have panic attacks before any kind of presentation to a group of people. I joined Toastmasters to try to address my public speaking fears, and it’s been absolutely amazing. The environment is really encouraging and the improvement you make, especially when you first join is pretty incredible. Since I joined Toastmasters, I’ve won a few prizes for my presentations, including one that offers sponsorship to go and present my research at a big conference in the US. In the past, that would have terrified me, but now I’m really excited about the opportunity.

I would strongly recommend that anyone who feels apprehensive about speaking in front of people visit a local Toastmasters club and see if it’s right for them. As a guest, there’s no obligation to get up and speak, and you get a great chance to hear some interesting speeches, as well as the constructive feedback that’s given to them, which can be applied to your own speaking as well. As an added benefit, it can also be a great place to meet new people and get help and advice if you’re new to an area.

 

 

Achievements

  • Best Student Lightning Talk: Canterbury ‘Omics Symposium 2016
  • Best Student Oral Presentation: New Zealand Microbiological Society Conference 2015. The prize included sponsorship to attend the American Society for Microbiology Conference in Boston 2016.
  • Traditional Poster Prize: Queenstown Molecular Biology Conference 2015
  • Awarded UC School of Biological Sciences Ph.D. Scholarship (2015-2017)
  • Awarded Biomolecular Interaction Centre Ph.D. Top-up Scholarship (2015-2017)
  • New Zealand Federation for Graduate Women (NZFGW) Sadie Balkind Award (2014)
  • Summer Scholarship recipient, University of Otago, 2012
  • Summer Scholarship recipient, University of Canterbury, 2011