Travel story: Qianhui Wan

Qianhui Wan from the Robinson Research Institute travelled to Brisbane in July to attend the Winter School in Mathematical & Computational Biology.

This is what Qianhui had to say about her experience.

What was a highlight of the travel?

The highlight of the travel was learning about the up-to-date methods and ideas about bioinformatics analysis, such as neural networks and deep learning.

Did you attend any workshops, labs, research facilities or attend any meetings associated with your travel?

Yes. In the 5-day Winter School, we had speakers representing 4 computational themes including next generation sequencing and bioinformatics, data science and machine learning for bioinformatics, bio-data analysis and visualisation, and advanced microscopy analysis and modelling. Apart from these presentations, we also had several other thought-provoking activities. First, we had very interesting panel discussion that made us think about where one lies on the bioinformatics skill spectrum and what we need to do as a community. PhD candidates Gabriel Foley and Alexandra Essebier talked about their projects and how they collaborate with other researchers. Gabriel Foley is also an organiser of COMBINE, a student-run Australian organisation for students in computational biology, bioinformatics, and related fields. Professor Sean O’Donoghue talked about his career spent in European Molecular Biology Laboratory (EMBL) and at Lion Bioscience. He pointed out that improving the visualisation of biomedical data such as 3D genomics and protein structure could help us clearly address complex phenomena. Other panel members including Dr Simone Linz and Aaron Darling showed that there are more researchers needed in bioinformatics field and encouraged people interested in data science and biology to engage in a project on bioinformatics. Second, we listened to the Friday Noon Seminar from Institute for Molecular Bioscience (IMB) in the University of Queensland. Professor Melissa Little talked about how her team generates human kidney organoids from human embryonic stem cells (hESC) and human induced pluripotent stem cells (hiPSC) and how they translated their results to use for drug testing and developing cellular therapy for chronic kidney disease. All the PPTs of the lecturers are online now at website http://bioinformatics.org.au/ws/category/wsol18/.

Did you visit any other labs or research facilities?

Yes, we visited the Institute for Molecular Bioscience (IBM) at the University of Queensland. In IBM, there are labs doing research on genomics of development and disease, cell biology and molecular medicine, and chemistry and structural biology. IBM had many research facilities based on cutting-edge technologies. We visited the microscopy facility, nuclear magnetic resonance (NMR) spectroscopy facility, Queensland Emory Drug Discovery Initiative and Centre for Pain Research. This visit will be useful to me because I know more cutting edge methods which could be potentially used for placental research. It is also essential to have professional people to deal with imaging and sequencing data from these platforms, and in this way these technologies could be the primary enablers of discovery and innovation.

Did you meet any researchers or collaborators of significance? Why are they important to your work?

Many speakers mentioned the Hidden Markov Model (HMM) and random forest as classification methods used in bioinformatics. I wanted to know more about these methods and talked with Dr Nicola Armstrong who is a statistical bioinformatician from Murdoch University. She recommended a book explaining HMM that is quite helpful to me. These methods could be potentially used in my project to find more patterns from the data we have.

How will the experience support you and your research going forward?

From the Winter School, I now know how other researchers are analysing data using mathematical and computational methods and what is the proper way of doing research in bioinformatics. I now feel more confident about my analyses, and at the same time feel there are a lot more skills that need to be learned and used to improve my data analyses. In addition, during Winter School, the representatives of COMBINE encouraged us to join the Australian Bioinformatics and Computational Biology Society (ABACBS) since COMBINE is the student subcommittee of ABACBS. I have become a member of ABACBS and will help review abstracts for the COMBINE student symposium later this year.

What was the most exciting thing you learned/experienced whilst traveling?

I found the translation of research is becoming faster. I did my Masters in a lab mainly focused on inducing porcine pluripotent stem cell (iPSC) from fibroblasts. At that time (in 2012), I expected iPSC could probably be used for clinical purposes after 50 years since iPSC only appeared in 2006. However, I saw translation of iPSC through presentations during Winter School (e.g. kidney organoid for drug testing), which is quite exciting progress.

What was the most interesting or unexpected moment of your travel?

The most unexpected moment was when the presenters showed how they combine physics with biological research. Professor Sean O’Donoghue showed data visualization using an immersive virtual reality headset. Professor Halina Rubinsztein-Dunlop presented using optical tweezers systems to manipulate the vestibular system in zebrafish. These interdisciplinary projects promote multifaceted and comprehensive understanding of biology.