Past Experiences

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An Interview with an ESCS speaker Alexandre Renaux

In this interview, one of the organizers of #ESCS2020, Pradeep Eranti is talking with Alexandre Renaux, a Flash talk presenter at the Student Council Symposium (SCS) 2019 symposium, held at Basel, Switzerland. He is currently a second-year PhD candidate at the Université Libre de Bruxelles (ULB) and at the Vrije Universiteit Brussel (VUB) in Belgium.

alexandre renaux

Pradeep Eranti: What are your research interests? What are you currently working on? 

 Alexandre Renaux: My research interests are mainly focused on human genomics, especially variant interpretation and on the topics of machine learning, network biology and data integration.

I am currently working on the development of new computational methods and tools to help in the diagnosis and understanding of complex genetic diseases. The diseases of interest in my team are called 'oligogenic', meaning that they are caused by mutations in a few numbers of different genes. The particular angle of my research is to provide geneticists with explanations and interpretable tools that would help them make sense of predictive results provided by machine-learning based approaches, by leveraging the information contained in multiple biological networks.

PE: How did you decide to make this the focus of your research?

AR: I have had the opportunity to work on different aspects of bioinformatics before (comparative genomics, protein annotation, ...) so I feel quite comfortable in exploring different biological levels and integrating them together. I think the field of genomic variant discovery/interpretation is a perfect candidate for these kinds of integrative approaches. 

I also believe that the current deluge of new computational methods (especially machine-learning based) in this field will mostly go to waste if we do not offer ways for experimentalists/clinicians to interpret and navigate predictive results. Biologists and clinicians usually do not trust black-box methods alone.

PE: How did your scientific journey begin?

AR: I studied bioinformatics at the master level after doing a bachelor’s in molecular biology. I thought at the time that the PhD was not for me, so I worked as a bioinformatician with a more 'software engineer' role at the Atomic Energy Commission in France and at the European Bioinformatics Institute in the UK. It was all very instructive and interesting, but I felt that my projects were becoming less and less research-oriented and more and more pure development. The PhD was really a way for me to go deeper into the science, the literature, and getting to know the process (and pain! :p) involved in research done independently.

The beginning of the PhD was definitely not easy, and I am still struggling with the high and sometimes contradictory expectations and the inherent uncertainty it involves. 

PE: What do you love most about being a researcher?

AR: I love the feeling of freedom I get when I explore and develop ideas in the first place. Especially, I love when I stumble upon THE paper, the one that connects all the dots in my head and gives me the aha moment, quickly followed by a big rush of productivity where I chaotically work on that idea. This is something unique you will hardly find in any other jobs.

PE: Was there something specific about ESCS that drew you to apply? 

AR: I participated in the ISMB conference (for the first time as a PhD student) so ESCS was a perfect opportunity for me to meet other fellow students from all over the world. I was accepted to give a flash talk and I felt it less intimidating than presenting to a crowd of more senior researchers as I did afterward at ISMB.

PE: What was your key takeaway from the symposium; and how did you plan to apply it to your work?

AR: I was really interested by the keynote presentation at (E)SCS2019 from Dr. Dessimoz about big data. He mentioned for example, the loss of intuition in the way models are built and the need to make use of prior knowledge. This is something that confirmed my views and inspired me to carry on my research.

PE: What feedback or advice would you share with someone considering participating in ESCS?

AR: ESCS is really a "safe space" for students to interact and present their work without all the pressure of ISMB/ECCB. I would advise you to use the coffee breaks and networking event(s) to engage with other students in a friendly way, what's the worst that could happen? :-)

PE: What did you like most about your participation in an ESCS event?

AR: The opportunity I had to present my work and then exchange with other students about it, and in general the approachability of the participants and organization team.

Follow Alex on twitter at @alex_rnx. Pradeep tweets as @pradeeperanti! For more content about the #ESCS2020 follow the official account @escs2020 and more Early Career Researchers’ lead activities of the ISCB student council at @iscbsc.

 

 

An Interview with an ESCS travel fellowship winner Renee Dale

In this interview, one of the organizers of #ESCS2020, Pradeep Eranti is talking with Renee Dale, a Travel fellowship winner of the European Student Council Symposium (ESCS) 2018 symposium. Dr. Renee Dale is currently a first-year post-doctoral researcher at Donald Danforth Plant Science Center, USA.

Dale

Pradeep Eranti: What are your research interests? What are you currently working on? 

Renee Dale: I am interested in mechanistic modeling and plant biology. My PhD was on mechanistic modeling in enzymes and cell biology, so I’m currently working on applying that perspective to plant phenotype (disentangling the “gene” by “environment” effects that produce different traits) and modeling the development of those traits over time.

PE: How did you decide to make this the focus of your research?

RD: I started this project during my PhD. I worked with mechanistic models and the issues with identifying and estimating parameters gave me a lot of trouble. Often reviewers or other biologists thought the model was too complex or left out too many biological components. I wanted to see if there was a way to take the network predictions from bioinformatic analyses of gene expression and test it with a mechanistic model.

PE: If you were not working on the same project during ESCS 2018, what were you working on then?

RD: I am still working on the project I presented at ESCS. I was working on taking a large drought stress signaling network and modeling it mechanistically using an algorithmic approach. Large mechanistic models have computational and parameter issues, and my idea was to bypass this by focusing on what we already know about that network.

PE: What impact do you hope to make through your work? 

RD: I hope my work can help bridge the gap between bioinformatic prediction of regulatory networks, and experimental testing of the predicted mechanisms and interactions inside those networks, with mechanistic modeling.

PE: Was there something specific about ESCS that drew you to apply?

RD: I was drawn to the idea of a grad-student led symposium. I think people around your career stage are probably the best to identify useful and interesting things, and it would make a great symposium.

PE: What was your key takeaway from the symposium; and how did you plan to apply it to your work?

RD: I enjoyed the poster session and opportunity to engage with everyone with their work. Many people’s work was either up- or down-stream of my work, and it helped me to contextualize and receive feedback of my work.

PE: What feedback or advice would you share with someone considering participating in ESCS?

RD: I’d definitely suggest going! ESCS had a great sense of community and talk lineup. You don’t always get a good sense of community from a gathering of early-career scientists like that. It’s organized and run by the students, and you can definitely see the immediate utility of the selected talks.

Follow Renee on twitter at @b10_m0del1ng . Pradeep tweets as @pradeeperanti! For more content about the #ESCS2020 follow the official account @escs2020 and more Early Career Researchers’ lead activities of the ISCB student council at @iscbsc.