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Hélène has been involved in several wheat projects, such as the BreedWheat French Stimulus Initiative project, where she worked on the development of an Affymetrix Axiom genotyping SNP array. In 2016, she worked on the annotation of chromosome 1B with TriAnnot , an annotation platform that has been used to improve the whole-genome reference developed by the IWGSC.

What motivated you to become a bioinformatician? How did you become involved in genomics?

It was during my last year as an undergraduate, in 2009, that I had my first experience with bioanalyses/bioinformatics and this led me to decide to continue in bioinformatics. This was a challenge for me as I had no experience in informatics at all. My first steps in genomics were highly linked with my involvement in the French pre-competitive project Breedwheat where I worked under the leadership of Dr. Etienne Paux at GDEC from 2012. It was exciting to have the opportunity to work with the latest sequencing technologies, on an organism I did not know much about.

In your daily work as a bioinformatician, what excites you the most?

I am very curious of the continuous progress in information technology (IT). Informatics and genomics are fast moving areas and I find this very stimulating because one is learning something new all the time.

You most recently worked to produce the IWGSC RefSeq annotation v1.1 and are currently working on v2.0; what do you find most challenging about your work on this project?

Delivering a high-quality annotation of a genome sequence is really challenging. We had the chance to work jointly on this task with colleagues at PGSB and Earlham Institute in the Annotation Team, to get the best from the two annotations analysis. Every step in the annotation is crucial. We spent time to find the best way to use TriAnnot with a realistic time (more than 3 month of calculation) to obtain our gene-models and the TEs annotations. For the release of IWGSC RefSeq annotation v2.0, the most challenging part concerns genes falling into regions that have been corrected in RefSeqv2 and also the traceability between the current annotation (v1.1) and the next one (v2.0). This is our main focus currently and it is challenging to produce the best results for the release of this new resource while also keeping track of the information from previous annotation.

What would you say are the benefits of being part of an international consortium?

The IWGSC is a powerful tool to bring together people and resources and work with common objectives. We can all benefit from the strength of the members and their network to move forward.

As a bioinformatician, is there a particular genome you would love to work on? Why?

I would not say a particular genome but rather a different field. For example, since I do not know much about AI, I would definitely like to explore this area and see how this can be used in wheat genomics.

According to you, what will be the biggest advances in wheat research in the next 5-10 year?

We are now having more and more data generated and these data are highly heterogenous (new genomes, expression, variations, phenotypes, on different time/tissues and cultivars etc.) I think the challenge now is to make the connections between all these data-types and to make them easily available for everyone to explore. I believe that the work done on graph databases might be useful to integrate all the work that is done in the community.

What are your future plans?

We have a project with URGI about data integration as part of the “Genomics Research Environment for Plants” INRA Engineer collective. We are currently collecting a lot of –omic data ( France Génomique project WheatOmics ). In that context, we need to have an integration system to allow researchers to query all these data sets which are highly heterogenous. I believe that the growing concept of graph databases will help. As part of this collective, I will work on this with wheat data-sets and I am convinced that this can be highly beneficial for the wheat community.

About Hélène

Publication date: 11/21/2019