Bastien Degardins

Les gens qui lisent ces articles ont déjà vu une chambre de résidence étudiante ? Je sais qu'on l'avait déjà dit pour Balkani mais l'apprentissage c'est la répétition, tout ça.

And many thanks to @guigau.bsky.social and Hanin Ali for using and promoting our methods in bacterial gene family analysis. Check their work !

bsky.app/profile/cami...

The latest presentation earned the prize of the best presentation of the mini-symposium.
Many thanks to all participants, voters, organizers and to @camillemrcht.bsky.social and Charles Paperman for the work we did together.

Next time we'll have to show some human Pangenomic examples 😀

I was delighted to participate to @jobim2025.bsky.social. I had the chance to present Vizitig twice, during the session on data structures and algorithms, and during the mini-symposium on Pangenomics.

Many thanks to the organizers for this amazing conference !

Photo de groupe prise avec les participants et participantes à JOBIM 2025.

👏 Ca y est, #JOBIM2025 est officiellement fini !

Au nom de toute l'équipe, merci pour votre participation, et pour toutes ces discussions scientifiques intenses et stimulantes.
Merci aussi pour votre enthousiasme, votre bienveillance et tous ces rires échangés pendant la conférence.

1/2 ⤵️

@cnrsecologie.bsky.social regrette profondément l'adoption de cette loi à la vision court-termiste & ses conséquences graves sur l’environnement, qui méprise santé & bien-être de la population & le rôle des espèces sauvages dans la prod. agricole. La communauté scientifique n'a pas été entendue.

Super proud that @bdegardins.bsky.social and Fiona Hak earned a Mini-symposium prize for the presentation and poster award at #JOBIM2025 🎉🏆

Meet Hanin Ali on July 9th at #JOBIM2025 at the poster session to talk about Bridging gene-level and sequence-level pangenome graph to explore microbial diversity
#INRAE #MaIAGE @guigau.bsky.social #UniversiteLille #CRIStAL @camillemrcht.bsky.social

Showing the last circRNAs we could spot

#JOBIM2025 @bdegardins.bsky.social presents his PhD work on Vizitig, a multi sample graph exploration tool, with a focus on RNA - this afternoon we'll do a demo on pangenomes with the same tool

A chance to get to know what's behind REINDEER2 and to see Vizitig in action

On day 3 our PhD students Mathilde Girard, @bdegardins.bsky.social and Yohan Hernandez Courbevoie will present in the sequence algorithms session

⌚ Les inscriptions pour #JOBIM2025 se sont clôturées ce week-end. Merci pour votre participation, et rendez-vous à Bordeaux du 8 au 11 juillet ! 🌞

Mais avant ça, et si vous jetiez un œil au programme des communications orales ? 👀
Il est disponible sur notre site Internet ➡️ jobim2025.labri.fr

A graph showing a circular RNA with colors for each exons and a clear circular junction between exons 2 and 5

From the same papers, this time in the FBXW4 gene 🙌🏻

Another circRNA in MAN1A2 human gene, first described in Mercer et al. 2015. I retrieved illumina data, built the graph, searched the gene in Vizitig and here it is!

@camillemrcht.bsky.social is back on stage to present Vizitig, an interactive visualization tool for sequencing datasets developped by @bdegardins.bsky.social

In this (rebutted) grant proposal I wrote that I thought we could see circular RNAs with Vizitig, despite being hard to detect and with low expression. Guess what? Looks very much like a circular RNA to me 😎 (in TET2 gene, human co-assembled cancer RNA-seq samples).

Vizitig: context-rich exploration of sequencing datasets https://www.biorxiv.org/content/10.1101/2025.04.19.649656v1

5/ @bdegardins.bsky.social is the main character of the story, follow him! I'll present his work during RECOMB-Seq.

1/ We made a tool called Vizitig to explore sequencing datasets visually, interactively, and with metadata.
It uses a colored de Bruijn graph under the hood.

Job offers: 1 funded PhD position and 1 postdoc in computational genomics between Univ Lille and Helsinki Uni, details: kamimrcht.github.io/webpage/jobs.html we're looking for candidates, please share 🙏🏻

@bdegardins.bsky.social added a cool features allowing to display bars that indicate abundances levels. It's our own sashimi plots. In a zoomed-in region, they help forming an opinion on whether a local variant is something worth digging or not

a graph of RNA molecule with colors showing different exons

Playing with #vizitig again to prepare for the 1.0 release. This is the SNAP25 human gene expressed in 3 SRA datasets linked to cancers.
Exons have one color each, and exon junctions are in yellow.
The rest is new/noise.

How helpful is a de Bruijn graph for visualizing alternative RNA variants? Here I requested our graph visualization tool Vizitig to show me the CIC human gene in my data (3 RNA-seq samples). I connected sequences to known genes using an annotation and colored CIC's exons in different tints.