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Reposted by Bastien Degardins

VivienM @vivienm.bsky.social · 19/03/2026

From my pangenomics story in @natmethods.nature.com, It's a colorful pangenome world, which is here www.nature.com/articles/s41... and here: rdcu.be/e8ZYC A comment from @camillemrcht.bsky.social

A comment from the story:It's a colorful pangenome world . From: It’s a colorful pangenome world... When digging into pangenomics methods to avoid reference bias, a hurdle is that “when you represent a lot of variations, it becomes, paradoxically, harder to correctly place the ‘nonaligners,’”
says Camille
Marchet. Aligning sequence
to graphs offers “no trivial
answer.” She and her team use
the De Bruijn graph and her
lab’s latest method is Vizitig.

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Bastien Degardins @bdegardins.bsky.social · 20/02/2026

I had the occasion of presenting nice results about the detection of biological events in De Bruijn Graph at #DSB2026, in the context of my PhD work on #Vizitig ! Thanks to the organizers and colleagues for this amazing and super-inspiring event (and @camillemrcht.bsky.social for the picture).

Presentation of scientific work on De Bruijn Graphs applied to the processing of sequencing data in the context of biology. The picture was taken in the conference room of the University of Venice, where a screen displays a slide that introduces De Bruijn Graphs, with the speaker standing in front of it. Being the screen is a large renaissance painting that spans from the floor to the roof.

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Camille Marchet ⚡ @camillemrcht.bsky.social · 21/10/2025

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.

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Bastien Degardins @bdegardins.bsky.social · 15/07/2025

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 !

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JOBIM 2025 @jobim2025.bsky.social · 11/07/2025

👏 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 ⤵️

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

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CNRS Écologie & Environnement @cnrsecologie.bsky.social · 09/07/2025

@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.

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Reposted by Bastien Degardins

Camille Marchet ⚡ @camillemrcht.bsky.social · 11/07/2025

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

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Unité INRAE MaIAGE @inrae-maiage.bsky.social · 08/07/2025

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

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Camille Marchet ⚡ @camillemrcht.bsky.social · 10/07/2025

Showing the last circRNAs we could spot

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Reposted by Bastien Degardins

Camille Marchet ⚡ @camillemrcht.bsky.social · 10/07/2025

#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

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Camille Marchet ⚡ @camillemrcht.bsky.social · 18/06/2025

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

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Reposted by Bastien Degardins

Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · 18/06/2025

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

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JOBIM 2025 @jobim2025.bsky.social · 16/06/2025

⌚ 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

jobim2025.labri.fr

Journées Ouvertes en Biologie, Informatique et Mathématiques - 2025

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Reposted by Bastien Degardins

Camille Marchet ⚡ @camillemrcht.bsky.social · 04/06/2025

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

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

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Reposted by Bastien Degardins

Camille Marchet ⚡ @camillemrcht.bsky.social · 03/06/2025

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!

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Reposted by Bastien Degardins

Igor Martayan @imartayan.bsky.social · 25/04/2025

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

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Camille Marchet ⚡ @camillemrcht.bsky.social · 06/05/2025

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).

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 22/04/2025

Vizitig: context-rich exploration of sequencing datasets www.biorxiv.org/content/10.1101/202…

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Camille Marchet ⚡ @camillemrcht.bsky.social · 23/04/2025

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

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Camille Marchet ⚡ @camillemrcht.bsky.social · 23/04/2025

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.

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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · 28/03/2025

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 🙏🏻

kamimrcht.github.io

PhD and Postdoc in computational genomics

CRIStAL, CNRS, Université de Lille

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Reposted by Bastien Degardins

Camille Marchet ⚡ @camillemrcht.bsky.social · 26/03/2025

@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

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Camille Marchet ⚡ @camillemrcht.bsky.social · 26/03/2025

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.

a graph of RNA molecule with colors showing different exons

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Reposted by Bastien Degardins

Camille Marchet ⚡ @camillemrcht.bsky.social · 16/01/2025

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.

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