Ca n'est pas si souvent, un article publié dans Nature met ma communauté à l'honneur (la bioinformatique des séquences). Je vous raconte ? www.nature.com/articles/d41...

Yohan Hernandez-Courbevoie chaired by Maxime Crochemore just before presenting REINDEER2 at #SPIRE2025 in London

Achievement unlocked: defend your habilitation thesis on the same day than your partner. That was quite a science + celebration day, thanks to all involved 💙✨

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A wonderful day for @bonsaiseqbioinfo.bsky.social, with @camillemrcht.bsky.social's and @npmalfoy.bsky.social's HDR defenses. Congrats for the amazing work! It's a great chance for the team to have you both!

Excited to attend #SEA2025 this week in Venice! I'll present our work on simd-minimizers on Thursday! Meanwhile, you can take a look at the slides here: igor.martayan.org/slides-sea-2...

Two talks for Bonsai this Thursday, one from @mikael-salson.univ-lille.fr during ISMB presenting a compressed representation for viral MSAs,

🖥️🧬: The ISMB 2025 proceedings are out! I’m looking forward to seeing many presentations on this work next week :). academic.oup.com/bioinformati...

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 !

Among other flash talks @imartayan.bsky.social presented recent techniques for rapid assessment of pangenome openness, and @bdegardins.bsky.social did a demo of Vizitig for exploring different small pangenomes

Congrats to both and to other award winners 🎊

#JOBIM2025 glad to have Jana Ebler as keynote speaker in our mini symposium on graphs for pangenomics

#JOBIM2025 Mathilde Girard ends the session with a simple but effective idea: re oder the reads before using an off the shelf compressor to improve compression gain

#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

Bonsai delegation enjoying #JOBIM2025 🌴and Bordeaux's weather

Our first keynote speaker Anouck Necsulea from LBBE on genomics for understanding phenotypic diversity, chaired by her LBBE fellow, post-punk and IFB master @komo625.bsky.social #JOBIM2025

All Bonsai related communications during #JOBIM2025. Come meet us 👇🏻

Could a "simple" read reordering have impact on the compression of your fasta file? Find out in this publication from Mathilde Girard, PhD student in the group.

Ouverture des candidatures au Prix de thèse Gilles Kahn décerné par la Société informatique de France www.socinfo.fr/recherche/pr...

Bonsai goes camping by the shore ☀️

I worked with Thomas during a three months research visit during his PhD, and it resulted in a paper in NAR. I highly recommend him. doi.org/10.1093/nar/...

Preprint alert from the group 🚨 super fast grep-like sequence selection

First Bonsai group's PhD to defend this year. You're a unique student Thomas, thanks for sharing these 3 years with us. Now we wish you the best.

It's the K-mer Days in Toulouse, a meeting between computational bioinformaticians and clinical bioinformaticians, discussing how k-mer based methods can be used in research/diagnostic... Here Yohan presents REINDEER2.

Our PhD student, Pierre Berriet, presented a poster at the Nancy Computational Structural Biology (NCSB) meeting, demonstrating how to map chains in large protein complexes to compare folding predictions.

Introduction to our group yesterday in Berlin 😊

Abundance indexes are super valuable in transcriptomics, and our team @bonsaiseqbioinfo.bsky.social is implied in some impactful work developing these methods through amazing consortium efforts. Check out their latest: link.springer.com/article/10.1... pmc.ncbi.nlm.nih.gov/articles/PMC...

Save the date! 🙆🏻‍♀️ The Workshop on Genomics 2026 will take place between the 11th and 24th of January, 2026! In Český Krumlov, Czechia. Regular applications will be oppening mid-July, keep an eye on updates! 🤗 evomics.org/2026-worksho... #evomics2026

REINDEER's successor is ready

REINDEER2: practical abundance index at scale https://www.biorxiv.org/content/10.1101/2025.06.16.659990v1

New crate updates to fix some outstanding feature requests :) - Packed-seq now directly supports reverse-complementing packed sequences. - Simd-minimizers now supports returning [canonical] minimizer values as u64, instead of only their positions. With @imartayan.bsky.social of course

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

New preprint by Florian and Bastien. More compression work from the group to come...

⌚ 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

Continuing with @imartayan.bsky.social and Lucas Robidou presenting Hyper-k-mers a novel efficient streaming k-mers representation. A joint work with @npmalfoy.bsky.social and Yoshihiro shibuya

We finally concluded the meeting. Thanks to all attendees for their scientific contributions and for traveling (near or far) to the meeting! Thanks to the local organizers for the infrastructure and catering, and thanks to the co-organizers @yaronorenstein.bsky.social @camillemrcht.bsky.social!

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

Now our @tmthrz.bsky.social presenting his approach for compressing collections of unitigs - Rayan Chikhi 🤝🏻 @npmalfoy.bsky.social

This time, @camillemrcht.bsky.social is on the other side of the stage to present the next version of REINDEER, a scalable index for k-mer abundances

On the second short-talks session today we heard about exploration of sequencing datasets @camillemrcht.bsky.social, isoform quantification, complex chromosomal rearrangements, and benchmarking read mapping

@bonsaiseqbioinfo.bsky.social friends in Seoul @rayanchikhi.bsky.social @imartayan.bsky.social @tmthrz.bsky.social 🫰🏻🫰🏻🫰🏻

Congratulations to @imartayan.bsky.social and @curiouscoding.nl whose paper on fast minimizer computation with simd has been accepted to SEA 2025 🙌🏻 www.biorxiv.org/content/10.1...

We also present a novel work at the main event @recombconf.bsky.social recomb.org/recomb2025/a..., by @imartayan.bsky.social

Part of our seminars, we were happy to recently host Lore Depuyt from Ghent, check out her works on pattern matching with move indexes!

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 🙏🏻

Bonsai group members will present 3 talks at @recombseq.bsky.social 2025 in Seoul recomb-seq.github.io/program/ excited to meet you there!

Excited to share a new preprint! We developed a new algorithm for POA, POASTA (pronounce it with your best Bo-ah-ston accent). It is based on the A* framework and inspired by other recent alignment algorithms such as the WFA and Astarix. www.biorxiv.org/content/10.1...

🎶 Last Christmas,i gave you m̶y̶ ̶h̶e̶a̶r̶t̶ 40 pages of delicious combinatorics 🎶 Choose any word W of size m. How many words of size k>m admit W as their smallest lexicographical subword of size m ? Find out in my latest preprint!

An example of k-mers data structures in action in a result result: with colleagues from CRCT Toulouse and IRMB Montpellier, we have identified an aberrant splicing mechanism in blood stem cells and certain aggressive forms of acute myeloid leukemia. 1/2

Preprint alert! Can we enumerate how many k-mers lexicographic minimizers have? Yes! (implicitly). Looking forward to applications of this 👌🏻 work by Florian Ingels, @mikael-salson.univ-lille.fr @camillemrcht.bsky.social arxiv.org/abs/2412.17492