The RECOMB-Seq 2026 program is now available! Join us May 24–25 in Thessaloniki, Greece, for two days of cutting-edge biological sequence analysis, with keynotes by Camille Marchet (CNRS) and Manolis Kellis (MIT). Full schedule: recomb-seq.github.io/seq2026/prog... #RECOMBseq

More and better human assemblies. Now annotate them to the minute. Special kudos @trhyker.bsky.social @jnalanko.bsky.social and @florisbarthel.bsky.social

Floris Barthel@florisbarthel.bsky.social · 5mo ago

The human genome's most variable and clinically important regions (centromeres, telomeres, and acrocentric short arms) have been hardest to study at scale. Thrilled to share KaryoScope, our new preprint that brings them within reach. 🧵 www.biorxiv.org/content/10.6...

#SEQBIM2025 is about to start, Bonsai presents 4 works this year in Nantes seqbim.cnrs.fr/seqbim-2025/...

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...

‘Google for DNA’ brings order to biology’s big data

MetaGraph compresses vast data archives into a search engine for scientists, opening up new frontiers of biological discovery.

nature.com

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 💙✨

🍾🍾

Mikaël Salson@mikael-salson.univ-lille.fr · last yr.

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!

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...

Volume 41 Issue Supplement_1 | Bioinformatics | Oxford Academic

Publishes scientific papers and review articles on new developments in bioinformatics and computational biology. Shorter papers report biologically interesting discoveries using computational methods ...

academic.oup.com

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 🎊

Camille Marchet ⚡@camillemrcht.bsky.social · last yr.

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

#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.

Antoine Limasset@npmalfoy.bsky.social · last yr.

Paper alert! We present Oreo a tools that reorder long reads datasets in a way to compress them efficiently with ANY universal compressor like gz, zstd, xz ... TLDR: You can get state of the art compression WITHOUT a dedicated compressor/decompressor! academic.oup.com/bioinformati... A thread!

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

Prix de thèse Gilles Kahn - Société Informatique de France

Le prix de la Société informatique de France (SIF) a été créé en 1998 pour récompenser chaque année une excellente thèse en informatique. Gilles Kahn, qui a présidé les trois premiers jurys…

socinfo.fr

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/...

Improved sub-genomic RNA prediction with the ARTIC protocol

Abstract. Viral subgenomic RNA (sgRNA) plays a major role in SARS-COV2’s replication, pathogenicity, and evolution. Recent sequencing protocols, such as th

doi.org

Camille Marchet ⚡@camillemrcht.bsky.social · last yr.

Thomas Baudeau defended his thesis on Studying the properties of viral long reads mapping methods - congrats docteur Baudeau you'll be deeply missed in the team. I'm very glad I got the chance to work with you. Thomas is also on the lookout for a postdoc 👀

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

Antoine Limasset@npmalfoy.bsky.social · last yr.

A common approach is to use k-mer indexes to identify datasets that share a significant number of k-mers with a query sequence. This problem has been studied extensively, and I recommend the survey of @camillemrcht.bsky.social, a great introduction to the subject genome.cshlp.org/content/31/1...

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.

Camille Marchet ⚡@camillemrcht.bsky.social · last yr.

Thomas Baudeau defended his thesis on Studying the properties of viral long reads mapping methods - congrats docteur Baudeau you'll be deeply missed in the team. I'm very glad I got the chance to work with you. Thomas is also on the lookout for a postdoc 👀

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 😊

Camille Marchet ⚡@camillemrcht.bsky.social · last yr.

Really enjoying my first attendance at @mdc-bimsb.bsky.social in Berlin. Thanks for the invitation!

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...

Transipedia.org: k-mer-based exploration of large RNA sequencing datasets and application to cancer data - Genome Biology

Indexing techniques relying on k-mers have proven effective in searching for RNA sequences across thousands of RNA-seq libraries, but without enabling direct RNA quantification. We show here that arbi...

link.springer.com