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Bonsai Sequence Bioinformatics

@bonsaiseqbioinfo.bsky.social
94 followers 56 following 36 posts

Research group in Lille, Fr.

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recombseq.bsky.social @recombseq.bsky.social · 03/05/2026
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
recomb-seq.github.io
Program
RECOMB-Seq 2026 Web Page
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Camille Marchet ⚡ @camillemrcht.bsky.social · 17/05/2026
More and better human assemblies. Now annotate them to the minute. Special kudos @trhyker.bsky.social @jnalanko.bsky.social and @florisbarthel.bsky.social
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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · 24/11/2025
#SEQBIM2025 is about to start, Bonsai presents 4 works this year in Nantes seqbim.cnrs.fr/seqbim-2025/...
seqbim.cnrs.fr
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Camille Marchet ⚡ @camillemrcht.bsky.social · 09/10/2025
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...
nature.com
‘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.
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Reposted by Bonsai Sequence Bioinformatics
Camille Marchet ⚡ @camillemrcht.bsky.social · 09/09/2025
Yohan Hernandez-Courbevoie chaired by Maxime Crochemore just before presenting REINDEER2 at #SPIRE2025 in London
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Camille Marchet ⚡ @camillemrcht.bsky.social · 05/09/2025
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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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · 08/09/2025
🍾🍾
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Mikaël Salson @mikael-salson.univ-lille.fr · 04/09/2025
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!
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Igor Martayan @imartayan.bsky.social · 21/07/2025
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...
igor.martayan.org
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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · 21/07/2025
Two talks for Bonsai this Thursday, one from @mikael-salson.univ-lille.fr during ISMB presenting a compressed representation for viral MSAs,
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Rob Patro @robp.bsky.social · 15/07/2025
🖥️🧬: The ISMB 2025 proceedings are out! I’m looking forward to seeing many presentations on this work next week :). academic.oup.com/bioinformati...
academic.oup.com
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 ...
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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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Camille Marchet ⚡ @camillemrcht.bsky.social · 11/07/2025
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
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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · 11/07/2025
Congrats to both and to other award winners 🎊
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Camille Marchet ⚡ @camillemrcht.bsky.social · 10/07/2025
#JOBIM2025 glad to have Jana Ebler as keynote speaker in our mini symposium on graphs for pangenomics
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Camille Marchet ⚡ @camillemrcht.bsky.social · 10/07/2025
#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
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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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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · 09/07/2025
Bonsai delegation enjoying #JOBIM2025 🌴and Bordeaux's weather
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Camille Marchet ⚡ @camillemrcht.bsky.social · 08/07/2025
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
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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · 08/07/2025
All Bonsai related communications during #JOBIM2025. Come meet us 👇🏻
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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · 03/07/2025
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.
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David Monniaux @monniauxd.bsky.social · 03/07/2025
Ouverture des candidatures au Prix de thèse Gilles Kahn décerné par la Société informatique de France www.socinfo.fr/recherche/pr...
socinfo.fr
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…
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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · 03/07/2025
Bonsai goes camping by the shore ☀️
Members enter the sea as the sun goes downA picture of the group with pretty dusk colors and the beach in the background Coastal landscape The group with tents
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Kristoffer Sahlin @ksahlin.bsky.social · 02/07/2025
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/...
doi.org
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
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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · 02/07/2025
Preprint alert from the group 🚨 super fast grep-like sequence selection
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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · 30/06/2025
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.
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Camille Marchet ⚡ @camillemrcht.bsky.social · 26/06/2025
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.
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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · 20/06/2025
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.
Pierre standing in front of his poster
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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · 20/06/2025
Introduction to our group yesterday in Berlin 😊
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Antoine Limasset @npmalfoy.bsky.social · 19/06/2025
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...
link.springer.com
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...
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Workshops @evomics.bsky.social · 17/06/2025
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
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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · 18/06/2025
REINDEER's successor is ready
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 17/06/2025
REINDEER2: practical abundance index at scale www.biorxiv.org/content/10.1101/202…
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Ragnar {Groot Koerkamp} @curiouscoding.nl · 17/06/2025
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
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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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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · 18/06/2025
New preprint by Florian and Bastien. More compression work from the group to come...
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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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Timothe Rouze @tmthrz.bsky.social · 27/04/2025
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
Igor and Lucas on Recomb's stage presenting their work
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recombseq.bsky.social @recombseq.bsky.social · 25/04/2025
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!
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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 · 25/04/2025
Now our @tmthrz.bsky.social presenting his approach for compressing collections of unitigs - Rayan Chikhi 🤝🏻 @npmalfoy.bsky.social
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Igor Martayan @imartayan.bsky.social · 25/04/2025
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
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recombseq.bsky.social @recombseq.bsky.social · 25/04/2025
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
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Camille Marchet ⚡ @camillemrcht.bsky.social · 25/04/2025
@bonsaiseqbioinfo.bsky.social friends in Seoul @rayanchikhi.bsky.social @imartayan.bsky.social @tmthrz.bsky.social 🫰🏻🫰🏻🫰🏻
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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · 01/04/2025
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...
biorxiv.org
SimdMinimizers: Computing random minimizers, fast
Motivation Because of the rapidly-growing amount of sequencing data, computing sketches of large textual datasets has become an essential preprocessing task. These sketches are typically much smaller ...
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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · 28/03/2025
We also present a novel work at the main event @recombconf.bsky.social recomb.org/recomb2025/a..., by @imartayan.bsky.social
recomb.org
RECOMB 2025 | PROGRAM
RECOMB 2025 - Yonsei University, Seoul
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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · 28/03/2025
Part of our seminars, we were happy to recently host Lore Depuyt from Ghent, check out her works on pattern matching with move indexes!
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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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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · 28/03/2025
Bonsai group members will present 3 talks at @recombseq.bsky.social 2025 in Seoul recomb-seq.github.io/program/ excited to meet you there!
recomb-seq.github.io
Program
RECOMB-seq is the RECOMB Satellite Conference on Biological Sequence Analysis
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Lucas van Dijk @lucasvandijk.nl · 28/05/2024
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...
biorxiv.org
Fast and exact gap-affine partial order alignment with POASTA
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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