Bonsai Sequence Bioinformatics
@bonsaiseqbioinfo.bsky.social
Research group in Lille, Fr.
#SEQBIM2025 is about to start, Bonsai presents 4 works this year in Nantes seqbim.cnrs.fr/seqbim-2025/...
seqbim.cnrs.fr
November 24, 2025 at 9:10 AM
#SEQBIM2025 is about to start, Bonsai presents 4 works this year in Nantes seqbim.cnrs.fr/seqbim-2025/...
Reposted by Bonsai Sequence Bioinformatics
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...
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.
www.nature.com
October 9, 2025 at 3:00 PM
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...
www.nature.com/articles/d41...
Reposted by Bonsai Sequence Bioinformatics
Yohan Hernandez-Courbevoie chaired by Maxime Crochemore just before presenting REINDEER2 at #SPIRE2025 in London
September 9, 2025 at 10:06 AM
Yohan Hernandez-Courbevoie chaired by Maxime Crochemore just before presenting REINDEER2 at #SPIRE2025 in London
Reposted by Bonsai Sequence Bioinformatics
Achievement unlocked: defend your habilitation thesis on the same day than your partner. That was quite a science + celebration day, thanks to all involved 💙✨
September 5, 2025 at 4:51 PM
Achievement unlocked: defend your habilitation thesis on the same day than your partner. That was quite a science + celebration day, thanks to all involved 💙✨
🍾🍾
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!
Congrats for the amazing work!
It's a great chance for the team to have you both!
September 8, 2025 at 9:57 AM
🍾🍾
Reposted by Bonsai Sequence Bioinformatics
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!
Congrats for the amazing work!
It's a great chance for the team to have you both!
September 4, 2025 at 4:40 PM
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!
Congrats for the amazing work!
It's a great chance for the team to have you both!
Reposted by Bonsai Sequence Bioinformatics
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
July 21, 2025 at 10:00 AM
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,
July 21, 2025 at 8:11 AM
Two talks for Bonsai this Thursday, one from @mikael-salson.univ-lille.fr during ISMB presenting a compressed representation for viral MSAs,
Reposted by Bonsai Sequence Bioinformatics
🖥️🧬: 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
July 15, 2025 at 2:52 PM
🖥️🧬: The ISMB 2025 proceedings are out! I’m looking forward to seeing many presentations on this work next week :). academic.oup.com/bioinformati...
Reposted by Bonsai Sequence Bioinformatics
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 !
Many thanks to the organizers for this amazing conference !
July 15, 2025 at 11:51 AM
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 !
Many thanks to the organizers for this amazing conference !
Reposted by Bonsai Sequence Bioinformatics
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
July 11, 2025 at 1:26 PM
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 🎊
Super proud that @bdegardins.bsky.social and Fiona Hak earned a Mini-symposium prize for the presentation and poster award at #JOBIM2025 🎉🏆
July 11, 2025 at 1:35 PM
Congrats to both and to other award winners 🎊
Reposted by Bonsai Sequence Bioinformatics
#JOBIM2025 glad to have Jana Ebler as keynote speaker in our mini symposium on graphs for pangenomics
July 10, 2025 at 1:19 PM
#JOBIM2025 glad to have Jana Ebler as keynote speaker in our mini symposium on graphs for pangenomics
Reposted by Bonsai Sequence Bioinformatics
#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
July 10, 2025 at 9:34 AM
#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
Reposted by Bonsai Sequence Bioinformatics
#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
July 10, 2025 at 8:44 AM
#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
July 9, 2025 at 12:10 PM
Bonsai delegation enjoying #JOBIM2025 🌴and Bordeaux's weather
Reposted by Bonsai Sequence Bioinformatics
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
July 8, 2025 at 12:18 PM
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 👇🏻
July 8, 2025 at 12:28 PM
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.
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!
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!
OReO: optimizing read order for practical compression
AbstractMotivation. Recent advances in high-throughput and third-generation sequencing technologies have created significant challenges in storing and mana
academic.oup.com
July 3, 2025 at 3:29 PM
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.
Reposted by Bonsai Sequence Bioinformatics
Ouverture des candidatures au Prix de thèse Gilles Kahn décerné par la Société informatique de France
www.socinfo.fr/recherche/pr...
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…
www.socinfo.fr
July 3, 2025 at 7:15 AM
Ouverture des candidatures au Prix de thèse Gilles Kahn décerné par la Société informatique de France
www.socinfo.fr/recherche/pr...
www.socinfo.fr/recherche/pr...
Bonsai goes camping by the shore ☀️
July 3, 2025 at 8:40 AM
Bonsai goes camping by the shore ☀️
Reposted by Bonsai Sequence Bioinformatics
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/...
July 2, 2025 at 11:48 AM
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
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...
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...
Data structures based on k-mers for querying large collections of sequencing data sets
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
genome.cshlp.org
July 2, 2025 at 1:38 PM
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.
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 👀
June 30, 2025 at 4:38 PM
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.
Reposted by Bonsai Sequence Bioinformatics
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.
Here Yohan presents REINDEER2.
June 26, 2025 at 3:26 PM
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.
Here Yohan presents REINDEER2.