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Camille Marchet ⚡ @camillemrcht.bsky.social · 29d

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

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Reposted by Bonsai Sequence Bioinformatics

Camille Marchet ⚡ @camillemrcht.bsky.social · Sep 5

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 · Sep 8

🍾🍾

Mikaël Salson @mikael-salson.univ-lille.fr · Sep 4

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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Reposted by Bonsai Sequence Bioinformatics

Mikaël Salson @mikael-salson.univ-lille.fr · Sep 4

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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Reposted by Bonsai Sequence Bioinformatics

Igor Martayan @imartayan.bsky.social · Jul 21

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 · Jul 21

And one from @imartayan.bsky.social and @curiouscoding.nl at SEA in Venice on simd computation of minimizers

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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · Jul 21

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 · Jul 15

🖥️🧬: 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

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Reposted by Bonsai Sequence Bioinformatics

Bastien Degardins @bdegardins.bsky.social · Jul 15

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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Reposted by Bonsai Sequence Bioinformatics

Camille Marchet ⚡ @camillemrcht.bsky.social · Jul 11

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 · Jul 11

Congrats to both and to other award winners 🎊

Camille Marchet ⚡ @camillemrcht.bsky.social · Jul 11

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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Camille Marchet ⚡ @camillemrcht.bsky.social · Jul 10

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

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Reposted by Bonsai Sequence Bioinformatics

Camille Marchet ⚡ @camillemrcht.bsky.social · Jul 10

#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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Reposted by Bonsai Sequence Bioinformatics

Camille Marchet ⚡ @camillemrcht.bsky.social · Jul 10

#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 · Jul 9

Bonsai delegation enjoying #JOBIM2025 🌴and Bordeaux's weather

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Camille Marchet ⚡ @camillemrcht.bsky.social · Jul 8

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 · Jul 8

On day 3, afternoon
Bonsai co-organises the Mini-symposium: Methods for Interfacing with Graphs of Genomic Sequences: novel pangenome

With two flash talks by @imartayan.bsky.social and @bdegardins.bsky.social

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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · Jul 8

11:10 – 11:30 OReO: Optimizing Read Order for practical compression by Mathilde Girard

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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · Jul 8

10:50 – 11:10 Reindeer2: practical abundance index at scale by Yohan Hernandez Courbevoie

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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · Jul 8

On day 3, morning in Amphi D

10:30 – 10:50 Vizitig: context-rich exploration of sequencing datasets by @bdegardins.bsky.social

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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · Jul 8

On day 2, posters :

122 Large Language Models-driven Reconstruction of Sequence Read Archive Metadata for Cancer Research by Fiona Hak

120 Bridging gene-level and sequence-level pangenome graph to explore microbial diversity by Hanin Ali

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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · Jul 8

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

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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · Jul 3

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 · Jul 3

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!

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

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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · Jul 3

Cyanotype workshop with the beach wrack to end our stay 🦀

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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · Jul 3

Visit of the marine station AND simd tutorial by @imartayan.bsky.social, pretty much sums up how wide bioinformatics can be

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