Bonsai Bioinformatics

We are a bioinformatics research group affiliated with the @UMR_CRIStAL, @univ_lille, @cnrs, based in Lille, France. Tweets in EN/FR.

[Bonsai Bioinformatics @Bonsai_Bioinfo]

We have a new website! Visit us 👉🏻 https://t.co/K6IqFULXd0

[Malfoy @BQPMalfoy]

I am super excited to share our latest preprint with @yhhshby, @IgorMartayan, and Lucas Robidou on k-mer representations, introducing Hyperkmer and a novel k-mer counter, KFC!

https://t.co/OS8kmnrKJK

🧵 A thread:

[Giulio Ermanno Pibiri @giulio_pibiri]

The next symposium of experimental algorithms (SEA'25) is going to be in Venice 😎 Amazing invited speakers: Sebastiano Vigna, Daniel Lemire, and Giulia Bernardini! + workshop on compressed self-indexes, featuring Roberto Grossi and Giovanni Manzini!
https://t.co/PkmRuMOgqE

[Bonsai Bioinformatics @Bonsai_Bioinfo]

Congratulations Dr. Marchand 💐very well done. The whole team wishes you all the best.

[Bonsai Bioinformatics @Bonsai_Bioinfo]

Lilian Marchand, student in Bonsai, will defend his PhD this afternoon, on methods for precise gene-level RNA isoform reconstruction with long reads (Méthodes pour la reconstruction du répertoire des transcrits d’un gène à partir de données RNA-seq de 3ème génération)

[Bonsai Bioinformatics @Bonsai_Bioinfo]

C'est parti!

[Kristoffer Sahlin @krsahlin]

Our study on methods to detect subgenomic RNAs (sgRNA) is now out. This is work from Thomas Baudeau (from @CamilleMrcht and @m_salson Mikaël Salson's groups), who visited my group last summer. https://t.co/7cd9XQXThh 1/5

[MIGGS @MIGGS_workshop]

The registration form for attending the MIGGS symposium is now open at the following link:

https://t.co/S7ueONGS9O

Thank you to all the authors for their contributions, which have helped us create this great program.

[Igor Martayan 🦋 @IgorMartayan]

I'll be presenting our work on CBL at #ISMB2024 tomorrow at 2:20pm. In the meantime, I'd like to share the slides of my talk: https://t.co/F3APH1cN1M
See you there!

[Bonsai Bioinformatics @Bonsai_Bioinfo]

On Sunday 07/14 @IgorMartayan will present his work #ISMB2024: CBL an exact dynamic representation of k-mer sets ⭐

[Camille Marchet @[email protected] @CamilleMrcht]

The de Bruijn graph, beyond assembly, allows us to index raw reads and scale to larger genome numbers. We have quite a rich and diverse literature to index k-mers sets and collections of set (here with highlighted partitions of our group in Lille and students)

[Igor Martayan 🦋 @IgorMartayan]

Quick announcement: the minimizer-iter crate is now part of the rust-seq org!
This new release provides canonical minimizers, to ensure that a sequence and its reverse complement will always select the same minimizers.
https://t.co/I0bdKuyj4u

[Bonsai Bioinformatics @Bonsai_Bioinfo]

"PAMPA: Protein Analysis by Mass Spectrometry for Ancient Species"

[Bonsai Bioinformatics @Bonsai_Bioinfo]

#JOBIM2024 Want to reckognize fossil taxa based on ancient proteins?
Meet Yohan and Karl at the paleoproteomics corner! They will present their posters:

[Bonsai Bioinformatics @Bonsai_Bioinfo]

"Reconstruction of protein sequences for taxonomic recognition of fossil taxa"

[INRAE MaIAGE @INRAE_MaIAGE]

@GUILLAUMEGAUTRE is waiting for you at poster 256 at @jobim2024 (Wednesday, June 26, from 11:30 to 12:30 a.m.) to talk about « A workshop on Methods for Interfacing with Graphs of Genomic Sequences ».
@MIGGS_workshop @ThomasDerrien7 @CamilleMrcht #JOBIM2024

[bioRxiv Bioinfo @biorxiv_bioinfo]

Constrained enumeration of k-mers from a collection of references with metadata https://t.co/mqYFL4CRB0 #biorxiv_bioinfo

[Zamin Iqbal @ZaminIqbal]

This year Genome Informatics will be in Hinxton, with sessions on Pangenomes, Genome assembly, Microbial/Metagenomes, Single Cell and Functional Genomics, with keynotes from Fabian Theis and @CamilleMrcht . Send us your abstracts (deadline 10 Sept), and join us!

[Bonsai Bioinformatics @Bonsai_Bioinfo]

🌿 Looking to work with Bonsai ? (sequence indexing, paleogenomics, transcriptomics, spaced seeds,... members include @BQPMalfoy @m_salson @CamilleMrcht) Contact us to apply to an international chair complete with a package and 8 weeks/year in France for 4 years! Please RT

[Bonsai Bioinformatics @Bonsai_Bioinfo]

https://t.co/8bJ8YhlNXu

[Malfoy @BQPMalfoy]

Our latest preprint is out!
TLDR:
We propose a novel model, the Tinted de Bruijn graph that associate to each kmer all the reads that contains it
We developed the K2R index that scale nicely on high coverage human datasets
(1/n)
https://t.co/35F22nWAHV

[Bonsai Bioinformatics @Bonsai_Bioinfo]

@TimotheRouze @IgorMartayan Caleb Smith and Léa Vandamme present their works at DSB this year (two preprints and one incoming)

[Eric Rivals @EricRivals]

Happy to share the
final schedule of DSB 2024
online at
https://t.co/R8GHPXxPCc
please check it out and feel free to distribute!
@CNRS @CNRSInformatics @umontpellier @lirmm_

[Bonsai Bioinformatics @Bonsai_Bioinfo]

https://t.co/c9seL054VE