BaudeauT

PhD Student in the bonsai team in the CRIStAL lab. Work on read mapping and rna structure probing.

[Michael Bertram @MichaelGBertram]

The first many-analysts study in ecology is finally published! 🥳🙌

300+ coauthors and 5+ years, this was a massive effort by @Elliot_Gould_ @HannahSFraser @TimParker88 and co.

Open access 👉 https://t.co/aA8QFN3bDs

[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)

[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

[kez cleal @kezcleal]

So happy to see this out today - our ultra-fast genome browser GW v1.0 #Genomics 🚀 https://t.co/GBcXHHetTR

[Bonsai Bioinformatics @Bonsai_Bioinfo]

New preprint by Léa Vandamme, Bastien Cazaux and Antoine Limasset

[Bonsai Bioinformatics @Bonsai_Bioinfo]

Mikaël Salson @m_salson obtained his HDR yesterday, with a defense entitled Méthodes sans alignement et indexation
pour l'analyse de données nucléiques massive (alignment free methods for massive nucleic sequences analysis).

[Mao-Jan Lin @MaoJanLin]

Recent alignment methods aim to reduce reference bias, where reads with non-ref alleles fail to align correctly. However, there's a lack of methods for analyzing reference bias. Here we present biastools, which measures and categorizes reference bias. 1/
https://t.co/Xcp1AoKkob

[Kristoffer Sahlin @krsahlin]

Alex's paper on isONform is now out and will be presented at the iRNA COSI at #ISMB23. Come talk to him :)

[bioRxiv Bioinfo @biorxiv_bioinfo]

Seq-InSite: sequence supersedes structure for protein interaction site prediction https://t.co/cibis5T30q #biorxiv_bioinfo

[Misha Kolmogorov @MishaKolmogorov]

A remaining hurdle for long-read sequencing is scalability and cost. Here, we developed a single flowcell ONT protocol + push-button pipeline that generates state-of-the-art small and structural variant calls and scales to 1000s of genomes: https://t.co/SNCQkvoKlY

[antisense. @razoralign]

Igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV) https://t.co/ed141Z2JBi

[bioRxiv Bioinfo @biorxiv_bioinfo]

mapquik: Efficient low-divergence mapping of long reads in minimizer space https://t.co/kvBD344a8P #biorxiv_bioinfo

[Mikаël Sаlson @m_salson]

Wonderful #Seqbim2022 in Bordeaux, thanks to the organizers!
By the way, did I mention that Lille will host the GDR BIM days in November 2023, that will be joint with #Seqbim23 ?

[BaudeauT @t_baudeau]

Nice talk @LeaVandamme7 !
Very promising results !

[BaudeauT @t_baudeau]

It's now @LeaVandamme7 turns. She will talk about Kmer2Reads her work in collaboration with @BQPMalfoy and Bastien Cazaux
#SeqBIM2022

[BaudeauT @t_baudeau]

It was a great talk ! Congratulations @TimotheRouze

[BaudeauT @t_baudeau]

@TimotheRouze will talk about Supersampler his work in collaboration with @CamilleMrcht and @BQPMalfoy
#SeqBIM2022

[Mushtaq Bilal, PhD @MushtaqBilalPhD]

Recently, I wrote a bunch of Zotero tutorials that went (mildly) viral on #AcademicTwitter.

Thought I'd put them all together so folks can find them easily.

So, here goes 👇

Zotero 101: A meta-thread 🧵

Retweet to share it with your friends/colleagues.

[Pesho Ivanov 🇺🇦 @peshotrie]

@curious_coding and I extended the seed heuristic to exact alignment of long (Mbps) erroneous (≤15%) sequences.

The empyrical near-linear runtime makes our aligner A*PA 250x faster than Edlib and WFA on synthetic data, and looks promising on human data.

https://t.co/YmqdAOml32

[bioRxiv Bioinfo @biorxiv_bioinfo]

Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment https://t.co/xW9AkuSSoH #biorxiv_bioinfo