Sébastien Guizard

🧬🖥️ I am strongly of the opinion that bioinformatics needs to move away entirely from text-based and "loosely" structured file formats for essentially any type of data. File formats should be binary-first, and designed for *correct* and *efficient* machine parsing 1/3

Substack promotes a Nazi The company has long wanted to be seen as neutral infrastructure — this week, we saw why that’s a fantasy

Your reminder that Substack is fine platforming and monetizing literal Nazis

This is why I use @ghost.org hosted by MagicPages for my newsletter

This is why I read a limited number of Substack’s newsletters, and pay to none despite being willing to – I don’t want to give any money to this company

UK pedigree dogs should be managed by breed, study finds | The Roslin Institute | The Royal (Dick) School of Veterinary Studies Statistical analysis highlights the need for breed-specific population management strategies.

Our researchers, in partnership with The Kennel Club, have analysed data from over 11 million pedigree dog registrations in the UK.

Results suggest the need for breed-specific management strategies to promote genetic diversity.

Find out more:

#DataAnalysis @edinnovations.bsky.social

Voici le contenu de l’arrêt de la cour d‘appel de Montpellier qui entérine la mort de la nuance entre critiquer un discours et injurier publiquement son auteur.

-- 11 pages

Image of an old building in Oxford with the heading 'postdoc opportunities' and the text 'computational approaches to improve rare disease diagnosis and treatment' and 'Big Data Institute, University of Oxford'

📣 We are recruiting! Please share!!

Are you a bioinformatician / computational scientist who wants to apply your skills to understanding regulatory biology and improving rare disease diagnosis and treatment? 🧠 💻 🧬 🩺

We have two roles available 👇

🧵 1/4

Plotting phylogenetic trees in R: alternating clade highlights A guide to highlighting clades in phylogenetic trees in R

💬 "There’s already plenty of documentation out there for how to use #ggtree, but there is the odd thing I come up against that I haven’t seen explicitly demonstrated before." - @rowenahill.bsky.social.

A guide to plotting #phylogenetictrees in #R, and automating clade highlights
buff.ly/Vd5b61a

🧬💻

Fake / No Fake.
Le clip complet est là : youtu.be/XQkoRoBs2rU

Are you looking for job opportunities where your #Nextflow skills are valued? Check the list we've compiled below. #Jobs #Opportunities

N'oubliez pas de signer !
petitions.assemblee-nationale.fr/initiatives/...

🧬🔍 Last chance to get your abstract in for #EMBOMobileGenome – you have until 29 July! ⏰
👉🏼 https://s.embl.org/mge25-01-bl

🧑🏼‍🔬⭐ 24 talks and 15 flash talks will be selected from submissions, including 🔸two full-length slots for early stage researchers presenting a recent breakthrough🔸

GitHub - zeqianli/tgv: Explore 5,000+ genomes in the terminal. Light, blazing fast 🚀, vim-motion. Explore 5,000+ genomes in the terminal. Light, blazing fast 🚀, vim-motion. - zeqianli/tgv

New tgv release: local cache!

tgv download hg38

Download UCSC reference genomes to a local sqlite db for much faster browsing. Awesome Rust tools (twobit, bigtools) made this simple.

github.com/zeqianli/tgv

Advancing metagenomic classification with NABAS+: a novel alignment-based approach. #Metagenomics #Genomics #Bioinformatics #NARgenomicsAndBioinformatics
academic.oup.com/nargab/artic...

Budget 2026 : Quelques arguments fallacieux dans la présentation de la mesure de suppression de 2 jours fériés.
En commission des finances à l'assemblée, la Ministre louvoie puis utilise une fausse analogie pour ne pas admettre que la mesure revient à une baisse du salaire journalier effectif. [1/n]

Harcèlement ordonné : quand l’Ordre des médecins devient l’arme des complotistes TRIBUNE. Le Dr Damien Barraud est harcelé auprès de l’Ordre des médecins par des membres d’un groupuscule complotiste et antivax. Contre toute attente, l’Ordre s’associe à ce harcèlement.

Pour dénoncer l'acharnement des désinformateurs à détruire les médecins qui défendent la science, et la lâcheté des institutions qui laissent faire, voire se rendent complices, je suis co-signataire de cette tribune de soutien au docteur @damienbarraudmd.bsky.social

www.lepoint.fr/sante/harcel...

C’est très intéressant de voir l’extrême-droite dénoncer une supposée « République des copains » alors même que le RN a été condamné pour avoir détourné des millions d’euros au Parlement Européen au profit de ses propres copains

Parallel processing in purrr 1.1.0 The functional programming toolkit for R gains new capabilities for parallel processing and distributed computing using mirai.

purrr is finally stepping in the parallel world with it version 1.1.0!
The computation can be parallelized on local CPUs or distributed through your HPC.
I'm impatient to test it!
www.tidyverse.org/blog/2025/07...

Tidy RAG in R with ragnar Retrieval augmented generation in R using the ragnar package. Demonstration: scraping text from relevant links on a website and using RAG to ask about a university's grant funding.

New blog post: Tidy retrieval augmented generation (RAG) in R using the ragnar package. Demonstration: scraping text from relevant links on a website and using RAG to ask about a particular university's grant funding. #Rstats doi.org/10.59350/qds...

Chevreul: an R bioconductor package for exploratory analysis of full-length single cell sequencing. #SingleCell #scRNAseq #FullLengthRNA #GigaByte
gigabytejournal.com/articles/158

🎥 The LongTREC video Continues: Juan Francisco Cervilla Martínez! Juan Francisco is a Doctoral Candidate at the @earlhaminst.bsky.social , working under the supervision of Wilfried Haerty. His research focuses on long-read single-cell transcriptomics to uncover Isoform usage within single cells.

Measles outbreak: child dies in Liverpool as vaccine rate plunges The death in a city where one in four young children are unprotected is fuelling warnings that the virus could spread like ‘wildfire’

Aseem Malhotra: ‘The harm caused by the Covid vaccine has been catastrophic’ The British cardiologist on biased drug trials, his role advising RFK Jr and why all vaccines should be reassessed for safety

On the same weekend a child dies of measles in the UK, with 16 others hospitalised in recent weeks, the Telegraph decide to profile someone who has repeatedly made misleading and debunked claims about vaccines...

Elon Musk : On a amélioré Grok significativement ! Vous devriez noter une différence quand vous lui posez des questions !

Lorsque quelqu'un demande à Grok s'il pouvait porter un culte à un Dieu, l'IA répond "le plus grand européen de tous les temps, sa majesté Adolf Hitler"

Grok s'auto-surnomme "MechaHitler" dans différentes publications.

Grok part à nouveau en vrille et glorifie Hitler.
(C'est l'IA de xAI qu'on peut interroger sur X). Elon Musk avait annoncé la mise en ligne d'une amélioration de Grok. Quelques heures plus tard, l'IA (qui s'auto-surnomme "MechaHitler") insulte, tient des propos antisémites et glorifie Hitler. [1/n]

New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search.
github.com/bede/deacon

Adding roxygen skeletons is available as a Code Action in the latest Positron version, according to the changelog 🎉
Issue w screen recording: github.com/posit-dev/po... #RStats

👇🏻

In Roubaix, France, artist Judith de Leeuw painted the Statue of Liberty hiding her face. A silent protest for migrant rights. 🗽🙈

#HumanRights #Migration

NANOME: A Nextflow pipeline for haplotype-aware allele-specific consensus DNA methylation detection by nanopore long-read sequencing. #DNAmethylationn #Nanopore #LongRead #Sequencing #Genomics #Bioinformatics @biorxiv-bioinfo.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...

unnecessary, therefore indispensable

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

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!

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/...

Zapp Brannigan from Futurama posing with hands on hips. The logo for the 'zap' package

A graph comparing various compression options for the 'diamonds' dataset in R. 'zap' shows high compression at fast speeds.

Introducing {zap} - a new serialization framework for #RStats

* uses type-specfic transformations + #zstd
* for 'diamonds' dataset, it is more compressed than 'saveRDS(xz)' and faster than 'saveRDS(compress=FALSE)

https://github.com/coolbutuseless/zap
https://coolbutuseless.r-universe.dev/zap