1/8 🛠️ Introducing logan_blaster — a command-line tool to locally align your sequences against Logan contigs or unitigs. github.com/pierrepeterlongo/logan_blaster

This is awful to hear, describing how Sean Eddy (HMMER, infernal, pfam, rfam) has been defunded. The letter said his work "had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated," www.npr.org/2026/05/21/n...

Testing the mutation accumulation hypothesis in aging with AlphaGenome https://www.biorxiv.org/content/10.64898/2026.05.10.724136v1

The Metappuccino paper is out in Bioinformatics! academic.oup.com/bioinformati... Given an input list of SRA sample IDs, Metappuccino infers and normalizes metadata over 15 categories, specially aimed at human transcriptomics studies 1/3

Impressive. That opens a new path to ncRNA functional classification.

La tribune du Monde était donc une opération de Pollinis (Tousse) « Parce que bien cuisiner commence par bien choisir » … il n’existe aucune preuve de différence intrinsèque gustatives entre variétés conventionnelles ou ogm mais on écrit ça tranquille

Happy to present the latest Corynephage discovered and characterized by Bachelor students at University Paris-Saclay @univparissaclay.bsky.social

cet article est un exemple chimiquement pur du bingo anti biotechnologies pathétique

comme attendu cette émission n'aura pas permis une juste information du public sur le sujet des NGT ! un fil de débunk (avec toutes les ressources à la fin) 🧵⬇️ 1/35

Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data. The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k... Figure 1 shows they key result

I had the occasion of presenting nice results about the detection of biological events in De Bruijn Graph at #DSB2026, in the context of my PhD work on #Vizitig ! Thanks to the organizers and colleagues for this amazing and super-inspiring event (and @camillemrcht.bsky.social for the picture).

👇 😨

PREPRINT ALERT I heard you craving for more combinatorics, here are some more for y'all !

More minimizer papers! 😆

www.biorxiv.org/cgi/content/... What’s behind Metapuccino? ☕️, by PhD student Fiona Hak, @camillemrcht.bsky.social and Melina Gallopin. A thread 👇

My algorithmic friends (@camillemrcht.bsky.social) doing LLM stuff : www.biorxiv.org/content/10.1...! And also, screaming last names in the author list ;P. Given my level of trust in Camille, though, perhaps it's time for me to engage more seriously with these models in research...

Interested in #lncRNA and #ArtificiaIntelligence? In the frame of our recently founded French-Korean bilateral project DHARP, we are recruiting a post-doc in bioinformatics and artificial intelligence in our team at @ips2parissaclay.bsky.social Application limit: 01/12/2025

PubMed is running on autopilot during shutdown, but key independent committee has been abolished www.bmj.com/content/391/... 🧪

New tool "bwt-svg" for making illustrations of the BWT and the many auxiliary arrays and other structures related to it. Pyodide-based no-installation-necessary interface here: benlangmead.github.io/bwt-svg/. (H/t to @robert.bio for pointing me to pyodide!) Full repo: github.com/benlangmead/....

The MSc. Bioinformatics students of U. Paris-Saclay are organizing the Junior Conference on Computational Biology (JC2B) 2025: AI and predictive models in bioinformatics November 13, 2025 - I2BC, CNRS, Gif-sur-Yvette, France Register for free : bioi2.i2bc.paris-saclay.fr/jc2b/#regist...

🦠🧍‍♀️From bacterial to human immunity. We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity. Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social www.science.org/doi/10.1126/...

Congratulations to Rayan Chiki, (Institut Pasteur) head of the “Sequence Bioinformatics” unit, for securing the ERC Proof of Concept 2025 for his project ENZYMINER! 👏 ‪@rayan.chiki.bsky.social #Bioinformatics

Ca a l'air bien, non? www.nature.com/articles/d41...

Paper Alert! Our preprint on the K2R index, being able to efficiently associate kmers to the reads containing them is finally out there! A thread! academic.oup.com/bioinformati...

New ENCODE4 long-read RNA-seq transcripts track for hg38 and mm10. Triplets (e.g. [1,1,3]) indicate start site, exon combination, and stop site for each transcript. Enrichment scores show how these change across tissue and cell line samples. Read more: genome.ucsc.edu/gold...

#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

#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

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!

Preprint alert from the group 🚨 super fast grep-like sequence selection

What a thread!

Now indexing 10k RNA-seq samples with accurate counts!

Hey yeast lovers. Do you like pangenomes? O'Donnel et al. 2023 produced T2T assemblies of different strains, including phased haplotypes for yeast. Here I selected 10 phased haplotypes and the S288C reference, and looked for the MST28 / YAR033W gene reported to contain SVs such as indels. 👇🏻👇🏻

A great and non technical, yet super relevant piece on implications of this scam

Just merged in an awesome new feature for xsra to support named pipes with @robp.bsky.social. This lets you skip an intermediary write step and go straight from SRA to downstream tools. It works with accessions that are both on- or off-disk.

gtexr: R interface to the GTEx Portal API docs.ropensci.org/gtexr/ #rstats

J'ai rarement vu une désinformation d'une telle ampleur, de la part d'un journal soi-disant sérieux, faisant dire à une expertise de l'Anses à peu près l'inverse de ce qu'elle dit vraiment... C'est fou. Même si c'est désormais récurrent. On reprend tout ? 🧵

This is so destructive and idiotic. mRNA vaccines are one of the most exciting opportunities to tackle diseases - from infectious disease to cancer and beyond - and these morons want to shut it down.

correct RNAhub webserver address rnahub.org

Bioinfo PhDs from abroad and french PhDs willing to return: There is still time to apply and be part of this super innovative project on cancer transcriptomics.

Remember, EuropePMC is actually better than #PubMed because it includes ALL preprints in search results, not just those including NIH-funded research. europepmc.org

Turning realms of "data" into a rectangular table is a most noble activity.

RNA xkcd.com/3056

One of the cooler things I saw at the Nextflow summit a few months ago. Can't wait to try this.

This comes up frequently. bioRxiv has a no reviews/hypotheses/commentary policy. The rationale is signal:noise and a focus on being a venue for new research not discussion of existing work (for which there are excellent other venues e.g. PubPeer). 1/n

Dear young investigator in cancer bioinformatics: check our postdoc position on reference-free, organ agnostic transcriptome signatures of cancer at I2BC, Gif sur Yvette. emploi.cnrs.fr/Offres/CDD/U...

@yannponty.bsky.social Good move!

This is just a fantastic ressource. It finds _any_ sequence in the whole SRA. That's 5 orders or magnitudes larger than NR/Genbank.

There are many papers about "predicting" lncRNAs from RNA-seq data. But I'm wondering: who ever needs to predict lncRNA? (1/3)

I am happy to see that both papers have been published. Pymportx is Python port of Tximport #bioinformatics academic.oup.com/nargab/artic...