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...