iiinova — where your digital self keeps evolving

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Zamin Iqbal @zaminiqbal.bsky.social · 02/09/2026

Crazy/incredible "Here we show that bacterial ribosomes can synthesize proteins encoded within their own RNA. We engineered a chimeric messenger–ribosomal RNA (mrRNA) by appending a protein-coding sequence to 16S rRNA. " www.nature.com/articles/s41...

nature.com

Rewiring the ribosome to translate proteins encoded in its own RNA - Nature

Bacterial ribosomes can synthesize proteins encoded within their own RNA.

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Paul Gardner @ppgardne.bsky.social · 15/07/2026

1/8 Systematic reviews and meta-analyses are at the top of the evidence hierarchy. They influence clinical practice, policy and future research. So I was surprised to find a series of 12 reviews with remarkably similar PRISMA literature-search figures.

Evidence pyramid from: https://commons.wikimedia.org/wiki/File:Research_design_and_evidence_-_Capho.svg

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dgautheret.bsky.social @dgautheret.bsky.social · 22/07/2026

Too bad we don't have this call in Europe

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Yann Duroc @durocyann.bsky.social · 12/07/2026

Toujours d’actualité avec des réactions dithyrambiques du moment

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Camille Marchet ⚡ @camillemrcht.bsky.social · 11/07/2026

No Transipedia mention here, I feel a bit 😐

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Camille Marchet ⚡ @camillemrcht.bsky.social · 11/07/2026

I think I get why from how Table 3 is constructed. Anyway cool work that was missing from the literature I think.

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dgautheret.bsky.social @dgautheret.bsky.social · 09/07/2026

"we introduce the π-compression: a column reordering that groups similar samples together by solving the Traveling Salesman Problem via a nearest-neighbor heuristic." I'm clueless but I like it anyway!

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dgautheret.bsky.social @dgautheret.bsky.social · 09/07/2026

I just find out the number of protein coding transcripts in Gencode has exploded from 65,000 in V45 to 278,000 in Gencode V50! This makes a huge difference. I guess this is due to their new CDS annotation of long reads, see 👇

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 08/07/2026

Might be useful. Here is a short blog entry describing a tool that annotates a PDF using a text file. I couldn't find anything that simply does this single task, so I created this. Blog post: pierrepeterlongo.github.io Git repo: github.com/pierrepeterl...

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Rob Patro @robp.bsky.social · 02/07/2026

Continuing the stream of new features following the salmon rust re-write (i.e. salmon 2), v2.3.0 has landed with a feature I've long wanted: you can now provide salmon with a genome BAM file (i.e. spliced alignments to the genome; still name collated though)! github.com/COMBINE-lab/... 1/2

github.com

Release v2.3.0 · COMBINE-lab/salmon

salmon 2.3.0 adds genome-alignment quantification, a deterministic alignment mode, and a dependency-graph cleanup. It is fully backward compatible with 2.2.x (CLI, index, and output formats unchang...

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 11/06/2026

Happy to see that K2Rmini was recommended today by PCI Mathematical & Computational Biology. "quickly evaluate whether an arbitrary sequence has a number of k-mer [of interest] matches above or below a threshold." by @imartayan.bsky.social and colleagues: www.biorxiv.org/content/10.1...

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 03/06/2026

🌎 🧬 🖥️ logan-search.org the tool to query all SRA sequences (Dec 2023 snapshot) — just got major updates. Here's what's new. 🧵 1/12

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Lincoln Michel @thelincoln.bsky.social · 03/06/2026

Ted Chiang on AI: www.theatlantic.com/philosophy/2...

Being open to the possibility that LLMs are conscious is the same as being open to the possibility that Microsoft Word is conscious, or, more precisely, that multiple distinct consciousnesses are dormant in every Word document containing a conversational transcript, and that they are awakened every time the document is loaded. Should you consider the possibility that every time you open a Word document you are bringing multiple conscious interlocutors into existence, and every time you close one you snuff their existence out? No. Contemplating that scenario is not a good use of your time. Even if the Microsoft Office team employed a philosopher who said you shouldn’t be so certain, because consciousness is not well understood, that would not be sufficient reason for you to take this idea seriously. We don’t need to fully understand the nature of consciousness to definitively say that certain things are not conscious, and conversational transcripts fall in that category.

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Zamin Iqbal @zaminiqbal.bsky.social · 25/05/2026

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...

npr.org

Researchers say the Trump administration is finding new ways to punish science

Even with federal grants largely restored, scientists say the Trump administration is still preventing those funds from reaching them. The consequences, they say, are already becoming clear.

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 15/05/2026

Testing the mutation accumulation hypothesis in aging with AlphaGenome www.biorxiv.org/content/10.64898/20…

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dgautheret.bsky.social @dgautheret.bsky.social · 05/05/2026

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

academic.oup.com

Metappuccino: Large Language Model-driven Reconstruction of Sequence Read Archive Metadata for Cancer Research

AbstractMotivation. High-throughput RNA-sequencing has significantly advanced transcriptomic profiling in oncology. Millions of RNA-seq datasets have accum

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dgautheret.bsky.social @dgautheret.bsky.social · 13/04/2026

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

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Yann Duroc @durocyann.bsky.social · 30/03/2026

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

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Ombeline Rossier @ombelinerossier.bsky.social · 27/03/2026

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

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Yann Duroc @durocyann.bsky.social · 26/03/2026

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

Les NGT vont contaminer toutes les cultures
La reglementation n'est pas scientifique
Ce n'est pas naturel
Les NGT ont été inventées pour ne ps dire OGM
On ne peut pas tracer les mutations secondaires
Kokopelli
IL n'y a aucune traçabilité
On n'a pas assez de recul sur les transgéniques alors sur les NGT ?
Ajouter des modifications aux effets inconnus c'est irresponsable
Les mutations hors cible sont un desastre
Crispr n'est ni précis ni infaillible
Les protocoles toxicologiques sur des rats pendant 90 jours sont insuffisants

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Yann Duroc @durocyann.bsky.social · 20/03/2026

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

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Páll Melsted @pmelsted.bsky.social · 06/03/2026

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

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Bastien Degardins @bdegardins.bsky.social · 20/02/2026

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).

Presentation of scientific work on De Bruijn Graphs applied to the processing of sequencing data in the context of biology. The picture was taken in the conference room of the University of Venice, where a screen displays a slide that introduces De Bruijn Graphs, with the speaker standing in front of it. Being the screen is a large renaissance painting that spans from the floor to the roof.

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Ragnar {Groot Koerkamp} @curiouscoding.nl · 04/02/2026

More minimizer papers! 😆

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Rob Patro @robp.bsky.social · 01/11/2025

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...

biorxiv.org

Metappuccino: Large Language Model-driven Reconstruction of Sequence Read Archive Metadata for Cancer Research

Motivation: High-throughput RNA-sequencing has significantly advanced transcriptomic profiling in oncology. Millions of RNA-seq datasets have accumulated in public databases such as the Sequence Read ...

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Thomas Blein @bleinthomas.bsky.social · 22/10/2025

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

PostDoc position in bioinformatics and artificial intelligence. PDF available upon request.

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Stephen Turner @stephenturner.us · 22/10/2025

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

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Ben Langmead @benlangmead.bsky.social · 14/10/2025

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/....

Illustration of Burrows-Wheeler Transform and many auxiliary structures from the input string how$now$brown$cow$#

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dgautheret.bsky.social @dgautheret.bsky.social · 01/10/2025

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...

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Aude Bernheim @audeber.bsky.social · 24/07/2025

🦠🧍‍♀️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/...

science.org

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Institut Pasteur | 130 years of biomedical research @pasteur.fr · 24/07/2025

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

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Antoine Limasset @npmalfoy.bsky.social · 05/07/2025

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...

academic.oup.com

K2R: Tinted de Bruijn graphs implementation for efficient read extraction from sequencing datasets

AbstractSummary. Biological sequence analysis often relies on reference genomes, but producing accurate assemblies remains a challenge. As a result, de nov

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UCSC Genome Browser @genomebrowser.bsky.social · 16/07/2025

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...

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Camille Marchet ⚡ @camillemrcht.bsky.social · 10/07/2025

#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

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Camille Marchet ⚡ @camillemrcht.bsky.social · 10/07/2025

#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

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Antoine Limasset @npmalfoy.bsky.social · 03/07/2025

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!

academic.oup.com

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

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Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · 02/07/2025

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

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dgautheret.bsky.social @dgautheret.bsky.social · 17/06/2025

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

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Camille Marchet ⚡ @camillemrcht.bsky.social · 11/06/2025

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. 👇🏻👇🏻

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Camille Marchet ⚡ @camillemrcht.bsky.social · 14/05/2025

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

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Noam Teyssier @noamteyssier.bsky.social · 09/05/2025

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.

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