Reposted by @dgautheret.bsky.socialZamin Iqbal @zaminiqbal.bsky.social · 02/09/2026Crazy/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.comRewiring the ribosome to translate proteins encoded in its own RNA - NatureBacterial ribosomes can synthesize proteins encoded within their own RNA. 1186
dgautheret.bsky.social @dgautheret.bsky.social · 30/08/2026I love sshash and a stranded query mode was much needed for RNA-seq. Thanks a lot for the update. 140
Reposted by @dgautheret.bsky.socialPaul Gardner @ppgardne.bsky.social · 15/07/20261/8 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. 2196
dgautheret.bsky.social @dgautheret.bsky.social · 25/07/2026Ce n'est pas très responsable de faire de tels appels quand on a près de 10,000 abonnés, dont surement des personnes influençables. Pourquoi vous ne foutez pas le feu vous même? 000
dgautheret.bsky.social @dgautheret.bsky.social · 22/07/2026Too bad we don't have this call in Europe 000
Reposted by @dgautheret.bsky.socialYann Duroc @durocyann.bsky.social · 12/07/2026Toujours d’actualité avec des réactions dithyrambiques du moment 173
Reposted by @dgautheret.bsky.socialCamille Marchet ⚡ @camillemrcht.bsky.social · 11/07/2026No Transipedia mention here, I feel a bit 😐 101
Reposted by @dgautheret.bsky.socialCamille Marchet ⚡ @camillemrcht.bsky.social · 11/07/2026I think I get why from how Table 3 is constructed. Anyway cool work that was missing from the literature I think. 001
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! 010
dgautheret.bsky.social @dgautheret.bsky.social · 09/07/2026I 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 👇 021
Reposted by @dgautheret.bsky.socialPierre Peterlongo @pierrepeterlongo.bsky.social · 08/07/2026Might 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... 062
Reposted by @dgautheret.bsky.socialRob Patro @robp.bsky.social · 02/07/2026Continuing 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/... 1/2github.comRelease v2.3.0 · COMBINE-lab/salmonsalmon 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... 2157
Reposted by @dgautheret.bsky.socialStephen Turner @stephenturner.us · 30/06/2026I took Claude Science for a test drive today blog.stephenturner.us/p/test-drivi...blog.stephenturner.usTest Driving Claude ScienceAnthropic released Claude Science today. I tried it out for an AIxBio literature review and for an analysis using the IUCN Red List API with R. 4288
Reposted by @dgautheret.bsky.socialPierre Peterlongo @pierrepeterlongo.bsky.social · 11/06/2026Happy 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... 074
Reposted by @dgautheret.bsky.socialPierre 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 13626
Reposted by @dgautheret.bsky.socialLincoln Michel @thelincoln.bsky.social · 03/06/2026Ted Chiang on AI: www.theatlantic.com/philosophy/2... 3336391069
Reposted by @dgautheret.bsky.socialPierre Peterlongo @pierrepeterlongo.bsky.social · 29/05/20261/8 🛠️ Introducing logan_blaster — a command-line tool to locally align your sequences against Logan contigs or unitigs. github.com/pierrepeterlongo/logan_blastergithub.comGitHub - pierrepeterlongo/logan_blaster: Given either a kmviz id (obtained from a Logan-Search query) or a query (fasta sequence), and a file containing a list of SRA accessions (provided or not by Lo...Given either a kmviz id (obtained from a Logan-Search query) or a query (fasta sequence), and a file containing a list of SRA accessions (provided or not by Logan-Search results) run a local blast ... 184
Reposted by @dgautheret.bsky.socialZamin Iqbal @zaminiqbal.bsky.social · 25/05/2026This 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.orgResearchers say the Trump administration is finding new ways to punish scienceEven 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. 7144112
Reposted by @dgautheret.bsky.socialbioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 15/05/2026Testing the mutation accumulation hypothesis in aging with AlphaGenome www.biorxiv.org/content/10.64898/20… 011
dgautheret.bsky.social @dgautheret.bsky.social · 05/05/2026Install metappuccino from here: github.com/chumphati/Me... Follow us for the complete annotation of 1 million human SRA samples. (Soon available) 3/3github.comGitHub - chumphati/Metappuccino: Automates metadata extraction and completion based on LLMs.Automates metadata extraction and completion based on LLMs. - chumphati/Metappuccino 000
dgautheret.bsky.social @dgautheret.bsky.social · 05/05/2026Annotated categories: Library selection Sequencing source Biopsy site Biopsy type Cell line Cell type Organ Disease Treatment Treatment time Response Age Sex Ethnicity Is cancer 2/3 100
dgautheret.bsky.social @dgautheret.bsky.social · 05/05/2026The 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 1/3academic.oup.comMetappuccino: Large Language Model-driven Reconstruction of Sequence Read Archive Metadata for Cancer ResearchAbstractMotivation. High-throughput RNA-sequencing has significantly advanced transcriptomic profiling in oncology. Millions of RNA-seq datasets have accum 132
dgautheret.bsky.social @dgautheret.bsky.social · 13/04/2026Impressive. That opens a new path to ncRNA functional classification. 000
Reposted by @dgautheret.bsky.socialYann Duroc @durocyann.bsky.social · 30/03/2026La 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 2279
Reposted by @dgautheret.bsky.socialElena Rivas @rivaselenarivas.bsky.social · 28/03/2026www.nature.com/articles/s42...nature.comWhat does it take to learn the rules of RNA base pairing? A lot less than you may think - Communications BiologyDeep-learning models typically require large parameter spaces and extensive training data. Here the authors demonstrate that learning the fundamental biological rules of RNA base pairing can be achiev... 0123
Reposted by @dgautheret.bsky.socialOmbeline Rossier @ombelinerossier.bsky.social · 27/03/2026Happy to present the latest Corynephage discovered and characterized by Bachelor students at University Paris-Saclay @univparissaclay.bsky.social 031
Reposted by @dgautheret.bsky.socialYann Duroc @durocyann.bsky.social · 26/03/2026cet article est un exemple chimiquement pur du bingo anti biotechnologies pathétique 1115
Reposted by @dgautheret.bsky.socialYann Duroc @durocyann.bsky.social · 20/03/2026comme 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 3258
Reposted by @dgautheret.bsky.socialPáll Melsted @pmelsted.bsky.social · 06/03/2026Excited 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 618887
Reposted by @dgautheret.bsky.socialBastien Degardins @bdegardins.bsky.social · 20/02/2026I 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). 1177
dgautheret.bsky.social @dgautheret.bsky.social · 11/02/2026Pour l'importance des pesticides dans l'incidence des cancers, voyez plutot ceci. Les expositions professionnelles (amiante, benzene) sont dans la barre bleue à droite, et les pesticides n'apparaissent nulle part faute de données suffisantes. www.nature.com/articles/s41... 020
dgautheret.bsky.social @dgautheret.bsky.social · 04/02/2026Pour l'importance des facteurs de risque de cancer, voyez plutôt ceci. La petite zone bleu clair, ce sont toutes les causes professionnelles: amiante, arsenic, etc. Les pesticides n'apparaissent nulle part faute de données suffisantes. Source: Fink et al. Nature Medicine, 2026 000
Reposted by @dgautheret.bsky.socialRagnar {Groot Koerkamp} @curiouscoding.nl · 04/02/2026More minimizer papers! 😆 132
dgautheret.bsky.social @dgautheret.bsky.social · 02/11/2025Stay tuned: We are now running Metapuccino on SRA’s 1 million human transcriptomes. 021
dgautheret.bsky.social @dgautheret.bsky.social · 02/11/2025This ms. covers the full methodology and discusses the limits of NLP and LLMs for NGS metadata completion. 100
dgautheret.bsky.social @dgautheret.bsky.social · 02/11/2025Usability was a top priority: Metapuccino runs on regular computers with open-source LLMs, but can also scale up on GPUs for large datasets. All it needs is a list of SRA IDs — no pre-processed tables required. 100
dgautheret.bsky.social @dgautheret.bsky.social · 02/11/2025Fiona Hak developed a clever LLM training strategy using the hardest SRA cases — the fine-tuned model is available on Hugging Face. 100
dgautheret.bsky.social @dgautheret.bsky.social · 02/11/2025Metapuccino fills and standardizes 19 key SRA metadata fields in human transcriptomics, using rule-based NLP and a large language model (LLM). 100
dgautheret.bsky.social @dgautheret.bsky.social · 02/11/2025Even simple tasks, like selecting tumor vs. normal samples for a cancer type, require expert curation across multiple tables, protocols, and abstracts. 100
dgautheret.bsky.social @dgautheret.bsky.social · 02/11/2025NCBI’s SRA is a fantastic resource for studying the human transcriptome. But its metadata is messy — over 70% of fields are empty, and information is often inconsistent. 100
dgautheret.bsky.social @dgautheret.bsky.social · 02/11/2025www.biorxiv.org/cgi/content/... What’s behind Metapuccino? ☕️, by PhD student Fiona Hak, @camillemrcht.bsky.social and Melina Gallopin. A thread 👇biorxiv.orgMetappuccino: Large Language Model-driven Reconstruction of Sequence Read Archive Metadata for Cancer ResearchMotivation: 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 ... 252
Reposted by @dgautheret.bsky.socialRob Patro @robp.bsky.social · 01/11/2025My 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.orgMetappuccino: Large Language Model-driven Reconstruction of Sequence Read Archive Metadata for Cancer ResearchMotivation: 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 ... 152
Reposted by @dgautheret.bsky.socialThomas Blein @bleinthomas.bsky.social · 22/10/2025Interested 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 031
Reposted by @dgautheret.bsky.socialStephen Turner @stephenturner.us · 22/10/2025PubMed is running on autopilot during shutdown, but key independent committee has been abolished www.bmj.com/content/391/... 🧪 079
Reposted by @dgautheret.bsky.socialBen Langmead @benlangmead.bsky.social · 14/10/2025New 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/.... 34021
dgautheret.bsky.social @dgautheret.bsky.social · 01/10/2025The 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... 022
