iiinova — where your digital self keeps evolving

Reposted by Antoine Limasset

Mark Chadbourn @chadbourn.bsky.social · 28/09/2026

US social media companies are interfering in the Brazilian elections in favour of the Far Right’s Flávio Bolsonaro. Meta is the latest. It’s just blocked the campaign account of President Lula in the final stretch of the election.

elespectador.com

Meta restringe la cuenta de Lula y su partido alerta por posible injerencia extranjera

De cara a las elecciones en Brasil, Lula enfrenta a Meta por restringir su cuenta mientras su partido alerta por posible injerencia extranjera.

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Christophe Dessimoz @dessimoz.bsky.social · 27/09/2026

ISMB is ranked A in CORE largely thanks to @yannponty.bsky.social ‘s tireless efforts. I believe ECCB could/should also be ranked A considering the scientific committee’s qualifications, acceptance rate etc. But it takes a lot of work to do the advocacy….

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froggleston @froggleston.carpentries.org · 28/09/2026

Don't tell me - the industry based on the largest wholesale theft in history... stole stuff you gave to it?

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Rob Patro @robp.bsky.social · 25/09/2026

Ok comp. bio / bioinformatics / genomics friends. Let's talk about @recombconf.bsky.social and, specifically, the way in which the "proceedings" have evolved. This seems like something that we, as a community, should address. RECOMB now has no "published" proceedings in the classic sense.

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Rob Patro @robp.bsky.social · 25/09/2026

Cuttlefish 3.0.3 is out! github.com/COMBINE-lab/... Fun little jaunt with Opus 5.5 to substantially reduce the memory requirement (especially at moderate thread counts). Now it's both non-trivially faster *and* more memory-frugal than the initial C++ implementation!

github.com

Release 3.0.3 · COMBINE-lab/cuttlefish

Release Notes Colored builds use far less memory at low and moderate thread counts. On 149,998 Salmonella assemblies at 16 threads, peak RSS falls from 22.4 GB to 8.9 GB (C++ Cuttlefish 3: 11.5 GB...

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Mat G @gienieczko.com · 25/09/2026

Trying to achieve something in C++ after having been immersed in the Rust ecosystem for the past few years is *wild*. Incredibly broken build systems, obscure linker errors from three CMakes deep, documentation snippets that don't compile, no info on which class is declared in which header...

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Wei Shen 沈伟 @shenwei356.bsky.social · 24/09/2026

SeqKit is now faster and uses 40% less memory when reading large FASTA records, such as human genomes, though it still uses more RAM than tools written in C/C++/Rust. Worth upgrading! github.com/shenwei356/s...

github.com

GitHub - shenwei356/seqkit: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation - shenwei356/seqkit

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Antoine Limasset @npmalfoy.bsky.social · 24/09/2026

Yet another example of "So much to do, so little time"

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Antoine Limasset @npmalfoy.bsky.social · 24/09/2026

This will be the "burn the Alexandria library" event of our lifetime

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Jarno N. Alanko @jnalanko.bsky.social · 21/09/2026

Exciting news regarding the SBWT rust API! We now have an implementation of the subset rank method in this preprint, written Anastasia Diseth. It takes the space down from 5 bits/kmer to 2.5 bits/kmer (double that if both strands are indexed). About 4-5 times slower. www.biorxiv.org/content/10.6...

biorxiv.org

New Space-Time Tradeoffs for Subset Rank and k-mer Lookup

Given a sequence S of subsets of symbols drawn from an alphabet of size σ , a subset rank query srank( i, c ) asks for the number of subsets before the i th subset that contain the symbol c . It was r...

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 21/09/2026

Gravlax: an annotation-independent molecular evidence archive for single-cell RNA-seq www.biorxiv.org/content/10.64898/20…

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Spyc @spycphd.eurosky.social · 21/09/2026

"self-centred men who are argumentative, stubborn, disagreeable and unempathetic are much more likely to own a high-status car such as an Audi, BMW or Mercedes."

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Nature @nature.com · 21/09/2026

Artificial-intelligence systems can generate hypotheses, design experiments and analyse data — but humans still need to decide what makes sense go.nature.com/3Vn4WUY

go.nature.com

AI co-scientists are revolutionizing how research is done

Artificial-intelligence systems can generate hypotheses, design experiments and analyse data — but humans still need to decide what makes sense.

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Rob Patro @robp.bsky.social · 21/09/2026

Explainer posts here: bsky.app/profile/robp...

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Rob Patro @robp.bsky.social · 21/09/2026

It's here! new preprint: Gravlax, an annotation-independent molecular evidence archive for scRNA-seq. A count matrix freezes one annotation. Molecules never change. Instead, gravlax keeps the evidence. Requantify, query, and discover under any annotation. 🧵 www.biorxiv.org/content/10.6...

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Rob Patro @robp.bsky.social · 21/09/2026

What excites me most about gravlax is that it breaks the dichotomy between tiny but *very limited* count matrix data that is shared and reanalyzed on a near constant basis and huge and compute intensive raw read/bam artifacts that are often too inconvenient for people to routinely reuse.

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Antoine Limasset @npmalfoy.bsky.social · 16/09/2026

My agent achieved to use my printer, ASI confirmed

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Jim Shaw @jimshaw.bsky.social · 15/09/2026

The sylph metagenome profiler is v1.0.0! sylph-docs.github.io A new DB format + approach --> huge performance gains: GTDB-R232 (200k species) now takes < 5 GB of RAM and ~30s (2GB fq.gz). Huge thanks to @benjwoodcroft.bsky.social and his ongoing performance efforts (github.com/wwood/weebill)

sylph-docs.github.io

Documentation for sylph - ultrafast, precise metagenomic profiling

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Nils Wilcke @nilswilcke.bsky.social · 13/09/2026

On est sûr que ça n'a rien à voir avec le (petit ahem) problème de financement de tout ce bazar... C'est comme construire des autoroutes sans avoir les moyens de les entretenir.

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Imani Gandy @angryblacklady.blacksky.app · 12/09/2026

The international chess Federation banned trans women from playing women's chess. CHESS. It's not about fairness. The fairness argument is intended to radicalize people into more violent forms of transphobia.

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Christopher Wheat @chriswheat.bsky.social · 11/09/2026

“we compared 5 foundation models and two other deep learning models against deliberately simple baselines for predicting transcriptome changes after single or double perturbations. None outperformed the baselines, .. highlights .. importance of critical benchmarking www.nature.com/articles/s41...

nature.com

Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines - Nature Methods

The analysis presented in this Brief Communication shows that, despite their complexity, current deep learning models do not outperform linear baselines in predicting gene perturbation effects, thus e...

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Jeremy Kun @jeremykun.com · 10/09/2026

Don't want OpenAI to steal your in-progress millennium prize proofs? Invest in homomorphic encryption today!

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Tien Chih @tienchihmath.bsky.social · 09/09/2026

What’s gonna happen if Overleaf decides they’re going to scrape user documents and starts scooping authors on in progress results?

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Trevor A. Branch @trevorabranch.bsky.social · 08/09/2026

Millennium math problem solved by OpenAI may have "regurgitated" competitors unpublished work... also they spent more than $22 million in computing power in one week to scoop them. techcrunch.com/2026/09/08/o...

techcrunch.com

OpenAI fought dirty on career-making math problem, says NYU mathematician | TechCrunch

There is a $1 million bounty for the first person providing a solution to the Navier-Stokes existence and smoothness problem.

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Ragnar {Groot Koerkamp} @curiouscoding.nl · 09/09/2026

Unfortunately, I don't think there's a need for the "really makes me think" qualifier here.

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🇵🇸Tim Henke (tɪm 'ɦɛŋ.kə) @timhenke.bsky.social · 09/09/2026

We should talk more about what a travesty the bibliography of OpenAI is 16 measly citations for a 165-page paper, of which 5 are just the problem statement. Only 7 are from this century. They failed to cite the method they used. And the guy whom they offered single-authorship & the Millennium Prize

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Michael Barany @mbarany.com · 08/09/2026

humanities academics watching the tech companies force the mathematicians to realise they were humanities academics all along

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Zach Weinersmith @zachweinersmith.bsky.social · 08/09/2026

For anyone not following the drama, there's been apparently a big development in ai math, along with some accusations of very bad behavior by OpenAI. But we don't have details yet. If I understand it, Buckmaster and Levent Alpoge made a big discovery on Navier-Stokes. Events go something like this:

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Ragnar {Groot Koerkamp} @curiouscoding.nl · 08/09/2026

Cute! So in general: x%b = (x+c*(x//b))%(b+c) (b=60, c=4)

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Mike Ensminger Fan Account @laplanck.bsky.social · 13/08/2026

First time I've seen a court issue sanctions for prompt injection in a brief. Pro se plaintiff tries prompt injection (here, white text in tiny font) because he thinks the judge will just use some LLM to read the papers and write a ruling. Judge sees through the ruse.

civilinquiry.jud.ct.gov

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Earth BioGenome Project 🌍 @ebpgenome.bsky.social · 13/08/2026

🧬 The VGP Phase I preprint is out! 🎉 The Vertebrate Genomes Project has completed Phase I, delivering 816 of the highest-quality vertebrate reference genomes ever produced. Explore this major new resource for vertebrate genomics: 📄 tinyurl.com/VGPphase1 @vertebrategenomes.bsky.social #Genomics

Graphic featuring a collage of diverse vertebrates, including a chameleon, sea turtle, frog, whale, bat, duck, axolotl, shark, echidna, salamander, bird, tropical fish, leopard, crocodile, cassowary, clownfish, Komodo dragon, snake and deep-sea fish. Text reads: “A New Milestone for Vertebrate Genomics.” The Vertebrate Genomes Project (VGP) has completed Phase I, delivering 816 high-quality reference genomes spanning 95% of vertebrate orders.

Underwater photograph of a humpback whale swimming beneath the ocean surface. Text reads: “Why Vertebrates? More than 70,000 vertebrate species inhabit our planet.” High-quality reference genomes help researchers understand evolution, biodiversity, conservation and adaptation.

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 10/08/2026

PanGBank: a large-scale resource of precomputed microbial pangenomes built with PPanGGOLiN www.biorxiv.org/content/10.64898/20…

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Steven Salzberg @stevensalzberg.bsky.social · 07/08/2026

I'm very pleased to be part of this paper on the first-ever complete diploid human genome, led by my (new!) Hopkins colleague @aphillippy.bsky.social and his lab, with contributions from Hayden Ji in my lab plus many other @jhu.edu and @hopkinsengineer.bsky.social faculty and students.

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naturepoker @binomicalabs.org · 05/08/2026

Normally I avoid company-associated lectures but this one looks genuinely interesting. Apparently aeonophile is a thing! Never heard of the term before, but I'm sure we've all asked the microbial life span question before. 🦠🧫 www.zymoresearch.com/pages/aeonop...

zymoresearch.com

Aeonophiles: Can an individual microbial cell live for a million years? | ZYMO RESEARCH

Explore how aeonophiles survive for millennia and what they reveal about evolution and biotechnology.

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Ragnar {Groot Koerkamp} @curiouscoding.nl · 03/08/2026

This is some really cool stuff! A chaining dynamic hashtable that uses *less* space than the input (by using quotienting), that actually seems to have quite competitive performance 🤯 And also a faster flat variant has 1.25 cache misses on average (and at most 2 or 3), that has super fast queries.

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Zach Weinersmith @zachweinersmith.bsky.social · 01/08/2026

There's lots of stuff LLMs can't do, but if you want to disbelieve all the recent math, you have to believe a bunch of Fields Medalists with long track records are just straightforwardly lying about the thing they care most about. Here's a recent blog by Gowers: gowers.wordpress.com/2026/05/08/a...

gowers.wordpress.com

A recent experience with ChatGPT 5.5 Pro

We are all having to keep revising upwards our assessments of the mathematical capabilities of large language models. I have just made a fairly large revision as a result of ChatGPT 5.5 Pro, to whi…

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tastewart 🦋 @tastewart.bsky.social · 31/07/2026

Jeanne Gibson, beloved “Rosie the Riveter,” passed away on July 29, 2026 at 100. Gibson became a welder at Todd Pacific Shipyards in Seattle, helping build destroyers for the Allied war effort during WWII. Gibson helped pave the way for millions of women who stepped into critical wartime roles.

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 01/08/2026

Pangenome Graph Node-Phenotype Association shows GWAS-like quality results with only few individuals www.biorxiv.org/content/10.64898/20…

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Ragnar {Groot Koerkamp} @curiouscoding.nl · 31/07/2026

I've been working on Pandedup the past weeks: a tool to quickly dedup the k-mer content of a pangenome (read: HPRCv2). Just uploaded a k=64 SPSS (k-mer spectrum preserving string set) as well: zenodo.org/records/2172... This reduces the ~1.5Tbp input to just 10.6Gbp. github.com/RagnarGrootK...

github.com

GitHub - RagnarGrootKoerkamp/pandedup: Pandedup uses minimizers to build a quick & dirty k-mer spectrum (SPSS) from a .AGC pangenome.

Pandedup uses minimizers to build a quick & dirty k-mer spectrum (SPSS) from a .AGC pangenome. - RagnarGrootKoerkamp/pandedup

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Tom Warren @tomwarren.co.uk · 30/07/2026

Microsoft-owned LinkedIn just added a “seems like AI slop” button to report posts that don’t feel human-written. It’s part of a broader push to get rid of AI slop on LinkedIn www.theverge.com/ai-artificia...

theverge.com

LinkedIn actually adds a ‘seems like AI slop’ button

It’s also removing an AI “enhance” feature.

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Zamin Iqbal @zaminiqbal.bsky.social · 30/07/2026

what the hell "The Anthropic copyright case set the precedent — the US court ruled that by making a digital copy and destroying the physical in a one-for-one transfer, the process is deemed “transformative” and therefore protected by fair use.

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Rob Patro @robp.bsky.social · 29/07/2026

New preprint🚨(*long* time coming)! We introduce seqproc: an efficient, flexible, and concise tool for describing and transforming sequencing-read geometry. The aim: make complex protocols easy to specify & transform without giving up speed or accuracy. www.biorxiv.org/content/10.6... 🧵

Crop of the preprint's first page. The title is "seqproc: An
efficient, flexible, and concise tool for sequence geometry description and
transformation." Authors are Noah Cape, Elan Fisher, Daniel Liu, and Rob Patro.
The abstract introduces seqproc, EFGDL, and the antisequence execution engine.

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Floris Barthel @florisbarthel.bsky.social · 28/07/2026

Excited to share a big KaryoScope update this past week: the HKS k-mer backend is now integrated, and you can build databases for any features of interest. The complete @humanpangenome.bsky.social HG002 assembly (~6.3 Gbp) now annotates in 21 minutes on a MacBook Pro. 🧵

Macbook laptop showing KaryoScope actively running alongside the final output karyotype plots

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Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 28/07/2026

ANR 2026, les résultats sont tombés anr.fr/fileadmin/aa...

anr.fr

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Janusz M. Bujnicki @jmbujnicki.bsky.social · 25/10/2025

Exciting news for the RNA research community! The Human RNome Project has been launched: a global effort to map all human RNAs and their chemical modifications. Proud to support it and contribute to the article in Genome Biology doi.org/10.1186/s130... #RNA #bioinformatics #RNAstructure #modomics

genomebiology.biomedcentral.com

Unlocking the regulatory code of RNA: launching the Human RNome Project - Genome Biology

The human RNome, the complete set of RNA molecules in human cells, arises through complex processing and includes diverse molecular species. While research traditionally focuses on four canonical nucl...

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