iiinova — where your digital self keeps evolving

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Judith Kribelbauer @jk-swietek.bsky.social · 12h

ui, a new regulatory sequence models from Kelley/Linder to play with - Cerberus! a new architecture with Hydra blocks replacing the transformer blocks. www.biorxiv.org/content/10.6...

biorxiv.org

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James Davies @jojdavies.bsky.social · 07/10/2026

Delighted to see our latest paper out in @natgenet.nature.com ! The brilliant @jhamley98.bsky.social developed MCCv, allowing chromatin architecture to be visualised at base-pair resolution for each allele—a powerful way to identify functional genetic variants. www.nature.com/articles/s41... 🧵

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Alejandro Fábregas-Tejeda @alejandrofabregastejeda.com · 06/10/2026

Please do get in touch if you are a philosopher or scientist (from any discipline) interested in these topics—I would love to collaborate and learn from you! If you would like to learn more about my research or find my contact info, please go to www.alejandrofabregastejeda.com

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Alejandro Fábregas-Tejeda @alejandrofabregastejeda.com · 06/10/2026

I am really happy to share that I have started as PI of an @fwovlaanderen.bsky.social-funded 3-year project @clpskuleuven.bsky.social. I'll investigate how scientists conceptualize, model & measure environments across the life, cognitive, social & Earth sciences! #philsci #philsky #evosky #envhum 🧪

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Kaili Fan @kailifan.bsky.social · 05/10/2026

1/13 The human body runs on one genome—but every cell reads it differently. How? To find out, we need to measure both gene expression and chromatin accessibility in the same nucleus. So we did, across 21 adult tissues and nearly half a million nuclei. 🧵 🔗 www.biorxiv.org/content/10.6...

biorxiv.org

Single-Nucleus Multi-Omic Atlas Maps Regulatory Architecture and Non-Coding Variant Effects across Adult Human Tissues

Diverse human cell types establish specialized functions through lineage- and context-specific regulatory programs. Interpreting non-coding genetic risk requires integrated multi-omic reference maps t...

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Julia M. Rohrer @dingdingpeng.the100.ci · 04/10/2026

This is very good. “Over 2.2 million cancer deaths can be attributed to Costco; that’s more than 20% of all cancer deaths between 2000 and 2018.”

Ridiculous things you can “prove” caused cancer mortality

Everything causes cancer. Sounds cliché; maybe those California warning tags were right all along. But thanks to the methodology created by Alwadi et al., we can now prove that anything and everything causes cancer. Oh, sorry, that is too strong of an assertion. To use the authors’ words, since they have claimed their papers don’t prove causality, we can create an association between any physical landmark and cancer and, from that association, figure out how much cancer is attributable to that thing. Which is totally not the same as saying “that thing causes cancer.”

For instance, living near a private four-year university is associated with a 15-fold increase in cancer mortality when compared

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Matt Henderson @matthen.com · 03/10/2026

Visualising the distribution of substrings in the genomes of different organisms. Going up to depth eight by recursively splitting into quadrants, we get these fractal-like pictures.

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samuel mehr @mehr.nz · 02/10/2026

early-career academics, if you don't have a website, make yourself one. yes it's annoying but just do it it can be plain text on a white background, or google sites, or even a free Wix one with ads. nobody cares we just need to be able to look you up, quickly, bc there's like 100 other apps here

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Dr Hannah M. Rowland @hannahmrowland.bsky.social · 01/10/2026

Hope your day was better than Darwin’s, on this day 165 years ago

I am very poorly today & very stupid & hate everybody &everything.

Charles Darwin
Letter to Charles Lyell
1st October 1861

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VIB.AI @vibai.bsky.social · 30/09/2026

Want to present your work in this room? The VIB Conference on AI & Computational Biology is coming to Leuven, with several talk slots selected from abstracts. Submit yours by 7 Oct: www.vibconferences.be/events/ai-and…

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Hubrecht Institute @hubrechtinstitute.bsky.social · 30/09/2026

Group leaders Danny Sahtoe and Alexander van Oudenaarden will supervise 2 of the 15 PhD positions that open in the ORFeus network, a Horizon Europe program studying the #DarkProteome, a group of recently discovered proteins linked to disease and new therapies. Apply 1–22 Oct via orfeus-dn.eu/apply

orfeus-dn.eu

Apply to ORFeus — 15 fully funded PhD positions

15 fully funded PhD positions across Europe, starting 2027. Applications open 1 October and close 22 October 2026. Rank up to three projects.

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Uwe Ohler @uweohler.bsky.social · 30/09/2026

Our #genome still holds many mysteries… Want to help figuring out what is actually translated into proteins and how it is regulated? Our research network #ORFeus is looking for motivated #PhD students to join projects across Europe. Deadline is soon (Oct 22), have a look! www.orfeus-dn.eu/apply/

orfeus-dn.eu

Apply to ORFeus — 15 fully funded PhD positions

15 fully funded PhD positions across Europe, starting 2027. Applications open 1 October and close 22 October 2026. Rank up to three projects.

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Brendan O’Kane @bokane.org · 15/07/2025

in the process of having an idea

An orange cat with white socks and a sweet heart, emerging slowly from croissant mode on the sofa. He appears to be thinking about something, which he is - sorry, little homie - not really equipped to do.

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Maitreya Dunham @maitreya.bsky.social · 24/09/2026

Exciting news: @uwgenome.bsky.social will be hiring for two tenure-track faculty positions this year, one open rank and one assistant professor. Both are “Genome Sciences” interpreted broadly so we welcome applicants working in a variety of fields and methods. Ad will be out shortly.

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Michalis Averof @michalis-averof.bsky.social · 23/09/2026

Nice example of how AI predictions are limited by the training set. AlphaFold has not learned the rules of protein folding, it's just great at predicting structures based on what it has already seen. Added constraints (e.g. alignment revealing conservation patterns) can help make a good prediction.

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Cas Blaauw @casblaauw.eurosky.social · 22/09/2026

Excited to show deepSCENIC to the world! GRNs meet sequence-to-function models: explicit TF-region and region-gene links, with the power of enhancer DL models, predicting RNA & ATAC at single-cell resolution. Check out the examples in the paper or try it on your own data: github.com/aertslab/Dee...

github.com

GitHub - aertslab/deepSCENIC: Deep learning for single-cell Gene Regulatory Networks

Deep learning for single-cell Gene Regulatory Networks - aertslab/deepSCENIC

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 22/09/2026

DeepSCENIC: transfer learning from sequence-to-function models enables causal gene regulatory network inference www.biorxiv.org/content/10.64898/20…

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John Timmer @jtimmer.bsky.social · 22/09/2026

Ok, this "there are two separate brains" thing appears to be making the rounds, and I want to be absolutely clear: this is a press office overhyping some perfectly reasonable science that won't come as a surprise to most developmental biologists.

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Matt Hodges @matthodges.bsky.social · 19/09/2026

Very quick and dirty Jev test for hiring bias. One resume for a Wall Street job; asked whether the applicant should get a first-round interview. 76 evaluations, changing only the first name. 19 of each: White-associated men/women, Black-associated men/women. console.typesafe.ai/playground?s...

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Stefan Schoenfelder @stefanschoenfelder.bsky.social · 20/09/2026

The number of MSCA Postdoctoral Fellowship applications in 2026 (21,627) has more than doubled since 2024 (10,360 proposals) and more than tripled since 2022 (7,044). Stating the obvious here but this is not sustainable.

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Arnaud Krebs @arnaudkr.bsky.social · 21/09/2026

We are recruiting! Wet&Dry either combined or separate. If you are excited about gene regulation, new methods in genomics and AI-based interpretation! Talk to us!

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Christophe 🔬 Leterrier @christlet.bsky.social · 20/09/2026

Acronyms in biology tools these days are either already used by another method or "Here we present sMLFNJCOIMZNJQM"

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Joe Bak-Coleman @jbakcoleman.bsky.social · 20/09/2026

For whatever reason the fact that LLMs manifest their task completion with language has had folks wanting to jump the gun on a big thorny question of whether/when they “think” in the sense that we all have come to understand it. They may simply not need “think” to to complete complex tasks.

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Richard Sever @richardsever.bsky.social · 20/09/2026

"All corners of academia will soon be flooded with AI-generated research....Maths and CS go first because their entire output is symbol manipulation...Biology comes later not because biologists are cleverer but because the rate-limiting step is physical" giorgio.gilest.ro/the-weimar-o...

giorgio.gilest.ro

The Weimar of knowledge – la bottega

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Christophe 🔬 Leterrier @christlet.bsky.social · 19/09/2026

I asked chatGPT and - Well I asked Toko the starling and he said he loves me so much and that's everything I need

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Eris ⌬ @eriskii.net · 18/09/2026

"Pope gifted green orb" "Trump threatens EU over Canada" "Chipotle partners with Palantir" What the fuck is going on anymore they're just making this shit up now

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Nicola Rennie @nrennie.bsky.social · 17/09/2026

I love overly honest READMEs

Screenshot of GitHub README saying known issues: coding style only a mother could love

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Thibaut Brunet @thibautbrunet.bsky.social · 17/09/2026

It had been theoretically predicted that the expansion of the Nature family of journals would inevitably lead to oxymoronic titles in the long run if left unchecked. This prediction has just been experimentally confirmed

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shri @shrikhalpada.dev · 16/09/2026

is there a word for hating an aesthetic you'd probably have liked 5 years ago, entirely because it's now the visual signature of AI slop? (thinking of Claude-generated UX with the parchment canvas, serif fonts, and muted earthy colors)

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Tanja Stadler @tanjastadler.bsky.social · 15/09/2026

🚀 Interested in joining our Computational Evolution group at ETH Zürich in Basel @bsse.ethz.ch as a Postdoc? We will be hosting ETH AI Center's Postdoc Fellows on AI x evolution, AI x single cell biology as well as AI x public health. Apply now 👉 ai.ethz.ch/apply Deadline: Oct 27, 2026

ai.ethz.ch

Fellowship Programs

The application portal for the ETH AI Center Fellowship Programs is now closed. The deadline for submitting reference letters is 23:59 CET on November 14, 2025.

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Stats For Bios @statsforbios.bsky.social · 16/09/2026

Reminder that "wiggly" is absolutely a technical statistical term. No discussion needed.

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Cas Blaauw @casblaauw.eurosky.social · 16/09/2026

As always, this makes Brussels politics's obsession with car lanes and parking spaces all the weirder - over half of households don't have a car!

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Centre de Regulació Genòmica (CRG) @crg.eu · 15/09/2026

We are at a critical moment for the future of European science. As @eu-life.bsky.social founder, and together with 100s of institutes and universities across the continent, we call for an ambitious funding pot for FP10. See Luis Serrano's comments in El Mundo. www.mundoamerica.com/entertainmen...

mundoamerica.com

European science calls for ambitious investment in research: "Current decisions determine Europe's future. We are falling behind China and the USA"

"To remain global leaders, a competitive economic power, and a sovereign actor, Europe needs strong science and innovation." Seven scientific organizations, representing...

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Sergey Ovchinnikov @sokrypton.org · 14/09/2026

Finally a more intuitaive way to learn pLDDT/pAE? 😎 sokrypton.github.io/protein_figh... (Character idea from @hannes-stark.bsky.social & Alex Waldherr)

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VIB.AI @vibai.bsky.social · 14/09/2026

New group leader recruitment call now open. 📣 Together with KU Leuven, we are looking for two Principal Investigators to join VIB.AI and build ambitious independent research programs on AI in biology. Apply by 15 November 2026 vib.ai/en/join-vibai-group-leader-a…

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Pedro Beltrao @pedrobeltrao.bsky.social · 03/09/2026

8.8% success rate for the ERC Starting Grant is not acceptable. It is a lottery at this point with so many great scientists and ideas left to be funded. We keep talking about the competitiveness of Europe and we can't agree to properly fund our best instrument for scientific innovation.

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Irene Gallego Romero @ee-reh-neh.bsky.social · 03/09/2026

Here's something a bit different that we've been noodling around with! Nearly 10y ago we established a panel of cell lines from Papuan donors, which let us check predictions from AlphaGenome against experimental data. If you've followed the field you'll know that expression prediction is very tough

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Cas Blaauw @casblaauw.eurosky.social · 31/08/2026

At ECCB this year as one of over 1500 attendees, let's chat if you're around! If you want to see what I'm up to, I'm giving a talk on Wednesday at 9 in the Transcriptomics track, room AD! ( #ECCB2026 )

A big stage with an ECCB welcome slide in the back, showing the big fountain in Geneva.

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Claus Wilke @clauswilke.com · 30/08/2026

I'm really frustrated by the constant fear-mongering about AI-designed superviruses. Can we focus on the things that should actually worry us, such as measles? blog.genesmindsmachines.com/p/im-sorry-y...

blog.genesmindsmachines.com

I'm sorry, you're not going to die from an AI-engineered supervirus

God save us from economists who think they can competently talk about biology

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Casper Albers 🟥 @casperalbers.nl · 31/08/2026

(en ja, er zijn te weinig studentenkamers, maar dat is niet de schuld van buitenlandse studenten maar van Stef fucking Blok)

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Shrew @shrewshrew.bsky.social · 28/08/2026

She's just like me fr I also sit in my living room and wait for motivation to fall from the sky

The torbie stares up to the ceiling in wait of the toys next descent

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Cas Mudde @casmudde.bsky.social · 28/08/2026

Such a missed opportunity for the EU and its (richer) member states. Both the UK and the US are weakening their university systems and there is a unique opportunity to use some of their top talent to lift up EUropean universities. Instead, they defund their core and add a few shiny stars.

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Adam Rutherford @adamrutherford.bsky.social · 27/08/2026

This is pretty funny tbh. The US gov wades in with its big bully boots to protect the 'academic freedom' of this scientifically illiterate weird little racist, who actively opposes the academic freedom of others, for a 1 yr postdoc on a subject he shows no track record for. Well done all concerned.

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shri @shrikhalpada.dev · 27/08/2026

My latest interactive explainer all about the technology behind record players is done! perthirtysix.com/how-the-heck...

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Carl T. Bergstrom @carlbergstrom.com · 24/08/2026

As LLMs get better at certain tasks and much more convincing, it's a useful exercise to ask about a subject you know intimately. Here, ChatGPT 5.6 diagrams the wrong game, doubles down, then finally admits its mistake. It cites a paper that doesn't exist, doubles down, and finally confesses again.

ChatGPT query: Diagram the enquist model of agonistic signaling

[poster output]

User: This is fucked up. So you just made that up.

ChatGPT: Yes. I did, and you’re right to call it out.

My first description was not a faithful account of Enquist’s model. I supplied a plausible generic sequence for agonistic assessment—“initial assessment → signaling → reassessment → escalation”—without having verified that those were actually the stages or assumptions in Enquist (1985). Then, when you challenged the “prior information” point, I compounded the problem by giving another specific reconstruction instead of checking the source first.

I’ve now checked secondary material explicitly discussing Enquist’s 1985 model, and it describes the model as one in which players choose among possible displays/actions in an agonistic game, with the evolutionary question being when those choices can constitute honest signaling. That is importantly different from the staged assessment process I initially gave you.

So: do not use either of my previous stage descriptions as a representation of Enquist (1985). I should have looked up the paper/model before answering a source-specific question.

ChatGPT: Yes. You’re right — again.

The poster actually says:

Enquist, M. (1985). “Communication during agonistic encounters.” In R. R. Hinde (Ed.), Advances in the Study of Behavior, Vol. 15, 65–106. Academic Press.

And that citation is not the original Enquist model paper I should have been using.

I made three separate errors here: I generated an unverified citation, then misreported what the poster said twice. That’s a basic source-handling failure.

If you want, I can now do this properly: verify the actual Enquist agonistic-signaling model from the primary paper and give you only the real sequence/stages, with no reconstruction.

User: The paper on the poster doesn't even exist.

ChatGPT: Correct. That poster citation is fabricated. I generated a title and book chapter that do not exist.

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roterote @roterote.bsky.social · 22/08/2026

Here is the full suspension letter from UGent that was sent to Nathan Cofnas, it shows ample reason for his suspension and potential termination. Including breach of contract, using the University of Ghent’s name and legitimacy to promote his racial supremacist views and causing reputational damage.

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Prasad Jallepalli, MD, PhD @prasad.bsky.social · 23/08/2026

there’s a world of difference between putting forth controversial ideas that are (1) testable but unproven; (2) testable and squarely disproven ; (3) untestable and yet argued as if they worthy of consideration

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roterote @roterote.bsky.social · 22/08/2026

33 more names added to the letter defending American Eugenicist Nathan Cofnas in the last 45 minutes. These people are caping for a man whose stated goal is to mainstream eugenics and fight wokeness.

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BeijingPalmer @beijingpalmer.bsky.social · 23/08/2026

I'm sorry, but if you think Nathan Cofnas being suspended for being a racist is an 'academic freedom' issue you are the dumbest fucking mark alive.

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