The other thing I feel needs continued emphasis is pretty much all these preprints are written with the expectation they will undergo peer review. That may reduce the tendency of authors to overclaim from the outset and it tells us little about what they would write without prospect of formal review

EMBL's new AI unit is recruiting. We are seeking a machine learning scientist to establish their independent research group bridging innovations in machine learning/AI with modern biology. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Excited that the {anndataR} 📦 publication is out academic.oup.com/bioinformati... 🎉! I hope this makes it easier to move single-cell data between R and Python and encourages people to take advantage of both languages. Check it out on @bioconductor.bsky.social bioconductor.org/packages/ann....

I have been working with polars a bit lately and was missing some of my favorite functions from {{forcats}} and {{santoku}} for dealing with enums/factors. So, naturally, I wrote a new package to fix this :) const-ae.github.io/polarstation/ #polars #python #rstats

Happy to see that `jgd` is now up on CRAN. An alternative #rstats graphics device that's fast and lightweight (mostly pure C). Try it out with our VS Code extension or Deno server. More details: github.com/grantmcdermo... Joint work with the indefatigable @eitsupi.bsky.social.

I don't think cell representation foundation models _should_ be good at zero-shot integrating data. How do you know which variation I want to integrate out?

Thrilled to join Isomorphic Labs—time to build better ML models of cells and create the drugs of the future!! 🧬🧫🧑‍💻🥳

Thrilled to join Isomorphic Labs—time to build better ML models of cells and create the drugs of the future!! 🧬🧫🧑‍💻🥳

We are super excited to welcome Dmitry Kobak @hippopedoid.bsky.social as a new VIB.AI group leader! The Kobak lab will officially kick off in April at the VIB.AI Ghent hub. More: vib.ai/en/news/dmit...

1/ Apply for an inter-disciplinary postdoc position in Heidelberg with the Health & Life Science Alliance Deadline: **31 March** Project proposals can be self-designed or adapt one of the outlines on the website ("List of project outlines for download") www.health-life-sciences.de/opportunitie...

I just made an account and voted for this biology laboratory made of LEGO to "promote biological research and inspire more people into the world of biology". They need 10K votes. Reposting and/or voting below would be helpful. 🤗 beta.ideas.lego.com/product-idea...

Biological Laboratory | LEGO® Ideas

This is a two-floor realistic Biological Laboratory building. In this design, I try to tell stories about biologists, introduce biology concepts to general publ…

beta.ideas.lego.com

www.deadlanguagesociety.com/p/how-far-ba... I cannot speak as to the accuracy of the piece yet I found it a fascinating exercise @adamroberts.bsky.social @drlauravarnam.bsky.social

How far back in time can you understand English?

An experiment in language change

deadlanguagesociety.com

screaming this from the rooftops

Luca Palmieri@lpalmieri.com · 6mo ago

The mainstream conversation around AI agents is stuck on "AI slop." There's more to it: we can use cheap agent code to do quality-raising work that didn't make economic sense before. What's viable now that writing code isn't the primary bottleneck? lpalmieri.com/posts/agenti...

Job offer: PhD-level biostatistician with ML&omics experience to work on prediction models for CAR T cell therapy, in an exciting clinical trial - spatial omics - data science consortium (LOOP/INTeRCePT3.0 centered in Zurich; this position in Heidelberg) embl.wd103.myworkdayjobs.com/en-GB/EMBL/j...

We wrote a review of representation learning methods of single-cell RNA-seq data, where we compare factor models, autoencoders, contrastive learning, and foundation models 🎉 rnajournal.cshlp.org/content/earl...

RNA Society Journal@rnajournal.bsky.social · 7mo ago

A review on representation learning of single-cell RNA-seq data by Constantin Ahlmann-Eltze (@const-ae.bsky.social), Florian Barkmann (@flobarkmann.bsky.social), Jan Lause (@janlause.bsky.social), Valentina Boeva (@valboeva.bsky.social), and Dmitry Kobak (@hippopedoid.bsky.social) bit.ly/49vWRSJ

Boeva Lab is #hiring postdocs and senior scientists in AI/ML for Cancer Biology! Check the offer and apply at: jobs.ethz.ch/job/view/JOP...

Postdoctoral Researcher or Senior Scientist (AI × Biology)

jobs.ethz.ch

Apply for the Ascona workshop "Statistical and AI methods for multi-modal multi-scale modeling of biological systems", 28 Jun-3 Jul 2026 on Monte Verità, Lago Maggiore at the foot of the Swiss Alps. ascona2026.sciencesconf.org

Save the date: April 9 from 4pm to 6pm CET. Our department is hosting an online seminar with @noeliaferruz.bsky.social @sdomcke.bsky.social @const-ae.bsky.social who will talk about models for protein design, large-scale perturbation screens, and benchmarking of perturbation prediction models.

Join me in 5.5h, when we discuss our benchmark of perturbation prediction models and what the right metric is to assess if a gene expression prediction is good!

Bioconductor@bioconductor.bsky.social · 8mo ago

⏰ Only a few hours left to register! Don’t miss today’s Bioconductor Seminar Series session: “Deep-learning-based Gene Perturbation Effect Prediction Does Not Yet Outperform Simple Linear Baselines.” 🗓️ December 2, 2025 🕒 9PM CET / 3PM EST / 12PM PST 👉 Register here: dfci.zoom.us/webinar/regi...

🚀 Excited to share our new preprint: msBayesImpute - A Versatile Framework for Addressing Missing Values in Biomedical Mass Spectrometry Proteomics Data 👉 Improves imputation accuracy, normalization, and differential expression detection 📝https://www.biorxiv.org/content/10.1101/2025.10.02.679746v1

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change. Ie: it's not us (Samtools team)! Be warned

We're excited to share that our preprint on anndataR, a new package bringing Python's AnnData to R, is now available on bioRxiv 🎉 🔗 Read the paper: www.biorxiv.org/content/10.1... 💻 Check the package in action: anndatar.data-intuitive.com

Now on CRAN, ggdiagram is a #ggplot2 extension that draws diagrams programmatically in #Rstats. Allows for precise control in how objects, labels, and equations are placed in relation to each other. wjschne.github.io/ggdiagram/ar...

Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉 www.nature.com/articles/s41... We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures! 🧵

🚨 PhD Position available in our lab 🚨 exploring the power of blood immune multi-omics to detect lung cancer years prior to clinical diagnosis in a unique cohort of >10,000 CT screened individuals. ✅ Wet & dry lab ✅ September 2025 enrolment ✅ UK tuition fees only www.ucl.ac.uk/medical-scie...

Pre-Cancer Immunology

The Pre-Cancer Immunology Lab (James Reading Lab) is mapping pre-invasive T cell dynamics during carcinogenesis to detect and intercept cancer development.

ucl.ac.uk

I wrote about AI foundation models for biology last year: www.nytimes.com/2024/03/10/s... Benchmarking tests since then aren't finding that they're better than simpler models of how genes and cells work.

A.I. Is Learning What It Means to Be Alive (Published 2024)

nytimes.com

Constantin Ahlmann-Eltze@const-ae.bsky.social · last yr.

Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉 www.nature.com/articles/s41... We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures! 🧵

An analysis shows that current deep learning models do not beat linear baselines in predicting gene perturbation effects, thus emphasizing the importance of further method development and evaluation. @const-ae.bsky.social @wkhuber.bsky.social @s-anders.bsky.social www.nature.com/articles/s41...

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...

nature.com

Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉 www.nature.com/articles/s41... We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures! 🧵

In October 2024, I twote that "something is deeply wrong" with what we now call virtual cell models. A lot has happened since then. How am I updating? New blog post: ekernf01.github.io/virtual-cell...

Going from methods dev to full on cancer bio has been tough. All the more excited to see this out at last— www.biorxiv.org/content/10.1... @pascual-reguant.bsky.social @brukerspatial.bsky.social @hoheyn.bsky.social

Tracing colorectal malignancy transformation from cell to tissue scale

The transformation of normal intestinal epithelium into colorectal cancer (CRC) involves coordinated changes across molecular, cellular, and architectural scales; yet, how these layers integrate remai...

biorxiv.org