Constantin Ahlmann-Eltze

Stoked to share our new perspective on ✨ Trait Causal Models ✨ as the next frontier for human genomics! It was a pleasure to put this together with @jeffspence.github.io and @jkpritch.bsky.social with guidance from @minetoota.bsky.social @jengreitz.bsky.social @marsonlab.bsky.social Thread 👇

I’m super excited that Isomorphic labs is part of the virtual biology initiative that will invest a total of 1.8$ billion (!!) to generate the data needed to train the next generation of machine leaving models for biology 🔬🧬💻

The @embl.org PhD programme closes in 48 hours - you still have time to rush in an application if you are a science, maths or computer science undergraduate wanting to do a PhD in one of the world's leading biology and AI institutes www.embl.org/about/info/e...

Yesterday, we released a new version of anvl: github.com/r-xla/anvl. You can use it to implement numerical algorithms in R and run it on CPU and GPU. The R Code is compiled, so you do not have interpreter overhead, and it also allows you to automatically compute gradients #rstats

Our work on systematic perturb-seq of primary human T cells is now out in Cell 🎉 www.cell.com/cell/fulltex... It's been a privilege to work with @ronghuizhu.bsky.social between @jkpritch.bsky.social @marsonlab.bsky.social labs, with a dream-team of co-authors ❤️ Highlights in preprint thread👇

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...

screaming this from the rooftops

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...

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...

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!

🚀 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...

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.

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...

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

With {tidylog}, you see friendly messages like: summarise: now 3 rows and 3 columns, ungrouped filter: removed 2 rows (67%), one row remaining ✨ It’s like having a gentle co-pilot, helping you track what each step is doing — super useful for debugging and learning!

New preprint out! We introduce 𝐬𝐩𝐚𝐭𝐢𝐚𝐥𝐩𝐫𝐨𝐭𝐞𝐨𝐦𝐢𝐜𝐬, a Python package for end-to-end processing and analysis of highly multiplexed immunofluorescence imaging data. Built on xarray and dask, with seamless integration into the scverse ecosystem. www.biorxiv.org/content/10.1...

(2/3) Constantin Ahlmann-Eltze showcased impressive work on assembling an atlas of T cells in precancerous samples. They developed the R packages treelabel and Shinytreelabel, which showed GITR+ Tregs are enriched in several precancerous samples, suggesting avenues for future treatments

🦎 Differential expression analysis relies on cluster identities, unless you perform a regression along continuous representation in latent space. LEMUR from @const-ae.bsky.social & @wkhuber.bsky.social does that neatly for scRNA-seq data! 🔗 doi.org/10.1038/s415... 🧪 @naturegenet.bsky.social

We are recruiting a PhD student in Computational Biology to work on omics data and spatial integration in cellular immunotherapy of cancer. Joint project with the group of Florian Büttner. @loewe-fci.bsky.social agimkeller.github.io/recruit.html

Blog post by @const-ae.bsky.social with a simple explanation of the manifold regression algorithm & code that underlies our paper “Analysis of multi-condition single-cell data with latent embedding multivariate regression” (doi.org/10.1002/eji....). const-ae.name/post/2025-01...

Abstract submissions are now open for the European Bioconductor Conference (EuroBioC2025), 17-19 September 2025 in Barcelona. This event will bring together the Bioconductor community in Europe to advance bioinformatics, data science, and open-source software. eurobioc2025.bioconductor.org

Thrilled to share that our work from Trumpp Lab @hi-stem @dkfz.bsky.social is out in Nature. We provide the first single-cell data on neurons infiltrating pancreatic tumors, offering new insights into cancer therapy. #cancerneuroscience @cn-hd.bsky.social www.nature.com/articles/s41...