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Constantin Ahlmann-Eltze

@const-ae.bsky.social
2.1K followers 691 following 70 posts

Scientist at Isomorphic Labs. Previously at UCL and EMBL working with Wolfgang Huber. Biology, ML, Python, R, cancer immunology

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Reposted by Constantin Ahlmann-Eltze
Emma Dann @emmamarydann.bsky.social · 28/08/2026
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👇
cell.com
Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits
A dynamic atlas of gene regulation was generated by perturbing every expressed gene across 22 million primary human CD4+ T cells under resting conditions and following re-stimulation. The resulting ma...
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Richard Sever @richardsever.bsky.social · 06/07/2026
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
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Wolfgang Huber @wkhuber.bsky.social · 01/07/2026
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...
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Luke Zappia @lazappi.bsky.social · 10/06/2026
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....
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Constantin Ahlmann-Eltze @const-ae.bsky.social · 26/05/2026
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
const-ae.github.io
polarstation
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Grant McDermott @gmcd.bsky.social · 29/04/2026
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.
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Valentine Svensson @nxn.se · 22/04/2026
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?
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Constantin Ahlmann-Eltze @const-ae.bsky.social · 22/03/2026
Thrilled to join Isomorphic Labs—time to build better ML models of cells and create the drugs of the future!! 🧬🧫🧑‍💻🥳
Picture of myself in front of the Iso logo
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Constantin Ahlmann-Eltze @const-ae.bsky.social · 22/03/2026
Thrilled to join Isomorphic Labs—time to build better ML models of cells and create the drugs of the future!! 🧬🧫🧑‍💻🥳
Picture of myself in front of the Iso logo
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Reposted by Constantin Ahlmann-Eltze
VIB.AI @vibai.bsky.social · 18/03/2026
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...
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Wolfgang Huber @wkhuber.bsky.social · 15/03/2026
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...
health-life-sciences.de
HEALTH + LIFE SCIENCE ALLIANCE | Interinstitutional Postdoc Call |…
Apply for the Alliance Interinstitutional Postdoc Program in health & life sciences. Two-year funded positions with interdisciplinary research support.
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Sjors Scheres @sjorsscheres.bsky.social · 16/10/2025
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...
beta.ideas.lego.com
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…
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Reposted by Constantin Ahlmann-Eltze
Mark O’Neill 🐻 @radiobeartime.com · 22/02/2026
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
deadlanguagesociety.com
How far back in time can you understand English?
An experiment in language change
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Davis Vaughan @davisvaughan.bsky.social · 16/02/2026
screaming this from the rooftops
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Wolfgang Huber @wkhuber.bsky.social · 13/02/2026
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...
Screenshot of Job AdEMBL site in HeidelbergZurich, incl. a bit of UZH/USZ
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Constantin Ahlmann-Eltze @const-ae.bsky.social · 21/01/2026
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...
rnajournal.cshlp.org
Representation learning of single-cell RNA-seq data
A monthly journal publishing high-quality, peer-reviewed research on all topics related to RNA and its metabolism in all organisms
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Valentina Boeva @valboeva.bsky.social · 20/01/2026
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...
jobs.ethz.ch
Postdoctoral Researcher or Senior Scientist (AI × Biology)
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Wolfgang Huber @wkhuber.bsky.social · 15/01/2026
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
View from the hotel roomPoster session 2024, with Valentina Boeva, Constantin Ahlmann-Eltze and othersWednesday afternoon hike incl. swim in the mountain riverAnother view from the hotel room
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christofseiler.bsky.social @christofseiler.bsky.social · 14/01/2026
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.
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Constantin Ahlmann-Eltze @const-ae.bsky.social · 02/12/2025
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!
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Junyan Lu @junyanlu.bsky.social · 07/10/2025
🚀 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
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James Bonfield @jbonfield.bsky.social · 15/09/2025
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
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Louise Deconinck @louisedck.bsky.social · 25/08/2025
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
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W. Joel Schneider @w-joel-schneider.bsky.social · 20/08/2025
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...
An arrow with a LaTeX equationTrigonometric functions and a unit circleA bivariate change model with structured residualsA hierarchical model of cognitive abilities
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Constantin Ahlmann-Eltze @const-ae.bsky.social · 04/08/2025
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! 🧵
Beeswarm plot of the prediction error across different methods of double perturbations showing that all methods (scGPT, scFoundation, UCE, scBERT, Geneformer, GEARS, and CPA) perform worse than the additive baseline.Line plot of the true positive rate against the false discovery proportion showing that none of the methods is better at finding non additive interactions than simply predicting no change.
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James Reading @jamesreading.bsky.social · 05/08/2025
🚨 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...
ucl.ac.uk
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.
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Carl Zimmer @carlzimmer.com · 04/08/2025
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.
nytimes.com
A.I. Is Learning What It Means to Be Alive (Published 2024)
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Nature Methods @natmethods.nature.com · 04/08/2025
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...
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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Constantin Ahlmann-Eltze @const-ae.bsky.social · 04/08/2025
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! 🧵
Beeswarm plot of the prediction error across different methods of double perturbations showing that all methods (scGPT, scFoundation, UCE, scBERT, Geneformer, GEARS, and CPA) perform worse than the additive baseline.Line plot of the true positive rate against the false discovery proportion showing that none of the methods is better at finding non additive interactions than simply predicting no change.
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Reposted by Constantin Ahlmann-Eltze
Eric Kernfeld @ekernf01.bsky.social · 28/07/2025
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...
ekernf01.github.io
A recap of virtual cell releases circa June 2025
In October 2024, I twote that “something is deeply wrong” with what we now call virtual cell models. A lot has happened since then: modelers are advancing new architectures and mining new sources of i...
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Helena Lucia Crowell @helucro.bsky.social · 27/06/2025
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
biorxiv.org
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...
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We Are RLadies+ @weare.rladies.org · 08/05/2025
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!
With {tidylog}, you see friendly messages like:
summarise: now 3 rows and 3 columns, ungrouped
filter: removed 2 rows (67%), one row remaining
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Matthias Meyer-Bender @matthiasmeybe.bsky.social · 05/05/2025
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...
Spatialproteomics orchestrates workflows to analyze highly multiplexed images. It segments cells, processes images, quantifies proteins, predicts cell types, and provides neighborhood analysis methods, all while integrating into the scverse ecosystem.
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T cell Vaccines Lab (Swadling UCL) 🧬👩🏽‍🔬 @tcellvaccineucl.bsky.social · 10/04/2025
(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
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Adlung Lab @adlunglab.com · 19/03/2025
🦎 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
doi.org
Analysis of multi-condition single-cell data with latent embedding multivariate regression
Nature Genetics - Latent embedding multivariate regression models multi-condition single-cell RNA-seq using a continuous latent space, enabling data integration, per-cell gene expression prediction...
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Katharina Imkeller @imkeller.bsky.social · 11/03/2025
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
agimkeller.github.io
Open positions - AG Imkeller
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Wolfgang Huber @wkhuber.bsky.social · 04/03/2025
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...
const-ae.name
LEMUR simplified | const-ae
A simplified implementation of the LEMUR algorithm.
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Wolfgang Huber @wkhuber.bsky.social · 28/02/2025
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
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Constantin Ahlmann-Eltze @const-ae.bsky.social · 19/02/2025
Is there some clever syntax to control when a quasi-quotation is evaluated so that the wrap_in_tibble function works? 🧐 (Context in stackoverflow.com/questions/79...) #Rstats #rlang
wrap_in_df <- function(...){
  dots <- rlang::enquos(...)
  eval_in_mtcars(data.frame(!!! dots))
}
wrap_in_tibble <- function(...){
  dots <- rlang::enquos(...)
  eval_in_mtcars(tibble::tibble(!!! dots))
}
eval_in_mtcars <- function(expr){
  quo <- rlang::enquo(expr)
  rlang::eval_tidy(quo, data = mtcars[1:3,])
}

wrap_in_df(mpg * 2, cyl + 3)
#>   X.mpg...2 X.cyl...3
#> 1      42.0         9
#> 2      42.0         9
#> 3      45.6         7
wrap_in_tibble(mpg * 2, cyl + 3)
#> Error: object 'mpg' not found
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verat-h.bsky.social @verat-h.bsky.social · 18/02/2025
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...
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Constantin Ahlmann-Eltze @const-ae.bsky.social · 12/02/2025
I just uploaded the first version of {{exactplot}} to github.com/const-ae/exa... 🎉 It produces figures with consistent font size, Latex labels, and millimeter-perfect layouting. It's an alternative to patchwork with less elegant syntax but much more flexibility. #rstats
Plot produced with exactplotxp_compose_plots(
  xp_text("Welcome to \\texttt{exactplot} with \\LaTeX{} support", x = 1, y = 2, 
          fontsize = xp$fontsize_large, fontface = "bold"),
  xp_text("A) Flipper length vs.\\ beak size", x = 1, y = 8),
  xp_plot(scatter_plot, x = 0, y = 12, width = 80, height = 40),
  
  xp_text("B) Beak sizes", x = 84, y = 8),
  xp_plot(beak_lengths, x = 82, y = 12, width = 58, height = 40),
  xp_text(density_formula, x = 99, y = 12, fontsize = xp$fontsize_small),
  
  width = 140, height = 52,
  keep_tex_file = FALSE, filename = "example.pdf"
)
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Will Townes @willtownes.bsky.social · 31/01/2025
@epigenci.bsky.social makes a pretty convincing case for pseudobulk (as opposed to GLMMs) in multi-sample single cell studies here: doi.org/10.1093/bioi... . #bioinformatics
doi.org
Pseudobulk with proper offsets has the same statistical properties as generalized linear mixed models in single-cell case-control studies
AbstractMotivation. Generalized linear mixed models (GLMMs), such as the negative-binomial or Poisson linear mixed model, are widely applied to single-cell
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Lukas Heumos @lukasheumos.bsky.social · 30/01/2025
We have additional available spots. Please consider joining! It will be a blast.
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Wolfgang Huber @wkhuber.bsky.social · 27/01/2025
CSAMA 2025 Biological Data Science Summer School in Brixen, South Tyrol, 7-11 July We cover (sc)-RNA-seq and spatial omics data analysis, underlying (bio)statistical topics, multi-omics, ... All hands-on using R/Bioconductor tools. csama2025.bioconductor.eu Registration opens on 1 Feb
A picture of the surroundings of Brixen/Bressanone together with key data on the summer school.
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Britta Velten @brittavelten.bsky.social · 14/01/2025
My first post here on BlueSky to share our recent work with Claudia Feng and @leopoldparts.bsky.social - a large-scale single cell CRISPR screen to chart out gene regulation and the role of genomic background in iPSCs. Check out the data here: www.sanger.ac.uk/tool/crispri...
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Annique Claringbould @anniquec.bsky.social · 09/01/2025
Come do a PhD with me! 🖥️🧬 We've got very exciting multiomics data coming in, you get to shape the project and there are lots of opportunities to collaborate and learn. Reach out here or via email if you have questions Please reskeet 🙏 www.werkenbijerasmusmc.nl/en/vacancy/1...
werkenbijerasmusmc.nl
Vacature: PhD candidate in gene regulatory mechanisms underpinning cardiovascular diseases
We are seeking a motivated PhD student to join our lab at Erasmus University Medical Centre in Rotterdam, exploring the gene regulatory mechanisms underpinning cardiovascular diseases. Type 2 diabetes...
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Constantin Ahlmann-Eltze @const-ae.bsky.social · 06/01/2025
For the Monday morning crowds :) Also take a look at my blog post where I compress the full lemur package into 100 lines of code and explain the core algorithm. const-ae.name/post/2025-01...
const-ae.name
LEMUR simplified | const-ae
A simplified implementation of the LEMUR algorithm.
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Constantin Ahlmann-Eltze @const-ae.bsky.social · 03/01/2025
After 4y in the making, I am super excited that my main PhD project is published 🎉🥳🎉🎉🥳 www.nature.com/articles/s41... LEMUR is a tool to analyze multi-condition single-cell data and model differential expression as a continuous function of the cell-state space. Some highlights⬇️
Overview of the LEMUR steps: (1) subspace alignment, (2) differential expression, (3) DE neighborhoods, (4) pseudobulking.
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Constantin Ahlmann-Eltze @const-ae.bsky.social · 11/12/2024
PSA for authors posting to bioRxiv, who don't want to miss if someone comments on their preprint or writes a review: Click "follow" on your papers! Otherwise, you won't be notified. ✉️🚨
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Constantin Ahlmann-Eltze @const-ae.bsky.social · 11/12/2024
@richardsever.bsky.social, is there a setting as an author on bioRxiv to be notified if someone posts a comment about one of my preprints? Or maybe get a notification from prereview.bsky.social? I received a comment in November and only saw it today!
prereview.bsky.social
PREreview (@prereview.bsky.social)
PREreview is a free and open platform for the crowdsourcing of #preprint reviews, a resource center, and a convener. Working to make science and scholarship more equitable, transparent, and collaborat...
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