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...

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

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

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

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...

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

@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

We have additional available spots. Please consider joining! It will be a blast.

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

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...

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...

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...

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⬇️

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. ✉️🚨

@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!

Formulaic is the go-to way to specify design formulas in Python, e.g. ~treatment + timepoint. To compare sth, one needs to specify a contrast, e.g "on treatment vs baseline". To make this easier, we developed "formulaic-contrasts": formulaic-contrasts.readthedocs.io/en/latest/

I wrote a new blogpost about working with D3 (or any other Javascript library) from R. Existing wrappers, like R2D3, where last updated in 2021. But with a few (low-level) function calls we can load any JS library and even send data from R to JS! const-ae.name/post/2024-12... #rstats

Extremely proud to see my PhD project exploring intra-tumor heterogeneity in complex karyotype AML finally out in @NatureGenet! 🎉 👩🏻‍🔬 They say that 10,000 hours make you an expert, so I guess after more than five years of work I’m half-way there 😅 ⬇️1/5 www.nature.com/articles/s41...

I made a starter pack for algorithmic genomics. It's certainly incomplete, but already has a ton of awesome peeps. Let me know if you know people I should add (with a focus on algorithms and data structures in genomics) go.bsky.app/TRWCnZs

🫣👀 Deep learning-based predictions of gene perturbation effects do not yet outperform simple linear methods https://www.biorxiv.org/content/10.1101/2024.09.16.613342v1

There's a lot of excitement about foundation models and their ability to learn biology 🧬💻 But current tools for perturbation prediction perform worse than simple linear models! We need more careful benchmarking to make progress. www.biorxiv.org/content/10.1...

Very excited to announce that I started a postdoc in James Reading's lab at UCL working on tumor immunology 🥳 So, if you are in London and want to meet for a coffee, hit me up :)

Over on mastodon, @teunbrand.bsky.social presented his new package {{gguidance}} to customize your legends and axis in #ggplot: fosstodon.org/@teunbrand/1... Now you can, for example, easily distinguish groups of discrete labels without facetting! #rstats

Great conference with lots of exciting science! 🧪🧬💻

I wrote a new ggplot2 extension to draw Bezier curves github.com/const-ae/ggb... 🎉 The curves are defined by a set of control points and the tangents at those points. This makes each parameter directly interpretable and easy to tweak! #rstats #ggplot2

Job at EMBL Heidelberg: Bioinformatician Scientific Data Manager and Research Software Engineer in Precision Oncology and Multiomics www.embl.org/jobs/positio...

I recently had to convert a manuscript written in Latex to Word and pandoc made the process mostly straightforward. In this blog post, I describe how I fixed some of the remaining edge cases :) const-ae.name/post/2024-08...

Over at Twitter, my colleague Paula has posted about our new R package {{fullRankMatrix}} available on CRAN twitter.com/PaulaH_W/sta... Check it out at github.com/Pweidemuelle... The package helps with design matrices that contain colinear columns. #rstats

Excited to announce pyLemur, a Python version of LEMUR pylemur.readthedocs.io/en/latest/no... Just run `pip install pyLemur` and predict diff. expr. without clusters! 🥳 🧬 🖥️ To learn more about LEMUR, check out my talk at the scverse-meeting from last month: youtu.be/cBkjJLoLX-g?...

Open Position: Scientific Lab and Project Manager at EMBL Heidelberg www.embl.org/jobs/positio...

Join me in 1.5h at the scverse community call (connection details at scverse.zulipchat.com#narrow/strea... ) to learn about LEMUR, differential geometry for single-cell, and get a sneak peek of an upcoming Python package! pylemur.readthedocs.io/en/latest/in...

Had a lot of fun teaching horizontal data integration at the EMBO multi-omics course! We went over strategies to neutralize batch effects and account for conditions in single-cell data. 🧬 🖥️ You can find my tutorial at htmlpreview.github.io?https://gith...

I just uploaded a new version of the LEMUR manuscript www.biorxiv.org/content/10.1... 🎉🥳 LEMUR disentangles observed and latent factors of multi-condition single-cell data and finds groups of cells with consistent differential expression for each gene. Details on the changes ⬇️

Doing multi-condition scRNA-seq and looking for alternatives to working with predefined discrete cell-type categories? Check out LEMUR for differential expression analysis in latent space. Revised version of ms with more application examples and easy-to-use Bioconductor pkg doi.org/10.1101/2023...