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...

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! 🧵

Our tool, RIDDEN (Receptor actIvity Data Driven inferENce) for predicting #receptor activity from #transcriptomics data is published in PLOS Computational Biology journals.plos.org/ploscompbiol... 1/n

Single-cell foundation models, trained on large-scale scRNA-seq datasets, are increasingly used for post-perturbation RNA-seq prediction. But how do they actually perform? Our new paper from @turbine-ai.bsky.social is now out in BMC Genomics. bmcgenomics.biomedcentral.com/articles/10.... 1/5

Hello #AACR25 !

We have an opening for a PhD/Postdoc in Spatial Omics for Cardiology in Heidelberg 🫀 #job #academicjob #phd #postdoc #cadiology 👇 jobrxiv.org/job/heidelbe...

Turns out the way we usually pre-train foundational cell models adds very little information to the system - definitely not enough to make drug effect predictions work. Not what I've expected. #virtualcells #foundationalmodels #compbio blog.turbine.ai/p/pretrainin...

easter holiday is coming: 2 revised versions submitted today

You’ve probably heard about how AI/LLMs can solve Math Olympiad problems ( deepmind.google/discover/blo... ). So naturally, some people put it to the test — hours after the 2025 US Math Olympiad problems were released. The result: They all sucked!

Does @iscb.bsky.social have a statement on this? We need to be there to support bioinformatics researchers.

based on some recent papers / presentations, the hill(s) I'll die on: 1) Raw IC50 values != good metrics for comparing cancer drug sensitivity 2) Raw TPMs / counts are meaningless for comparing gene expression similarity 3) Diverging color palettes need a meaningful midpoint.

Post-doc opening to join our lab @ebi.embl.org to develop&apply #bioinformatics and #machine-learning methods to study intra-/extra cellular networks to extract disease mechanisms from #single-cell and #spatial multiomic data - please share 🙏 : embl.wd103.myworkdayjobs.com/EMBL/job/Hin...

We will be hosting the International Conference on Systems Biology (ICSB) in Dublin this year – 5-9th October icsb2025.com/registration/ #ICSB2025

It's been over 24 hours since #AdventOfCode 2024 ended! This AoC season: - 273,313 users collected at least one star - 3,654,949 stars were collected Since 2015: - 779 users have all 500 stars - 1,077,226 users collected at least one star - 23,170,305 were collected

holiday season is coming: 2 papers submitted today

[first 🦋] Receptors are essential for cell-cell communication, yet most comp CCC tools focus on ligand/receptor expression, not receptor activity. To address this, we developed RIDDEN, a model that infers activity for 229 receptors from transcriptomics data. 1/n www.biorxiv.org/content/10.1...

I just completed "Historian Hysteria" - Day 1 - Advent of Code 2024 #AdventOfCode adventofcode.com/2024/day/1

We have created a starterpack to make it easier to follow current members and alumni from our lab, check it out 👇 (DM us if we forgot about you) Also juliosaezrod.bsky.social has recently joined Bluesky go.bsky.app/5ZtPHPz

Hi 🦋 This is the saezlab (saezlab.org) bluesky account. We integrate #omics data with mechanistic molecular knowledge into statistical and machine learning #ML methods, and we share our tools as free #opensource packages (github.com/saezlab/) #systemsbiology #biology #compbio