Introducing ParTIpy, a python package for Pareto Task Inference that scales to large-scale datasets, including single-cell and spatial transcriptomics. 🔗 Manuscript: www.biorxiv.org/content/10.1... 💻 Code: partipy.readthedocs.io

My favorite part of last-year #scverse conference was to finally meet in-person many developers that I only knew from their GitHub username! Submissions and travel grant applications close in 3 days. Find out more and apply at scverse.org/conference2025 @scverse.bsky.social

A-tack-seq OR attack-seq? Explain your answer.

Been digging through GEO for multiome single-cell data, frustrating how much is unusable 🫠 (missing annotations, frag files, raw data). Uploading properly takes effort, but it makes your dataset so much more impactful... Props to (most of) the authors who fixed things when I reached out, though 👍

@niklaskemp.bsky.social will present our new CREsted framework at the next scverse community meeting! CREsted allows you to train sequence-to-function models tailored to cell type-specific enhancers (including synthetic enhancer design) www.biorxiv.org/content/10.1... github.com/aertslab/cre...

1/ First preprint from @jdemeul.bsky.social lab 🥳! We present our new multi-modal single-cell long-read method SPLONGGET (Single-cell Profiling of LONG-read Genome, Epigenome, and Transcriptome)! www.biorxiv.org/content/10.1...

Join EMBL as a research group leader in AI in biology. EMBL AI is our new initiative aiming to exploit the full potential of ML/AI-based approaches to advance our understanding of the most complex system in the known universe - life on Earth. embl.wd103.myworkdayjobs.com/en-US/EMBL/j... (1/3)

Bro… please reinspect and change the acronym.

👋 Time to say goodbye to another one of our PhD students, @smuellerdott.bsky.social. She was working on the integration of phosphoproteomics and transcriptomics data and will now join the Computational Oncology Team at Merck. We wish her all the best for this new chapter! 🚀 ✨

I've read the abstract 3 times and I still don't understand the phenomenon www.nature.com/articles/s41...

I always find it funny that we obsess over sample size, yet peer review relies on the arbitrary opinions of just 2/3 people. That would be fine if editors were truly engaged, but given the workload, they don’t have the time, or don’t care enough. Anyway, I’m just glad it finally got published! 👏

🚨 New in PNAS! 🧬 64% of disease co-occurrences can be explained by transcriptomic similarities. Comorbidities aren’t random—they have a molecular basis. Here’s how we found it 👇 (1/n) 🔗 doi.org/10.1073/pnas.2421060122 @alfonsovalencia.bsky.social

1/ Everything that could go wrong in paper publishing… did. A story of patience, absurdity, and persistence 🌀 <1min From Alfonso Valencia’s lab and a very stubborn PhD student (me).

🎉scverse conference 2025 Call for Abstracts DEADLINE EXTENDED! 🎉 We're excited to announce that the deadline to submit abstracts for the scverse Conference 2025 has been extended to September 15, 2025! 🧵 #scverse #scverse2025 #SingleCell #Conference

Meet the keynote speakers for the 2025 scverse conference! Elham Azizi, Associate Professor of Cancer Data Research and Biomedical Engineering at Columbia University 🧵 @elhamazizi.bsky.social @columbiauniversity.bsky.social #scverse #scverse2025 #machinelearning #genomics #cancerimmunology

In the genomics community, we have focused pretty heavily on achieving state-of-the-art predictive performance. While undoubtedly important, how we *use* these models after training is potentially even more important. tangermeme v1.0.0 is out now. Hope you find it useful!

scVerse conference is at Stanford this year! Encourage folks (especially Bay Area/West coast folks) to sign up and attend. Cool workshops/talks and other events + great community of developers for one of the most widely used open source software for single cell data analysis!

🧫 Meet the keynote speakers for the 2025 scverse conference! Erika Alden DeBenedictis, Co-founder of The Align Foundation & CEO of Pioneer Labs @erika-alden.bsky.social ‪ @alignbio.bsky.social @pioneerlabs.bsky.social #scverse #scverse2025 #StructuralBiology #Biotech #Stanford

We're bringing together the single-cell and spatial omics community for three days at Stanford University this November. Whether you're developing methods, translating research, or exploring the latest technologies, consider submitting an abstract or registering.

Our Systema framework for evaluating genetic perturbation response prediction methods is now out in @natbiotech.nature.com ✨ Systema helps to evaluate perturbation response prediction methods by focusing on perturbation-specific effects rather than systematic variation 🎯

A Visual Guide to Gene Delivery - press.asimov.com/articles/gen...

Collective cell motion has many forms, but rotation is the coolest of them all. I'm @onenimesa.bsky.social , and in this short🧵, I'll highlight some instances of global tissue rotation like this one from @BauschLab

Academia may not give you job security, flexibility, or wealth, but it will let you unexpectedly connect to eduroam in foreign cities

"I want to vibe code the genome" —the illustrious @casey.greenelab.com as quoted by @jperkel.bsky.social @nature.com 🧬🖥️ #MLSky www.nature.com/articles/d41...

@jengreitz.bsky.social l & my lab want to co-hire a computational biologist/biostatistician with project management expertise to help map the regulatory code of the human genome and discover genetic mechanisms of disease. Details below careersearch.stanford.edu/jobs/computa... Plz RT

Job Alert: A stealth startup focused on non-cancer diagnostics is keen to hire a deep learning for genomics/bio engineer. I am an advisor for the startup & closely involved. Please see the job description below and get in touch if interested. Plz forward.

Our paper is now out in final form at Nature Genetics! For those who missed the preprint, we used large-scale Perturb-seq targeting transcription factors to push primary fibroblasts into diverse transcriptional states, including those observed in cell atlas studies.

Introducing five concepts from dynamical systems to decode developmental regulatory mechanisms, have a read! @perez-carrasco.bsky.social‬ @roederlab.bsky.social @mpipz.bsky.social This effort started in a morphogenesis meeting @kitp-ucsb.bsky.social‬ in 2023. journals.biologists.com/dev/article/...

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...

Biological engineering is an aspirational term. Tinkering is often more apt. Mostly, we do not understand biological systems to engineer them in the same way we engineer cars and aircraft.

🎉 scverse conference 2025 Registration & Call for Abstracts NOW OPEN! 🎉 We're excited to announce that registration and the call for abstracts are officially open for the scverse Conference 2025! Details in thread! 🧵 1/3

the print link www.biorxiv.org/content/10.1...

Hello everyone, OmniPath is coming to Bluesky, this is our very first post here! 🐦 Check out our poster at #ISW2025 Visegrad: static.omnipathdb.org/poster-isw20... We're preparing exciting new updates in the next months, follow us here! 🌟 @saezlab.bsky.social

Thanks to @riyavsinha.bsky.social in my lab, the IGV browser will natively support dynseq (dynamic sequence tracks) in an upcoming release. These tracks are very useful to directly visualize base-resolution scores (e.g. contribution scores from ML models, conservation etc). 1/

Can’t wait to introduce bird-based storage into my backup system

1. Here's a fish swimming upstream. Nothing unusual about that. What's unusual is that this particular fish is *dead*. Vortices in the water as it flows past the fish cause the fish's body to flex, maintaining orientation and actually propelling it forward. (D. N. Beal et al 2006 J. Fluid. Mech.)

Wow Karolinska Institutet is recruiting 20 outstanding early-career researchers for assistant professor positions ki.se/en/about-ki/...

Better version of the meme.

Doing a post doc

🎉 The revised version of CORNETO, our unified Python framework for knowledge-driven network inference from omics data, is published in peer reviewed form 🔗 Paper: www.nature.com/articles/s42... 📖 News & Views: www.nature.com/articles/s42... 💻 Code: corneto.org 🧵 Thread 👇

Advances in DNA-synthesis technologies are allowing large volumes of DNA to be pumped out a low cost go.nature.com/4mrIh2j

I'm excited to share work on a research direction my team has been advancing: connecting machine learning derived genetic variant embeddings to downstream tasks in human genetics. This work was led by the amazing Divyanshi Srivastava! www.biorxiv.org/content/10.1...

New tgv release: local cache! tgv download hg38 Download UCSC reference genomes to a local sqlite db for much faster browsing. Awesome Rust tools (twobit, bigtools) made this simple. github.com/zeqianli/tgv

*Easter egg alert* NOT in the published paper. We also benchmarked Evo 2 and while it did better than other gLMs (consistent that scale can improve gLMs), it still falls short of a basic CNN trained using one-hot sequences and far short of supervised SOTA

We found a new asymmetry in the large-scale chromosome structure: sister chromatids are systematically shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! The work was led by Flavia Corsi, in close collaboration with the Daniel Gerlich lab. www.biorxiv.org/content/10.1... 1/

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

Help me build a virtual version of my apartment by training a hugeee (like so huge) neural network on temperature data from my stove. Call to action from the community to achive this ambitious goal!

FYI: New online! RNA polymerase II transcription compartments — from factories to condensates

🧵 1/9 I want to share some (inconclusive) thoughts about the generalization capabilities of protein language models under this main question: ¿what does it mean IN distribution generalization and what does it mean OUT of distribution generalization in (protein) biology?