Pau Badia i Mompel

Congrats Britta! 🎉

Arc is looking for an outstanding early-career scientist to be our next Science Fellow. This program provides resources and freedom for those looking to transition into a principal investigator role immediately after doctoral training. Apply here: arcinstitute.org/programs/sea...

Which mutations rewire function of regulatory DNA?

Excited to share SEAM: Systematic Explanation of Attribtuion-based Mechanisms. SEAM is an explainable AI method that dissects cis-regulatory mechanisms learned by seq2fun genomic deep learning models.

Led by @EESetiz

1/N 🧵👇

🌟 Thank You to Our Gold Sponsor: Stellaromics! 🌟

We're proud to recognize Stellaromics as a Gold Sponsor of scverse conference 2025! 🥇

@stellaromics.bsky.social
#scverse2025 #SpatialBiology #3DSpatial #ComputationalBiology #SingleCell #Stellaromics #SpatialOmics #Bioinformatics

Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians!

The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.

Loops of DNA Equipped Ancient Life To Become Complex | Quanta Magazine New work shows that physical folding of the genome to control genes located far away may have been an early evolutionary development.

I adored writing this piece. It brings together several of the things preoccupying me right now, like chromatin organization and gene regulation. There's so much more to be said on that. Also, these marine critters look gorgeous.
www.quantamagazine.org/loops-of-dna...

🧠 Arc Workshop at the upcoming scverse conference 2025 🧠

Processing and Modeling Large-Scale Single-Cell Perturbation Data with Machine Learning
🧵

@arcinstitute.org

#scverse2025 #PerturbSeq #MachineLearning #SingleCell #CRISPR #GenomicScreening #VirtualCells

"… Goodall’s … is a story of genuine scientific curiosity, determination, and respect for nature and humanity …" H. Holden Thorp, Editor-in-chief, Science journals

Jane Goodall has died at the age of 91.

In 2020, Goodall spoke with Science Editor-in-Chief H. Holden Thorp for a #ScienceEditorial reflecting on the 60th anniversary of her arrival in Gombe to study wild chimpanzees. Read more: https://scim.ag/472Chb8

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...

ikea-style logo of splongget

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! 🚀 ✨

Best of luck at Merck @smuellerdott.bsky.social ! 😜

One mother for two species via obligate cross-species cloning in ants - Nature In a case of obligate cross-species cloning, female ants of Messor ibericus need to clone males of Messor structor to obtain sperm for producing the worker caste, resulting in males from the same moth...

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 There are at least 10,000 known monogenic diseases. When attempting to cure them, how do clinicians decide which gene-therapy delivery method is best?

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