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Pau Badia i Mompel

@paubadiam.bsky.social

730 followers 630 following 39 posts

Postdoctoral researcher at @anshulkundaje.bsky.social‬ Machine learning #ML, gene regulatory networks #GRN, single cell and spatial #omics. Previously at @saezlab.bsky.social Developer of https://decoupler.readthedocs.io/

decoupler.readthedocs.io

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Pau Badia i Mompel @paubadiam.bsky.social · Dec 23

The final chapter of my PhD thesis is now out! 🎉 We compared the latest gene regulatory network (#GRN) inference methods for #single-cell multimodal datasets and evaluated their performance across various tasks. Hard to believe this journey started in March 2021 and has finally reached this point 😅🥳

Saez-Rodriguez Group @saezlab.bsky.social · Dec 23

We present Gene Regulatory nETwork Analsyis (GRETA), a framework to infer, compare and evaluate gene regulatory networks #GRNs. With it, we have benchmarked multimodal and unimodal GRN inference methods. Check the results here 👇
Paper: doi.org/10.1101/2024.12.20.629764
Code: github.com/saezlab/greta

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Reposted by Pau Badia i Mompel

Philip Ball @philipcball.bsky.social · 18h

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...

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.

www.quantamagazine.org

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Reposted by Pau Badia i Mompel

scverse @scverse.bsky.social · 17h

🧠 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

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Reposted by Pau Badia i Mompel

Science Magazine @science.org · 7d

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

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

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Saez-Rodriguez Group @saezlab.bsky.social · 23d

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

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Reposted by Pau Badia i Mompel

Luca Marconato @lucamarconato.bsky.social · 26d

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

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Reposted by Pau Badia i Mompel

Mike Feigin 🥯 @mikefeigin.bsky.social · 27d

A-tack-seq OR attack-seq?

Explain your answer.

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Pau Badia i Mompel @paubadiam.bsky.social · 27d

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 👍

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Reposted by Pau Badia i Mompel

Stein Aerts @steinaerts.bsky.social · 27d

@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...

scverse @scverse.bsky.social · 28d

We will have our next community meeting on Tuesday, 2025-09-16 at 18:00 CEST! Niklas Kempynck will be presenting on CREsted, a package for training enhancer models on scATAC-seq data.
(Zoom registration link and more information in thread!)
🧵

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Reposted by Pau Badia i Mompel

Alexandra P @alexanrna.bsky.social · 28d

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...

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Reposted by Pau Badia i Mompel

Wolfgang Huber @wkhuber.bsky.social · 29d

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)

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Reposted by Pau Badia i Mompel

Rob Patro @robp.bsky.social · Sep 8

Bro… please reinspect and change the acronym.

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Sep 8

Pathway impact analysis (PIS) for robust and comprehensive interpretation of differentially expressed genes (DEGs) https://www.biorxiv.org/content/10.1101/2025.09.08.674792v1

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Reposted by Pau Badia i Mompel

Saez-Rodriguez Group @saezlab.bsky.social · Sep 1

👋 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! 🚀 ✨

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Pau Badia i Mompel @paubadiam.bsky.social · Sep 4

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

Reposted by Pau Badia i Mompel

Alejandro Montenegro @aemonten.bsky.social · Sep 3

I've read the abstract 3 times and I still don't understand the phenomenon

www.nature.com/articles/s41...

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...

www.nature.com

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Pau Badia i Mompel @paubadiam.bsky.social · Sep 3

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! 👏

Beatriz Urda @beatrizurda.bsky.social · Sep 2

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).

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Reposted by Pau Badia i Mompel

Beatriz Urda @beatrizurda.bsky.social · Sep 2

🚨 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

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Reposted by Pau Badia i Mompel

Beatriz Urda @beatrizurda.bsky.social · Sep 2

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).

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Reposted by Pau Badia i Mompel

scverse @scverse.bsky.social · Sep 1

🎉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

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scverse @scverse.bsky.social · Aug 28

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

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Jacob Schreiber @jmschreiber91.bsky.social · Aug 27

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!

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Anshul Kundaje @anshulkundaje.bsky.social · Aug 26

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!

scverse @scverse.bsky.social · Aug 2

🎉 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

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scverse @scverse.bsky.social · Aug 26

🧫 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

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Pau Badia i Mompel @paubadiam.bsky.social · Aug 26

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.

scverse @scverse.bsky.social · Aug 2

Reposted by Pau Badia i Mompel

Maria Brbic @mariabrbic.bsky.social · Aug 25

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 🎯

Nature Biotechnology @natbiotech.nature.com · Aug 25

Systema: a framework for evaluating genetic perturbation response prediction beyond systematic variation - @mariabrbic.bsky.social @mornitzan.bsky.social go.nature.com/4791kda

Systema: a framework for evaluating genetic perturbation response prediction beyond systematic variation - Nature Biotechnology

An evaluation framework isolates perturbation-specific effects in perturbation datasets.

go.nature.com

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Valentine Svensson @nxn.se · Aug 25

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

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?

press.asimov.com

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