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Pau Badia i Mompel

@paubadiam.bsky.social
756 followers 640 following 42 posts

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

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Reposted by Pau Badia i Mompel
Rory Maizels @rorymaizels.bsky.social · 10/03/2026
How can we hope to understand organismal development when it is controlled by huge, complex networks of interacting genes? 
One option is to move away from molecular details and focus on learning representations and rules. Check out the new perspective from me and @jamesbriscoe.bsky.social
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James Briscoe @jamesbriscoe.bsky.social · 09/03/2026
New Perspective form Rory Maizels & me: "Gene regulatory networks: from correlative models to causal explanations" Gene regulatory networks are supposed to give us mechanistic explanations of development, so why are we drowning in 'hairballs' of statistical correlations? rdcu.be/e7zx7
rdcu.be
Gene regulatory networks: from correlative models to causal explanations
Nature Reviews Genetics - In this Perspective, Maizels and Briscoe discuss the limitations of current models of gene regulatory networks and outline solutions to harness data abundance without...
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Nature Reviews Genetics @natrevgenet.nature.com · 10/03/2026
New online! Gene regulatory networks: from correlative models to causal explanations
dlvr.it
Gene regulatory networks: from correlative models to causal explanations
Nature Reviews Genetics, Published online: 09 March 2026; doi:10.1038/s41576-026-00939-1In this Perspective, Maizels and Briscoe discuss the limitations of current models of gene regulatory networks and outline solutions to harness data abundance without compromising explanatory power.
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Seppe De Winter @seppedewinter.bsky.social · 15/01/2026
We are thrilled to share our new pre-print: “System-wide extraction of cis-regulatory rules from sequence-to-function models in human neural development”. S2F-deeplearning models can accurately encode enhancers, yet decoding these models into human-interpretable rules remains a major challenge.
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IRB Barcelona @irbbarcelona.org · 30/12/2025
🧪 The #IRBBarcelona #PhD Call is still open! We are offering PhD #fellowships to talented young scientists from around the world who wish to pursue a doctoral degree in #biomedicine! Learn more and apply by January 9! General call ➡️ bit.ly/3LtzIXi IRB DRIVE call ➡️ bit.ly/4hODx5B
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Alejandro Montenegro @aemonten.bsky.social · 18/12/2025
"We find that while TAD boundaries pair more frequently than non-boundary regions, these interactions are infrequent and are uncorrelated with transcriptional activity of genes within the TAD. (...) These results suggest that TAD boundary architecture and gene activity are largely uncoupled"
biorxiv.org
TAD boundary architecture and gene activity are uncoupled
Topologically associating domains (TADs) are prominent features of genome organization. A proposed function of TADs is to contribute to gene regulation by promoting chromatin interactions within a TAD...
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Britta Velten @brittavelten.bsky.social · 03/12/2025
Happy to see this out now in Cell Genomics: A genome-scale single-cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines: www.cell.com/cell-genomic...
cell.com
A genome-scale single-cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines
Feng et al. present the first genome-scale CRISPR interference perturbation map with scRNA-seq readout across many genetic backgrounds in human pluripotent cells, pioneering population-scale CRISPR pe...
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Giovanni Palla @giopll.bsky.social · 27/11/2025
As more single-cell perturbation data become available, it is crucial to establish a consensus on measures of success for perturbation prediction models. I reviewed recent literature and collected some thoughts on the current state of affairs. open.substack.com/pub/giovanni...
open.substack.com
Virtual Cell Perturbation Metrics Reloaded
Thoughts on metrics for perturbation prediction models
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Randall Munroe @xkcd.com · 26/11/2025
Fifteen Years xkcd.com/3172/
Comic. Panels up to the 10-year point are grayed out. New panels since the Ten Years comic, which chronicles the first ten years of PERSON 1's journey with cancer: (1) [two people in bed] PERSON 1 (woman): One more chapter? PERSON 2 (man): Don’t we both have to get up early? PERSON 1: Nnnnnggggh PERSON 2: Sure, good point. (2) [many people wearing masks, walking while looking at graphs on their phones] (3) [birds landing on people] PERSON 2 in beanie and scarf: Hah! They like *my* seeds best. PERSON 1 in scarf holding phone with a bird sitting on it: Wait, how do I take a picture of this one? (4) [two people rowing boats with tree landscape] (5) [Person 1 carries overflowing stack of things to Person 2 in bed] PERSON 1: I brought you honey lemon tea, more pillows, a cinnamon roll, Tylenol, another blanket, a– PERSON 2: It was just Appendicitis, I’m really– PERSON 1: *It is my turn to take care of you and I am going to do it right!* (6) [Two people in car] (7) [still in car) PERSON 1: Oh my god. PERSON 2: Oh my god. (8) [car driving] PERSON 1: Pull over! PERSON 2: I am! (9) [both people get out of car] (10) [Large colored panel of aurora borealis over water with both people looking on] (11) [Person 1 sits against tree while Person 2 lies on the ground] PERSON 1: Fifteen years. No sign of the cancer. (12) I *am* having some weird symptoms. Joint pain. Fatigue. I think I’m losing my close-up vision. PERSON 2: Yeah. Me too. (13) PERSON 2: I think we’re getting old. (14) PERSON 1: I guess that’s okay. PERSON 2: It’s all I wanted.
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scverse @scverse.bsky.social · 26/11/2025
We wrapped up an inspiring week with a visit to NVIDIA headquarters right after the scverse conference. Huge thanks to the NVIDIA Healthcare team and @severin7.bsky.social for hosting us and for the great discussions on scaling single-cell analysis and accelerating open science ⚡️
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Kurzgesagt – In a Nutshell @kurzgesagt.org · 25/11/2025
Trees are amazing! They build their bodies from thin air, move water with pressures that would crush a human, and grow using a system of living cables wrapped in layers of corpses. Watch our video to find out how they work, and why they might even be immortal: kgs.link/TreesAreDead
An illustration of a cross-section of a tree trunk, highlighting the core labeled "Undead wood" and a glowing ring-shaped layer labeled "Alive part".
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Mikhail Spivakov @mspivakov.bsky.social · 25/11/2025
I'm guest-editing a collection on "Enhancer-promoter interactions" at Genome Biology. Please send us your exciting stories! link.springer.com/collections/...
link.springer.com
Enhancer-promoter interactions
Genome Biology is calling for submissions to our Collection on enhancer-promoter interactions. Enhancer–promoter interactions are central to the regulation ...
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Saez-Rodriguez Group @saezlab.bsky.social · 20/11/2025
📍 Latest OmniPath paper is out now! ➡️ academic.oup.com/nar/advance-...
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Pau Badia i Mompel @paubadiam.bsky.social · 21/11/2025
scverse conference 2025 done ✅ Really engaging week at Stanford with scPerturb-seq work, agentic models in biology, and strong interest in scaling software to millions of cells. Organizing alongside the rest of the @scverse.bsky.social team was a blast! Hope attendees found it productive 😄
All scverse attendeesscverse conference organizersFirst session
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Selin Jessa @selinjessa.com · 07/11/2025
A highlight of my summer was this collab w/ @twangmdphd.bsky.social ! CRISPR base editors are driving several clinical trials, but it's hard to quantify off-target edits and their effects. Tong developed a sequencing assay to identify off-targets *in primary cells* 🧬🖥️🧪 #genomics #chromatin #CRISPR
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Pau Badia i Mompel @paubadiam.bsky.social · 06/11/2025
Can't make it to Stanford? We've just opened remote attendance for scverse Conference 2025! Join us online Nov 17-18 via Zoom 👇
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Tomer Ullman @tomerullman.bsky.social · 03/11/2025
Nature suggests you use their "Manuscript Adviser" bot to get advice before submitting I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:
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Sebastian Lobentanzer @slobentanzer.bsky.social · 27/10/2025
How do we know whether our AI solutions are up to our standards, for instance in clinical recommendations? We try to contribute to the answer by our recent study on *Benchmarking large language models for personalized, biomarker-based health intervention recommendations* rdcu.be/eMVeL
rdcu.be
Benchmarking large language models for personalized, biomarker-based health intervention recommendations
npj Digital Medicine - Benchmarking large language models for personalized, biomarker-based health intervention recommendations
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Arc Institute @arcinstitute.org · 13/10/2025
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...
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Peter Koo @pkoo562.bsky.social · 09/10/2025
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 🧵👇
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scverse @scverse.bsky.social · 09/10/2025
🌟 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
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Jacob Schreiber @jmschreiber91.bsky.social · 07/10/2025
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.
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Philip Ball @philipcball.bsky.social · 08/10/2025
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...
quantamagazine.org
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.
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scverse @scverse.bsky.social · 08/10/2025
🧠 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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Science Magazine @science.org · 01/10/2025
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: 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 · 15/09/2025
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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Luca Marconato @lucamarconato.bsky.social · 12/09/2025
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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Mike Feigin 🥯 @mikefeigin.bsky.social · 11/09/2025
A-tack-seq OR attack-seq? Explain your answer.
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Pau Badia i Mompel @paubadiam.bsky.social · 12/09/2025
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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Stein Aerts @steinaerts.bsky.social · 11/09/2025
@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...
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Alexandra P @alexanrna.bsky.social · 10/09/2025
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...
ikea-style logo of splongget
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Wolfgang Huber @wkhuber.bsky.social · 09/09/2025
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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Rob Patro @robp.bsky.social · 08/09/2025
Bro… please reinspect and change the acronym.
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Saez-Rodriguez Group @saezlab.bsky.social · 01/09/2025
👋 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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Alejandro Montenegro @aemonten.bsky.social · 03/09/2025
I've read the abstract 3 times and I still don't understand the phenomenon www.nature.com/articles/s41...
nature.com
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...
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Pau Badia i Mompel @paubadiam.bsky.social · 03/09/2025
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! 👏
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Beatriz Urda @beatrizurda.bsky.social · 02/09/2025
🚨 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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Beatriz Urda @beatrizurda.bsky.social · 02/09/2025
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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scverse @scverse.bsky.social · 01/09/2025
🎉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 · 28/08/2025
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 · 27/08/2025
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 · 26/08/2025
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!
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scverse @scverse.bsky.social · 26/08/2025
🧫 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 · 26/08/2025
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.
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Maria Brbic @mariabrbic.bsky.social · 25/08/2025
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 🎯
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Valentine Svensson @nxn.se · 25/08/2025
A Visual Guide to Gene Delivery - press.asimov.com/articles/gen...
press.asimov.com
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?
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epithelial mechanics fan club @epimechfc.bsky.social · 23/08/2025
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
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Alexander Luckmann @aluckmann.bsky.social · 20/08/2025
Academia may not give you job security, flexibility, or wealth, but it will let you unexpectedly connect to eduroam in foreign cities
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Michael Hoffman @michaelhoffman.bsky.social · 18/08/2025
"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...
nature.com
Beyond AlphaFold: how AI is decoding the grammar of the genome
Scientists are seeking to decipher the role of non-coding DNA in the human genome, helped by a suite of artificial-intelligence tools.
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Anshul Kundaje @anshulkundaje.bsky.social · 19/08/2025
@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
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