All right it’s time for the annual “please tell us about one (or a few if you are ambitious) paper from 2025 that really impressed you and why we should all read it“! Go! If you tell us how it changed your view of the world and what makes it so powerful and consequential It would be excellent.

If you ever need to fuzzy search some DNA, sassy is your tool. Please spread the word; I think many people just outside my own circle could benefit from this :) cc @rickbitloo.bsky.social github.com/RagnarGrootK...

Excited to share new preprint led by Sergio Salas on “unassigned RNAs” in imaging-based spatial transcriptomics. Across technologies, 30-40% of transcripts fall outside segmentation, & many show structured, biologically meaningful extrasomatic patterns. 📄 www.biorxiv.org/content/10.6...

I wrote a guide on constructive peer review. This is a polished version of an internal guide I had for my group. Of course, constructive feedback is welcome, peers! deboer.bme.ubc.ca/2025/12/09/g...

A new lab preprint is up: Work led by our MSc student Jan Sprengel comparing Interventional Causal Structure Learning Algorithms for Gene Regulatory Network Inference from single cell CRISPR perturbation screens 👇 www.biorxiv.org/content/10.6...

ISCO (Innovations in Single-Cell OMICS) will be back in beautiful Barcelona! 🗓️ 28th/29th of May 2026 📍Barcelona Biomedical Research Park @prbb.org (beachfront!) Keynotes: @bartdeplancke.bsky.social and @bocklab.bsky.social Submit your abstract and present your research! www.isco-conference.eu

I wrote a blog post about the often stated but never explained assumption that communities in graphs should always be connected. This is inconsistent with statistical significance and null models that underlie the most widely employed methods. skewed.de/lab/posts/co...

Great to see this published: Fitting dynamical landscape models to single-cell data, creating interpretable maps of cell decision making & developmental logic Applied to neural tube patterning, we show how morphogen signals reshape landscapes and drive fate decisions www.pnas.org/doi/10.1073/...

Related with my last post, I entered X and found this bioRxiv preprint: doi.org/10.1101/2025... I'm going to say some consciously exaggerated comments below.

I'm lately liking Bluesky. These ~2 months has been full of interesting papers & discussions (thanks Paper Skygest @paper-feed.bsky.social). Not crypto-bros, not so many AI-bros - just like in Twitter/X

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...

Congratulations to the new cohort of 28 EMBO Young Investigators! They are joining an international network of more than 800 life scientists – Welcome! Read the press release here: https://www.embo.org/press-releases/twenty-eight-group-leaders-become-embo-young-investigators/

We've been using this for years - I'm still surprised how Xist alone is so good for sex classification at single-cell level. Credit where should be given: original idea by Daniel Fernández-Pérez (a.k.a the best postdoc!)

Sample-level modeling of single-cell data at scale with tinydenseR https://www.biorxiv.org/content/10.1101/2025.11.26.690752v1

"Bulk RNA-seq to the rescue of differential expression analysis in single-cell transcriptomics" 🧫 📑 A new PCI Genomics recommendation by @mireyaplass.bsky.social: doi.org/10.24072/pci...

Your periodic reminder that science is not done by a few selected "stars scientists". Science is done by hundred of thousands. Siloed money mean a few flashy discoveries and a lot of waste. Want to change things? Make funding accessible and stop funding calls with less than 2% success rate.

🧬 New preprint out on bioRxiv! Using single-cell WGS and Bayesian phylodynamics, we show that some CRC tumors arise decades before diagnosis, remain indolent, then expand rapidly in the last ~2 years. 📄 doi.org/10.1101/2025... 🙏 Huge thanks to all co-authors

k-spaces: Mixtures of Gaussian latent variable models https://www.biorxiv.org/content/10.1101/2025.11.24.690254v1

IMO the contributions section of scientific articles should be standardized: credit.niso.org

This is important for 🧪🔬 www.embopress.org/doi/full/10....

Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA. Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions). It’s been a joy working with you @estellayixingdong.bsky.social!

This seems AMAZING: CRIPSR-All!

We are looking for a postdoc to join our team! If you're interested in translating a cutting edge genomics technology (www.nature.com/articles/s41...) to real-life applications in hematology, this is for you. We offer a unique working environment ON THE BEACH: recruitment.crg.eu/content/jobs...

Would you like to model and analyze sample-specific regulatory networks? Check out our latest BioRxiv pre-print in which we present 𝐒𝐢𝐒𝐚𝐍𝐀, a command line workflow that makes modeling and analysis of single-sample networks really easy, transparent, and reproducible 🪄: www.biorxiv.org/content/10.1...

Are you using any of our factor models, such as MOFA? 🛵 You might’ve found it challenging to tailor them to your specific use cases - not anymore! Introducing MOFA-FLEX: a flexible, modular factor analysis framework designed for customizable modeling across diverse multi-omics data scenarios. 1/n

𝗖𝗮𝗻 𝗰𝗲𝗹𝗹𝘀 𝗲𝘃𝗲𝗿 𝘁𝗿𝘂𝗹𝘆 𝗿𝗲𝗰𝗼𝘃𝗲𝗿 𝗳𝗿𝗼𝗺 𝗗𝗡𝗔 𝗱𝗮𝗺𝗮𝗴𝗲?Excited to share our new study “Repair of DNA double-strand breaks leaves heritable impairment to genome function”, revealing DNA repair’s hidden cost, out now @science.org tinyurl.com/5n6zw3ye. Led by @sbantele.bsky.social and Jiri Lukas.🧵👇1/n

Big New! @elife.bsky.social @genetics-gsa.bsky.social #G3journal are joining editorial forces with @reviewcommons.org - bringing not just field-specific expertise to the process but also making #PreprintPeerReview a truly collaborative effort!🎉👏 Read more to find out👇 www.embo.org/features/pub...

1/ @reviewcommons.org, @embo.org's preprint peer review platform, is taking an important step forward. Multiple publishers, including eLife, are now jointly running the peer-review process on behalf of the platform. 🔗 buff.ly/Rm1XotK

This is really interesting doi.org/10.1038/s415...

Training other methods on the same data may not be feasible due to compute limitations. Training on other much smaller data won’t be the same task. Training your implementation or with your compute limitations is not representative of the original method.

Academics also can be driven and intelligent, but the driver is often personal curiosity and understanding, with a fair bit of showing off (academic egos are something else; I am self aware enough to realise I am not immune to this though I do try to tame it).

Thread on the intellectual landscape around LLMs 👇 I love progress and am happy to see investment in it—but wonder if the amounts currently going into genAI are a missed opportunity to invest in more mundane "data plumbing" and digitalisation. Which could eventually have higher societal benefits.

Proud of the latest edition of my free intro biostats book. gitrepo: github.com/ybrandvain/b... book: ybrandvain.github.io/biostats/ Not complete but at a good point to take a break, and I think its quite usable dm me with comments , ideas etc

Hey Yaniv Brandvain is not on Bluesky but his most recent biostats ebook is live ybrandvain.github.io/biostats/. His stats resources have been so helpful to me as I develop my own stats course, so check it out. Github repo here: github.com/ybrandvain/b...

Are professors who don’t teach or mentor, just academic executives who raise money and market other people’s work? When did teaching stop being an important part of this job?

How can we scale subcellular spatial proteomics across many experiments and conditions? Our new paper presents a genetic algorithm and evaluation framework that optimizes bait subsets for proximity proteomics platforms like BioID enabling context-specific proteome mapping.

Discovery and engineering of retrons for precise genome editing - @texasscience.bsky.social go.nature.com/4nkr7DE

Correlation isn’t causation, as the mantra goes—but statistical noise in correlational data can reveal causal information. When X and Y are causally linked, their noise tends to be asymmetric & this can guide #CausalInference. Check out our 📃👇 doi.org/10.1111/nous... #philsky #philsci #StatsSky #HPS

🧵1/17 📣Thrilled to share our latest study just out in Cancer Discovery! ➡️ aacrjournals.org/cancerdiscov...

New “discrete state” model of hematopoiesis published in Nature Immunology. rdcu.be/eL8oO We propose a hierarchical model of hematopoiesis where stable “discrete states” serve as key regulatory nodes.

🧠 The Lipid #Brain Atlas is out now! If you think #lipids are boring and membranes are all the same, prepare to be surprised. Led by @lucafusarbassini.bsky.social with Giovanni D'Angelo's lab, we mapped membrane lipids in the mouse brain at high resolution. www.biorxiv.org/cgi/content/...

BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 (thread 👇)

15 years in the making, we confirmed that mitochondria - the powerhouse of the cell - have an unusual localization in patients who experience psychosis (including schizophrenia and bipolar disorders). You’ll never guess what kind of patient cells we used to make this discovery… 🧵

I read and write, I explore and I question, I design and script and analyse, I interpret and communicate. I do this to train my mind in the hopes of one day generating new knowledge. New knowledge that might even be useful, and that no algorithm can yet be trained on.

Our benchmark + guidelines for atlas-level differential gene expression of single cells is online: academic.oup.com/bib/article/... Bottom line: Use pseudobulk + DESeq2 in simple and pseudobulk + DREAM in more complex settings. Collab w/ @leonhafner.bsky.social @itisalist.bsky.social

Model organisms as platforms for training scientific minds www.nature.com/articles/s41...

Fantastic review on the importance of rigorous experimental design. Amen. 😊 "'To consult the statistician after an experiment is finished is often merely to ask him to conduct a post mortem examination. He can perhaps say what the experiment died of.' – Ronald A. Fisher" @manuelkleiner.bsky.social

How can mitophagy be an effective quality control mechanism if mtDNA mutations reach high enough levels to cause disease? This question led us into a dark path, full of concepts of evolutionary genetics, germline stem cell biology and mito-nuclear compatibility. www.science.org/doi/10.1126/...