Does this mean the end of the central dogma?

I am so excited to share our new findings with you! We provide the structural evidence for a direct protein-to-DNA information pathway, showing how a bacterial enzyme 'reads' its own structure to 'write' DNA. www.science.org/doi/10.1126/...

Spectral multiplexing is typically limited to 4-5 channels. Our new preprint introduces a framework that utilizes DNA barcoding and signal tuning to enable robust spectral unmixing and ground-truth benchmarking to achieve 15-plex subcellular profiling without cycling
www.biorxiv.org/content/10.6...

🚨 Why can’t mammals regenerate limbs like frog tadpoles or salamanders?
In our new paper in @science.org , we show that species-specific oxygen sensing acts as a gatekeeper for initiating limb regeneration 🐭🐸
🔗 www.science.org/doi/10.1126/... #EvoDevo

MPRAs are the gold-standard tool for measuring how DNA sequences drive gene expression and prioritizing variant effects.
In this preprint we asked: does it matter WHERE you place a variant in an MPRA?
Spoiler: yes, and it might lead you to miss disease-causing variants. 1/6
doi.org/10.64898/202...

Ever wondered how a eukaryotic transcription factor finds its specific DNA motif in the vast genome? In this preprint, we directly measured the dynamics of this search process in living cells, revealing a cooperative mechanism mediated by disordered regions. 1/10 doi.org/10.64898/202...

New OpenFold3 preview out! (OF3p2)

It closes the gap to AlphaFold3 for most modalities.

Most critically, we're releasing everything, including training sets & configs, making OF3p2 the only current AF3-based model that is functionally trainable & reproducible from scratch🧵1/9

@events.embl.org

This week I was at the amazing AI and Biology conference at @embl.org I had the chance to meet with so many brilliant researchers and was inspired by many talks. Also presented Corgi of course!

Thanks to all the organizers! #EESAIBio

🧬 How do immune disease-relevant variants affect gene regulatory networks in CD4+ T cells?

🧪🖥️ We coupled two large-scale CRISPRi screens (>4M cells) to map the downstream cascades of thousands of SNPs

More details in the thread below 👇 or in the article 📖 on biorxiv tinyurl.com/CD4screens

Some molecular machines, like ribosomes, can persist for long periods of time in cells.

Could molecular aging of ribosomes shape how proteins are made?

In our new preprint we track ribosomes as they age in cells and uncover unexpected effects on translation (1/10)

www.biorxiv.org/content/10.6...

@matthewkraushar.bsky.social

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.

New online! Gene regulatory networks: from correlative models to causal explanations

Single intramuscular injection of self-amplifying RNA of Nppa to treat myocardial infarction Self-amplifying RNA (saRNA) enables sustained protein expression from a single administration. In this study, we developed an intramuscular saRNA-lipid nanoparticle (saNppa-LNP) therapy encoding natri...

www.science.org/doi/10.1126/...

This is clever, very clever

We wrote a perspective "How to build the regulatory genome: a constructionist guide to the cis-regulatory code", out in Development yesterday. Title says it all. Find it here:

journals.biologists.com/dev/article/...

Our most recent work on the “function and evolution” of #nuclear-speckles is now online at Cell @cp-cell.bsky.social
doi.org/10.1016/j.ce...
Read the thread👇 for the highlights of our findings.

A small polymerase ribozyme that can synthesize itself and its complementary strand The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...

Ooooh. Cool new paper on origins of life. A simple 45-nucleotide RNA molecule that can perfectly copy itself.

www.science.org/doi/10.1126/...

Exciting Postdoc Opportunities – Alliance Interinstitutional Program
**Deadline:** March 31, 2026 (5:00 pm CEST)
🔗 Two shared positions: www.syn-gen.de/alliance-pos...
🔗 Full call & application info:: www.health-life-sciences.de/opportunitie...

We are thrilled that our study on the evolution of gene regulation in mammalian cerebellum development – led by @ioansarr.bsky.social, @marisepp.bsky.social and @tyamadat.bsky.social, in collaboration with @steinaerts.bsky.social – is now out in @ScienceMagazine! www.science.org/doi/10.1126/...

OpenAI’s latest product lets you vibe code science Prism is a ChatGPT-powered text editor that automates much of the work involved in writing scientific papers.

“The idea is to put ChatGPT front and center inside software that scientists use to write up their work in much the same way that chatbots are now embedded into popular programming editors.

It’s vibe coding, but for science.”

Antisense transcription can induce expression memory via stable promoter repression - Genome Biology Background The capacity of cells to retain a memory of previous signals enables acquisition of unique fates and adaptation to their environment. The underlying gene expression memory can arise from mu...

⚠️ The final work of two former PhD students Till @tschwammle.bsky.social and Verena @verenamutzel.bsky.social is out!
➡️⬅️ They dissect how memory can arise from antisense transcription using mathematical modelling 💻, genomics 🧬 and synthetic biology ⚒️! link.springer.com/article/10.1...

Ah I see, makes sense then! Thanks for the explanation.

I understand the answer to the first question after skimming the paper, but I have to check CREsted first. Though I think my point still stands, it would be more appropriate to compare such a TFBS prediction with something that uses motif+some data, like TF footprinting maybe.

Very interesting work! Is TF-MINDI cell type agnostic? What I mean is does it use the entire S2F model (e.g. all 7000 Borzoi tracks) or when predicting in PMBC you use only the PMBC channels?

Also, I'm not sure if motif enrichment is the right comparison here. S2F models learn from data after all

TF-MINDI is out! A new method to learn cis-regulatory codes through rich embeddings of TF binding sites. TF-MINDI decomposes motif neighbourhoods, and works downstream of any sequence-to-function deep learning model. We deeply study the enhancer code in human neural development, check out the thread

In remembrance of Peer Bork  | EMBL EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.

very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...

This sounds like it's from a sci-fi novel!

Save the date: April 9 from 4pm to 6pm CET. Our department is hosting an online seminar with @noeliaferruz.bsky.social @sdomcke.bsky.social @const-ae.bsky.social who will talk about models for protein design, large-scale perturbation screens, and benchmarking of perturbation prediction models.

An expanded registry of candidate cis-regulatory elements - Nature The existing ENCODE registry of candidate human and mouse cis-regulatory elements is expanded with the addition of new ENCODE data, integrating new functional data as well as new cell and tissue types...

Our paper on the newest version of the Registry of candidate cis-Regulatory Elements (cCREs) is out 🧬

Huge thanks to the many collaborators, experimentalists, analysts and software developers who made this work possible — truly a team effort!

A "meme-torial" of the science is coming soon 👀

Venezuelan president Maduro captured and flown out of country following ‘large scale’ US attack, Trump says – live US president says ‘the United States of America has successfully carried out a large scale strike against Venezuela’

The Empire strikes back, not just to grab oil and other riches but, fundamentally, to hide its own weakness at home – and to prepare the ground for subjugating its own people, in Chicago, Portland, NYC etc. Meanwhile, a vassal Europe watches in silence... www.theguardian.com/world/live/2...