Ekin Deniz Aksu

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...

📣 I hereby make my Bluesky debut to announce that our work linking DNA binding affinities and kinetics 𝘪𝘯 𝘷𝘪𝘵𝘳𝘰 and 𝘪𝘯 𝘷𝘪𝘷𝘰 for the human transcription factor KLF1 just got published in Cell! @cp-cell.bsky.social

www.cell.com/cell/fulltex...

Key findings in a thread (1/6):

My first @umasschan.bsky.social/@impvienna.bsky.social affiliated paper is up!

tomtom-lite is a re-implementation of tomtom targeting the ML age of genomics. Fast annotations ("what is this motif?") and simple large-scale discovery of motifs.

Check it out!

academic.oup.com/bioinformati...

Hey authors! Check to see if Anthropic stole your book to train their slop generator on. You’re entitled to $1500 per stolen Work.

Look up your work, and if you’re in the database, file a claim
secure.anthropiccopyrightsettlement.com/lookup/

Today I was happy to present Corgi at the @broadinstitute.org Broad Institute at the ML in Drug Discovery Symposium.

If you want to use it for predicting genomic tracks, Corgi is now published on GitHub: github.com/ekinda/corgi

Three new research groups joining the MPIMG

We are excited to welcome @fueyoraquel.bsky.social, @sedonamurphy.bsky.social, and @jmstein.bsky.social as new group leaders at our institute!
Read more about their work:
--> www.molgen.mpg.de/2025-10-31-n...
All three are recruiting in the IMPRS PhD Call!
--> www.molgen.mpg.de/IMPRSPhDproj...

Last chance to turn it off.

On Monday, November 3rd, Microsoft will start using your LinkedIn data for AI training. And remember, you're opted in by default.

To toggle it off 👉 Account - Settings & Privacy > Data privacy > Data for Generative AI Improvement.

Introducing the CodonFM Open Model for RNA Design and Analysis | NVIDIA Technical Blog Open research is critical for driving innovation, and many breakthroughs in AI and science are achieved through open collaboration. In the field of digital biology research, NVIDIA Clara supports this...

The genetic code is full of synonymous codons that, for decades, were assumed to be interchangeable.

Today, with NVIDIA, co-led by @genophoria.bsky.social, we announce CodonFM, a family of open-source AI models that reveal the grammar underlying codon choice: developer.nvidia.com/blog/introdu...

Enhancer-promoter compatibility is mediated by the promoter-proximal region Gene promoters induce transcription in response to distal enhancers. How enhancers specifically activate their target promoter while bypassing other promoters remains unclear. Here, we find that the p...

What is a promoter? And how does it work?

We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters

www.biorxiv.org/content/10.1...

Neural anticipation of virtual infection triggers an immune response - Nature Neuroscience Serino et al. show that seeing an infectious avatar approach the body in virtual reality triggers an immune response, indicating that the brain prepares the body to fight infections even for perceived...

Neural anticipation of virtual infection triggers an immune response
www.nature.com/articles/s41...

Reporter CRISPR screens decipher cis-regulatory and trans-regulatory principles at the Xist locus - Nature Structural & Molecular Biology Here Schwämmle et al. develop CRISPR reporter screens to map transcription-factor-regulatory element interactions at the Xist locus, revealing a two-step mechanism integrating developmental and X-dosage signals to initiate X-chromosome inactivation.

⚠️ Paper alert: Using a novel CRISPR screening approach, we mapped the entire regulatory network controlling Xist—key for X-chromosome inactivation.
👉 We discover how sex and development signals are decoded at a single gene locus.
www.nature.com/articles/s41...
👇 Bluetorial

Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq - Nature Genetics This study introduces single-cell transcription factor (TF) sequencing, a single-cell barcoded and doxycycline-inducible TF overexpression approach that reveals dose-sensitive functional classes of TFs and cellular heterogeneity by mapping TF dose-dependent transcriptomic changes during the reprogramming of mouse embryonic multipotent stromal cells.

🧵1/ Excited to share our new paper introducing a new #singlecell assay: scTF-seq, a high-throughput single-cell approach to explore how transcription factor (TF) dose shapes cell identity and reprogramming outcomes. 🔗 www.nature.com/articles/s41... Big congrats to the entire team @EPFL & @SIAT_China

⚡⚡Excited to announce I'll be starting my lab at the Max Planck Institute of Molecular Genetics (@molgen.mpg.de) in Berlin in December! Leaving sunny California to join a fantastic environment with colleagues who do super cool work.
🔬🦠I'm hiring at all levels! 🔬🦠Check: www.molgen.mpg.de/fueyo-lab

It's conference week in Cambridge. Yesterday I presented Corgi in the MIT/MGB AI Cures conference, and today I'm at the Broad Institute for the Variant to Function conference.