Ekin Deniz Aksu

📣 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.

A complete diploid human genome benchmark for personalized genomics Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...

Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)

Just got my flu vaccine shot.

Don't forget yours this season!

Congratulations!! 🎉

🥳 Thrilled to share that our lab has been awarded an ERC StGrant for our project SigReg: Signal to Regeneration!

How can we unlock limb regeneration in adult mammals?

It’s time to apply what we learned from 🐸 ➡️ 🐭

Thank you @erc.europa.eu for supporting ambitious science!!!

Juliane Glaser receives an ERC Starting Grant – portrait of Juliane with text on the left.

New ERC Starting Grant for Juliane Glaser to study role of epigenetic mechanisms, specifically the control of transposable elements, in mammalian embryonic development.

Read all details here: www.ie-freiburg.mpg.de/6057908/2025...

Congratulations @julianeg.bsky.social

@erc.europa.eu #ERCStG

4-panel Comic. (1) STUDENT: If the wavefunction only collapses when I observe it, does that mean my consciousness affects the universe? (2) [Bad:] PROFESSOR: Yes, quantum entanglement proves that we all have souls. (3) [Good:] PROFESSOR: No, consciousness plays no role here. It’s just physical measurement. (4) [Chaotic:] PROFESSOR: No. The wavefunction collapses when *I* look at it because I’m a full professor. It won’t collapse for an undergraduate.

Wavefunction Collapse

xkcd.com/3134/

Update: Trans perturbations are very tricky. The model has some capability of this, but mostly the output is not very sensitive to single perturbations. In hindsight this isn't surprising to me.

New preprint alert!

Corgi imitates cellular gene regulation and integrates DNA sequence and trans-regulator information.

This allows Corgi to make accurate predictions in unseen cell types. Also, it can simulate trans-regulator perturbations in silico.

If you like transcription regulation and its mechanisms, this WIP list is for you.

I'm sure I've forgotten lots of people, so don't hesitate to let me know so I can add you to the list.

go.bsky.app/8vTgeXB

Thanks! :)

Amazing list, thank you! I'd like to be included as well. I work on deep learning models of human gene regulation.

I think it makes sense, in that genomic DNA that is not a promoter has, through evolution, committed to being not a promoter. So its distribution is shifted away from promoters. Random DNA shouldn't have such a shift.

Phenology changes for the Japanese cherry tree (Prunus jamasakura) in Kyoto. Left: Day of the year of the flowering peak for the period between 812 and 2024. Right: Relation between March mean air temperature (°C) in Kyoto and the day of the year of the Japanese cherry tree peak flowering for the period between 1890 and 2024. https://jgpausas.blogs.uv.es/2025/06/11/134-years-of-climate-warming-effects/

Climate warming is not a recent phenomenon; it has had detectable impacts on plants for at least 134 years!

The onset of phenological plant response to climate warming @newphyt.bsky.social
nph.onlinelibrary.wiley.com/doi/10.1111/...

🧪🌎🌿🌐🌳 🍁 #PlantBiology @cideinvestiga.bsky.social @csic.es

Looking forward to spending the next couple of months at MIT, collaborating with @bergerlab.bsky.social on deep learning methods in computational biology!

Congrats!!