Ekin Deniz Aksu
@ekindea.bsky.social
450 followers 610 following 18 posts
Scientist and medical doctor. Gene regulation, DNA sequence models, transcription factor binding. Doing a PhD in computational biology at @molgen.mpg.de.
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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.
Reposted by Ekin Deniz Aksu
⚡⚡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.
Reposted by Ekin Deniz Aksu
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...
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Just got my flu vaccine shot.

Don't forget yours this season!
Reposted by Ekin Deniz Aksu
🥳 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!!!
Massive congratulations to @canaztekin.bsky.social for being awarded an ERC Starting Grant @erc.europa.eu ! 🎉 His "Signal to Regeneration" (SigReg) project will explore the potential of limb regeneration in mammals.

Read more and watch Can introduce his project: s.gwdg.de/cLAmJE
Reposted by Ekin Deniz Aksu
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
Juliane Glaser receives an ERC Starting Grant – portrait of Juliane with text on the left.
Reposted by Ekin Deniz Aksu
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.
Reposted by Ekin Deniz Aksu
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.
Reposted by Ekin Deniz Aksu
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
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.
Reposted by Ekin Deniz Aksu
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
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/
Looking forward to spending the next couple of months at MIT, collaborating with @bergerlab.bsky.social on deep learning methods in computational biology!
Reposted by Ekin Deniz Aksu
@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