Ekin Deniz Aksu
@ekindea.bsky.social
Scientist and medical doctor. Biology AI/ML methods, gene regulation, DNA sequence models, single cells. Doing a PhD in computational biology at @molgen.mpg.de.
Pinned
Ekin Deniz Aksu
@ekindea.bsky.social
· Jun 26
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.
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.
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
If you want to use it for predicting genomic tracks, Corgi is now published on GitHub: github.com/ekinda/corgi
November 7, 2025 at 11:36 PM
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
If you want to use it for predicting genomic tracks, Corgi is now published on GitHub: github.com/ekinda/corgi
Reposted by Ekin Deniz Aksu
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...
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...
Three new research groups joining the MPIMG
www.molgen.mpg.de
November 6, 2025 at 4:00 PM
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...
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...
Reposted by Ekin Deniz Aksu
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.
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.
October 31, 2025 at 1:37 PM
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.
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.
Reposted by Ekin Deniz Aksu
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...
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...
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...
developer.nvidia.com
October 28, 2025 at 8:55 PM
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...
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...
Reposted by Ekin Deniz Aksu
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...
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...
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...
www.biorxiv.org
October 16, 2025 at 3:06 PM
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...
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...
Reposted by Ekin Deniz Aksu
Neural anticipation of virtual infection triggers an immune response
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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...
www.nature.com
July 28, 2025 at 3:51 PM
Neural anticipation of virtual infection triggers an immune response
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Ekin Deniz Aksu
⚠️ 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
👉 We discover how sex and development signals are decoded at a single gene locus.
www.nature.com/articles/s41...
👇 Bluetorial
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.
www.nature.com
October 6, 2025 at 1:02 PM
⚠️ 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
👉 We discover how sex and development signals are decoded at a single gene locus.
www.nature.com/articles/s41...
👇 Bluetorial
Reposted by Ekin Deniz Aksu
🧵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
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.
www.nature.com
October 6, 2025 at 6:57 AM
🧵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
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
🔬🦠I'm hiring at all levels! 🔬🦠Check: www.molgen.mpg.de/fueyo-lab
October 6, 2025 at 1:46 PM
⚡⚡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
🔬🦠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.
September 23, 2025 at 3:00 PM
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
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]
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 ...
www.biorxiv.org
September 22, 2025 at 5:01 PM
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]
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...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 5:29 AM
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)
www.biorxiv.org/content/10.1...
(1/n)
Just got my flu vaccine shot.
Don't forget yours this season!
Don't forget yours this season!
September 4, 2025 at 9:47 PM
Just got my flu vaccine shot.
Don't forget yours this season!
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!!!
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
Read more and watch Can introduce his project: s.gwdg.de/cLAmJE
September 4, 2025 at 1:27 PM
🥳 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!!!
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!!!
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
Read all details here: www.ie-freiburg.mpg.de/6057908/2025...
Congratulations @julianeg.bsky.social
@erc.europa.eu #ERCStG
September 4, 2025 at 10:43 AM
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
Read all details here: www.ie-freiburg.mpg.de/6057908/2025...
Congratulations @julianeg.bsky.social
@erc.europa.eu #ERCStG
Reposted by Ekin Deniz Aksu
![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.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:cz73r7iyiqn26upot4jtjdhk/bafkreic2mhmdvsftki6qe275hycolgt22msekbwzdyqoujt56qzpcbm3hm@jpeg)
August 28, 2025 at 9:27 PM
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.
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.
June 26, 2025 at 7:46 AM
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.
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
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
August 28, 2025 at 12:48 PM
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
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
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
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
June 11, 2025 at 12:21 PM
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
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!
August 21, 2025 at 2:59 PM
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
Details below
careersearch.stanford.edu/jobs/computa...
Plz RT
August 19, 2025 at 12:29 AM
@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
Details below
careersearch.stanford.edu/jobs/computa...
Plz RT
Reposted by Ekin Deniz Aksu
Honored to receive the @isrbio.bsky.social Rising Star Award for our work in regeneration biology! Grateful to the committee and our colleagues for the recognition. A huge motivation for the lab. Excited to give the award talk in Madison next week and connect with everyone! 😎🥳🍾 shorturl.at/LnkSt
2025 Award Winners
www.isrbio.org
August 7, 2025 at 3:27 PM
Honored to receive the @isrbio.bsky.social Rising Star Award for our work in regeneration biology! Grateful to the committee and our colleagues for the recognition. A huge motivation for the lab. Excited to give the award talk in Madison next week and connect with everyone! 😎🥳🍾 shorturl.at/LnkSt
Reposted by Ekin Deniz Aksu
I really dislike how science has started calling almost any fancy computational technique AI. 🧪
The framing of this entire article makes it sound like a benevolent AI independently made these drugs.
That is *pure fantasy*.
Instead: a team of scientists made a machine learning model for a study.
The framing of this entire article makes it sound like a benevolent AI independently made these drugs.
That is *pure fantasy*.
Instead: a team of scientists made a machine learning model for a study.
August 15, 2025 at 6:14 AM
I really dislike how science has started calling almost any fancy computational technique AI. 🧪
The framing of this entire article makes it sound like a benevolent AI independently made these drugs.
That is *pure fantasy*.
Instead: a team of scientists made a machine learning model for a study.
The framing of this entire article makes it sound like a benevolent AI independently made these drugs.
That is *pure fantasy*.
Instead: a team of scientists made a machine learning model for a study.
Reposted by Ekin Deniz Aksu
Hiding in plain sight - how close are we to mapping ALL 🧬enhancers🧬 in the genome?
Our new paper by Mannion et al. takes a systematic look at "hidden enhancers" and why they remain so hard to find. With @mosterwalder.bsky.social, @jlopezrios.bsky.social & many more
www.nature.com/articles/s41...
Our new paper by Mannion et al. takes a systematic look at "hidden enhancers" and why they remain so hard to find. With @mosterwalder.bsky.social, @jlopezrios.bsky.social & many more
www.nature.com/articles/s41...
August 8, 2025 at 6:10 PM
Hiding in plain sight - how close are we to mapping ALL 🧬enhancers🧬 in the genome?
Our new paper by Mannion et al. takes a systematic look at "hidden enhancers" and why they remain so hard to find. With @mosterwalder.bsky.social, @jlopezrios.bsky.social & many more
www.nature.com/articles/s41...
Our new paper by Mannion et al. takes a systematic look at "hidden enhancers" and why they remain so hard to find. With @mosterwalder.bsky.social, @jlopezrios.bsky.social & many more
www.nature.com/articles/s41...