Ekin Deniz Aksu

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...
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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!!

@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

Congrats!

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

Article on BBC news. Title: AI designs antibiotics for gonorrhoea and MRSA superbugs Description: Two new potential drugs have been designed by AI to kill drug-resistant bacteria, in a major Massachusetts Institute of Technology study.

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.

A busy tool wall in a shed. At the bottom there are instructions saying "Find the 10 hidden enhancers!" Across the wall between the tools are 10 enhancers, represented as DNA helices, but they are difficult to find in the style of a "hidden object" puzzle. Original photo by Lachlan Donald, https://www.flickr.com/photos/lox/9408028555

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 paper is now out in final form at Nature Genetics! For those who missed the preprint, we used large-scale Perturb-seq targeting transcription factors to push primary fibroblasts into diverse transcriptional states, including those observed in cell atlas studies.

Beeswarm plot of the prediction error across different methods of double perturbations showing that all methods (scGPT, scFoundation, UCE, scBERT, Geneformer, GEARS, and CPA) perform worse than the additive baseline.

Line plot of the true positive rate against the false discovery proportion showing that none of the methods is better at finding non additive interactions than simply predicting no change.

Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉

www.nature.com/articles/s41...

We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!

🧵

🧬 New study from the Kinkley Lab! 🧬 In collaboration with the Vingron and Hnisz labs at the MPIMG the team has gained new insights how the epigenetic reader PHF13 regulates it´s affinity to bind to chromatin.
Read more: www.molgen.mpg.de/2025-07-28-o...
Congrats to first author Francesca Rossi!

Open Call for Expressions of Interest in Max Planck Directorships: Expressions of interest can be submitted until 31 October 2025.

Director at Max Planck - a unique position! The Open Call for Expressions of Interest in Max Planck Directorships is open now and can be submitted by the 31st of October 2025. ➡️ mpg.de/directors - Please share the Open Call among potential candidates.