Daniel Ibrahim

Advancing regulatory variant effect prediction with AlphaGenome - Nature AlphaGenome, a deep learning model that inputs 1-Mb DNA sequence to predict functional genomic tracks at single-base resolution across diverse modalities, outperforms existing models in variant effect...

I had intended to post something about this new Google DeepMind paper that appeared yesterday in Nature, but the press coverage has added to what there is to say. So this is a long 🧵
www.nature.com/articles/s41...

I'd just add one further comment. I'm very keen to write about the work being done to unravel the complexities of gene regulation. As the whole premise of AlphaGenome implies, this is really where much of the action is in molecular biology, and is central to how we work. But...

AlphaGenome is out in @nature.com today along with model weights! 🧬

📄 Paper: www.nature.com/articles/s41...

💻 Weights: github.com/google-deepm...

Getting here wasn’t a straight path. We discussed the story behind the model, paper & API in the following roundtable: youtu.be/V8lhUqKqzUc

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...

🧬Sign up to our free online 2026 Genome Writing Workshop 🧬
www.thedarkmatterproject.org/2026-genome-...

I think I might be able to get my hands on some.

🧬 We’re #Hiring a #Bioinformatician/ Computational Biologist!
#Single-cell genomics, #Epigenomics & #3Dgenome biology in #Zebrafish #DevBio 🐟
📍 @cabd-upo-csic.bsky.social, CABD, Seville (Spain)
🕒 Full-time, 3-year position (start March 2026)
📅 Apply by Feb 15, 2026
👉 drive.google.com/file/d/1M8rp...

Technologieoffen!

Welcome! You are invited to join a webinar: The 3D Regulatory Genome: Can chromatin organization store memories?. After registering, you will receive a confirmation email about joining the webinar. Join our guest speaker, Dr. Sedona Murphy, in this exciting seminar on the 3D Regulatory Genome, sponsored by Enhanced Genomics.

I am very excited to kick off our 2026 @enhancedgenomics.bsky.social seminar series ‘The 3D Regulatory Genome’ with @sedonamurphy.bsky.social’s talk “Can chromatin organization store memories?”.

📅 08 Jan 2026 (tomorrow!)
⏰ 4 pm GMT

Please join us:
us02web.zoom.us/webinar/regi...

JOB ALERT! 📢 For the scientists who love science communication: we’re hiring at @kurzgesagt.org !🌍 Come join our team, the vibes are impeccable.

✍️ Scriptwriter (Remote) kurzgesagt.org/careers/scri...
🔍 Fact-Checker & Researcher (Munich/Berlin/Remote) kurzgesagt.org/careers/seni...

The combined life-hours lost by "verifying that you're human" after clicking on links ......

This is progress, right?

maybe a Dpnl digest prior to RT in the protocol?

Very happy to share the published version of our study on the benefits of sodium sulfite + trolox (SST) as oxygen scavenger for #DNA-PAINT - now out in Small!

Thanks to the reviewers for helpful comments and again congrats, Becky, on your PhD's first paper!!

tinyurl.com/54m2pt9c

I do find it interesting trying to explain to people that historians deal in arguments, not in facts. History isn’t a catalogue of dates and names, but what happened around those things, and how we now and those who were alive at the time perceived and responded to those events.

I‘ve been having a similar hunch as @triggerloop.bsky.social, but not a good way to test it.
a model could be that CTCF constrains replication domains to some degree (thereby helping with DSBs and HDR) and gene regulatory roles evolved on top of that.
multilayered molecular fxn = muddled results

I have done both and I‘m not surprised at all.also, it turns nothing on its head

Contacts between boundaries should be rare and unless there’s a CRE directly next to it, there‘s no reason to assume that TAD boundaries influence the activity within the domain

looking fwd to read the full MS though!

Programmatic design and editing of cis-regulatory elements The development of modern genome editing and DNA synthesis has enabled researchers to edit DNA sequences with high precision but has left unsolved the problem of designing these edits. We introduce Le...

After a huge amount of work w/ @alex-stark.bsky.social's group, a new version of our Ledidi preprint is now out!

In an era of AI-designed proteins, the next leap will be controlling when, where, and how much of these proteins are expressed in living cells.

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

JASPAR goes Deep Learning! - NCMBM - Norwegian Centre for Molecular Biosciences and Medicine A new era for motif resourcesThe team behind JASPAR, led by Anthony Mathelier at NCMBM, has released the 11th update. JASPAR is built and maintained by an international consortium of research groups, ...

Together, these approaches create a uniquely powerful platform for exploring how transcription factors interpret the genome.”

📰 Read the full story: www.med.uio.no/ncmbm/englis...

Congrats to the entire JASPAR community for driving this resource forward to shape the future of regulatory genomics!

🔬 Hot #PhD topic: Single-molecule fluorescence and super-resolution microscopy! Use quantitative nanoscale imaging to map nuclear organization. Apply by Jan 7 to join Johannes Stein’s Lab @jmstein.bsky.social & #IMPRS-BAC #gradschool!

👉 www.molgen.mpg.de/5098010/stei...

i’m intrigued - sounds like a niche arms race that I want to follow.

if the user would in the end just do it themselves….*sigh*

I 100% subscribe to this post!
I really do not want to read a paraphrased version of whatever is written on my website. Just write me a nice email if you're interested.

Very proud of our new paper! Great job @mweilert.bsky.social, our experimentalists and modeling collaborator Rosa Martinez-Corral. It was fun to see the story grow and get feedback from various experts. Thank you all!

IMPRS-BAC #gradschool: Our new groupleader @sedonamurphy.bsky.social has an open PhD project in her lab. Topic: Spatial feedback between epigenetic regulation and chromatin regulation. Apply by Jan 7, 2026!
👉 www.molgen.mpg.de/5091778/Murp...

1. We start a major consortium programme funded by the sLoLa of BBSRC (shorturl.at/aUbnt) to decipher the semantic rules of enhancer arrangements driving regulator genes of development (shorturl.at/6qcjW).

This mural has gone up in Kingston, ostensibly for Christmas but AI has ensured it's actually to celebrate the return of our dark lord Cthulhu

🚨Reposts appreciated‼️If I had read this PhD offer five years ago, I wouldn’t have hesitated for a second to apply 😉
Passionate about gene regulation, chromatin, and developmental biology? Just contact @radaiglesiaslab.bsky.social at @ibbtec.bsky.social 🧬✨

#PhD #3DGenome

We recently reported that promoter competition can contribute to the robust insulation of gene regulatory domains (www.nature.com/articles/s41...).
We now offer a 4-years PhD contract to investigate whether the dirsuption of this regulatory mechanism can lead to congenital defects. More details 👇

Job announcement: The image has a solid dark blue background with a clean, minimal layout. In the top left corner, the word “JOBS” appears in all-capital red sans-serif text. Below, large white sans-serif text spans several lines and reads: “Three Independent Group Leaders in Bioengineering Approaches to Human Health m/f/d.” Near the bottom left, smaller white sans-serif text reads: “Apply by November 16, 2025,” followed by “Max Delbrück Center (Berlin-Buch)” in lighter gray. In the bottom right corner is the Max Delbrück Center logo in white and blue.

🚀 WE ARE HIRING 3️⃣ Independent Group Leaders for #mdcBerlin's new cutting-edge Bioengineering Cluster within our Biomedical Engineering Program.

Lead cutting-edge research at the interface of biology, engineering, and medicine in Berlin.

👉 Apply now: www.mdc-berlin.de/career/jobs/...

Happy to share our latest publication, in which we show that the arrangement of nucleosomes around CTCF sites contributes to higher-order organisation of chromatin into TADs: www.embopress.org/doi/full/10....

Thanks! Obvsly, I have many thoughts on that. I think enhancer-reporters tell you a lot about what expr. the enhancer might be driving, but that could be quite different from what it does endogenously.
And pairing the same enhancer with different core promoters in vivo - could be another story 😉