Daniel Ibrahim

A digital CAPTCHA verification window titled "Select all squares with PIPES" against a plain white background. The window contains a 3×3 grid of numbered squares, mixing literal hardware, smoking pipes, and programming syntax.

These captchas just keep getting harder #rstats

And I'm very excited to share our latest work with you and discuss about the 3D genome. This will be cool - See you later!

sign up if you have the time!!

Our most recent work on the “function and evolution” of #nuclear-speckles is now online at Cell @cp-cell.bsky.social
doi.org/10.1016/j.ce...
Read the thread👇 for the highlights of our findings.

fully agree, maybe we even find brendan eventually 😂🤣

Participants of the meeting posing on a staircase looking fantastic.

Thanks to co-authors Charles C. Bell, Brendan R. Camellato,
M. Joaquina Delás, Daniel M. Ibrahim, and @michaeltmont.bsky.social
And also to all the participants of the 2024🤨 Company of Biologists meeting that inspired this.

huhu 👋 @joadelas.bsky.social and I were hiding in the comment section 😉

We wrote a piece on how easy it is to write gene regulatory sequences. - Turns out, it isn't that easy even though we know a lot about cis-regulation.

huge credit to @carldeboer.bsky.social to seeing this through so our thoughts aren't lost. I promise, it's a worthwhile read!

This will be fun!
Rally looking forward to present our latest story next week and discuss long-range gene regulation form the promoter's point of view!

Betreiber kleiner Anlagen mit einer Kapazität von weniger als 25 Kilowatt müssen sich künftig selbst erst einen Abnehmer für ihren Strom suchen, ehe sie diesen ins Netz speisen dürfen. Bisher mussten die Netzbetreiber ihnen den Strom stets abnehmen.

Ah, das muss dieser berühmte Bürokratieabbau sein

www.spiegel.de/wirtschaft/u...

I had a lot of fun putting this together with @suminkim.bsky.social and @andersshansen.bsky.social! Glad to have had the chance to work on it!

This is absolutely awesome!

A small polymerase ribozyme that can synthesize itself and its complementary strand The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...

Why hasn't this paper gotten more attention?

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!