Daniel Ibrahim
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danielibrahim.bsky.social
Daniel Ibrahim
@danielibrahim.bsky.social
1K followers 290 following 72 posts
Group Leader @ BIH Berlin and MPI Molecular Genetics. I play around with DNA because I‘d like to know how the genome functions.
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danielibrahim.bsky.social
Daniel Ibrahim @danielibrahim.bsky.social · Oct 16
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...
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
danielibrahim.bsky.social
This is absolutely awesome!
edogia.bsky.social Edoardo Gianni @edogia.bsky.social · 1d
How could a simple self-replicating system emerge at the origins of life? RNA polymerase ribozymes can replicate RNA, but existing ones are so large that their self-replication seems impossible. Could they be smaller?

Excited to share our latest work in @science.org on a new small polymerase.
1/n
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 ...
www.science.org
February 13, 2026 at 3:53 PM
Reposted by Daniel Ibrahim
delalamo.xyz
Why hasn't this paper gotten more attention?
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 ...
www.science.org
February 13, 2026 at 1:40 AM
Reposted by Daniel Ibrahim
philipcball.bsky.social
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...
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...
www.nature.com
January 30, 2026 at 9:47 AM
Reposted by Daniel Ibrahim
philipcball.bsky.social
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...
January 30, 2026 at 11:10 AM
Reposted by Daniel Ibrahim
avsecz.bsky.social
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
January 28, 2026 at 9:02 PM
Reposted by Daniel Ibrahim
eddaschulz.bsky.social
⚠️ 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...
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...
link.springer.com
January 20, 2026 at 11:02 AM
Reposted by Daniel Ibrahim
darkmatterproject.bsky.social
🧬Sign up to our free online 2026 Genome Writing Workshop 🧬
www.thedarkmatterproject.org/2026-genome-...
January 20, 2026 at 7:23 PM
Reposted by Daniel Ibrahim
martinfranke.bsky.social
🧬 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...
Job offer 2026.pdf
drive.google.com
January 12, 2026 at 3:57 PM
danielibrahim.bsky.social
Technologieoffen!
January 8, 2026 at 6:38 AM
Reposted by Daniel Ibrahim
stefanschoenfelder.bsky.social
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...
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.
us02web.zoom.us
January 7, 2026 at 5:14 PM
Reposted by Daniel Ibrahim
prokaryota.bsky.social
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...
Job listing for (Senior) Fact-Checker & Researcher (all genders) | kurzgesagt
Want to work with kurzgesagt? We have an open role as (Senior) Fact-Checker & Researcher (all genders). Apply now to become part of a great team and start an exciting career!
kurzgesagt.org
January 7, 2026 at 12:37 PM
danielibrahim.bsky.social
The combined life-hours lost by "verifying that you're human" after clicking on links ......

This is progress, right?
January 5, 2026 at 11:05 PM
Reposted by Daniel Ibrahim
jmstein.bsky.social
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
December 19, 2025 at 2:00 PM
Reposted by Daniel Ibrahim
hallierubenhold.bsky.social
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.
December 7, 2025 at 5:43 PM
Reposted by Daniel Ibrahim
jmschreiber91.bsky.social
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...
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...
www.biorxiv.org
December 10, 2025 at 3:18 PM
Reposted by Daniel Ibrahim
ncmbm.bsky.social
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!
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, ...
www.med.uio.no
December 2, 2025 at 7:38 AM
Reposted by Daniel Ibrahim
molgen.mpg.de
🔬 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...
November 25, 2025 at 2:18 PM
danielibrahim.bsky.social
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.
biyolokum.bsky.social Dr. B. Duygu Özpolat (she/her) @biyolokum.bsky.social · Nov 21
Students applying for grad school, or reaching out to professors. I have an important piece of advice for you: STOP DOING THIS 👇 (a thread) #STEM #PhD #gradschool #academictips
November 24, 2025 at 10:23 AM
Reposted by Daniel Ibrahim
juliazeitlinger.bsky.social
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!
November 19, 2025 at 11:38 PM
Reposted by Daniel Ibrahim
molgen.mpg.de
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...
November 18, 2025 at 4:05 PM
Reposted by Daniel Ibrahim
ferencmueller.bsky.social
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).
shorturl.at
November 18, 2025 at 12:48 PM
Reposted by Daniel Ibrahim
mattthr.bsky.social
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
November 18, 2025 at 9:44 AM
Reposted by Daniel Ibrahim
mariamafau.bsky.social
🚨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
November 15, 2025 at 9:53 AM
Reposted by Daniel Ibrahim
radaiglesiaslab.bsky.social
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 👇
November 6, 2025 at 6:37 PM
Reposted by Daniel Ibrahim
mdc-berlin.bsky.social
🚀 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/...
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.
October 9, 2025 at 11:00 AM