Daniel Ibrahim

The cover of Nature Genetics July 2025 issue. Digital art of a mouse paw skeletal prep on dark background, digits I to IV disintegrating into viral particles. A caption says “An endogenous retrovirus causes limb malformation”.

Pretty surreal to see my artwork on the cover of Nature Genetics! Big congrats to @julianeg.bsky.social, @stemundi.bsky.social and the others, and thank you Juliane for letting me help bring your research to life visually.

www.nature.com/ng/volumes/5...

Thrilled to see our revised preprint now published in Nature Ecology & Evolution!
If you’re curious about how to build a bat wing by re-using existing gene programs, check out the link or the tutorial below. Big congratulations to all co-authors!! Thanks to reviewers!

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

multalin.toulouse.inra.fr/multalin/ind...

this is my favourite for a long time. the website has last been updated 2002 or so. still does the job for a quick check.

after that - edit in word

SOOOO MANY GENOMICS MODELSSSS! 😱 Often unclear which is best since they benchmark differently! In this preprint, we introduce GAME, a new framework that utilizes APIs to enable sustainable, uniform model evaluation so we can see which is actually best for each task. doi.org/10.1101/2025...

The evolution of high-order genome architecture revealed from 1,000 species www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/xjtu-omics/H...

so many cool things in there!!

My favourite is the cell-type specific TE activity, others might prefer the viral-like particle mechanismone way or another - very much worth the read! congratulations 🙌

Liebenberg syndrome severity arises from variations in Pitx1 locus topology and proportion of ectopically transcribing cells - Nature Communications Here the authors show that reducing enhancer-promoter distance at the Pitx1 locus increases proportion of Pitx1 forelimb expressing cells, worsening skeletal defects in Liebenberg syndrome. They also ...

Our work bridging enhancer-promoter proximity to phenotypic outcomes in vivo is out! Shout out to @olimpiabompadre.bsky.social, to Marie Kmita's lab, and to all the co-authors. www.nature.com/articles/s41...

Range extender mediates long-distance enhancer activity - Nature The REX element is associated with long-range enhancer–promoter interactions.

Our paper describing the Range Extender element which is required and sufficient for long-range enhancer activation at the Shh locus is now available at @nature.com. Congrats to @gracebower.bsky.social who led the study. Below is a brief summary of the main findings www.nature.com/articles/s41... 1/

In Nature Genetics, @danielibrahim.bsky.social (MPIMG/BIH) and his team have developed a bioinformatic tool to identify evolutionary conserved regulatory regions of the genome that have transformed so much over time that their DNA sequences have changed completely.

👉 www.molgen.mpg.de/4927054

It just takes one change Here, I run though three examples of evolutionary novelty driven by single non-coding DNA changes: limb loss in snakes, gliding in sugar gliders, and coat coloration in African striped mice. These …

Mustering the courage to share my latest scicomm endeavour: I channelled my love for writing into a blog where I can hopefully bring the marvels of evolutionary biology and non-coding DNA to all Science lovers!

darkgenomevo.wordpress.com/2025/06/22/i...

Transcriptional and post-transcriptional regulation of transposable elements and their roles in development and disease - Nature Reviews Molecular Cell Biology Transposable elements (TEs) comprise nearly half of the human genome. This Review discusses transcriptional and post-transcriptional mechanisms that repress TE activity, how TEs escape this suppressio...

We wrote a review on Transposable Elements (TEs) and almost all aspects of TE silencing and their roles in biological processes & disease.
www.nature.com/articles/s41...

Paper alert! I am really pleased to share the final version of the work led by Irène Amblard in the team on a regulatory switch controlling Cdx2 expression during posterior body development! #regulatorylogic #devbio @mrc-lms.bsky.social @imperialmed.bsky.social

We are looking for a research assistant to join our lab and support ongoing projects with genome engineering in mouse embryonic stem cells! Please get in touch if you are interested.
www.fmi.ch/education-ca...

I'm supposed to give a 20 min talk right after @avsecz.bsky.social at ASBMB in Kansas City on Friday. I'm planning to use the "Ziga ate my slides for lunch" excuse (which is the dog ate my homework excuse in AI for genomics) & stand quietly in the corner for 20 mins. 😂😂😂 1/

Portrait photo of Dr. Juliane Glaser

We are excited to officially welcome a new group leader at the MPI-IE in #Freiburg. 🎉

Dr Juliane Glaser 🥳 – she studies epigenetic mechanisms of embryonic development, with a focus on transposable elements. 👉 Interview: www.ie-freiburg.mpg.de/6043545/2025...

Welcome, @julianeg.bsky.social!

this is so cool! happy to see it out!!!

Hey y'all, grant-pending, I may be unemployed starting from October. If you have any leads on biotech / postdoc positions in the German-speaking part of Switzerland, I'd greatly appreciate a message. I'm great with Data Analysis, Molecular Biology, and Teaching. (Plz RT!)

More at timothyfuqua.com

Excited to share our new paper in @cellreports.bsky.social that reshapes our understanding of chromosome organization's deep evolutionary roots! Our work dives into the origins of the machinery that structures our very genomes.

🔗: doi.org/10.1016/j.ce...

#Genomics #Evolution #CellBiology #LECA

A meme-style comic panel with three parts. Left: A stylized enhancer with a mutation, surrounded by colored blocks representing functional motifs, a neural network diagram, chromatin accessibility signal traces, and a sequence motif. Two cartoon mouse embryos below show different LacZ reporter activity patterns. Top right: A hand hovers anxiously between two red buttons labeled “Experiments” and “AI,” with the caption “HOW DO ENHANCERS REALLY WORK?” Bottom right: A sweating superhero wipes his forehead, looking stressed about the difficult choice.

Textbooks: “Enhancers are just a bunch of TFBSs”

But how do they REALLY work?

New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social

A 🧵 (1/n)

Free access link: rdcu.be/erD22

cool cool cool !

‘Killswitch’ protein lets scientists study immobilized cellular droplets Synthetic peptide fixes biomolecular condensates, revealing how these enigmatic cell structures actually work.

Check out a technology feature in @nature.com by Elie Dolgin regarding our recent 'Killswitch' publication
www.nature.com/articles/d41...

Thank you for the comments and first impressions by Rick Young, Isaac Klein, @danfengcai.bsky.social @superscijew.bsky.social
@yaotianzhang.bsky.social

oh yeah - those papers (there are a couple of really nice drosophila papers) are definitely motivation pursuing this!

Conservation of regulatory elements with highly diverged sequences across large evolutionary distances - Nature Genetics Combining functional genomic data from mouse and chicken with a synteny-based strategy identifies positionally conserved cis-regulatory elements in the absence of direct sequence conservation.

4) Speaking of conservation, synteny, and enhancer turnover, the next paper is from @danielibrahim.bsky.social 's group:

What controls condensate composition and function beyond binding stoichiometry? We show that condensate microenvironments play a key role, and can be probed by a micropeptide killswitch in live cells. www.nature.com/articles/s41... in @nature.com ‬ with @yaotianzhang.bsky.social Denes Hnisz & team.

Honored that our lab made the shortlist for Best Research Environment. Awesome initiative by Junge Akademie and proud of the incredible Gaebler Lab team and the entire Infectious Disease Department at Charité/BIH that makes this place what it is! 👏 @libuchauer.bsky.social @sanderlab.bsky.social

Conservation of regulatory elements with highly diverged sequences across large evolutionary distances - Nature Genetics Combining functional genomic data from mouse and chicken with a synteny-based strategy identifies positionally conserved cis-regulatory elements in the absence of direct sequence conservation.

📢 ONLINE @natgenet.nature.com

📰 Conservation of regulatory elements with highly diverged sequences across large evolutionary distances.

By Mike Phan, @danielibrahim.bsky.social and colleagues.

⬇️

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

portrait of a man

@drmrobson.bsky.social has won two grants from @dfg.de & @hfspo.bsky.social totaling over €2 million. He and his lab now work to decode the mechanics of #chromatin, hoping to finally define its physical state and better understand how it governs gene regulation
www.mdc-berlin.de/news/news/mi...

that's 🧬🔥!

I am excited to see the method we used in DANIO-CODE now fully developed as #IPP — and successfully tested on heart enhancers between chicken 🐔 and mouse 🐭! 🧬 Thanks to @danielibrahim.bsky.social for leading this. Proud to be part of it! Exciting times for future comparative regulatory analyses 🚀

1/"I have a presentation tomorrow."
If you've ever collaborated with wet lab scientists as a bioinformatician…
you’ve heard this. And died inside a little.