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Daniel Ibrahim

@danielibrahim.bsky.social
1.1K followers 310 following 86 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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Reposted by Daniel Ibrahim
Arnaud Krebs @arnaudkr.bsky.social · 10/09/2026
EMBL QBMM is back this year with an outstanding line-up! Plenty of talks will be selected from submitted abstracts, with emphasis on junior scientists and representation across diverse fields. The abstract deadline is the end of this week, so don’t miss out! www.embl.org/about/info/c...
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Mariana Schuster @marischuster.bsky.social · 07/09/2026
I'm excited to share that my newly funded #ERCStG FRONTERA is recruiting two postdoctoral researchers at @ipbhalle.bsky.social 🌱🔬 If you are passionate about plant immunity, proteolysis, membrane proteins, or proteomics, I'd love to hear from you. 🧵 Please RT/share!
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Paul Byrne @theplanetaryguy.com · 09/09/2026
Astrophotographer Adam (AJ) Smadi caught this image a few hours ago from Washington state. A thin crescent Moon, sunlight illuminating the rugged lunar surface. And 2,400 times farther away—and on the other side of the Sun—mighty Jupiter, and its moons Io (left) and Ganymede (right).
A crescent Moon seen during the day, arcing from upper left to lower right of the frame. At lower centre is the full disk of Jupiter; the small dots to its upper left and lower right and Io and Ganymede, respectively.
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Daniel Ibrahim @danielibrahim.bsky.social · 27/08/2026
I AM SCREAMING NANOPORE! seriously, @nanoporetech.com: you eed to look into this for you lib prep & sequencing. it might make your tech way more reliable!
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Shenzhi Chen @shenzhichen1999.bsky.social · 25/08/2026
Excited to share our paper in @natgenet.nature.com on the de novo design of tissue-specific mammalian enhancers that function in vivo in mouse embryos. 🧬🐭 www.nature.com/articles/s41...
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Evgeny Kvon @evgenykvon.bsky.social · 26/08/2026
Breakthroughs like this rely on standing on the shoulders of giants. Beyond new DL models, this work was only possible thanks to high-quality epigenomic #ENCODE datasets and massive VISTA collection of validated enhancers built over 20+ years by @axelvisel.bsky.social, Pennacchio and Rubin labs.
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rev. howard arson @theophite.bsky.social · 19/08/2026
the mechanism behind this is that if you don't do your homework you don't learn the topic
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Teresa Rayon @trayon.bsky.social · 15/08/2026
Our work on the role of the proteasome in developmental tempo is out!!!! 🐭⌛️👤⏳ Six years after identifying an association between protein stability and developmental tempo, we now demonstrate a causal link between protein turnover and developmental tempo through proteasomal degradation
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Bjørt K.Kragesteen @kragesteen-lab.bsky.social · 12/08/2026
📢Job alert! 👩🏽‍💻🧑🏼‍💻 @amandaanderssonr.bsky.social and I are hiring a computational scientist to work on sc/spatial data 🧬🧫 organ development and oxygen homeostasis 📍Karolinska Institute, Stockholm ⏰ 1 year-with potential for permanent contract Apply by 15th Sept👇🏼 ki.varbi.com/what:job/job...
ki.varbi.com
Computational Staff Scientist - shared between 2 labs - in spatial and single cell omics
Do you want to contribute to top quality medical research? Come and join the Andersson & Kragesteen labs at the department of Medical Biochemistry and Biophysics (MBB) at Karolinska Institutet/Bio
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Jonathan Pritchard @jkpritch.bsky.social · 09/08/2026
Must-know numbers in human genetics -- As many of you know, I'm writing a free online textbook in human genetics. In this blog post I cover a key skill for genome scientists from that book: how to use mental math to figure out key genome properties. jkpritchard.substack.com/p/on-fermi-p...
jkpritchard.substack.com
On Fermi Problems in Human Genetics
and some very useful numbers about human genomes to get you started!
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Selin Jessa @selinjessa.com · 06/08/2026
Massive effort from many in @anshulkundaje.bsky.social lab to train and curate this collection of 1000s of sequence-to-function deep learning models and the predictive features they learn - check out their blog posts on how to use the resource!
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Daniel Ibrahim @danielibrahim.bsky.social · 31/07/2026
really impressive scaling feat! i’m jealous of it. very neat assay, wonderful acronym. i’m all for it though lit refs could be better and are 5 x1kb fragments really a mammalian locus?
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Judith Kribelbauer @jk-swietek.bsky.social · 30/07/2026
Obviously a strong supporter of this type of tool, but troubled by the literature review. No reference to @chribue.bsky.social work on combinatorial enhancers, and our EXTRA-seq -> kilobase-scale E-P landscapes in a native locus (no minP). Same principle, just ONT.
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nellykanata.bsky.social @nellykanata.bsky.social · 28/07/2026
I am very excited to share the work of my PhD with @eddaschulz.bsky.social, now on BioRxiv! 🎉 🧵⬇️ (1/9) How does the transcription↔️chromatin crosstalk ensure monoallelic expression?
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Sarah Vergult @svergult.bsky.social · 27/07/2026
40 individuals with the clinical picture of FOXG1 syndrome and a completely intact FOXG1 gene. So what’s going wrong then? Our new paper in @natcomms.nature.com traces the answer to a stretch of non-coding DNA 665 kb away from the gene. (1/7)
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Albert Blanch-Asensio @ablanchasensio.bsky.social · 20/07/2026
The STRAIGHT-IN (Dual) kit is now available via @addgene.bsky.social! 🧬 A complete 24-plasmid toolkit for installing up to two orthogonal CLYBL landing pads, DASIT-based enrichment without FACS, and efficient large DNA integration in human cells. Link: www.addgene.org/kits/gallowa... 🧵
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David Shiffman, Ph.D. 🦈 @whysharksmatter.bsky.social · 16/07/2026
When I was writing this piece about the Ocean Cleanup, I had a surreal experience: They assured me that they only kill invasive species, and sent me a published paper to demonstrate that. But the paper said the opposite! I wonder how many journalists just took their word for it and didn't check?
therevelator.org
Why The Ocean Cleanup Hasn’t Solved the Plastic Pollution Crisis • The Revelator
Global problems are rarely solved by one person or invention. The Ocean Cleanup didn’t work, for the reasons experts said it wouldn’t. What can we learn from this?
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Luca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 15/07/2026
Our preprint is now out in @natgenet.nature.com ! doi.org/10.1038/s415... We measured Sox2 promoter bursting dynamics with the SCR enhancer positioned at different distances within a genomic locus devoid of confounding effects in mESC: Main findings in the 🧵 below:
doi.org
Enhancer control of promoter activity and variability via frequency modulation of clustered transcriptional bursts - Nature Genetics
Tünnermann et al. use live-cell imaging to study promoter activity under the control of an enhancer inserted at different genomic distances. RNA production from the promoter occurs in clusters of tran...
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Daniel Ibrahim @danielibrahim.bsky.social · 27/06/2026
really good take from Aydan! I‘m also quite disturbed by the whole 1% marketing gag. masterful click-baiting as expected from oded (worked for me). but it kind of feels like a right out of a Black Mirror episode. As if it wouldn’t lead to a new glorification of articles ranked well by an AI.
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lilastromech (Mischa) @mischajaye.bsky.social · 26/06/2026
The cooling system was installed by the village AC technician, Thermodynamix 😊
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Jonas Koeppel @jonaskoeppel.bsky.social · 04/06/2026
1/n What fraction of the human genome is essential for cells? Excited to share our preprint that explores this question by combining an unusual CRISPR system, phage promoters, and thousands of deletion launchpads. @sudpinglay.bsky.social @jshendure.bsky.social www.biorxiv.org/content/10.6...
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Jonas Koeppel @jonaskoeppel.bsky.social · 04/06/2026
22/n On a personal note, I’ll soon start an independent research group in the Genome Biology Unit at EMBL Heidelberg. If you enjoy this type of work and want to engineer genomes at the largest scale, please reach out! jonas-koeppel.github.io/koeppellab/ www.embl.org/groups/koepp...
jonas-koeppel.github.io
Koeppel Lab | Structural Variation and Genome Engineering
Genome engineering research led by Jonas Koeppel, developing scalable technologies to design structural variants and study mammalian genome function.
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Ferenc Mueller @ferencmueller.bsky.social · 01/06/2026
Join is in Budapest in October! For the 6th time, all things epigenetics, gene and genome regulation and more. A fantastic opportunity to present, to talk to speakers and colleagues in a friendly, informal setting at a great location. Please note, travel grant deadline will expire soon.
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Max Planck Institute of Immunobiology and Epigenetics @mpi-ie.bsky.social · 27/05/2026
We are over the moon! 🎈 Dr. Marieke Oudelaar joins the MPI-IE as a new #MaxPlanck Director, heading the newly established Department of Genome Biology She studies how the 3D folding of DNA controls gene expression – more details below ⬇️ Welcome to #Freiburg, @mariekeoudelaar.bsky.social!
ie-freiburg.mpg.de
Marieke Oudelaar becomes new Director at MPI-IE in Freiburg
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Arnaud Krebs @arnaudkr.bsky.social · 08/05/2026
An historical figure of the transcription field has gone. Founder of @igbmc.bsky.social where I started my career. A great enabler as well.
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Denis Duboule @denisduboule.bsky.social · 07/05/2026
Pierre Chambon was a great scientist. And a good man too. He alone opposed to leading British embryologists during the evaluation of a case of scientific misconduct more than 40 years ago, to defend young scientists against an establishment to which he belonged. An unforgettable lesson. RIP Pierre 💐
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Addgene @addgene.bsky.social · 04/05/2026
And more plasmids for using STRAIGHT-IN Dual from the Galloway Lab here: www.addgene.org/browse/artic...
addgene.org
Addgene: Gene syntax defines supercoiling-mediated transcriptional feedback.
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MyPet Health by Vetcation @vetcation.com · 01/05/2026
In 2015, the Los Angeles SPCA gave their annual National Hero Dog award to a tabby cat named Tara. Yes, you read that right, a cat was given a dog award.
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Albert Blanch-Asensio @ablanchasensio.bsky.social · 04/05/2026
⭕️ The STRAIGHT-IN dual plasmids are now available on Addgene! 🧬 @addgene.bsky.social A full STRAIGHT-IN kit with 20+ plasmids, including everything needed to set up and run the platform, is coming soon 🔥 Stay tuned 🚀
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Alexis Barr @alexisbarr.bsky.social · 29/04/2026
Excellent opportunity @mrc-lms.bsky.social for a human physiologist to start their own group. Deadline 4th May. Core funding, excellent package. Please repost! lms.mrc.ac.uk/work/vacanci...
lms.mrc.ac.uk
Programme Leader Track - MRC Laboratory of Medical Sciences
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Romain Koszul @rkoszul.bsky.social · 16/04/2026
Happy to share our review of the past, recent, and future applications of synthetic genomics in studying the 3D functional organization of chromosomes, a set of approaches that are gaining momentum! www.sciencedirect.com/science/arti...
sciencedirect.com
Synthetic chromosomes for 3D functional genomics: from principles to AI-guided design
The role of genome 3D organization for fundamental chromatin processes, such as long-range promoter-activator regulatory interactions, remains ambiguo…
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MRC Laboratory of Medical Sciences @mrc-lms.bsky.social · 16/04/2026
A new study shows how different regulatory genetic elements control when a key developmental gene is active in the body. The findings could explain subtle differences seen in patients with congenital limb malformations, for which the underlying disease mechanisms often remain unknown.
lms.mrc.ac.uk
Waves of regulation control an important developmental gene
In a new study published in Genes & Development, research led by Dr Lila Allou at the MRC Laboratory of Medical Sciences (LMS) in London and Professor Stefan Mundlos at the Max Planck Institute for Mo...
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Sally Lowell @cellysally.bsky.social · 10/04/2026
Just look at this graph (Fig 5A,B from Koeber et al). Amazing. Congratulations to the Pollard lab and all authors. www.nature.com/articles/s41...
Data. A mouse model of glioblastoma leads to inevitable death within 50 days. Delivery of HSV+TK plus IL2, driven by a strong and specific synthetic superenhancer, allows almost all mice to survive even after nearly 150 days.  From Fig5 of Koeber et al 2026
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Arne Semsrott @arnesemsrott.bsky.social · 15/04/2026
Die Bundesregierung will geheimhalten, wo sie neue fossile Infrastruktur in Deutschland plant. Wir schaffen Transparenz und zeigen, wo neue Kraftwerke, Bohrungen, Pipelines und Flüssiggas-Terminals entstehen sollen – und wie ihr dagegen aktiv werden könnt: fragdenstaat.de/aktionen/cli...
Deutschlandkarte mit Planungsorten von Gaskraftwerken, Bohrungen und Pipelines. Es finden sich vor allem in der Nordsee und in allen Teilen Westdeutschlands Planungen
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Informationsdienst Wissenschaft - idw @idw-online.de · 28/02/2025
Meilenstein in der Neurochirurgie: Neue Methode ermöglicht personalisierte Präzisionschirurgie bei Hirntumoren Forschende des Universitätsklinikums Schleswig-Holstein (UKSH), Campus Kiel, der Christian-Albrechts-Universität zu Kiel (CAU) un... weiterlesen
Dr. Alena van Bömmel, zuletzt Postdoc am MPIMG, Prof. Dr. Helene Kretzmer, zuletzt Gruppenleiterin „Computational Genomics“ am MPIMG, und Mara Steiger, Doktorandin (v. l.) - Copyright MPIMG
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Anders Sejr Hansen @andersshansen.bsky.social · 13/04/2026
Harvey Yang and I were fortunate to contribute polymer simulations to this paper from @nicholas-aboreden.bsky.social Zhao... Zhang, Blobel showing that most CRE loops can form de novo after mitosis without loop extrusion www.nature.com/articles/s41...
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Max Planck Institute of Molecular Cell Biology and Genetics @mpi-cbg.de · 10/04/2026
Meet people @mpi-cbg.de and their younger selves! At MPI-CBG, 500 curiousity-driven individuals, from over 50 countries & from the most diverse backgrounds, explore fundamental molecular and cellular processes underlying the formation of organs and organisms and their healthy maintenance. #thisiswho
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cxqiu.bsky.social @cxqiu.bsky.social · 09/04/2026
New preprint @cxqiu.bsky.social @jshendure.bsky.social ! Can we learn regulatory grammars of human cell types — by training on mouse development and transferring across 241 mammalian genomes? Introducing STEAM & a whole-organism scATAC-seq atlas from E10 to birth. www.biorxiv.org/content/10.6...
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Arnaud Krebs @arnaudkr.bsky.social · 24/03/2026
Want to know how histone marks regulate your favorite gene? Go single molecule with ChromSMF: integrated measure of chromatin accessibility and histone marks + DNA methylation, TF footprints and genotype for free! Very proud of @mpalamin.bsky.social ! @embl.org
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Michela Palamin @mpalamin.bsky.social · 24/03/2026
ChromSMF preprint is out!🚀 tinyurl.com/ChromSMF We often piece together chromatin regulation layer by layer from separate assays. But this can be limiting! In @arnaudkr.bsky.social's lab, we developed a method to directly study multiple layers on the same DNA molecule! 🧬 What does this unlock? ⬇️
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canaztekin.bsky.social @canaztekin.bsky.social · 10/04/2026
🚨 Why can’t mammals regenerate limbs like frog tadpoles or salamanders? In our new paper in @science.org , we show that species-specific oxygen sensing acts as a gatekeeper for initiating limb regeneration 🐭🐸 🔗 www.science.org/doi/10.1126/... #EvoDevo
science.org
Species-specific oxygen sensing governs the initiation of vertebrate limb regeneration
Why mammals cannot regenerate limbs like amphibians do presents a long-standing puzzle in biology. To uncover the underlying differences, we compared amputation responses of embryonic mouse (Mus musculus) and Xenopus laevis tadpole limbs. Lowering ...
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Jacob Schreiber @jmschreiber91.bsky.social · 09/03/2026
The Programmable Genomics Lab at @umasschan.bsky.social just officially launched our site! We have a "simple" goal: to develop synthetic regulatory elements that target every cell type in every tissue, and control payload dosage/duration Check it out! programmable-genomics.github.io
programmable-genomics.github.io
Programmable Genomics Laboratory | Home
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Jonathan Froehlich @jjfroehlich.bsky.social · 11/03/2026
I started Awesome Life Science Resources: a curated list of resources on work culture, career, and communication for life scientists. Built for PhD students, postdocs, and PIs. Check it out: github.com/jjfroehlich/...
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Noura Maziak @nmaziak.bsky.social · 10/03/2026
Excited to share my PhD work! The question: How is genome organization established? Here, we developed a low-input Micro-C method, Pico-C, and used it to map chromatin architecture across early stages of fly development. Here’s a quick Blue-torial 🙂 (1/n) www.nature.com/articles/s41...
nature.com
Three-dimensional genome reorganization foreshadows zygotic genome activation in Drosophila - Nature Genetics
Pico-C, a low-input Micro-C approach, reveals that dynamic three-dimensional genome folding precedes zygotic genome activation in Drosophila.
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Hadley Wickham @hadley.nz · 05/03/2026
These captchas just keep getting harder #rstats
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.
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Daniel Ibrahim @danielibrahim.bsky.social · 05/03/2026
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!!
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Tugce Aktas @aktast.bsky.social · 25/02/2026
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.
doi.org
Redirecting
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Carl de Boer @carldeboer.bsky.social · 25/02/2026
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.
Participants of the meeting posing on a staircase looking fantastic.
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Daniel Ibrahim @danielibrahim.bsky.social · 27/02/2026
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!
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Daniel Ibrahim @danielibrahim.bsky.social · 27/02/2026
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!
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