Daniel Ibrahim

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...

New preprint drop! I think this fun little story on Berkson's paradox will become essential reading for computational biology/genomics, where I think it commonly occurs but is poorly known. www.biorxiv.org/content/10.6...

I'm happy to share some good news: I finished my PhD after many great years at @molgen.mpg.de Next, I am starting my own group on AI for Biology at @mdc-berlin.bsky.social as an Independent Fellow. I will continue my work on designing biology-inspired AI models for gene regulation and single cells.

The flies arrived in Cambridge this morning—healthy and happy! So nice to see another successful shipment! And great to draw one of our all-time-best customers out of retirement long enough to recreate our first order! Here’s to another 40 years of the BDSC helping to make fly genetics happen!

40 years ago today, the BDSC made its 1st shipment. To celebrate, Trudy Kaufman, who packed the 1st shipment, boxed up the same kinds of flies for John Roote at Cambridge, who placed the 1st order. Watch for pics of the arrival next week. We’ve shipped 4,882,378 vials total. That’s a lot of flies!

IMO the paper of the year in the gene regulation field - such a clean and clear study, showing how promoter-enhancer contacts mediate transcriptional activation. www.cell.com/cell/abstrac...

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...

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!

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).

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!

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...

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.

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

📢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...

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...

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?

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?

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)

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... 🧵

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?

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:

The cooling system was installed by the village AC technician, Thermodynamix 😊

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...

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...

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.

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!

An historical figure of the transcription field has gone. Founder of @igbmc.bsky.social where I started my career. A great enabler as well.

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 💐

And more plasmids for using STRAIGHT-IN Dual from the Galloway Lab here: www.addgene.org/browse/artic...

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.

⭕️ 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 🚀

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...

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...

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.

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...

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...

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

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...

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

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...

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

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? ⬇️

🚨 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

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

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/...