Reposted by Daniel IbrahimArnaud Krebs @arnaudkr.bsky.social · 10/09/2026EMBL 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... 02312
Reposted by Daniel IbrahimMariana Schuster @marischuster.bsky.social · 07/09/2026I'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! 18884
Reposted by Daniel IbrahimPaul Byrne @theplanetaryguy.com · 09/09/2026Astrophotographer 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). 187165305074
Daniel Ibrahim @danielibrahim.bsky.social · 27/08/2026I 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! 030
Reposted by Daniel IbrahimShenzhi Chen @shenzhichen1999.bsky.social · 25/08/2026Excited 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... 35826
Reposted by Daniel IbrahimEvgeny Kvon @evgenykvon.bsky.social · 26/08/2026Breakthroughs 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. 1213
Reposted by Daniel Ibrahimrev. howard arson @theophite.bsky.social · 19/08/2026the mechanism behind this is that if you don't do your homework you don't learn the topic 23644112
Reposted by Daniel IbrahimTeresa Rayon @trayon.bsky.social · 15/08/2026Our 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 712947
Reposted by Daniel IbrahimBjørt 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.comComputational Staff Scientist - shared between 2 labs - in spatial and single cell omicsDo 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 045
Reposted by Daniel IbrahimJonathan Pritchard @jkpritch.bsky.social · 09/08/2026Must-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.comOn Fermi Problems in Human Geneticsand some very useful numbers about human genomes to get you started! 918570
Reposted by Daniel IbrahimSelin Jessa @selinjessa.com · 06/08/2026Massive 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! 083
Daniel Ibrahim @danielibrahim.bsky.social · 31/07/2026really 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? 270
Reposted by Daniel IbrahimJudith Kribelbauer @jk-swietek.bsky.social · 30/07/2026Obviously 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. 1153
Reposted by Daniel Ibrahimnellykanata.bsky.social @nellykanata.bsky.social · 28/07/2026I 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? 24720
Reposted by Daniel IbrahimSarah Vergult @svergult.bsky.social · 27/07/202640 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) 293
Reposted by Daniel IbrahimAlbert Blanch-Asensio @ablanchasensio.bsky.social · 20/07/2026The 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... 🧵 11911
Reposted by Daniel IbrahimDavid Shiffman, Ph.D. 🦈 @whysharksmatter.bsky.social · 16/07/2026When 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.orgWhy The Ocean Cleanup Hasn’t Solved the Plastic Pollution Crisis • The RevelatorGlobal 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? 14509202
Reposted by Daniel IbrahimLuca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 15/07/2026Our 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.orgEnhancer control of promoter activity and variability via frequency modulation of clustered transcriptional bursts - Nature GeneticsTünnermann 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... 48345
Daniel Ibrahim @danielibrahim.bsky.social · 27/06/2026really 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. 130
Reposted by Daniel Ibrahimlilastromech (Mischa) @mischajaye.bsky.social · 26/06/2026The cooling system was installed by the village AC technician, Thermodynamix 😊 6449491404
Reposted by Daniel IbrahimJonas Koeppel @jonaskoeppel.bsky.social · 04/06/20261/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... 28134
Reposted by Daniel IbrahimJonas Koeppel @jonaskoeppel.bsky.social · 04/06/202622/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.ioKoeppel Lab | Structural Variation and Genome EngineeringGenome engineering research led by Jonas Koeppel, developing scalable technologies to design structural variants and study mammalian genome function. 3349
Reposted by Daniel IbrahimFerenc Mueller @ferencmueller.bsky.social · 01/06/2026Join 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. 01512
Reposted by Daniel IbrahimMax Planck Institute of Immunobiology and Epigenetics @mpi-ie.bsky.social · 27/05/2026We 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.deMarieke Oudelaar becomes new Director at MPI-IE in Freiburg 17219
Reposted by Daniel IbrahimArnaud Krebs @arnaudkr.bsky.social · 08/05/2026An historical figure of the transcription field has gone. Founder of @igbmc.bsky.social where I started my career. A great enabler as well. 0103
Reposted by Daniel IbrahimDenis Duboule @denisduboule.bsky.social · 07/05/2026Pierre 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 💐 37119
Reposted by Daniel IbrahimAddgene @addgene.bsky.social · 04/05/2026And more plasmids for using STRAIGHT-IN Dual from the Galloway Lab here: www.addgene.org/browse/artic...addgene.orgAddgene: Gene syntax defines supercoiling-mediated transcriptional feedback. 011
Reposted by Daniel IbrahimMyPet Health by Vetcation @vetcation.com · 01/05/2026In 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. 6975321271
Reposted by Daniel IbrahimAlbert 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 🚀 0132
Reposted by Daniel IbrahimAlexis Barr @alexisbarr.bsky.social · 29/04/2026Excellent 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.ukProgramme Leader Track - MRC Laboratory of Medical Sciences 01616
Reposted by Daniel IbrahimRomain Koszul @rkoszul.bsky.social · 16/04/2026Happy 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.comSynthetic chromosomes for 3D functional genomics: from principles to AI-guided designThe role of genome 3D organization for fundamental chromatin processes, such as long-range promoter-activator regulatory interactions, remains ambiguo… 02215
Reposted by Daniel IbrahimMRC Laboratory of Medical Sciences @mrc-lms.bsky.social · 16/04/2026A 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.ukWaves of regulation control an important developmental geneIn 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... 2207
Reposted by Daniel IbrahimSally Lowell @cellysally.bsky.social · 10/04/2026Just 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... 22613
Reposted by Daniel IbrahimArne Semsrott @arnesemsrott.bsky.social · 15/04/2026Die 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... 431430816
Reposted by Daniel IbrahimInformationsdienst Wissenschaft - idw @idw-online.de · 28/02/2025Meilenstein 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 082
Reposted by Daniel IbrahimAnders Sejr Hansen @andersshansen.bsky.social · 13/04/2026Harvey 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... 14311
Reposted by Daniel IbrahimMax Planck Institute of Molecular Cell Biology and Genetics @mpi-cbg.de · 10/04/2026Meet 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 2173
Reposted by Daniel Ibrahimcxqiu.bsky.social @cxqiu.bsky.social · 09/04/2026New 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... 15127
Reposted by Daniel IbrahimArnaud Krebs @arnaudkr.bsky.social · 24/03/2026Want 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 17118
Reposted by Daniel IbrahimMichela Palamin @mpalamin.bsky.social · 24/03/2026ChromSMF 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? ⬇️ 311551
Reposted by Daniel Ibrahimcanaztekin.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/... #EvoDevoscience.orgSpecies-specific oxygen sensing governs the initiation of vertebrate limb regenerationWhy 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 ... 21270115
Reposted by Daniel IbrahimJacob Schreiber @jmschreiber91.bsky.social · 09/03/2026The 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.ioprogrammable-genomics.github.ioProgrammable Genomics Laboratory | Home 1218
Reposted by Daniel IbrahimJonathan Froehlich @jjfroehlich.bsky.social · 11/03/2026I 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/... 34621
Reposted by Daniel IbrahimNoura Maziak @nmaziak.bsky.social · 10/03/2026Excited 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.comThree-dimensional genome reorganization foreshadows zygotic genome activation in Drosophila - Nature GeneticsPico-C, a low-input Micro-C approach, reveals that dynamic three-dimensional genome folding precedes zygotic genome activation in Drosophila. 17024
Reposted by Daniel IbrahimHadley Wickham @hadley.nz · 05/03/2026These captchas just keep getting harder #rstats 8630141
Daniel Ibrahim @danielibrahim.bsky.social · 05/03/2026And 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!! 030
Reposted by Daniel IbrahimTugce Aktas @aktast.bsky.social · 25/02/2026Our 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.orgRedirecting 912560
Reposted by Daniel IbrahimCarl de Boer @carldeboer.bsky.social · 25/02/2026Thanks 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. 263
Daniel Ibrahim @danielibrahim.bsky.social · 27/02/2026We 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! 02812
Daniel Ibrahim @danielibrahim.bsky.social · 27/02/2026This 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! 020