Terrific new feature presented by @theo.io on @pathoplexus.org called SeqSets for generating DOIs for sequence subsets used in publications, that can then be tracked for impact via CrossRef that will allow data generators to track impact! #IMMEMXiV

Honoured to be in Birmingham to mark Bryan Turner’s retirement- a gentleman and giant of epigenetics.

Interested in zebrafish as a disease model for NF1? We are seeking a motivated PhD student to join our team and become an expert in high-resolution imaging/precise genome editing in collab with AZ. gw4biomed.ac.uk/establishing... @lsiexeter.bsky.social @zebrafishrock.bsky.social @izfs.bsky.social

This is not a HiC map! Ever wondered if multiple enhancers get activated simultaneously? We measured chromatin accessibility on thousands of molecules by nanopore to create genome-wide co-accessibility maps. Proud of @mathias-boulanger.bsky.social @kasitc.bsky.social Biology in the thread👇

#zebrafish genome update, our T2T assembly of the inbred strain of AB (M-AB) generated by my buddy Nori Sakai has now been released at NCBI and will be a second reference genome for zebrafish (GRCz12ab):

Check out our new collaborative preprint about Affinity-ligand purification of native human low-abundance multi-protein complexes doi.org/10.1101/2025...

Excited to share the latest work from the lab led by @eharo84.bsky.social, in which we have used synthetic biology to explore the mechanisms by which different types of long-range enhancers ensure robust and precise developmental gene expression www.biorxiv.org/content/10.1...

📢One month left to apply to our Group Leader position! 🌟A chance to be part of @nordicembl.bsky.social: “The Partnership connects us with an exceptional network of researchers, facilities, and complementary expertise. It opens doors to meaningful scientific exchange”, says @amathelier.bsky.social.

So excited and grateful to receive R24 NOA from NIH ORIP to create an integrated #zebrafish omics, histology and microCT 3D atlas! Looking forward to an exciting work with Dr. Postlethwait of U of Oregon, who is the co-PI of the grant.

Wrote a big review with my friend and colleague @varshneylab.social on the state-of-the-art in CRISPR used experimentally in vivo. We wanted to focus on their use in experimental vertebrate animals (apparently passé now but we persist).

#IZFC2025 #zebrafish #DANIO-CODE data coordination centre is back online. Note changed address: danio-code-dcc.genereg.net

The winners of the 2025 George Streisinger Award are the Course Directors of the Zebrafish Development and Genetics course at MBL, for their tremendous contributions to our amazing community for >25 years! #izfc2025

Dear #izfc2025 participants, if anyone of you are interested in how transcription control defines mRNA fate and translation in zebrafish development, there are/will be several PhD and postdoctoral positions (funded by the Wellcome Trust) for this research. Please find me if interested.

Genome Biology conference in Birmingham UK in September. Check out our great invited speakers! Lots of slots for talks selected from abstracts too! Please repost 😀

Do you use EMBL-EBI data resources? We would really appreciate your feedback! Our Interim Director Jo McEntyre explains how you can help us demonstrate the value of our data resources: www.ebi.ac.uk/about/news/a... Survey closes on 16 July: www.surveymonkey.com/r/QGFMBH8?ch... Thank you!

After a quarter of a century, the UCSC Genome Browser remains an essential tool for navigating the genome and understanding its structure, function and clinical impact https://go.nature.com/40wPxkB

The Birmingham Centre for Genome Biology invites you to join us at our 10th year anniversary conference! Website and Registration here: shorturl.at/rvJSr Fantastic speakers, and a very cost-efficient meeting for ECRs and all. Talk slots are available. See you in Brum on 11-12th September 2025!

Birmingham Centre for Genome Biology 2025 Anniversary Conference, 11-12 September! This symposium covers DDR and gene regulation. Register here: uobevents.eventsair.com/birmingham-c...

Join us! This will be a great meeting.

Are you a biologist with a research interest in #embryogenesis or synthetic biology? Join our upcoming residential scientific meeting in Brighton on the topic of generative biology: royalsociety.org/science-even... ‪@jcornwallscoones.bsky.social ‪@dbenzinger.bsky.social @cellysally.bsky.social

In the new issue of @cp-trendsgenetics.bsky.social, @wiringthebrain.bsky.social & Nick Cheney seek out a better metaphor. They propose a generative model concept to capture the indirect, distributed, & non-linear relationship between info in the genome & form of the organism. Worth a read: 🧬👇🧪 11/11

If you love Daniocell, but wish it could generate analyses specific to YOUR genes & cell types of interest, check out DaniocellDesktop - a new point-and-click app for Mac and Windows that enables reanalysis of the Daniocell data without programming: daniocell.nichd.nih.gov/desktop/ (1/4)

#Zebrafish genome reference update: it is now "live" on the UCSC genome browser at: genome.ucsc.edu/cgi-bin/hgTr... I am working on getting it included in the zebrafish genome pull down menu with the previous assemblies but that isn't working yet.

URGENT: FlyBase has lost practically all its funding overnight; even user fees are tied up in denied grant funding. 🤬🤯 Any lab using @flybase.bsky.social please donate using the link in post below. This incredible community, on whose backs our #Drosophila labs depend, can't be left out to dry.

ICYMI

Excited to share my first contribution here at Illumina! We developed PromoterAI, a deep neural network that accurately identifies non-coding promoter variants that disrupt gene expression.🧵 (1/)

We put a lot of effort into creating an easy to implement #github presence: github.com/tobiaszehnde... and deposited pre-processed files so that anyone can easily use #IPP on any human, mouse, or chicken bed-file to find conserved positions in all our different species. Go on and use it!

How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭 Check out our paper - fresh off the press!!! We find widespread functional conservation of enhancers in absence of sequence homology Including: a bioinformatic tool to map sequence-diverged enhancers! rdcu.be/enVDN github.com/tobiaszehnde...

Sequence-alignment is not the best way to detect conserved cis-regulatory elements? Tobi Zehnder from Vingron-Lab developed #IPP a synteny based algorithm with @ferencmueller.bsky.social, @borislenhard.bsky.social& @da-bar.bsky.social We used it to find conserved enhancers with diverged sequences

#DanioDigest (April 2025) Community News: Prof Wendy Bickmore @wbickmor.bsky.social elected as an International Member of the US National Academy of Sciences (NAS). Prof Dr Andrea Rentmeister @rentmeisterlab.bsky.social#DanioDigestreceives 2024 Franco-German Georg Wittig - Victor Grignard Prize. (1/46)

It was a pleasure to write a N&Vs on @danielibrahim.bsky.social's latest paper in @natgenet.nature.com. Enhancers tend to stay put even if their sequence changes beyond recognition. Quoting Il Gattopardo, everything must change so that everything can stay the same: www.nature.com/articles/s41...

Very happy to see that the work by Magdalena Karpinska from @mariekeoudelaar.bsky.social's lab at @mpi-nat.bsky.social is now out in NSMB! Mariano Barbieri from my lab contributed modeling that (we think) nicely explain CTCF contribution to multiway E-P interactions. www.nature.com/articles/s41...

Some exciting news! NCBI has finished the annotation pipeline for our new #zebrafish reference sequence GRCz12tu: www.ncbi.nlm.nih.gov/refseq/annot... This is a big step up in data depth and quality and should be super helpful going forward.

Welcome @burgesslab.bsky.social as an Associate Editor for #GENETICS 👋 Burgess, who will be joining the Experimental Technologies and Resources section, studies tissue regeneration in zebrafish and genome function. We’re delighted to have him on the team! Read more: buff.ly/k0yDk5c

Friday we celebrated my 40 years of scientific career in France, with present and past lab members and many friends. It was a fantastic day full of emotions, memories and great science. Thanks for making the day so memorable !

It has been a while since I advertised some of the tools we have released to help researchers analyze the zebrafish genome. So a brief Bluetorial on our zebrafish genomics UCSC public data hub and the bigger effort led by @ferencmueller.bsky.social to create a zebrafish ENCODE project (Danio-CODE):

Milestone reached: We’ve just surpassed 500 active monthly users on the Slack tankspace for the first time! 🤩 If you’d like to join, register your interest at our website: linktr.ee/zebrafishrock #RockOn

Do you need a certificate to work with fish models? Transgenic lines or mutants generated by Sanger or Tübingen? Get in touch with us at www.ezrc.kit.edu! #Zebrafish

Day 1 #PFAS are industrial chemicals that contaminate humans and the environment. One type of PFAS, called PFOA, was banned in 2020 because of its toxic effects. Despite the ban, it is still found in most living organisms along with complex mixtures of structurally similar PFAS.

We have a fully funded 4-year PhD position in the Monteiro Lab (rb.gy/osbkxv) to investigate novel modulators of blood stem cell fitness in GATA2 deficiency. Deadline for application: 6th April 2025 NOTE: only UK Home candidates are eligible to apply! rb.gy/7qffpf please share!

I have one open PhD position. Maybe one of the last PhD positions in the lab as I'm planning changes in what we do and how we will do it some five years from now. I'm offering freedom (pun intended), respect, an interesting project, and a good full time contract w. health insurance.

We are #hiring a postdoc to study the epigenetic imprinting of cell fate during adipogenesis. Cool interdisciplinary project to analyze ChIP-seq, ATAC-seq, Hi-C, and CAGE. The postdoc will be co-supervised by @chymkowitchlab.bsky.social and me. Spread the word! www.jobbnorge.no/en/available...

Last day to apply!!

📣 Hiring, please forward widely!! Two postdoc openings to work on genomics of diabetes 1. Computational regulatory genomics/statistical genetics. 2. Experimental cell-based modeling DM if interested @crg.eu shorturl.at/O3wMi shorturl.at/ieyZy

We wrote an opinion article inspired by the recent exciting reports on the sequence determinants of TSS selection + old observations on TFs activation domains. More posts on this soon! Q-rich activation domains: flexible ‘rulers’ for transcription start site selection? www.cell.com/trends/genet...

After 3 years of procedure, review by 3 specialists, and a final seminar, I officially received my habilitation today! I am now qualified to teach at the university and supervise Ph.D. students. I’ve been doing this for over 20 years without the title, but now I’m officially a Privatdozent!

RNA polymerase II transcription initiation in holo-TFIID-depleted mouse embryonic stem cells. www.cell.com/cell-reports...

PhD position(s) available in #development #genomics:  tinyurl.com/9dk9m29d European (#MSCA) doctoral training network,  #DanioreCODE (tinyurl.com/2rz4mdsa). How does  #transcription initiation regulation control #brain injury response and  #regeneration in #zebrafish?

🚀 Great Opportunity! The Danio ReCode EU consortium is offering **15 PhD positions** across diverse biological fields, from development to computer science! 🌱💻 apply here: 🔗 [https://euraxess.ec.europa.eu/jobs/290548](euraxess.ec.europa.eu/jobs/290548) #zebrafish #positions

PhD position available! We have a position available as part of the @MIBTP_BBSRC programme (warwick.ac.uk/fac/cross_fa...) on epigenetic regulation of stem cell fate in collaboration with the Cowley lab @uniofleicester. Deadline for applications - 16th January 2025 DM for more info Please share!