AlphaGenome is out in @nature.com today along with model weights! 🧬 📄 Paper: www.nature.com/articles/s41... 💻 Weights: github.com/google-deepm... Getting here wasn’t a straight path. We discussed the story behind the model, paper & API in the following roundtable: youtu.be/V8lhUqKqzUc

Over the past weeks I have been reading the earliest papers on zebrafish development, and came to realize that in the “canonized" version of zebrafish history we neglect some important people pre-Streisinger. I will try to correct here the record. Let’s start with Edward C. Roosen-Runge. (1/7)

“Development, regulatory genomics & AI on April 22-24 www.stowers.org/events/stowe...

2025 is a wrap! That’s the end of our coverage of all things #zebrafish for the year. We hope you have a safe and rejuvenating holiday season. Look out for us in the New Year! #RockOn

Open Team Leader position @embl.org to head & reshape our Genomics Core facility. Interested in providing & developing state-of-the art omics tech to a wide community? A very vibrant, dynamic place to work with fantastic colleagues. Closing Sept 30th embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Applications are now open 🚀for our fully funded Medical Research Council 4-year 🎓studentships 🎓 across our 3 partner institutions @unibirmingham.bsky.social @uniofleicester.bsky.social and @uniofnottingham.bsky.social See👉 more.bham.ac.uk/mrc-aim/phd-... to find out more and apply *by 9 Jan 2026*.

Together, these approaches create a uniquely powerful platform for exploring how transcription factors interpret the genome.” 📰 Read the full story: www.med.uio.no/ncmbm/englis... Congrats to the entire JASPAR community for driving this resource forward to shape the future of regulatory genomics!

Come join us in Heidelberg for the first German fish meeting 👩‍🔬👨‍🔬🧬🔬🐟🐠

Folks, it is finally out! Our paper on T2T assemblies of the zebrafish genome is on BioRxiv: www.biorxiv.org/content/10.1...

1. We start a major consortium programme funded by the sLoLa of BBSRC (shorturl.at/aUbnt) to decipher the semantic rules of enhancer arrangements driving regulator genes of development (shorturl.at/6qcjW).

🐟Meet the DANIO-ReCODE team!🐟 This week:Parth Bhatia and Prof @ferencmueller.bsky.social from @unibirmingham.bsky.social Parth´s research focuses on the annotation,characterisation and dynamics of cis-regulatory elements (CREs) in telencephalon injury 📢Stay tuned! #DANIO #MSCA @obog.bsky.social

PhD position (funded, competitive, shorturl.at/3zcmP, application details: shorturl.at/RDzd6) and postdoctoral fellow position (shorturl.at/UWtUV) are available in our lab. Topics: transcription regulation control of metabolism in development and upon toxic chemical exposures.

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...

If you've benefited from ZebrafishRock and its community, you can thank ZFIN. i.e. ZebrafishRock is actually Kevin searching ZFIN

🏆 First Prize – DevBio Art Contest 🖼️
“A Model Meeting” by Karla Akari Garcia Inspired by The Quaker Meeting, this watercolor honors animal research models, from mouse to axolotl, that have advanced developmental biology 🎨 A tribute to science’s often unsung heroes. #DevBioArt

🐟DANIO-ReCODE MSCA DN🐟 As part of Consortium DCs training, PhDs attended a "Career Development Workshop" led by Amani Said, career coach. They took part in two sessions focused on how maximizing their PhD journey #DANIO #MSCA @obog.bsky.social @ec.europa.eu @cabd-upo-csic.bsky.social

It is with great sadness that we heard of John Gurdon’s passing this week. Not just one of our 100 extraordinary biologists, but truly one of a kind, he was a pioneer, whose vision and personality inspired biologists worldwide.

Cell nuclei movements (color-coded for direction) during early zebrafish development. Credit to Dr. Philipp Keller @hhmijanelia.bsky.social. #ZebrafishZunday

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...