Ferenc Mueller

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

A new level of gene regulation in tumour heterogeneity in colorectal cancer organoid models at University of Birmingham on FindAPhD.com PhD Project - A new level of gene regulation in tumour heterogeneity in colorectal cancer organoid models at University of Birmingham, listed on FindAPhD.com

Still time to apply for these PhD opportunities (Deadline 9th January)! Check out this project on transcription initiation regulation, metabolism and cancer heterogeneity: shorturl.at/LSnsy. More on applications here: shorturl.at/O5VST

Photograph and signature of Edward Roosen-Runge taken from an obituary.

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)

Stowers Research Conferences: Development, Regulatory Genomics & AI Organized by Julia Zeitlinger, Ph.D., Neşet Özel, Ph.D., and Tatjana Sauka-Spengler, Ph.D.

“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

Good luck with the quest! In the meantime, how about these drawings by Galileo Galilei of the 50% epiboly embryo. Note the first depiction of the YSL nuclei.

Team Leader – Genomics Core Facility and Method Development Are you ready to lead a cutting-edge Genomics Core facility while developing state of the art genomics methods? Join us at EMBL! We are seeking talented scientists to develop and lead a cutting-edge G...

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...

Fantastic training opportunities, interdisciplinary projects spanning across 2-3 institutions

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*.

JASPAR goes Deep Learning! - NCMBM - Norwegian Centre for Molecular Biosciences and Medicine A new era for motif resourcesThe team behind JASPAR, led by Anthony Mathelier at NCMBM, has released the 11th update. JASPAR is built and maintained by an international consortium of research groups, ...

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...

3. 9 positions will be available, watch this space and usual sites for post-doc and PhD adverts!

2. with C Varnai, Y Hadzhiev (@unibirmingham.bsky.social), @wbickmor.bsky.social, S. Bhatia (@edinburgh-uni.bsky.social), @borislenhard.bsky.social (@mrc-lms.bsky.social), P Cai, J James (@manchester.ac.uk), B Davies (@crick.ac.uk) and @andrewyatz.bsky.social (@ebi.embl.org)

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

From food to phenotype - defining how cancer cells modify their transcriptome in response to the nutrient environment? at University of Birmingham on FindAPhD.com PhD Project - From food to phenotype - defining how cancer cells modify their transcriptome in response to the nutrient environment? at University of Birmingham, listed on FindAPhD.com

Another PhD position for those interested in working with cancer organoids and transcription initiation control of metabolism and growth (shorturl.at/wh6nW)

Training opportunities include - and/or experience with desired: zebrafish gene editing, transgenesis, genomics (bulk and single cell)

How does the interplay between metabolism control and gene regulation shape embryo development? at University of Birmingham on FindAPhD.com PhD Project - How does the interplay between metabolism control and gene regulation shape embryo development? at University of Birmingham, listed on FindAPhD.com

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.

Enhancer-promoter compatibility is mediated by the promoter-proximal region Gene promoters induce transcription in response to distal enhancers. How enhancers specifically activate their target promoter while bypassing other promoters remains unclear. Here, we find that the p...

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):