Ferenc Mueller
- Reposted by Ferenc MuellerAlphaGenome 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
- Reposted by Ferenc MuellerOver 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)
- Reposted by Ferenc Mueller“Development, regulatory genomics & AI on April 22-24 www.stowers.org/events/stowe...
- Reposted by Ferenc Mueller2025 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
- Reposted by Ferenc MuellerOpen 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...
- Reposted by Ferenc MuellerApplications 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*.
- Reposted by Ferenc MuellerTogether, 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!
- Reposted by Ferenc MuellerCome join us in Heidelberg for the first German fish meeting 👩🔬👨🔬🧬🔬🐟🐠
- Reposted by Ferenc MuellerFolks, 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).
- 3. 9 positions will be available, watch this space and usual sites for post-doc and PhD adverts!
- Reposted by Ferenc Mueller🐟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.
- Another PhD position for those interested in working with cancer organoids and transcription initiation control of metabolism and growth (shorturl.at/wh6nW)
- Reposted by Ferenc MuellerWhat 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...
- Reposted by Ferenc MuellerIf you've benefited from ZebrafishRock and its community, you can thank ZFIN. i.e. ZebrafishRock is actually Kevin searching ZFIN
- Want an easy way to support your model organism databases? Cite them! Depending on the #zebrafish data you retrieve from ZFIN, you can show your support by using one of the formats below 🙏 🧪 #ZebrafishFunFacts
- Reposted by Ferenc Mueller🏆 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
- Reposted by Ferenc Mueller🐟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
- Reposted by Ferenc MuellerIt 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.
- Reposted by Ferenc MuellerCell nuclei movements (color-coded for direction) during early zebrafish development. Credit to Dr. Philipp Keller @hhmijanelia.bsky.social. #ZebrafishZunday
- Reposted by Ferenc MuellerTerrific 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
- Reposted by Ferenc MuellerHonoured to be in Birmingham to mark Bryan Turner’s retirement- a gentleman and giant of epigenetics.
- Reposted by Ferenc MuellerInterested 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
- Reposted by Ferenc MuellerThis 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👇
- Activity of most genes is controlled by multiple enhancers, but is there activation coordinated? We leveraged Nanopore to identify a specific set of elements that are simultaneously accessible on the same DNA molecules and are coordinated in their activation. www.biorxiv.org/content/10.1...
- Reposted by Ferenc Mueller#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):
- Reposted by Ferenc MuellerCheck out our new collaborative preprint about Affinity-ligand purification of native human low-abundance multi-protein complexes doi.org/10.1101/2025...
- Reposted by Ferenc MuellerExcited 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...
- Reposted by Ferenc Mueller📢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.
- Reposted by Ferenc MuellerSo 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.
- Reposted by Ferenc MuellerWrote 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
- Track hub for UCSC browser: trackhub2genereg.net/DANIO-CODE/D...
- Correction: trackhub2.genereg.net/DANIO-CODE/D...
- Reposted by Ferenc MuellerThe 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.
- Reposted by Ferenc MuellerGenome Biology conference in Birmingham UK in September. Check out our great invited speakers! Lots of slots for talks selected from abstracts too! Please repost 😀
- 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!
- Reposted by Ferenc MuellerDo 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!
- Reposted by Ferenc MuellerAfter 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 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!
- Reposted by Ferenc MuellerBirmingham Centre for Genome Biology 2025 Anniversary Conference, 11-12 September! This symposium covers DDR and gene regulation. Register here: uobevents.eventsair.com/birmingham-c...
- Reposted by Ferenc MuellerJoin 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
- Reposted by Ferenc MuellerAre 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
- Reposted by Ferenc MuellerIn 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
- Reposted by Ferenc MuellerIf 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)
- Reposted by Ferenc Mueller#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.
- Reposted by Ferenc MuellerURGENT: 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.
- My lab studies bacterial infections. We spend a lot of time looking at (or for) species-specific genetic and genomic databases for hosts and microbes. FlyBase is the best of all—there is literally no comparison. Its existence is under threat. Please donate. www.philanthropy.cam.ac.uk/give-to-camb...
- Reposted by Ferenc MuellerICYMI
- #ICYMI Bioinformatics Bootcamp – Zebrafish Special Edition @kevinthiessen.bsky.social compiled a very useful collection of resources for those working with #zebrafish and beyond. Have fun exploring!
- Reposted by Ferenc MuellerExcited 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/)
- Reposted by Ferenc MuellerWe 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!
- Reposted by Ferenc MuellerHow 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...
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View full threadReposted by Ferenc MuellerSequence-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
- Reposted by Ferenc Mueller#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 receives 2024 Franco-German Georg Wittig - Victor Grignard Prize. (1/46)
- Reposted by Ferenc MuellerIt 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...
- Reposted by Ferenc MuellerVery 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...
- Reposted by Ferenc MuellerSome 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.
- Reposted by Ferenc MuellerWelcome @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
- Reposted by Ferenc MuellerFriday 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 !
- Reposted by Ferenc MuellerIt 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):
- Reposted by Ferenc MuellerMilestone 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
