Reposted by Ferenc MuellerMwahahahahahadScientist @mads100tist.bsky.social · 18/09/2026With my co-conspirator Sepand @rastapopolus.bsky.social 2241
Reposted by Ferenc MuellerErik van Nimwegen @erikvannimwegen.bsky.social · 09/05/2025Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...biorxiv.orgBonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics dataSingle-cell omics methods promise to revolutionize our understanding of gene regulatory processes during cell differentiation, but analysis of such data continues to pose a major challenge. Apart from... 9335108
Reposted by Ferenc MuellerShawn Burgess @burgesslab.bsky.social · 27/07/2026De novo annotations on the AB genome are still in the pipeline, hopefully to be released in the next few months, but until then, these tracks can be downloaded if you need annotations for AB and don't want to do a liftoff/liftover yourself. Genome is here: genome.ucsc.edu/cgi-bin/hgTr...genome.ucsc.edu 132
Reposted by Ferenc MuellerRobert Krautz @robertkrautz.bsky.social · 19/05/2026Absolutely thrilled 💣 to share our preprint 🖨️: "Mapping active cis-regulatory elements from transcription initiation events”. www.biorxiv.org/content/10.6... We introduce nucCAGE and PRIME to identify active cis-regulatory elements (CREs) and disease-associated, non-coding variants.biorxiv.org 1227
Ferenc Mueller @ferencmueller.bsky.social · 21/07/2026Join us in Budapest in October! There is still time to register with an abstract. Talk and flash talk slots, a great speaker line up at an informal meeting on epigenetics, gene and genome regulation etc. in a beautiful city. shorturl.at/fOuCZ. For that to do list before the holidays! 1125
Reposted by Ferenc MuellerAlexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 16/07/2026In memory of Pierre Chambon (1931–2026): a visionary pioneer of modern molecular biology by Hinrich Gronemeyer in @embojournal.org link.springer.com/article/10.1...link.springer.comIn memory of Pierre Chambon (1931–2026): a visionary pioneer of modern molecular biology - The EMBO JournalThe EMBO Journal - 01910
Ferenc 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 Ferenc MuellerPatricia Bernal @pbernalt6ss.eurosky.social · 31/05/2026Excessive paperwork and inefficient systems are sabotaging scientific progress. Really proud to be part of this global manifesto spearheaded by @kentimmis.bsky.social. We need action at all levels to tackle the root causes. Our analysis & proposals @microbiotech.bsky.social: doi.org/10.1111/1751...doi.orgScientists' Warning to Humanity: Unnecessary Bureaucracy Is a Global Impediment to Productivity, Advancement of Human and Planetary Wellbeing, Science and SustainabilityUnnecessary bureaucracy is a global impediment to progress and productivity that increases stress and lowers workplace morale and motivation. In research it smothers creativity and innovation that ar.... 02117
Reposted by Ferenc MuellerRob Klose @robklose.bsky.social · 29/05/2026Help please! We need to do some large(ish) cell culture inhibiting E-cadherin with a monoclonal antibody. Does anyone have the DECMA-1 hybridoma cell line so we could purify our own antibody? or a similar monoclonal that would do the job. Any help greatly appreciated, just DM me. Please repost! 01241
Reposted by Ferenc MuellerZebrafish Rock! @zebrafishrock.bsky.social · 17/05/2026ICYMI… Huge congrats to Prof. David Grunwald @utah.edu for winning this year’s George Streisinger Award from IZFS! #RockOn 🐟 #zebrafish 2207
Reposted by Ferenc MuellerAlexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 07/05/2026#RIP Pierre Chambon (1931-2026) via @alainberetz.bsky.social one of the last giants in biology: PARP, nuclear receptors, RNA Pol II, nucleosome, promoters, split genes 310052
Reposted by Ferenc MuellerRichard Sever @richardsever.bsky.social · 04/04/2026CRUK goes green [OA] news.cancerresearchuk.org/2026/04/01/w...news.cancerresearchuk.orgWhy we won’t be funding open access publishing any more - Cancer Research UK - Cancer NewsThe open access movement was bold and promising, but ultimately disappointing. Now is the time to stop and call for a new way to make publishing work… 33727
Reposted by Ferenc MuellerFerenc Mueller @ferencmueller.bsky.social · 17/02/2026We are hiring 2 Postdoctoral fellows for our lab (www.mueller-lab.org): 1, Transcription control of metabolic adaptation in development (shorturl.at/oeG6U). 2, Semantic rules of developmental gene regulation (shorturl.at/KdHmJ) #jobs #transcription #zebrafish #zebrafishrock #IZFSshorturl.atResearch Fellow at University of BirminghamDiscover Research Fellow jobs and more in higher education on jobs.ac.uk. Apply for further details on the top job board. 2115
Ferenc Mueller @ferencmueller.bsky.social · 17/02/2026We are hiring 2 Postdoctoral fellows for our lab (www.mueller-lab.org): 1, Transcription control of metabolic adaptation in development (shorturl.at/oeG6U). 2, Semantic rules of developmental gene regulation (shorturl.at/KdHmJ) #jobs #transcription #zebrafish #zebrafishrock #IZFSshorturl.atResearch Fellow at University of BirminghamDiscover Research Fellow jobs and more in higher education on jobs.ac.uk. Apply for further details on the top job board. 2115
Reposted by Ferenc MuellerCraig Kaplan @triggerloop.bsky.social · 16/02/2026This is a fascinating paper that reveals defined and clear mechanism for a phenomenon that for some seemed unbelievable- the up regulation of genes paralogous to those with specific types of inactivating mutations. This is called transcriptional adaptation 1/ www.science.org/doi/10.1126/...science.orgMechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptationTranscriptional adaptation (TA) is a genetic robustness mechanism through which mutant messenger RNA (mRNA) decay induces sequence-dependent up-regulation of so-called adapting genes. How cytoplasmica... 411953
Reposted by Ferenc MuellerŽiga Avsec @avsecz.bsky.social · 28/01/2026AlphaGenome 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 48740
Reposted by Ferenc MuellerMáté Varga @mvargam.eurosky.social · 02/01/2026Over 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) 12312
Reposted by Ferenc MuellerJulia Zeitlinger @juliazeitlinger.bsky.social · 30/12/2025“Development, regulatory genomics & AI on April 22-24 www.stowers.org/events/stowe...stowers.orgStowers Research Conferences: Development, Regulatory Genomics & AIOrganized by Julia Zeitlinger, Ph.D., Neşet Özel, Ph.D., and Tatjana Sauka-Spengler, Ph.D. 132
Reposted by Ferenc MuellerZebrafish Rock! @zebrafishrock.bsky.social · 20/12/20252025 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 0241
Reposted by Ferenc MuellerEileen Furlong @eileen-furlong.bsky.social · 11/08/2025Open 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...embl.wd103.myworkdayjobs.comTeam Leader – Genomics Core Facility and Method DevelopmentAre 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... 03032
Reposted by Ferenc MuellerMRC AIM DTP @mrcaimdtp.bsky.social · 03/12/2025Applications 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*.more.bham.ac.ukPhD Opportunities – MRC AIM 132
Reposted by Ferenc MuellerNorwegian Centre for Molecular Biosciences and Medicine (NCMBM) @ncmbm.bsky.social · 02/12/2025Together, 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!med.uio.noJASPAR goes Deep Learning! - NCMBM - Norwegian Centre for Molecular Biosciences and MedicineA 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, ... 086
Reposted by Ferenc MuellerArica Beisaw @abeisaw.bsky.social · 22/11/2025Come join us in Heidelberg for the first German fish meeting 👩🔬👨🔬🧬🔬🐟🐠 1209
Reposted by Ferenc MuellerShawn Burgess @burgesslab.bsky.social · 17/11/2025Folks, it is finally out! Our paper on T2T assemblies of the zebrafish genome is on BioRxiv: www.biorxiv.org/content/10.1...biorxiv.org 16830
Ferenc Mueller @ferencmueller.bsky.social · 18/11/20251. 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).shorturl.at 2247
Reposted by Ferenc MuellerDANIO-ReCODE @daniorecode.bsky.social · 11/11/2025🐟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 053
Ferenc Mueller @ferencmueller.bsky.social · 28/10/2025PhD 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.shorturl.atHow does the interplay between metabolism control and gene regulation shape embryo development? at University of Birmingham on FindAPhD.comPhD Project - How does the interplay between metabolism control and gene regulation shape embryo development? at University of Birmingham, listed on FindAPhD.com 261
Reposted by Ferenc MuellerDaniel Ibrahim @danielibrahim.bsky.social · 16/10/2025What 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...biorxiv.orgEnhancer-promoter compatibility is mediated by the promoter-proximal regionGene 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... 217374
Reposted by Ferenc MuellerKevin Thiessen, PhD @kevinthiessen.bsky.social · 22/10/2025If you've benefited from ZebrafishRock and its community, you can thank ZFIN. i.e. ZebrafishRock is actually Kevin searching ZFIN 1154
Reposted by Ferenc MuellerSociety for Developmental Biology @socdevbio.bsky.social · 22/10/2025🏆 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 33911
Reposted by Ferenc MuellerDANIO-ReCODE @daniorecode.bsky.social · 10/10/2025🐟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 082
Reposted by Ferenc MuellerThe Company of Biologists @biologists.bsky.social · 10/10/2025It 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. 1358
Reposted by Ferenc MuellerZebrafish Rock! @zebrafishrock.bsky.social · 05/10/2025Cell nuclei movements (color-coded for direction) during early zebrafish development. Credit to Dr. Philipp Keller @hhmijanelia.bsky.social. #ZebrafishZunday 0465
Reposted by Ferenc MuellerNick Loman @pathogenomenick.bsky.social · 19/09/2025Terrific 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 24718
Reposted by Ferenc MuellerWendy Bickmore @wbickmor.bsky.social · 11/09/2025Honoured to be in Birmingham to mark Bryan Turner’s retirement- a gentleman and giant of epigenetics. 29115
Reposted by Ferenc MuellerSteffen Scholpp @scholpplab.bsky.social · 02/09/2025Interested 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.socialgw4biomed.ac.uk 012
Reposted by Ferenc MuellerArnaud Krebs @arnaudkr.bsky.social · 18/08/2025This 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👇 1011334
Reposted by Ferenc MuellerShawn Burgess @burgesslab.bsky.social · 15/08/2025#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):ncbi.nlm.nih.govJBQAYU000000000.1 Danio rerio :: NCBI 34117
Reposted by Ferenc MuellerLászló Tora @tlaszlo.bsky.social · 12/08/2025Check out our new collaborative preprint about Affinity-ligand purification of native human low-abundance multi-protein complexes doi.org/10.1101/2025...doi.orgAffinity-ligand purification of native human low-abundance multi-protein complexes for structure determinationIn human cells, large multi-protein transcription co-activators, such as chromatin remodelers or histone acetyltransferases, play critical roles in gene-expression regulation and are often implicated ... 12011
Reposted by Ferenc MuellerRada-Iglesias Lab @radaiglesiaslab.bsky.social · 11/08/2025Excited 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...biorxiv.orgSynthetic engineering demonstrates that synergy among enhancers involves an increase in transcriptionally productive enhancer-gene contactsEnhancers are non-coding cis-regulatory elements that control the expression of distally located genes in a tissue- and time-specific manner. Recent studies indicate that enhancers can differ in their... 56637
Reposted by Ferenc MuellerNorwegian Centre for Molecular Biosciences and Medicine (NCMBM) @ncmbm.bsky.social · 08/08/2025📢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. 276
Reposted by Ferenc MuellerKhaiChung (KC) @khaichung.bsky.social · 05/08/2025So 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. 0124
Reposted by Ferenc MuellerShawn Burgess @burgesslab.bsky.social · 31/07/2025Wrote 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).nature.comCRISPR-based functional genomics tools in vertebrate models - Experimental & Molecular MedicineRecent advances in DNA sequencing have allowed scientists to gather vast amounts of genetic data, but understanding what those sequences actually do requires additional tools that allow scientists to ... 24317
Ferenc Mueller @ferencmueller.bsky.social · 13/07/2025#IZFC2025 #zebrafish #DANIO-CODE data coordination centre is back online. Note changed address: danio-code-dcc.genereg.netdanio-code-dcc.genereg.netDANIO-CODE DCCThis Data Coordination Center allows DANIO-CODE consortium members to submit and view their data sets annotated with standard metadata nomenclatures. 3179
Reposted by Ferenc MuellerKristen Kwan @blockintheback.bsky.social · 11/07/2025The 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 0244
Ferenc Mueller @ferencmueller.bsky.social · 11/07/2025Dear #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. 078
Reposted by Ferenc MuellerAga Gambus @agagambus.bsky.social · 25/06/2025Genome Biology conference in Birmingham UK in September. Check out our great invited speakers! Lots of slots for talks selected from abstracts too! Please repost 😀 075
Reposted by Ferenc MuellerEMBL-EBI @ebi.embl.org · 30/06/2025Do 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!ebi.ac.ukUser survey to understand the value of open data resourcesEMBL-EBI user survey opens – please complete it before 16 July 01211
Reposted by Ferenc MuellerNature @nature.com · 30/06/2025After 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/40wPxkBgo.nature.com’We couldn’t live without it’: the UCSC Genome Browser turns 25After a quarter of a century, the website remains an essential tool for navigating the genome and understanding its structure, function and clinical impact. 07932
