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
Ferenc Mueller @ferencmueller.bsky.social · 31/07/2026Abstract deadline has been extended to 15th Aug! epigenetics2026.febsevents.org 000
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 1237
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 · 17/02/2026and a funded PhD position/Research associate is also available. details here:https://shorturl.at/O9eKd 110
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
Ferenc Mueller @ferencmueller.bsky.social · 05/01/2026Still 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/O5VSTshorturl.atA new level of gene regulation in tumour heterogeneity in colorectal cancer organoid models at University of Birmingham on FindAPhD.comPhD Project - A new level of gene regulation in tumour heterogeneity in colorectal cancer organoid models at University of Birmingham, listed on FindAPhD.com 000
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
Ferenc Mueller @ferencmueller.bsky.social · 13/12/2025Good 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. 050
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... 03132
Ferenc Mueller @ferencmueller.bsky.social · 03/12/2025Fantastic training opportunities, interdisciplinary projects spanning across 2-3 institutions 000
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 · 18/11/20253. 9 positions will be available, watch this space and usual sites for post-doc and PhD adverts! 000
Ferenc Mueller @ferencmueller.bsky.social · 18/11/20252. 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) 021
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 · 28/10/2025Another PhD position for those interested in working with cancer organoids and transcription initiation control of metabolism and growth (shorturl.at/wh6nW)shorturl.atFrom food to phenotype - defining how cancer cells modify their transcriptome in response to the nutrient environment? at University of Birmingham on FindAPhD.comPhD 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 020
Ferenc Mueller @ferencmueller.bsky.social · 28/10/2025Training opportunities include - and/or experience with desired: zebrafish gene editing, transgenesis, genomics (bulk and single cell) 000
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
