What happened to Ensembl? 😭 Why was it destroyed? I came here to browse a genome, not fight for my life against the bad UI.

#zebrafish An update on the M-AB genome assembly and annotations: In the process of comparing the annotations between GRCz12ab and GRCz12tu, we discovered that 2 chromosomes, chr4 and chr19, were incorrectly uploaded. The sequences are actually from GRCz12tu. We have corrected the error

And a final track that shows all variants identified from sequencing multiple fish from our TU/AB hybrid fish NHGRI-1 which will show common SNV in both strains:

Yet another #zebrafish genome update: We just updated our ZebrafishGenomics public datahub for the UCSC browser (available all the way at the bottom here: genome.ucsc.edu/cgi-bin/hgHu...). We added several useful tracks including:

The 1996 Development issue reporting the zebrafish screen (and the special issue commemorating it 25 years later) are now free to read, thanks @biologists.bsky.social journals.biologists.com/dev/collecti...

Gaurav Varshney@varshneylab.bsky.social · 3mo ago

In 2021, the journal Development published a special issue, “The Zebrafish Issue: 25 Years On.” Unfortunately, all the articles are behind a paywall. At the very least, special issues like this should be made open access. journals.biologists.com/dev/collecti...

In 2021, the journal Development published a special issue, “The Zebrafish Issue: 25 Years On.” Unfortunately, all the articles are behind a paywall. At the very least, special issues like this should be made open access. journals.biologists.com/dev/collecti...

What if I do not want to use my institutional email?

Excited to share that Dr. Wei Qin from my lab will present his base editing work on June 25!

International Zebrafish Society@izfs.bsky.social · 4mo ago

Join us for a NEW IZFS WEBINAR: Franklin-Prasher-Kimmel (FPK) Series! On June 25th at 10 am EDT with speakers Stefan Choy and Wei Qin. Read more & register here: lnkd.in/g383zP7 This IZFS Webinar is FREE to all registrants, thanks to the #YoRC! #IZFSWebinar #Zebrafish

📣 Hiring a postdoc! My lab is hiring a postdoc to model rare genetic diseases in zebrafish utilizing CRISPR, high-throughput phenotyping, and multi-omics approaches.

Special shoutout to Wei Qin from @varshneylab.bsky.social lab. He has done the hard work to make precise editing in zebrafish a snap! Also shout out to all the other speakers in the series!

Cleaning freezers before I move to a new place. Found these plates from @burgesslab.bsky.social, these plates made my career, hard to throw them now.

Is Ensembl dead? Never worked for me for the last few months.

A powerful new technology developed at OMRF could dramatically speed up the process of diagnosing rare genetic diseases. Read more: omrf.org/2026/02/03/o...

High-efficiency TadA cytosine base editors for precise modelling of human disease variants

High-efficiency TadA cytosine base editors for precise modelling of human disease variants

Nature Biomedical Engineering, Published online: 28 January 2026; doi:10.1038/s41551-025-01607-1A suite of TadA-derived cytosine base editors was optimized to improve efficiency, reduce sequence bias, expand PAM compatibility and minimize artefacts, enabling precise genetic interrogation of variants of uncertain significance (VUS) in zebrafish.

nature.com

Our paper on TCBE-Umax is out in @natbiomedeng.nature.com! We developed these high-efficiency cytosine base editors for zebrafish, enabling rapid functional testing of disease variants. This work is led by a talented scientist, Wei Qin. www.nature.com/articles/s41...

High-efficiency TadA cytosine base editors for precise modelling of human disease variants - Nature Biomedical Engineering

A suite of TadA-derived cytosine base editors was optimized to improve efficiency, reduce sequence bias, expand PAM compatibility and minimize artefacts, enabling precise genetic interrogation of vari...

nature.com

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

Published October 25 years ago, “Effective targeted gene ‘knockdown’ in zebrafish” by Nasevicius & Ekker detail use of antisense morpholino-modified oligonucelotides or #morpholinos that inhibit translation. This landmark spurred a revolution in targeted gene knockdown in vivo. #ZebrafishFunFacts 🧪

While I'm sad our cover submission wasn't selected for our recent human duplication paper, check out the super cool illustration created with @lazaroillustration.bsky.social ! Certainly, you will be seeing Dennis lab members running around with "fishman" t-shirts at future meetings, inspired by Ohno

Javier Lazaro - scientific illustration@lazaroillustration.bsky.social · last yr.

"Fishman", proposal for a journal cover. Commissioned by MY Dennis' lab @mydennis.bsky.social for a study focused on identifying human-specific gene duplications and their role in brain evolution using genomics and zebrafish as model. @dcsoto.bsky.social #art #digitalart #sciart #fish

Does anyone have #zebrafish LC3 reporter lines and would be willing to share them with us? #askzebrafish

#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):

CRISPR technologies have transformed genetic research since their adaptation for genome editing in 2012. @burgesslab.bsky.social and I summarize key functional genomics tools being used in vertebrate models. www.nature.com/articles/s12...

CRISPR-based functional genomics tools in vertebrate models - Experimental & Molecular Medicine

Recent 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 ...

nature.com

Congratulations, Megan! As always inspiring work.

Megan Dennis@mydennis.bsky.social · last yr.

Check out our latest work co-led by @dcsoto.bsky.social and @jmuribescr.bsky.social identifying hundreds of human duplicated gene families using the new T2T-CHM13 assembly, with a focus on those potentially contributing to brain evolution 🧪: authors.elsevier.com/a/1lTQtL7PXu...

Our paper on TadA-based cytosine base editors is now online in Advanced Science. We introduce zTadCBEs—a next-generation CRISPR base editor optimized for zebrafish. advanced.onlinelibrary.wiley.com/doi/10.1002/...

Rationally Designed TadA‐Derived Cytosine Editors Enable Context‐Independent Zebrafish Genome Editing

A next-generation cytosine base editor (zTadCBE) and other variants are developed by combining the high-efficiency (TadCBEa) and low-indel (TadCBEMax) architectures, followed by the introduction of z....

advanced.onlinelibrary.wiley.com

Congratulations!

Christian Mosimann@chrmosimann.bsky.social · last yr.

Grateful to receive an R24 NOA from NIH/ORIP to advance phiC31-based transgenesis tools in #zebrafish. 🐟 Collab with @aburger2009.bsky.social & Breuss labs @cuanschutz.bsky.social. 🧬 ...and: big THX to everyone who already helped w/ sharing #pIGLET reagents! 🐽 #ShareYourTools #MakeMoreTransgenics

🚨🚨🚨 Tol2kit announcement! We have rebuilt the wiki that was corrupted a few months ago! We’re in the process of also linking it to the original address. Please visit us here: tol2kitkwan.genetics.utah.edu Thank you for your patience!! #zebrafish #transgenesis #plasmids #sharing

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.

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

The new impact factors are out: Development – 3.6, Developmental Cell – 8.7. Why the steady decline in two of Dev Bio's flagship journals?

Please read and share this opinion piece written by Carole LaBonne (our fellow Xenopus researcher) published in STAT in support for animal models in biomedical research. www.statnews.com/2025/05/19/a... #science #devbio #xenopus #frogs

There is no replacement (yet) for animal models in medical research

The NIH is “reducing animal use in research.” But there is no replacement for animal models.

statnews.com