iiinova — where your digital self keeps evolving

Jeff Farrell @jeffreyafarrell.bsky.social · 13/08/2026

Sorry, you know how I am with social media. Thanks for your patience hahahaha 😘

Jeff Farrell @jeffreyafarrell.bsky.social · 13/08/2026

Also, if you're interested in this topic, our colleague Ken Wallace has a paper out at the same time dissecting the contribution of individual Notch receptor family members to best4+ cell specification! www.sciencedirect.com/science/arti...

sciencedirect.com

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Jeff Farrell @jeffreyafarrell.bsky.social · 13/08/2026

And what a pleasure to work with the team at @genesdev.bsky.social! A model for what publishing can be like. Stay tuned to hear more about how best4+ cells develop from the Farrell Lab and more about what they do from @abhinavsur.bsky.social!

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Jeff Farrell @jeffreyafarrell.bsky.social · 13/08/2026

Overall, we find that intestinal secretory progenitors respond to a second Notch signaling event by expressing meis1b to become best4+ cells, rather than enterochromaffin cells. pbx3a then works to make them spatially heterogeneous in gene expression and function.

Model cartoon of best4+ cells' developmental program.

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Jeff Farrell @jeffreyafarrell.bsky.social · 13/08/2026

Additionally, we improved the electron microscopy showing the morphology of basolateral projections significantly, added some additional stainings, and the entire manuscript is leaner and meaner, all thanks to comments from invested and helpful reviewers.

Electron microscopy of a best4+ cell basolateral projection against the basement membrane (labeled by silver-enhanced immunogold against best4:GFP)

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Jeff Farrell @jeffreyafarrell.bsky.social · 13/08/2026

While under review, Ella managed to watch best4:pHluorin2 cells live in vivo while exposing them to different pHs and showed that best4+ cells are functionally heterogenous: anterior ones respond to acidic pH but not posterior by intracellularly acidifying.

More acidic solutions cause more dramatic intracellular pH changes in anterior best4+ cells, while posterior best4+ cells respond the same to solutions of different pHs.

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Jeff Farrell @jeffreyafarrell.bsky.social · 11/08/2026

Thank you, Edan!!! We are very happy to see it out. Guess I need to compose a bleat for real hahahaha

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Jeff Farrell @jeffreyafarrell.bsky.social · 31/07/2026

I would be delighted to read that paper. Truly.

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Jeff Farrell @jeffreyafarrell.bsky.social · 30/07/2026

I bet the producers of Real Housewives have a statistical model to quantify drama. Maybe a great collaboration opportunity.

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Reposted by Jeff Farrell

Nick Desnoyer @nickdesnoyer.bsky.social · 27/07/2026

So honored to receive the @socdevbio.bsky.social SciCom award and to share my work with the wonderful people in this community! This #2026SDB conference was a celebration of biodiversity 🧵

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Reposted by Jeff Farrell

Mike Piacentino @mikepiacentino.bsky.social · 21/07/2026

Come join us! 🔬🐣 The Piacentino Lab at Johns Hopkins @hopkinsmedicine.bsky.social is recruiting a postdoc to study membrane lipids, cell migration, and invasion in neural crest and embryonic models! @socdevbio.bsky.social @ascbiology.bsky.social #devbiol #cellbio #lipids

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Reposted by Jeff Farrell

Society for Developmental Biology @socdevbio.bsky.social · 14/07/2026

✨Jeffrey Farrell @jeffreyafarrell.bsky.social is a Stadtman Investigator at the NIH. He has led seminal work constructing single-cell RNAseq atlases for entire embryos using zebrafish. We are excited to host Jeffrey at the #2026SDB in Las Vegas! 🔬

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Jeff Farrell @jeffreyafarrell.bsky.social · 01/05/2026

Hard to say goodbye today to the lab’s first postdoc, but so excited to see what @abhinavsur.bsky.social will do in his new lab at U Arizona. We’re going to miss you deeply over here. Safe travels and knock em dead.

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Jeff Farrell @jeffreyafarrell.bsky.social · 27/02/2026

Apply to this course!!! The deadline is soon, but if you are considering using zebrafish for the first time in your career, this is an incredible opportunity. I took this in 2013, and it changed my career - and started several friendships and scientific relationships that persist to today!

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Reposted by Jeff Farrell

Roberto Mayor Lab @mayorlab.bsky.social · 08/02/2026

It’s a real honour to receive the Viktor Hamburger Outstanding Educator Prize from the SDB. Teaching is one of the most rewarding parts of my life. Thanks to the SDB and the hundreds of students and faculty at the Quintay course who have made it such a joy.

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Jeff Farrell @jeffreyafarrell.bsky.social · 05/02/2026

Thanks so much, Zebrafish Rock!!! 💖

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Jeff Farrell @jeffreyafarrell.bsky.social · 05/02/2026

Oh man! What a crazy honor to receive this award from SDB!! I love being a part of SDB so much - it has led to so many awesome ideas, collaborations, and friendships over the last 13 years, so this is really exciting. Looking forward to seeing you all at the meeting. Thank you, SDB!!!

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Jeff Farrell @jeffreyafarrell.bsky.social · 29/01/2026

Our lab website is mildly out of date, but up to date publications are here: www.ncbi.nlm.nih.gov/myncbi/jeffr... If you or someone you know is driven and curious and might be a good fit for my lab, please let me know.

ncbi.nlm.nih.gov

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Jeff Farrell @jeffreyafarrell.bsky.social · 29/01/2026

Postbacs typically carry out a independent 2 year project with mentoring from me and a postdoc in the lab, present publicly, have support to apply to MD or PhD, and receive a healthy stipend and insurance. Apply centrally (www.training.nih.gov/research-tra...) and notify me.

training.nih.gov

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Jeff Farrell @jeffreyafarrell.bsky.social · 29/01/2026

Postdocs should send a cover letter about their past work, their interests, and why they want to come to my lab (or what they want to do if they already have ideas), info for three references, and their CV.

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Jeff Farrell @jeffreyafarrell.bsky.social · 29/01/2026

Lab interests include development of intestinal epithelium and stroma, ‘messy’ outcomes/errors during cell fate decisions, developmental programs of uncharacterized cell types, or large-scale sc genomics. PDs also can propose any project that my lab would be well suited to support in some way.

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Jeff Farrell @jeffreyafarrell.bsky.social · 29/01/2026

I’m recruiting new members to the Farrell Lab this summer. We will have space for 1 postdoc (since Abhinav is leaving to start his own lab at U Arizona!!) and 2 postbacs, since my current two will leave for PhD programs at the end of the summer. More details in thread:

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Jeff Farrell @jeffreyafarrell.bsky.social · 09/01/2026

The work is just beginning! Abhinav's new lab (starting this year!) will study their function and how they communicate with other cell types. We will keep studying their development. Read Abhinav's thread for more details or better yet, read it! Feedback welcome. www.biorxiv.org/content/10.6...

biorxiv.org

Developmental regulation of intestinal best4+ cells

best4 +/CFTR-high expressing cells are a recently described intestinal epithelial cell type potentially altered in inflammatory bowel disease and colorectal cancer. However, their developmental origin...

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Jeff Farrell @jeffreyafarrell.bsky.social · 09/01/2026

We began testing their function, focusing on pH regulation. In ZF, they're not req'd for proper gut pH homeostasis, but their intracellular pH varies spatially. Eliminating spatial variation non-autonomously affects goblet cell mucus modifying enzymes, suggesting best4+ cells coordinate other cells.

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Jeff Farrell @jeffreyafarrell.bsky.social · 09/01/2026

While conserved, best4+ cells are absent in mice, so zebrafish will be a key in vivo model. We made fish that label best4+ cells to live image them (they extend dynamic projections to touch other cells!) and the first in vivo models that remove best4+ cells.

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Jeff Farrell @jeffreyafarrell.bsky.social · 09/01/2026

We tested best4+ cell development from birth to differentiation. We IDed the conserved best4+ cell gene expression program, lineage traced them to ID their progenitors, tested the signals that specify them, IDed the TF that confers their identity, and IDed a TF required for their spatial diversity.

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Jeff Farrell @jeffreyafarrell.bsky.social · 09/01/2026

Happy New Year! NEW LAB PREPRINT testing how best4+ intestinal epithelial cells develop! best4+ cells are conserved across vertebrates and altered in IBD & colorectal cancer. But they were first molecularly IDed in 2019. We barely know anything about them yet! What do they do?? HOW DO THEY GET MADE?

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Reposted by Jeff Farrell

Shawn 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.gov

JBQAYU000000000.1 Danio rerio :: NCBI

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Jeff Farrell @jeffreyafarrell.bsky.social · 05/08/2025

Just because I am seeing new reposts of this: this outage was resolved last week, about 48 hours after we found out about it. Thankfully, there has not been a second one 😎

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Jeff Farrell @jeffreyafarrell.bsky.social · 31/07/2025

Ok, friends! If you’re a Daniocell user, it’s now available again outside of the NIH. Very sorry for any inconvenience this posed for any of you and thanks for your patience. We’re taking additional steps to hopefully prevent similar outages in the future. Happy surfing 🎣

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Jeff Farrell @jeffreyafarrell.bsky.social · 29/07/2025

Hey friends - Daniocell is experiencing a temporary outage right now. The NICHD server it is hosted on got dropped from the NIH’s firewall list & so currently can’t be accessed outside the NIH. The relevant IT teams are working to resolve it. Sorry for any inconvenience. It’ll be back soon!!

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Jeff Farrell @jeffreyafarrell.bsky.social · 29/07/2025

It was super fun working on this interview with Saanjbati Adhikari about my path during my scientific training.

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Jeff Farrell @jeffreyafarrell.bsky.social · 26/06/2025

Thank you Kevin for creating something truly incredible. ZebrafishRock has been such an important contribution to our community. I’m glad that the Slack will live on - see you there, and hopefully at a meeting some time soon. Be well!

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Reposted by Jeff Farrell

Rebecca D. Burdine, PhD @rburdine1.bsky.social · 22/06/2025

@mads100tist.bsky.social calling attention to the awesomeness of #zebrafish #devbio and community. #SDB

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Jeff Farrell @jeffreyafarrell.bsky.social · 13/06/2025

Sure, but it’s a few extra steps. (1) Use a small screwdriver to unscrew the front panel of your Switch. (2) Use a hot glue gun to glue that front panel to the screen of your Mac laptop. (3) Start DaniocellDesktop and shrink the window to show through the front panel. (4) Voila! How easy is that?

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Jeff Farrell @jeffreyafarrell.bsky.social · 13/06/2025

Big props to Alicia Evans, Matt Breymaier, and the NICHD BSPC team for key contributions. It feels strange to announce new things these days, but hopefully this tool will bring some of you a little joy and some great new hypotheses. (4/4)

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Jeff Farrell @jeffreyafarrell.bsky.social · 13/06/2025

After installing, it'll download a copy of the Daniocell data for you and runs locally on your computer, meaning your interactions are private and can persist long-term. Check out the tutorials and give it a try: daniocell.nichd.nih.gov/desktop/ (3/4)

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Jeff Farrell @jeffreyafarrell.bsky.social · 13/06/2025

DaniocellDesktop lets you define custom cell populations, perform differentially expressed gene analysis, and generate publication-ready plots to show gene expression patterns, co-expression, and temporal changes for any genes or cell populations you wish. (2/4)

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Jeff Farrell @jeffreyafarrell.bsky.social · 13/06/2025

If 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)

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Reposted by Jeff Farrell

James Gagnon @james-gagnon.bsky.social · 02/06/2025

To dissect the gene regulatory networks used to build organisms, we need Perturb-seq-like tools that work in whole animals. For this purpose, we developed MIC-Drop-seq, a tool that couples high-throughput CRISPR in zebrafish embryos with single-cell RNAseq. www.biorxiv.org/content/10.1...

biorxiv.org

MIC-Drop-seq: Scalable single-cell phenotyping of mutant vertebrate embryos

Pooled perturbation screens can reveal cellular regulatory networks, yet scaling these techniques for large-scale screens in animals remains challenging. To address this, we developed MIC-Drop-seq, wh...

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Reposted by Jeff Farrell

Kristen Kwan @blockintheback.bsky.social · 21/05/2025

It was so awesome to have @jeffreyafarrell.bsky.social here to give a departmental seminar today!!

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Reposted by Jeff Farrell

Todd Macfarlan @toddmacfarlan.bsky.social · 29/04/2025

I am looking for postdocs to join my group at NIH. Are you interested in Development, Evolution, Genetics, Genomics, and Human health? Please apply! www.training.nih.gov/jobs/pdf-mb-...

training.nih.gov

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Jeff Farrell @jeffreyafarrell.bsky.social · 29/04/2025

We also did some such comparisons between ZF and human in our 2023 dev cell paper and some code you could use as a starting point is in the GitHub repo.

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Jeff Farrell @jeffreyafarrell.bsky.social · 29/04/2025

Hey Ivan! The data is available from the Daniocell front page, but LMK if you have questions

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Jeff Farrell @jeffreyafarrell.bsky.social · 29/04/2025

Kevin, I think what you do is super important, and I’m thankful for everything that Zebrafish Rock! has done!!! It helps me keep up with the community and helps make people aware of cool resources they should know about. Sorry there are some unappreciative jerks, but many of us love ZR deeply.

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