Jeff Farrell

genesdev.cshlp.orgA conserved Notch–Meis1–Pbx cascade specifies secretory progenitors into spatially diverse intestinal best4+ cells A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields

Super happy to see our work investigating best4+ cell development and function now out in Genes & Development, with some exciting new data! genesdev.cshlp.org/content/earl...

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!

sciencedirect.comsciencedirect.com

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...

Super happy to see our work investigating best4+ cell development and function now out in Genes & Development, with some exciting new data! genesdev.cshlp.org/content/earl...

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.

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.

Super happy to see our work investigating best4+ cell development and function now out in Genes & Development, with some exciting new data! genesdev.cshlp.org/content/earl...

@nickdesnoyer.bsky.social

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.

Jeff Farrell reposted

Nick Desnoyer

27 July

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 🧵

Jeff Farrell reposted

Alex Eve

@amjeve.uk

26 July

Congratulations, @jeffreyafarrell.bsky.social, on winning the @socdevbio.bsky.social #2026SDB Elizabeth D. Hay New Investigator Award! Learn more about Jeff's science and career in his @dev-journal.bsky.social interview with @saanjbati.bsky.social.

doi.orgTransitions in development – an interview with Jeffrey FarrellJeffrey Farrell is an Earl Stadtman Investigator at the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), USA, where he heads the Unit on Cell Specification and ...

Jeff Farrell reposted

Mike Piacentino

@mikepiacentino.bsky.social

21 July

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

Society for Developmental Biology

16 July

This morning!! Tune in!

International Zebrafish Society@izfs.bsky.social

FOUR DAYS AWAY: #IZFS Webinar on July 16 at 10 am EDT! Join in for How Specialized Cell Types Arise in Evolution and Development: Insights from Brain and Gut with Megan Y Dennis and Jeffrey Farrell. Red more and register here: www.izfs.org/education/we... #IZFSWebinar #brainandgut

Jeff Farrell reposted

@socdevbio.bsky.social

14 July

✨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! 🔬

30 Apr

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.

mbl.eduZebrafish Development and Genetics | Marine Biological LaboratoryOver the past 30 years, the zebrafish has emerged as a powerful model system for the study of vertebrate development and disease. This course will focus on the development and genetics of zebrafish an...

27 Feb

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!

Pauli Group (posts by Andi Pauli)@pauligroup.bsky.social

Interested in expanding your zebrafish skills or completely new to zebrafish as model system for your research question? Then this course is for YOU! Deadline for applying is on March 2nd, so get your applications in. PS: It's a fantastic course - changed my own career! www.mbl.edu/education/ad...

Jeff Farrell reposted

Roberto Mayor Lab

@mayorlab.bsky.social

8 Feb

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.

Society for Developmental Biology@socdevbio.bsky.social

Congrats to the 2026 SDB Award Winners! Conklin Medal: Lee Niswander SDB Lifetime Achievement Award: Alexandra Joyner Hamburger Outstanding Educator Prize: Roberto Mayor Hay New Investigator Award: Jeffrey Farrell SDB Trainee SciComm Award: Nicholas Desnoyer bit.ly/4afnjiC

5 Feb

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!!!

Society for Developmental Biology@socdevbio.bsky.social

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:

training.nih.govtraining.nih.gov

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.

ncbi.nlm.nih.govncbi.nlm.nih.gov

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.

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.

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.

biorxiv.orgDevelopmental regulation of intestinal best4+ cellsbest4+ /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...

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?

Abhinav Sur@abhinavsur.bsky.social

Closing out 2025 with our new preprint where @jeffreyafarrell.bsky.social and I explore development and function of zebrafish intestinal best4+ cells – molecularly described in 2019, conserved in evolution, absent in 🐭, and altered in inflammatory bowel disease. www.biorxiv.org/content/10.6...

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.

biorxiv.orgDevelopmental regulation of intestinal best4+ cellsbest4 +/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...

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...

Abhinav Sur@abhinavsur.bsky.social

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.

ncbi.nlm.nih.govJBQAYU000000000.1 Danio rerio :: NCBI

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.

Jeff Farrell reposted

Shawn Burgess

@burgesslab.bsky.social

15 Aug 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):

29 July 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!!

5 Aug 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 😎

30 July 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 🎣

29 July 2025

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

Development@dev-journal.bsky.social

Transitions in development – an interview with Jeffrey Farrell @jeffreyafarrell.bsky.social talks about becoming a group leader, his insights on advocacy for developmental biology and his belief in unifying single-cell biology with classical approaches. journals.biologists.com/dev/article/...

Jeff Farrell reposted

Rebecca D. Burdine, PhD

@rburdine1.bsky.social

22 June 2025

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

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)

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)

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)

@james-gagnon.bsky.social

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)

Jeff Farrell reposted

James Gagnon

2 June 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.orgMIC-Drop-seq: Scalable single-cell phenotyping of mutant vertebrate embryosPooled 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...

Jeff Farrell reposted

Todd Macfarlan

@toddmacfarlan.bsky.social

29 Apr 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.govtraining.nih.gov

Jeff Farrell reposted

Alex Chesler

@alexchesler.bsky.social

23 Apr 2025

An example of what we in the NIH Intramural program can accomplish. Excited to share our latest paper in close collaboration with Nick Ryba's group. We examined how inflammation transforms representation in somatosensory neurons to cause pain. Lots of surprises here: www.nature.com/articles/s41...

nature.comnature.com

Jeff Farrell reposted

Zebrafish Rock! 🎃

@zebrafishrock.bsky.social

16 Apr 2025

“These findings support the use of zebrafish as a useful comparative model for studying the meninges, provide a foundational description for future zebrafish meningeal research” New work from @biomarina-vg.bsky.social & Weinstein Lab at NIH 🐟

bioRxiv Developmental Biology@biorxiv-devbio.bsky.social

Anatomical and Molecular Characterization of the Zebrafish Meninges https://www.biorxiv.org/content/10.1101/2025.04.09.646894v1

Jeff Farrell reposted

Katherine W. Rogers

@katwrog.bsky.social

21 Apr 2025

Happy to share a new preprint from my lab! We characterize the on/off kinetics, light dosage-dependence, and more for a suite of optogenetic signaling activators in zebrafish embryos 💡 www.biorxiv.org/content/10.1...

biorxiv.orgAn optogenetic toolkit for robust activation of FGF, BMP, and Nodal signaling in zebrafishCell signaling regulates a wide range of biological processes including development, homeostasis, and disease. Accessible technologies to precisely manipulate signaling have important applications in ...