Jeff Farrell
@jeffreyafarrell.bsky.social
Cell states & cell fates in zebrafish development
Lab Head since 2020
Imaging, Genetics, scRNAseq
Represents my personal opinions 🏳️🌈
Lab Head since 2020
Imaging, Genetics, scRNAseq
Represents my personal opinions 🏳️🌈
Reposted by Jeff Farrell
#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):
JBQAYU000000000.1 Danio rerio :: NCBI
www.ncbi.nlm.nih.gov
August 15, 2025 at 4:17 PM
#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):
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 🎣
July 30, 2025 at 11:44 PM
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 🎣
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!!
July 29, 2025 at 9:58 PM
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!!
It was super fun working on this interview with Saanjbati Adhikari about my path during my scientific training.
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/...
@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/...
July 29, 2025 at 3:33 PM
It was super fun working on this interview with Saanjbati Adhikari about my path during my scientific training.
Reposted by Jeff Farrell
@mads100tist.bsky.social calling attention to the awesomeness of #zebrafish #devbio and community. #SDB
June 22, 2025 at 6:14 PM
@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)
June 13, 2025 at 2:30 PM
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)
Reposted by Jeff Farrell
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...
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...
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...
www.biorxiv.org
June 2, 2025 at 4:13 PM
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...
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...
Reposted by Jeff Farrell
It was so awesome to have @jeffreyafarrell.bsky.social here to give a departmental seminar today!!
May 21, 2025 at 4:41 AM
It was so awesome to have @jeffreyafarrell.bsky.social here to give a departmental seminar today!!
Reposted by Jeff Farrell
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-...
www.training.nih.gov
April 29, 2025 at 2:59 PM
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-...
Reposted by Jeff Farrell
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...
www.nature.com
April 23, 2025 at 5:31 PM
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...
Reposted by Jeff Farrell
“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 🐟
New work from @biomarina-vg.bsky.social & Weinstein Lab at NIH 🐟
Anatomical and Molecular Characterization of the Zebrafish Meninges https://www.biorxiv.org/content/10.1101/2025.04.09.646894v1
April 16, 2025 at 4:35 PM
“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 🐟
New work from @biomarina-vg.bsky.social & Weinstein Lab at NIH 🐟
Reposted by Jeff Farrell
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...
An optogenetic toolkit for robust activation of FGF, BMP, and Nodal signaling in zebrafish
Cell signaling regulates a wide range of biological processes including development, homeostasis, and disease. Accessible technologies to precisely manipulate signaling have important applications in ...
www.biorxiv.org
April 21, 2025 at 1:47 PM
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...
If you want to make it easy for editors to find reviewers for your manuscript, pre-print it so that prospective reviewers can quickly scan through it to make sure it's within their expertise and not going to be a slog. I am 5x more likely to accept if I can spend 5 minutes looking at the figs.
December 15, 2024 at 9:07 PM
If you want to make it easy for editors to find reviewers for your manuscript, pre-print it so that prospective reviewers can quickly scan through it to make sure it's within their expertise and not going to be a slog. I am 5x more likely to accept if I can spend 5 minutes looking at the figs.
Reposted by Jeff Farrell
The life of each of us began when a sperm and an egg came together. But what happens at a molecular level?
Our latest work in Cell led by @vdeneke.bsky.social & Andreas Blaha reveals a conserved fertilization complex that bridges sperm and egg in vertebrates! (1/11)
www.cell.com/cell/fulltex...
Our latest work in Cell led by @vdeneke.bsky.social & Andreas Blaha reveals a conserved fertilization complex that bridges sperm and egg in vertebrates! (1/11)
www.cell.com/cell/fulltex...
December 13, 2024 at 7:43 PM
The life of each of us began when a sperm and an egg came together. But what happens at a molecular level?
Our latest work in Cell led by @vdeneke.bsky.social & Andreas Blaha reveals a conserved fertilization complex that bridges sperm and egg in vertebrates! (1/11)
www.cell.com/cell/fulltex...
Our latest work in Cell led by @vdeneke.bsky.social & Andreas Blaha reveals a conserved fertilization complex that bridges sperm and egg in vertebrates! (1/11)
www.cell.com/cell/fulltex...
Out now in Dev Cell! scRNAseq trajectories describe the cascade of gene expression as cells differentiate, but turning them into a clear understanding of the underlying biology of a cell type's development remains challenging. authors.elsevier.com/c/1k9qj5Sx5g... (1/)
November 26, 2024 at 3:49 PM
Out now in Dev Cell! scRNAseq trajectories describe the cascade of gene expression as cells differentiate, but turning them into a clear understanding of the underlying biology of a cell type's development remains challenging. authors.elsevier.com/c/1k9qj5Sx5g... (1/)
So happy that we got to work with Jamie a little bit on this project. Congrats to Andy Sposato on her awesome work!!!!
How does the testis age? Our first paper on this topic is now out in Development. Spermatogonia become less able to contribute to sperm production in older males, and in some cases we see really wild gene expression, like pluripotency genes and even ovary genes!
doi.org/10.1242/dev....
doi.org/10.1242/dev....
Germ cell progression through zebrafish spermatogenesis declines with age
Summary: Single-cell RNA sequencing reveals an age-related decline in zebrafish spermatogenesis. Aged testes show reduced sperm production, altered spermatogonial gene expression and expanded immune c...
doi.org
November 22, 2024 at 4:25 PM
So happy that we got to work with Jamie a little bit on this project. Congrats to Andy Sposato on her awesome work!!!!
NICHD Intramural (Bethesda, MD) is having a faculty search this year, focused on neural development. Apply by Sep 30 via two routes (Stadtman + direct, see thread).
Details: (1/5)
Details: (1/5)
November 17, 2024 at 6:55 PM
NICHD Intramural (Bethesda, MD) is having a faculty search this year, focused on neural development. Apply by Sep 30 via two routes (Stadtman + direct, see thread).
Details: (1/5)
Details: (1/5)
In my usual fashion, extremely slow to post something, but thanks so much for hosting me for an amazing visit to Penn, @bushranraj. Had so much fun visiting with you, your colleagues, and your awesome lab members!
November 17, 2024 at 6:55 PM
In my usual fashion, extremely slow to post something, but thanks so much for hosting me for an amazing visit to Penn, @bushranraj. Had so much fun visiting with you, your colleagues, and your awesome lab members!
The lab’s first preprint! Super excited to share our work profiling cell types and gene expression cascades during zebrafish development & release a corresponding website (Daniocell) so you can dig through the data too! (1/10)
November 17, 2024 at 6:55 PM
The lab’s first preprint! Super excited to share our work profiling cell types and gene expression cascades during zebrafish development & release a corresponding website (Daniocell) so you can dig through the data too! (1/10)
Happy #NationalComingOutDay to all my queer and questioning scientists! A journey that I began 23 years ago, but always remains ongoing. Thankfully, developmental biology has been a truly supportive career and always embraced me for who I am. (1/3)
November 17, 2024 at 6:55 PM
Happy #NationalComingOutDay to all my queer and questioning scientists! A journey that I began 23 years ago, but always remains ongoing. Thankfully, developmental biology has been a truly supportive career and always embraced me for who I am. (1/3)
#AQMHD2022 Genomic Tools Workshop (here introduced by @FishEvoDevoGeno) today was some awesome science. So exciting to get to participate.
November 17, 2024 at 6:55 PM
#AQMHD2022 Genomic Tools Workshop (here introduced by @FishEvoDevoGeno) today was some awesome science. So exciting to get to participate.
Amazing first day of #GfE2022 (here introduced by organizers @WalentekLab and @RosiFeistel). I learned so much already on day one, and there are so many cool people here to meet. Come chat with me!!
November 17, 2024 at 6:54 PM
Amazing first day of #GfE2022 (here introduced by organizers @WalentekLab and @RosiFeistel). I learned so much already on day one, and there are so many cool people here to meet. Come chat with me!!
What a day! Congrats to @abhinav_sur on CRUSHING IT today giving the first conference presentation from a lab trainee!! Come be our colleague! We’re recruiting so get in touch. #SDB2022
November 17, 2024 at 6:54 PM
What a day! Congrats to @abhinav_sur on CRUSHING IT today giving the first conference presentation from a lab trainee!! Come be our colleague! We’re recruiting so get in touch. #SDB2022
So excited to catch up with you wonderful dev biologists at #SDB2022! Hope to see you at @abhinav_sur's talk about our new zebrafish scRNAseq data, shared gene modules, and uncharacterized cell types. And so much more he can't fit in the talk - chat with him after!
November 17, 2024 at 6:54 PM
So excited to catch up with you wonderful dev biologists at #SDB2022! Hope to see you at @abhinav_sur's talk about our new zebrafish scRNAseq data, shared gene modules, and uncharacterized cell types. And so much more he can't fit in the talk - chat with him after!