#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 🎣

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.

@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)

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...

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

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-...

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...

“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 🐟

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.

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...

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!!!!

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)

Looking forward to seeing everyone at #TAGC24 and hearing so much incredible new science!

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)

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.

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

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!

Very bittersweet see Eric and Jeremy off to their next steps this week after two awesome years as post-bacs in the lab. So proud of everything they accomplished and can't wait to see what they do next. Especially looking forward to finding out which lab Eric joins @WashUDevBio.

Huge congratulations to @abhinav_sur on winning a poster award at #IZFC2022. And just so we’re clear, it was an award for scientific content, not its incredible, record setting size. #proudpi

Wow! What a great first day of #IZFC2022. Amazing to see old zebrafish friends and to make new ones! DM me if you want to say hi or grab a meal or drink together — to catch up or if you’re potentially interested in the lab — we’re recruiting for funded positions at all levels!

The Farrell lab is looking for a post-doc to join the lab in 2022. Are you at #SDB2021 / #2021SDB and finishing your graduate studies? If you’re interested in our work (), reach out so I can come learn about yours and meet you!

Congratulations to @YiqunWang3, newly minted Dr. Wang! So proud of you today - your accomplishments and what a strong scientist you've become - and so thankful for so many excellent years working together. It was a major highlight of my post-doc. Cannot wait to see what's next!

A compelling reason to document your software well is that someday the person reading that documentation to figure out how a function works will be YOURSELF. Is this PI brain or 2020 brain?

Regardless of what gets published, I'm very thankful for the incredible female mentors that I've had during my career, both formal (Barbara Panning, Aviv Regev) and informal (@PauliGroup, @Juliano_Lab) who have all been crucial for my growth as a scientist.

NICHD Intramural Program is hiring a tenure-track investigator this year! Looking for innovative developmental biology -- any organism, any question.

As usual, day one of #2020SDB and I already have science envy where I briefly wonder if I should just scrap everything and start doing new work inspired by the awesome stuff I just saw. Great session on imaging approaches in dev bio @radikes and @dave_matus!

Did not expect that the most emotionally powerful experience (so far) of opening a lab was going to be seeing zebrafish embryos glowing under the microscope after being injected with a new transgenesis construct and feeling that we've really made something new here.

Farrell lab opens Jan 2020 @ NICHD w/ fully funded positions for creative, motivated postdocs, students & postbacs to study zebrafish development (cell fate, genetics of differentiation, embryonic DNA damage w/ scRNAseq, imaging & genetics) #ZebrafishJobs

This weekend, celebrated my PhD mentor Pat O’Farrell’s 70th birthday with most of the rest of the former members of the O’Farrell lab. We were all thankful to be shaped by his curiosity, passion, rigor, and generosity. He gives us all a high bar to live up to.

Super pumped to announce that I'm starting my own lab as an NIH intramural investigator in the NICHD and NHLBI institutes this fall. Can't wait to do some amazing science with my great new colleagues. And keep your eyes peeled, as I'll soon be recruiting post-doc applicants 😃

New Spiderman gets it right: PETER: Step Two: Find the head scientist's computer. MILES INTERRUPTS HIS IMAGE OF A CLASSIC SCIENTIST. M: That lady with the bike is the head scientist. I saw her in this documentary at school. P: Cool. Step Three: I re-examine my personal biases.

Mind blown that our work is part of the @sciencemagazine Top Breakthrough of 2018 & that my micrograph gets to represent this amazing field. Congrats to authors of the 11+ included studies (esp. @schierlab crew: Yiqun Wang, @james_gagnon & @bushranraj)

This year, we & several other groups reconstructed cells' gene expression trajectories during development. Super honored that Science has chosen this group effort as one of their 2018 Top Breakthroughs. The vote is still open! Maybe click that zebrafish...

Look at these two ultra successful @cnidofest organizers. Thanks so much for inviting this interloper to speak at your meeting.