James Gagnon
@james-gagnon.bsky.social
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I'm an associate professor @UofUBiology, Utah, USA gagnonlab.org | fish stuff in and out of the tank
pinned post!
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...
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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...
https://www.biorxiv.org/content/10.1101/2025.05.27.656468v2
7 months ago
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James Gagnon
Braasch Lab @ Michigan State University
3 days ago
Happy Coelacanth Day!
add a skeleton here at some point
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James Gagnon
Molly Przeworski
3 days ago
Happy to highlight an essay I wrote together with
@marcdemanuel.bsky.social
,
@natanaels.bsky.social
and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species:
www.biorxiv.org/content/10.6...
1/n
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What sets the mutation rate of a cell type in an animal species?
Germline mutation rates per generation are strikingly similar across animals, despite vast differences in life histories. Analogously, in at least one somatic cell type, mutation rates at the end of l...
https://www.biorxiv.org/content/10.64898/2025.12.19.695482v1
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James Gagnon
Needhi Bhalla 💅🏽
6 days ago
She let me know that they recently received guidance that, ONLY for the January EI deadline (1/27/2026) and the February ESI deadline (2/3/2026), PIs can submit MIRAs even if their previous application (R35, R01, R15, R21, and R37) is still considered under review.
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Máté Varga
12 days ago
I was today years old when I learned that there is a superb (freely available) documentary from 1961 on early zebrafish development by J.V. Durden.
collection.nfb.ca/film/embryon...
(1/2)
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FYI - if you already have a pending MIRA application, you need the summary statement in hand by Jan 27th to hit this first FOA deadline.
add a skeleton here at some point
14 days ago
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James Gagnon
Jim Heys
16 days ago
Neuro grad students! Applications for the 6th annual - Rising Stars in Neuroscience - due Jan 9! Don’t miss this chance to present research, sharpen science communication skills and connect with peers & faculty. Plus you’ll get to experience stunning Utah!
medicine.utah.edu/neurobiology...
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Parichy Lab | Dave Parichy
16 days ago
We have a new preprint on bioRxiv from postdoc Delai Huang and colleagues. It's not about peacocks.
www.biorxiv.org/content/10.6...
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Chris Miles
23 days ago
I'm hiring a postdoc through Utah Math. Deadline Dec 15. If you work in math/comp bio (SciML, stochastic modeling, single-cell data), please apply! Vibrant math bio community & unbeatable outdoors. Mention me in your cover letter & reach out with any questions.
www.mathjobs.org/jobs/list/27...
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MathJobs from the the American Mathematical Society
Mathjobs is an automated job application system sponsored by the AMS.
https://www.mathjobs.org/jobs/list/27080
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James Gagnon
Anna Allen
21 days ago
***Important*** BIO will host a Virtual Office Hour (VOH) on Thurs, Dec 18th, 2025, 1 - 2 pm ET. In this VOH, we’ll be joined by leadership to outline updates to NSF’s review process & share news relevant to all areas of research funded by BIO. Register here:
nsf.zoomgov.com/webinar/regi...
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Webinar Registration - Zoom
https://nsf.zoomgov.com/webinar/register/WN_VckBbTuSRa2IE9cQxVJNsg#/registration
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James Gagnon
James Briscoe
22 days ago
Applications are open for
@dev-journal.bsky.social
2026 Pathway to Independence (PI) programme, supporting postdocs applying for group leader positions: Mentoring Profile raising Leadership training Network building Spread the word...
www.biologists.com/grants/devel...
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Development's Pathway to Independence Programme
Our grants support and encourage the sharing of knowledge throughout the community by facilitating international collaboration, event attendance and the organisation of scientific meetings, conference...
https://www.biologists.com/grants/development-pathway-independence/
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John Wallingford
about 1 month ago
SAVE THE DATE! Stoked to organize the 2026 Santa Cruz Developmental Biology Meeting with
@rashmi-priya.bsky.social
,
@lowelab.bsky.social
, and Shelbi Russell. Come learn about Biomedicine, Biomechanics, and the Biosphere, August 24-28, 2026. Registration dates, etc., coming soon! Please RT
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John F. Rawls
about 2 months ago
Part 6: For decades, the zebrafish has helped scientists unlock the mysteries of genetics, development, & disease. But the fish that power most discoveries have spent generations inside lab tanks. This video captures footage of zebrafish in their natural environment in Nepal.
youtu.be/cCZhZpPALqw
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Zebrafish in the wild
YouTube video by John Rawls
https://youtu.be/cCZhZpPALqw
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James Gagnon
Molly Schumer
about 1 month ago
I am so excited to share new work on a TE insertion that regulates iridescence in swordtails, led by fantastic grad student
@nadiahaghani.bsky.social
and with help from many coauthors! In a time that has been so difficult to navigate, this & other projects have kept my spirits up:
shorturl.at/NE65A
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Insertion of an invading retrovirus regulates a novel color trait in swordtail fish
For over a century, evolutionary biologists have been motivated to understand the mechanisms through which organisms adapt to their environments. Coloration and pigmentation are remarkably variable wi...
https://shorturl.at/NE65A
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Carl Zimmer
about 1 month ago
An engineer wanted to make a quiet high-speed train. “The question then occurred to me — is there some living thing that manages sudden changes in air resistance as a part of daily life?” The answer: the kingfisher. See my story today for more tales of bioinspiration. Gift link:
nyti.ms/4otNQyl
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Matthew Neville
3 months ago
Now published! Our paper on: (1) Accurate sequencing of sperm at scale (2) Positive selection of spermatogenesis driver mutations across the exome (3) Offspring disease risks from male reproductive aging [1/n]
www.nature.com/articles/s41...
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Sperm sequencing reveals extensive positive selection in the male germline - Nature
A combination of whole-genome NanoSeq with deep whole-exome and targeted NanoSeq is used to accurately characterize mutation rates and genes under positive selection in sperm cells.
https://www.nature.com/articles/s41586-025-09448-3
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James Gagnon
D. Allan Drummond
3 months ago
Cat flea, homage to Hooke. Micron in Moleskine. 🔬🖊️
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James Gagnon
Josh Currie
3 months ago
💥OUR LAB IS HIRING!!💥 We are hiring a research assistant/lab manager to assist with managing our axolotl colony and enabling some kick-ass science! Looking for high levels of organization, collaboration, problem solving and curiosity. Application link:
tinyurl.com/3tpvphpm
#SciJob
#JobAlert
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James Gagnon
Mathieu Preußner
3 months ago
1🧵 Excited to share my first PhD paper, published in
@dev-journal.bsky.social
What if fish gills —often overlook —hold secrets about development, patterning, and function? We uncovered how early patterning shapes adult gill architecture.
journals.biologists.com/dev/article/...
#DevBio
#Zebrafish
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Martin Haesemeyer
3 months ago
Come be my colleague in the department of neuroscience at OSU. We are hiring for an open rank tenure track faculty position in several focus areas.
neurojobs.sfn.org/job/39081/te...
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Tenure-track faculty positions in Neuroscience - Columbus, Ohio job with The Ohio State University, Dept of Neuroscience | 39081
Faculty studying mechanisms underlying normal nervous system function and/or how these mechanisms and interactions are affected by disease or injury
https://neurojobs.sfn.org/job/39081/tenure-track-faculty-positions-in-neuroscience/
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James Gagnon
pikaole
4 months ago
Just keep thinking about fish
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Maxwell Shafer
4 months ago
Now published
@natecoevo.nature.com
with
@annika-nichols.bsky.social
, our latest on the evolution of 𝘴𝘭𝘦𝘦𝘱 across 𝟲𝟬 𝘀𝗽𝗲𝗰𝗶𝗲𝘀 of cichlid fishes!
doi.org/10.1038/s415...
with members of the
@schierlab.bsky.social
and Salzburger labs, as well as the burgeoning Shafer lab
@uoftcellsysbiol.bsky.social
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James Gagnon
The Salt Lake Tribune
6 months ago
Proposed cuts to the National Institutes of Health and the National Science Foundation “would cause immense and largely irreversible damage to the successful American scientific enterprise,” write Jerry Kaplan and Dana Carroll in an op-ed.
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Voices: Federal funding cuts to genetic research will be devastating for years to come
Proposed cuts to the National Institutes of Health and the National Science Foundation “would cause immense and largely irreversible damage to the successful American scientific enterprise,” write Jerry Kaplan and Dana Carroll in an op-ed.
https://www.sltrib.com/opinion/commentary/2025/07/08/voices-cuts-science-funding-will/?utm_campaign=snd-autopilot
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John Murray
6 months ago
Happy to announce our paper comparing embryonic gene expression between C. elegans and C. briggsae, work led by Christopher Large with Rupa Khanal and in collaboration with Junhyong Kim and Bob Waterston.
www.science.org/doi/10.1126/...
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Lineage-resolved analysis of embryonic gene expression evolution in C. elegans and C. briggsae
The constraints that govern the evolution of gene expression patterns across development remain unclear. Single-cell RNA sequencing can detail these constraints by systematically profiling homologous ...
https://www.science.org/doi/10.1126/science.adu8249
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James Gagnon
International Zebrafish Society
7 months ago
We are excited to announce the winner of the Chi-Bin Chien Award, Dr. Victoria Deneke! See more about Dr. Deneke and the CBC Award here:
www.izfs.org/news/congrat...
@impvienna.bsky.social
@vdeneke.bsky.social
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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...
loading . . .
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...
https://www.biorxiv.org/content/10.1101/2025.05.27.656468v2
7 months ago
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James Gagnon
Aaron Quinlan (he/him)
8 months ago
The Department of Human Genetics at the University of Utah is sponsoring the Rising Stars in Genetics and Genomics symposium! - We are seeking nominations bu June 1. - September 18-19, 2025 - Please share with the star postdocs that you know.
docs.google.com/forms/d/e/1F...
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Katherine W. Rogers
8 months ago
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...
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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 ...
https://www.biorxiv.org/content/10.1101/2025.04.17.649426v1.abstract?%3Fcollection=
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This is an exciting time for reproductive research in fish, let's get together and talk about it at the Reproduction session!🪺 If you are on team germ cells and gonads, please RT and send in abstracts
@marymullins.bsky.social
@yanivelkouby.bsky.social
@erezraz.bsky.social
@zebrafishrock.bsky.social
add a skeleton here at some point
10 months ago
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James Gagnon
Nature Reviews Genetics
10 months ago
Featured article: The lives of cells, recorded
go.nature.com/4g2gRwG
by Amjad Askary, Wei Chen,
@choijunhong.bsky.social
, Lucia Y. Du,
@elowitzlab.bsky.social
,
@james-gagnon.bsky.social
,
@schierlab.bsky.social
,
@seidels.bsky.social
,
@jshendure.bsky.social
,
@tanjastadler.bsky.social
& Martin Tran
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James Gagnon
Gina Baucom
11 months ago
Letter from the SSE/SSB/ASN councils on the scientific understanding of sex and gender, pls RT
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Letter to the US President and Congress on the Scientific Understanding of Sex and Gender
President Donald J Trump Washington, DC Members of the US Congress Washington, DC February 5, 2025 RE: Scientific Understanding of Sex and Gender Dear President Trump and Members of the US Congr...
https://www.evolutionsociety.org/news/display/2025/2/7/letter-to-the-us-president-and-congress-on-the-scientific-understanding-of-sex-and-gender/
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John Wallingford
11 months ago
So, everyone knows the story about the time the 5th Dalai Lama wrote the Editor to complain that Ernst Haeckel hadn’t cited his work from 200 years earlier? Right? Right? Coming soon….
#devbiol
#SciHist
#TheLongBibliography
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James Gagnon
Titus Brown
12 months ago
Hello everyone, the MBL Gene Regulatory Networks for Development course still has openings for its 2025 offering, Apr 6-18. We’d love to receive some more applications! The deadline is Jan 3, but if you start the application by then and get us the letters later, we will be happy to consider you!
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Gene Regulatory Networks for Development | Marine Biological Laboratory
This course introduces the concepts of Gene regulatory networks (GRNs), and teaches experimental and computational methods used to study them, through highly interactive lectures, discussions, group p...
https://www.mbl.edu/education/advanced-research-training-courses/course-offerings/gene-regulatory-networks-development
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James Gagnon
Mary
about 1 year ago
New preprint out now! The history of some RNA virus lineages that infect vertebrates might date back to our invertebrate ancestors. Read more here:
biorxiv.org/cgi/content/...
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Simon Fisher
about 1 year ago
Beethoven, one of the most celebrated musicians in history, scored unremarkably on the musicality-related polygenic index, ranking between the 9th & 11th percentile based on modern samples. In our paper we explain why this is no surprise & how it offers a nice example for teaching complex genetics.
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Today is the final lecture of my 7th (and possibly last) time teaching undergraduate Cell Biology. Over the years 2,554 students have finished my class! 20+ years ago, this class convinced me to be a biologist, and I hope I passed that spark along to some of my students 🧬🔬🦠🧑🔬
about 1 year ago
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James Gagnon
Clay Carey Photography
about 1 year ago
I took this picture of the night sky over this neat rock formation while camped out in the eastern Sierra back in October. I loved how the milky way seemed to erupt from the rocks.
#landscapephotography
#astrophotography
#nature
#photographer
#nikon
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I loved working on this future-focused review with an absolute Murderer's Row of smarties in the DNA recording field. Hope we can all meet in person some day!
add a skeleton here at some point
about 1 year ago
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James Gagnon
Tony Gamble
over 1 year ago
This short graphic novel about Fish Sex Determination from Sophia Breslin, John Postlethwait, & Thomas Desvignes
@notothentoma.bsky.social
is AMAZING!
blogs.uoregon.edu/fishsexdeter...
🧪🐠🧬
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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....
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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...
https://doi.org/10.1242/dev.204319
about 1 year ago
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