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James Gagnon

@james-gagnon.bsky.social
634 followers 567 following 110 posts

I'm an associate professor @uofubiology.bsky.social, Utah, USA gagnonlab.org | fish stuff in and out of the tank

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Reposted by James Gagnon
Nature Reviews Genetics @natrevgenet.nature.com · 17/09/2026
ICYMI: New online! Zebrafish relatives as models for functional comparative genetics and genomics
dlvr.it
Zebrafish relatives as models for functional comparative genetics and genomics
Nature Reviews Genetics, Published online: 10 September 2026; doi:10.1038/s41576-026-01007-4Comparative functional genetics and genomics across Danio, Devario and Danionella species reveal molecular and cellular bases of phenotypic divergence, establishing danionin fishes as powerful model systems for understanding a wide range of evolutionary innovations.
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Reposted by James Gagnon
Emma R Andersson @anderssonlab.bsky.social · 23/09/2026
🧬 Preprint! 🧵 Our goal is to genetically manipulate every embryonic germ layer to enable high throughput in vivo studies. We previously showed mouse ectoderm can be targeted by amniotic injection, enabling cell-specific manipulation, lineage tracing, and knockouts. But how to reach mesoderm?
Schematic of method developed and application. At embryonic day 7.5, a lentiviral library carrying unique 30-nucleotide barcodes and a fluorescent reporter is injected into the mouse exocoelomic cavity. An E8 embryo cross-section shows that this cavity is continuous with the intraembryonic coelomic cavity, allowing the virus to reach and barcode mesodermal progenitors, including lateral plate and paraxial mesoderm.
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Saba Parvez @sparvez.bsky.social · 23/09/2026
My lab at Northwestern University is recruiting a postdoctoral fellow to study alternative splicing, NMD, and gene regulation in vertebrate development and regeneration. We use zebrafish large-scale functional genetics, genomics, and high-throughput phenotyping.
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Yuan He @yuanhejhu.bsky.social · 22/09/2026
A big week for the lab! Two new papers on how cells repair DNA double-strand breaks: one on getting NHEJ started in chromatin, one on processing the ends before ligation. Years of work by a fantastic team.
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International Zebrafish Society @izfs.bsky.social · 01/09/2026
🚨 Travel. Learn. Collaborate. The #IZFS Knowledge Exchange Grant supports researchers seeking to visit another lab, gain new experience, and expand their knowledge. Learn more and apply: www.izfs.org/awards/knowl... #ZebrafishGrant #ExchangeGrant
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Tom Sasani @tomsasani.bsky.social · 02/09/2026
How long does DNA damage last? @aaronquinlan.bsky.social and I found evidence that lesions are transmitted from parent (P0) to offspring (F1) in C. elegans. If they segregate unrepaired for multiple cell divisions, lesions generate multi-allelism in the F1 germline. www.biorxiv.org/content/10.6...
biorxiv.org
Inherited DNA damage generates multi-allelic mutations in C. elegans
Exogenous and endogenous mutagens generate a wide variety of DNA lesions, including bulky adducts, chemical modifications, and single- or double-stranded breaks. A phenomenon called “lesion segregation,” in which lesions evade repair and persist for multiple cell divisions, has recently been documented in tumors and healthy somatic tissues from mice and humans, respectively. Persistent lesions can generate multi-allelic variants (MAVs) by serving as templates for multiple rounds of error-prone replication. By reanalyzing data from a large C. elegans mutagenesis experiment, we observed robust evidence for MAVs at a small fraction (∼0.2%) of mutated sites in the offspring of strains treated with alkylating agents. Because these sequencing data were derived from the progeny of a single F1 animal — itself the offspring of a mutagenized P0 — all mutations should be biallelic. The presence of multi-allelic variation implies that some DNA lesions are transmitted to the F1 zygote, evade repair, and are repeatedly bypassed by error-prone polymerases during embryogenesis. We suspect that many more lesions are inherited than is suggested by MAV prevalence, and that a large fraction of biallelic mutations are also caused by inherited lesions. Our results demonstrate that DNA lesions serve as durable, transgenerational templates for mutagenesis in C. elegans . We speculate that lesion segregation in the early embryo may be a source of mosaicism and genetic diversity in humans, as well. ### Competing Interest Statement The authors have declared no competing interest. National Institutes of Health, https://ror.org/01cwqze88, R01HG012252
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Molly Schumer @mollyschumer.bsky.social · 03/09/2026
Help needed! Does anyone know of a lab that has glass (pigmentless) guppies? We are interested in getting them for a project
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Tom Near @tjnear.bsky.social · 29/08/2026
1/11 🐟 2nd new preprint today from @chasedbrownstein.bsky.social We investigated how losing the swim bladder, the organ that most fishes use to control their buoyancy, has shaped the diversity of ray-finned fishes over 90 million years of Earth history. The results surprised us. 🧵
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Jason Shepherd @jasonsynaptic.bsky.social · 28/08/2026
My department is hiring! Come join a vibrant and thriving neuroscience group. New faculty are exceptionally well supported and we offer a very collaborative/collegial environment. employment.utah.edu/salt-lake-ci...
employment.utah.edu
Founded in 1850, The University of Utah is the flagship institution of higher learning in Utah, and offers over 100 undergraduate and more than 90 graduate degree programs to over 30,000 students. University of Utah Jobs
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Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 28/08/2026
I am delighted to announce that The Department of Human Genetics at the University of Utah is continuing a multi-year recruiting initiative for multiple tenure-track faculty positions at the rank of Assistant Professor. Please share and consider applying! utah.peopleadmin.com/postings/208...
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Raphaël Clément @raphclement.bsky.social · 27/08/2026
A developmental biologist's guide to mechanics, just out in Development! In which we learn about the three pillars of any mechanical model: forces, mechanical properties, and boundary conditions. @pflenne.bsky.social @alessandrochppr.bsky.social @caojialing1002.bsky.social @dev-journal.bsky.social
journals.biologists.com
A developmental biologist's guide to mechanics
Summary: A guide to mechanics in development: unlock how forces, material properties and geometry shape the forms of life.
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Kristen Kwan @blockintheback.bsky.social · 21/08/2026
📣 The Department of Ophthalmology and Visual Sciences @utah.edu is recruiting! We seek researchers addressing exciting questions in vision science using innovative approaches. Join our community @moraneyecenter.bsky.social! Repost and contact me with questions! utah.peopleadmin.com/postings/206...
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Maxwell Shafer @maxshafer.bsky.social · 14/08/2026
Do you have trouble sleeping when away from home or your partner and family? In our latest, we find that shells 🐚🏠 (homes) and conspecifics 🐟❤️ (family) control (or mask) circadian rhythms in shell dwelling cichlid fish: www.biorxiv.org/content/10.6...
static.klipy.com
Callipterus Cichlid Collecting Shell
Alt: Callipterus Cichlid Collecting Shell
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Shawn Burgess @burgesslab.bsky.social · 13/08/2026
NHGRI is recruiting genomics oriented researchers through the Stadtman mechanism. It is also open to any kind of research, the goal is to match your interests to an institute. The applications are now open until Oct. 1st. Details below:
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Jeff Farrell @jeffreyafarrell.bsky.social · 13/08/2026
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...
genesdev.cshlp.org
A 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
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Development @dev-journal.bsky.social · 10/08/2026
Influential articles from 2024 A subject collection compiling a selection of articles that represent the most-read and discussed publications in Development, all now free to read. Topics range from climate change to ageing. Browse now: journals.biologists.com/dev/collecti...
A screenshot of the "Influential articles from 2024" Development subject collection.
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Reposted by James Gagnon
Nick Desnoyer @nickdesnoyer.bsky.social · 05/08/2026
If Flower Bioengineering & Breeding sparks your curiosity, explore more at openflower.bio 🌸🧬 Designed and built by me, with love 🌱
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James Gagnon @james-gagnon.bsky.social · 04/08/2026
In a new (ish) preprint, we used CRISPR barcodes to label germline stem cell clones in zebrafish, then tracked their contributions to sperm production for 2 years. Instead of staying stable, individual clones rose, fell, and disappeared over time. www.biorxiv.org/content/10.6...
biorxiv.org
Clonal dynamics deviate from neutral drift in zebrafish spermatogenesis
Spermatogonial stem cells (SSCs) maintain male fertility, but how their clonal dynamics change with age remains poorly understood. Here, we use in vivo CRISPR barcoding in zebrafish to label SSCs and ...
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Jay Shendure @jshendure.bsky.social · 31/07/2026
Thrilled to post thread re: new single-cell lineage of mouse embryo reconstructed w/ DNA Typewriter. One animal, zygote to late organogenesis (E13.5). Tree has 1,340,794 transcriptionally profiled, annotated tips (cells), 1,142,588 dated internal nodes, rooted at zygote 1/n
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Daniel Gorelick @danielgorelick.bsky.social · 14/07/2026
The 1996 Development issue reporting the zebrafish screen (and the special issue commemorating it 25 years later) are now free to read, thanks @biologists.bsky.social journals.biologists.com/dev/collecti...
journals.biologists.com
The zebrafish issue: 25 years on | Development | The Company of Biologists
Welcome to Development’s 2021 Subject Collection celebrating the 25th anniversary since the publication of the zebrafish issue. The issue, originally publi
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Kristen Kwan @blockintheback.bsky.social · 09/07/2026
It was an absolute JOY to be in Vienna to see my colleague David Grunwald be awarded the @izfs.bsky.social George Streisinger Award! David gave us an inspiring reminder of who we are as a community, how we got here, and what we can accomplish when we work together. #zebrafish #EZM2026
Lila Solnica-Krezel introducing David Grunwald, the recipient of the 2026 George Streisinger AwardDavid telling us about George, scientific courage, and communityDavid reminding us what makes our zebrafish community so special
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Dr. Solomon David @solomonrdavid.bsky.social · 02/07/2026
There were more people at the DNR Fish Pond at the 2025 Minnesota State Fair (as there should be)! Their Reflecting Pool was much clearer too…AND HAD GAR 😎👍
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James Gagnon @james-gagnon.bsky.social · 29/06/2026
📣 Meeting announcement - the SDB Southwest Regional meeting will be at the University of Utah from March 5-7, 2027! Developmental biologists from Denver to Mexico City and from Reno to New Orleans, join us to share your research and celebrate our community. Details soon. @socdevbio.bsky.social
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William DeWitt @wsdewitt.github.io · 27/06/2026
Spectacular preprint led by @sydsat.bsky.social in @ohnolog.bsky.social lab, @uwgenome.bsky.social. Neutrophils precede gastrulation in killifish and rapidly patrol the yolk. (1/2)
doi.org
Early immune cell development precedes gastrulation in annual killifish
During embryogenesis, cell types arise in a predictable order because developmental regulators act sequentially. But how evolutionary changes in morphogenesis reshape the signaling environments that a...
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Zebrafish Rock! @zebrafishrock.bsky.social · 20/06/2026
Cool new tool from Keir Balla Lab @czbiohub.bsky.social 🐟🧬 Give it a try: portal.rnaquarium.org
portal.rnaquarium.org
RNAquarium Portal
Explore, visualize, and interact with RNAquarium project data.
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Mike Dorrity @mwdorr.bsky.social · 19/06/2026
(1/X) Assembling a time- and embryo-resolved sci-RNA-seq atlas of (slow) medaka development from blastula to hatch, we use comparative analysis of (fast) zebrafish to understand global + cell type-specific trends in developmental timing. Excited to get this resource out to the fish community!
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Stand Up for Science! @standupforscience.net · 15/06/2026
What? You heard SUFS made wheatpasting posters? We totally DO NOT have wheatpasting posters on our website for you to print at home and totally DISCOURAGE you from pasting them! DO NOT visit the link in our bio or this link to print them: zurl.co/QHtb4 Learn how to avoid wheatpasing below! 🧵
The graphic displays various Stand Up for Science posters that advocate for science and agaisnt the Trump admin's attacks on science and public health. The graphic also contains the red Stand Up for Science logo. The graphic reads: "WE DIDN'T MAKE WHEATPASTING POSTERS, Here's how to NOT use them" (an arrow points downwars to the thread below).
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James Gagnon @james-gagnon.bsky.social · 15/06/2026
Our new paper on interferon signaling during the response to heart injury is out today. doi.org/10.1242/bio....
doi.org
Interferon signaling is required for early neutrophil recruitment after zebrafish heart injury
Summary: Interferon-Φ1 signaling is required for early neutrophil recruitment after zebrafish heart injury, revealing a key immune trigger that shapes inflammation and may influence efficient cardiac ...
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Raju Tomer @rtomer.bsky.social · 09/06/2026
HySIL / pLSM-SCOPE / SLICE work out now in Nature Biotechnology (open article)!
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MwahahahahahadScientist @mads100tist.bsky.social · 07/06/2026
At 10k followers I start spilling the tea on model organisms starting with frogs
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Maxwell Shafer @maxshafer.bsky.social · 02/06/2026
Have you ever wondered if fish yawn? (and if they do, what that tells us about yawning?) The first preprint from the lab and a serendipitous observation ⬇️ www.biorxiv.org/content/10.6...
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Dionna Kasper @dionnakasper.bsky.social · 02/06/2026
🚨The Kasper lab is hiring! Funded positions for a postdoc and research assistant.🚨 We study regulatory mechanisms regulating vascular and hematopoietic development using zebrafish 🐟. For postdocs, contact me dionna.m.kasper@dartmouth.edu. For RAs, apply here: searchjobs.dartmouth.edu/postings/85822
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James Gagnon @james-gagnon.bsky.social · 01/06/2026
A fascinating video about the return of riparian habitats as Lake Powell water levels drop. youtu.be/eMaa0vEAbZA?...
youtu.be
See what’s emerging in Glen Canyon as Lake Powell recedes
YouTube video by The Salt Lake Tribune
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Nicolas Robine 🇪🇺🇫🇷🇺🇸 @nicorobine.bsky.social · 29/05/2026
Single Cell Genomics Day: A (Virtual) Practical Workshop. June 12, 2026, organized by @nygenome.org's Rahul Satija Free, livestreamed, no registration.
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James Gagnon @james-gagnon.bsky.social · 28/05/2026
Excited to share the published version of MIC-Drop-seq @natcomms.nature.com! Shoutout to co-lead authors @claycarey.bsky.social @sparvez.bsky.social for driving this work. Excited to see where this new scale of single-cell perturbation screening goes next. www.nature.com/articles/s41...
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Victoria Deneke @vdeneke.bsky.social · 22/05/2026
How do sperm and egg fuse? Surprisingly, we still don’t fully know… Our field has uncovered many pieces of the fertilization puzzle, but not how they fit together. We identify ✨ SPARK ✨ - a conserved sperm complex that couples sperm-egg binding to fusion. tinyurl.com/34cm4xat Read on! 🧵👇
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James Gagnon @james-gagnon.bsky.social · 22/05/2026
Support a great cause. Spread the shrimp gospel. Everyone wins.
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Molly Schumer @mollyschumer.bsky.social · 12/05/2026
Do you know any students who are planning to apply to graduate school this cycle? Encourage them to apply to the Biology Preview Program! We provide intensive workshops to help students w/ their applications + 1:1 mentorship.
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Society for Developmental Biology @socdevbio.bsky.social · 19/05/2026
🎉 The new #SDB Merch Store is officially LIVE! 👕🧢☕ Grab your favorite SDB gear including t-shirts, sweatshirts, caps, mugs & more ✨ 🛍️ Visit the store via the SDB homepage or shop directly here: sdb-official-merch.printify.me Show off your dev bio pride 🔬🧬🐟 #DevelopmentalBiology
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Molly Schumer @mollyschumer.bsky.social · 14/05/2026
Help needed! Does anyone have experience extracting nuclei from flash frozen tissue? Especially helpful if it is fish skin or tail tissue! We are trying to get some precious melanoma samples processed for snRNAseq but are having issues with either nuclei number and/or quality
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James Gagnon @james-gagnon.bsky.social · 13/05/2026
LEARN THE TRUTH NOW 🥵🐟
A silly meme that emphasizes how zebrafish use behavior fever to respond to an infection, through mechanisms conserved with mammals.
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Martin Haesemeyer @haesemeyerlab.bsky.social · 13/05/2026
New preprint from the lab, led by Bradley Cutler. With the @james-gagnon.bsky.social lab we use zebrafish to show that fever is not a reduction in the perception of warmth. Immune signals instead increase the valence of warming stimuli while cooling turns aversive. www.biorxiv.org/content/10.6...
Conceptual model of how PGE2 signaling alters temperature encoding in medullary circuits to change the valence of heating and cooling stimuli.
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Christian Mosimann @chrmosimann.bsky.social · 08/05/2026
Open-rank search: 2 (!) PI positions in Pulmonary Biology at @cuanschutz.bsky.social 🌄 We are looking for new colleagues @cupediatrics.bsky.social, working in lung fibrosis, focusing on #devbio, stem cell, & regen.biology of the lung 🫁🫀. Please help spread the word! cu.taleo.net/careersectio...
cu.taleo.net
Open Rank- Assistant Professor, Associate Professor, or Professor
Click the link provided to see the complete job description.
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Ali Seleit @aliseleit.bsky.social · 05/05/2026
(1/15) Thrilled to share new Evo-Devo work where we address the molecular, cellular & morphometric basis of an extreme axis segmentation program in the Japanese eel — an animal that forms 120 vertebrae.
biorxiv.org
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Chris Miles @chrismil.es · 30/04/2026
I'm very sad to share that my advisor and colleague Jim Keener has passed away. Jim's impact on mathematical biology, through his writing and prolific mentorship, is hard to overstate. I'll write more personal reflections soon, but given his influence on so many, I wanted to share the news.
Headshot of mathematician Jim Keener, standing in front of a bookshelf.
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James Gagnon @james-gagnon.bsky.social · 29/04/2026
Applications due tomorrow!
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James Gagnon @james-gagnon.bsky.social · 28/04/2026
Using light-activated CRISPR in zebrafish, we triggered synchronized DNA breaks and track the repair process. ⚡🐟⚡ 

 Well ... DNA repair is very different in embryos compared to tissue culture cells. Embryos repair DNA breaks incredibly fast - within minutes! www.biorxiv.org/content/10.6...
A cartoon showing how a caged guide RNA poises CRISPR cleavage until release by light. Below, a cartoon of injection of "light-activated CRISPR" into the embryo, followed by activation.
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Nick Leigh @niche-leigh.bsky.social · 27/04/2026
🐸Do salamanders need adaptive immunity to regenerate limbs and tails? 🐸 Nope! 🚨Check out back-to-back pre-prints from PhD student in our lab Chimezie (tinyurl.com/42wst3bh) and from our collaborators the Max Yun lab (tinyurl.com/b92rzwzr)
illustration by Elsa Pi Börjesson of a salamander surrounding the edges of a white background.
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Molly Schumer @mollyschumer.bsky.social · 23/04/2026
Please share widely! We will imminently be posting a technician position in our lab group since @rheasood.bsky.social is off to grad school 🙌! If you know of anyone excited about molecular biology, evolution, and functional genomics please have them reach out (schumer at stanford). Start date ~June
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Surfin' NuRD @surfinnurd.bsky.social · 13/04/2026
A very moving tribute to one of the founders of modern Stem Cell Biology: Gail Martin. Well worth a read. www.pnas.org/doi/10.1073/...
pnas.org
Gail R. Martin (1944–2026): Embryonic stem cell pioneer, developmental biologist, and student of Asian art and ceramics | PNAS
Gail Roberta Martin, Professor Emerita of Anatomy at the University of California, San Francisco, and one of the founding figures of modern stem ce...
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