James Gagnon
@james-gagnon.bsky.social
I'm an associate professor @UofUBiology, Utah, USA
gagnonlab.org | fish stuff in and out of the tank
gagnonlab.org | fish stuff in and out of the tank
Pinned
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
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 James Gagnon
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
youtu.be/cCZhZpPALqw
Zebrafish in the wild
YouTube video by John Rawls
youtu.be
October 28, 2025 at 2:09 PM
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
youtu.be/cCZhZpPALqw
Reposted by James Gagnon
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
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...
shorturl.at
November 12, 2025 at 8:34 PM
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
Reposted by James Gagnon
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
November 10, 2025 at 5:10 PM
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
Reposted by James Gagnon
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...
(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...
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.
www.nature.com
October 8, 2025 at 3:51 PM
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...
(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...
Reposted by James Gagnon
Cat flea, homage to Hooke. Micron in Moleskine. 🔬🖊️
September 30, 2025 at 2:12 PM
Cat flea, homage to Hooke. Micron in Moleskine. 🔬🖊️
Reposted by James Gagnon
💥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
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
September 18, 2025 at 7:30 PM
💥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
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
Reposted by James Gagnon
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
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
September 17, 2025 at 1:59 PM
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
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
Reposted by James Gagnon
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...
neurojobs.sfn.org/job/39081/te...
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
neurojobs.sfn.org
September 16, 2025 at 4:01 PM
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...
neurojobs.sfn.org/job/39081/te...
Reposted by James Gagnon
Just keep thinking about fish
September 2, 2025 at 6:45 PM
Just keep thinking about fish
Reposted by James Gagnon
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
with members of the @schierlab.bsky.social and Salzburger labs, as well as the burgeoning Shafer lab @uoftcellsysbiol.bsky.social
August 28, 2025 at 2:18 PM
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
with members of the @schierlab.bsky.social and Salzburger labs, as well as the burgeoning Shafer lab @uoftcellsysbiol.bsky.social
Reposted by James Gagnon
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.
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.
www.sltrib.com
July 8, 2025 at 9:25 PM
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.
Reposted by James Gagnon
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/...
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 ...
www.science.org
June 20, 2025 at 8:25 PM
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/...
Reposted by James Gagnon
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
@impvienna.bsky.social @vdeneke.bsky.social
June 3, 2025 at 7:56 PM
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
@impvienna.bsky.social @vdeneke.bsky.social
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 James Gagnon
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...
- 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...
April 28, 2025 at 5:20 PM
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...
- 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...
Reposted by James Gagnon
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...
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
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
There is only one week left to submit your oral abstract for the 19th IZFC! If you choose to submit an Oral Abstract, and your abstract is not selected for an oral presentation you will be offered a poster presentation. Submit here today: www.izfs.org/education/19...
Abstracts | IZFS
www.izfs.org
March 4, 2025 at 5:12 PM
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
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
Reposted by James Gagnon
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
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
February 20, 2025 at 4:51 PM
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
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
Reposted by James Gagnon
Letter from the SSE/SSB/ASN councils on the scientific understanding of sex and gender, pls RT
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...
www.evolutionsociety.org
February 7, 2025 at 10:11 PM
Letter from the SSE/SSB/ASN councils on the scientific understanding of sex and gender, pls RT
Reposted by James Gagnon
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
Coming soon….
#devbiol
#SciHist
#TheLongBibliography
January 29, 2025 at 1:47 AM
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
Coming soon….
#devbiol
#SciHist
#TheLongBibliography
Reposted by James Gagnon
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!
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...
www.mbl.edu
December 30, 2024 at 12:32 AM
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!
Reposted by James Gagnon
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/...
Read more here: biorxiv.org/cgi/content/...
December 17, 2024 at 4:10 AM
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/...
Read more here: biorxiv.org/cgi/content/...
Reposted by James Gagnon
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.
December 5, 2024 at 9:05 PM
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.
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 🧬🔬🦠🧑🔬
20+ years ago, this class convinced me to be a biologist, and I hope I passed that spark along to some of my students 🧬🔬🦠🧑🔬
December 5, 2024 at 8:53 PM
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 🧬🔬🦠🧑🔬
20+ years ago, this class convinced me to be a biologist, and I hope I passed that spark along to some of my students 🧬🔬🦠🧑🔬
Reposted by James Gagnon
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
#landscapephotography #astrophotography #nature #photographer #nikon
November 29, 2024 at 7:24 PM
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
#landscapephotography #astrophotography #nature #photographer #nikon