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Shawn Burgess

@burgesslab.bsky.social
2.2K followers 772 following 1.5K posts

zebrafish researcher, genetics and genomics of regeneration All posts are my personal opinions and do not reflect the position of the NIH or US government

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Shawn Burgess @burgesslab.bsky.social · 11h
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Margaret Alexander @margaretalexander.bsky.social · 15h
New NIH F31 stipend just dropped, I'm thinking of going back to graduate school. Credit to student Kate Stack in finding this exciting update! www.nia.nih.gov/research/tra...
New F31 stipend $289,364
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Matti Pronker @mfpronker.bsky.social · 16h
Check out our new preprint: Affinity maturation of a single-domain antibody via rational mutagenesis informed by artificial intelligence 🧬🧫🧪🤖 www.biorxiv.org/content/10.6...
biorxiv.org
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Shawn Burgess @burgesslab.bsky.social · 14h
It was based on this article: futurism.com/future-socie...
futurism.com
Eyebrows Raise When Elon Musk's Twitter Engagement Shrivels After Destruction of Russian Data Centers
Could Ukraine's destruction of Russian data centers really be impacting Elon Musk's engagement on his own platform?
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Shawn Burgess @burgesslab.bsky.social · 19h
Problem is the vast majority of accounts there are not people.
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En Buen Ora @enbuenora.bsky.social · 20h
It can't be said too often: in the days when Twitter was much less Nazi-ish, it was dismissed by commentators & journalists as "not real life". The moment it was taken over by a literal Nazi white supremacist CSAM breeder freak who remade it as an ultraright bigot algorithm, it became real life.
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Chen @xenopuselegans.bsky.social · 14/10/2026
I put together a list of neuroscience job openings to make it easier for people at my Institute to find jobs. I wanted to share it here too 🧠 Tabs cover assistant professor, senior, and related non-PI roles. Updated Oct 12. The Read Me explains more. Please share! #neuroscience #neurojobs #postdoc
docs.google.com
Oct_12_2026_Neuroscience_Openings_Columbia_Zuckerman_Institute_Chen_Wang.xlsx
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Bradley P. Moss @bradmossesq.bsky.social · 23h
But giving water to voters waiting in long lines to vote is illegal
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Roland Hatzenpichler @environmicrobio.bsky.social · 21h
Here the direct link to the study for folks who are interested. #saynotoAI intellicat.ai/traces/index...
intellicat.ai
AI Models + Bad Science
We tested 30 leading AI models on 42 unreliable papers. They went along with the bad premise 93% of the time.
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Derek Lowe @dereklowe.bsky.social · 21h
Can the LLM-based AI agents that are supposed to be able to help with scientific research distinguish real work from pseudoscience, from fraud, or from long-discredited retracted starting papers? Take a guess.
science.org
How LLMs Deal With Fraudulent Papers
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Nature Structural & Molecular Biology @natsmb.nature.com · 23h
ICYMI: New online: Alternative splicing fine-tunes modular protein interfaces to control protein localization
dlvr.it
Alternative splicing fine-tunes modular protein interfaces to control protein localization
Nature Structural & Molecular Biology, Published online: 14 October 2026; doi:10.1038/s41594-026-01875-8Kjer-Hansen et al. show that alternative splicing reshapes how proteins interact and where they localize in cells, with tiny microexons making a disproportionate contribution to protein organization and cellular function.
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ʟᴇɢꜱ ʙᴇɴᴇᴅɪᴄᴛ ✨ @maybecam.blacksky.app · 22h
*continues to reject every cookie* you will never know me!!!
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Gabriel Flynn @gabrielflynn.bsky.social · 14/10/2026
AI researchers warn technology 'months away' from being able to connect to wifi using eduroam
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Biology Open @biologyopen.bsky.social · 23h
BiO is proud to be a PCI-friendly journal. Submit your PCI recommended preprint to BiO for a decision within five days. Find out more: peercommunityin.org/pci-friendly...
peercommunityin.org
Submit to PCI-friendly journals - Peer Community In
The authors of a PCI-recommended article have the possibility to publish in a variety of journals, including a selection of PCI-friendly journals.
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Yusuke Mori @yusuke-mori.bsky.social · 14/10/2026
Our work is finally out! How do organs get the right shape and size on time? Using the zebrafish inner ear canal, we show that a mechanical feedback loop between the ECM and Yap1 drives timely tissue growth, and a built-in termination system shuts it down once morphogenesis is done.
nature.com
A self-limiting mechanotransduction feedback loop ensures robust organ formation - Nature Communications
Developing tissues must acquire the correct shape. This study shows that mechanical feedback between the extracellular matrix and Yap sustains timely tissue growth, while Adgrg6 terminates the feedbac...
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Evgeny Kvon @evgenykvon.bsky.social · 14/10/2026
Are weak TF motifs important? Weilert et al use deep learning to systematically map low-affinity pioneer binding sites in mESCs and show that they cooperate with strong pioneer motifs to drive chromatin opening. Paper: www.cell.com/cell-genomic... Preview w/ Grace Bower: www.cell.com/cell-genomic...
cell.com
Deep learning uncovers hidden power of low-affinity motifs
Low-affinity transcription factor binding sites are functionally important but difficult to map and mechanistically poorly understood. In this issue of Cell Genomics, Weilert et al. leverage sequence-...
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Shawn Burgess @burgesslab.bsky.social · 14/10/2026
This is very cool...
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Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 06/10/2026
What's next: an in-person Cell Tracking Workshop at Biohub in Redwood City, Nov 30 to Dec 3, bringing the tracking and bioimaging community together, with our prize winners invited. Time to compare notes and chart where the field goes next! 🧬
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Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 06/10/2026
It all stays open: CC0 data, winning code under MIT, writeups already up. 1st-place writeup: kaggle.com/competition... Metric code: github.com/royerlab/ka... #OpenScience
github.com
GitHub - royerlab/kaggle-cell-tracking-competition
Contribute to royerlab/kaggle-cell-tracking-competition development by creating an account on GitHub.
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Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 06/10/2026
The task: detect every cell in light-sheet microscopy movies of zebrafish embryos, link each one from frame to frame, and catch every division, so that cell lineages can be rebuilt. By node and edge count, it's the largest cell tracking dataset published to date. #Zebrafish #DevBio
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Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 06/10/2026
🏁 That's a wrap! The @biohub.org Cell Tracking machine learning challenge on @kaggle.com is over: 4,478 participants, 3,947 teams, 120 countries, 95,438 submissions, tracking every cell of zebrafish embryos. 🧪🔬🧵 kaggle.com/competition... #microscopy
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Maxim Greenberg @maxvcg.bsky.social · 14/10/2026
I'm reviewing a grant right now that is so cool, it would be such a shame to waste this experience on a robot
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Anyi Mazo-Vargas @anyimv.bsky.social · 14/10/2026
🎉 First work from my lab at Duke University 🦋 Led by @tianshenbio.bsky.social Shen Tian, whose in situs are 😚🤌, with key contributions from @yf-joye-zhou.bsky.social Joye Zhou. Exploring the evolution of the WntA regulatory network in butterfly wing patterning. www.biorxiv.org/content/10.6...
biorxiv.org
Genetic circuit rewiring underlies a lineage-specific patterning machinery on butterfly wings
Phenotypes evolve through changes in gene regulatory networks (GRNs), but how changes in network topology contribute to phenotypic evolution is still poorly understood. Butterfly wing color patterns p...
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olderthandirt1.bsky.social @olderthandirt1.bsky.social · 13/10/2026
A moment of silence 😆😆
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Maureen Barr @barrlab.bsky.social · 14/10/2026
The Hobert lab (Chien-Po Liao and Hongzhu Ji) created yet another tool/resource for the C. elegans community! Super useful to study sexual dimorphisms in the nervous system and in animal physiology. www.biorxiv.org/content/10.6...
biorxiv.org
Genome-engineered C. elegans strains with sex-transformed neurons and gut
The sexual identity of specific tissues can be altered through cell-autonomous manipulation of the sex determination pathway in the nematode Caenorhabditis elegans . Previously described sexually mosa...
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Pawel Burkhardt @pawelburkhardt.bsky.social · 13/10/2026
Can a comb jelly choose whether to reproduce as a larva or grow up first? 🪼 Our new preprint shows that in Mnemiopsis leidyi, this depends on the density of other comb jellies. A story of surprising developmental plasticity! www.biorxiv.org/content/10.6... 🧵 1/4 📸 @beziostudio.bsky.social
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Shawn Burgess @burgesslab.bsky.social · 14/10/2026
static.klipy.com
Grateful Dead Live: Jerry Garcia in 1987
ALT: Grateful Dead Live: Jerry Garcia in 1987
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Anil Dash @anildash.com · 14/10/2026
Based on a browser funded with public money, and made the founders multimillionaires. One went on to cofound the biggest venture firm in the world and hired a man as a partner because he choked my unarmed neighbor to death. The people who *didn't* become millionaires are still making a free browser.
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Needhi Bhalla 💅🏽 @needhibhalla.bsky.social · 13/10/2026
“This is the part of my column where usually I wrap things up by writing something darkly witty and sardonic. But this time I can only say: God damn these people. God damn them to hell.”
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Sharon Clark 🦋 @sharonclark.bsky.social · 13/10/2026
According to Aaron Parnas: Musk is trying to trick everyone by sending them to his own phony site when they go to check their registration. DO NOT go to votesafe.org When you enter your information, Elon Musk will steal it. DO NOT go to that website! Pass it on...
votesafe.org
VOTE SAFE | Home
We provide you with the information you need to vote with confidence. Sign up for election reminders and get help with voter registration and voting by mail.
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Shawn Burgess @burgesslab.bsky.social · 13/10/2026
I want a Guy Ritchie reboot of Wild Wild West.
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dan sinker @dansinker.com · 12/10/2026
An Open Letter To The People Writing Lengthy Posts About 'Why I'm Going Back to Twitter' dansinker.com/posts/2026-1...
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Shawn Burgess @burgesslab.bsky.social · 13/10/2026
I encourage this behavior
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Kevin Bird @stairwaytokevin.bsky.social · 11/10/2026
New work to share! Pangenome studies treat gene presence/absence independently, but genes work together in pathways. By focusing on the covariance of gene loss, we show the Arabidopsis dispensable genome has modular co-evolutionary structure reflecting the biological organization of the plant 1/
biorxiv.org
Gene functional-state covariance reveals modular structure in the Arabidopsis thaliana dispensable genome
Classical multilocus theory predicts that selection acting on combinations of loci can maintain non-random associations among allelic states, causing selection to act on multilocus genotypes rather than individual alleles. Across eukaryotic species, pangenome studies have documented thousands of genes that vary in functional status between individuals, yet this variation is analyzed as if each gene evolves independently. Here we test for non-random association within the dispensable pangenome across 1,012 natural genotypes of Arabidopsis thaliana to better understand the structure and evolution of eukaryotic pangenomes. Genome-wide pairwise association testing of loss-of-function alleles across genotypes identified 150,033 significantly covarying gene pairs among 5,679 unique genes after controlling for kinship and population structure. Most associations were between genes on different chromosomes, and covarying gene pairs showed greater co-expression and functional similarity than expected by chance. Network analysis revealed a non-random higher-order architecture comprising stable functional communities with distinct biological functions and structured connectivity among communities. The enriched functions and connectivity of communities revealed a tight coupling of modules involving plant immunity, environmental response, and specialized metabolism, highlighting how these systems integrate and evolve in response to dynamic ecological pressures. Taken together, these results show that the dispensable genome has a complex higher-order structure driven by functionally interacting genes, and that variation in gene content provides a population-scale resource for investigating the organization and evolution of biological systems. ### Competing Interest Statement The authors have declared no competing interest. Division of Integrative Organismal Systems, 2208944
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Nicholas Grossman @nicholasgrossman.bsky.social · 11/10/2026
Uh oh, did someone’s website and personal account experience a big drop in activity after Ukraine hit a Russian data center?
Elon Musk: “Zelensky has gone too far”

https://x.com/elonmusk/status/2109033017184338141
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JD Long @jdlong.cerebralmastication.com · 11/10/2026
Snort.
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🦋 C.G., PhD 🐸 (🪖"Prima" AKA "Battle" to One)🌻 @tcrg2012.bsky.social · 10/10/2026
💪🏽 #ONEV1 #Pinks 🌸 #Voices4Victory
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Mark Peifer (He, him) @peiferlabunc.bsky.social · 11/10/2026
Here's another excellent story about David Sinclair as a snake-oil salesman www.nmn.com/news/disgrac...
nmn.com
Dr. David Sinclair Steps Down from Prominent Aging Research Position Amidst Backlash Surrounding ‘Reverse Aging’ Claim
Harvard’s Dr. David Sinclair has claimed achievement of “age reversal” in animal models, prompting a whirlwind of criticism from fellow scientists and his resignation as president of the Academy for H...
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Mark Peifer (He, him) @peiferlabunc.bsky.social · 11/10/2026
Centromeres are key to mitotic spindle attachment and high fidelity chromosome segregation but change rapidly during evolution. Check out these novel insights into the relative role of particular DNA sequences, using powerful chromosome manipulation tools in Drosophila! 🧪
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Richard Sever @richardsever.bsky.social · 11/10/2026
Important legal distinction. Training AI with your text (currently) falls under Fair Use. But if it reproduces that text verbatim as output that’s copyright breach. Much like if I write about your paper that’s fine, but if I copy it word for word I have to ask*. *unless you’ve open licensed it
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Mark Histed @markhisted.org · 11/10/2026
Please stop using Musk’s version of Twitter. Everyone who uses it is having their mind poisoned (slowly) by a pedophilia MechaHitler machine, yes. But worse they’re having their minds poisoned by a thousand small nudges, “reply guys calling [good values] cope and cringe.”
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Prisonculture @prisonculture.bsky.social · 08/10/2026
The deployment of National Guard troops into cities has been so normalized that it barely merits a mention in the press or among the public anymore. D.C. remains occupied, Memphis is occupied, so is New Orleans... It's incredible to me.
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Oliver Willis @owillis.bsky.social · 08/10/2026
a big difference between me in 2026 and me in 2006 is i no longer believe democrats are just helpless little guys buffeted by forces beyond their control. decades of writing about this stuff makes it clear: while dems face very evil people, the party is complicit in not fighting.
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Isle McElroy @islemcelroy.bsky.social · 17/09/2026
I start teaching at the Columbia mfa today. Here’s the AI statement from my syllabus. Feel free to borrow.
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Elizabeth Jacobs, PhD @elizabethjacobs.bsky.social · 08/10/2026
It’s simply unimaginable that CDC Director Dr. Erica Schwartz has just bowed to RFK Jr. and approved funding for an utterly unethical clinical trial that will withhold the birth dose of HepB vaccine in Guinea Bissau. It is to be conducted by researchers accused of academic misconduct.
rollingstone.com
CDC Is Moving Forward With a Previously Shelved Controversial Hepatitis B Vaccine Study
“It’s a wholly unethical trial, and it shouldn’t be allowed,” says Dr. Paul Offit of Guinea-Bissau study
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Lauren Slosky @laurenslosky.bsky.social · 08/10/2026
Our Department of Pharmacology at the University of Minnesota is looking for another tenure-track Assistant Professor! Please pass along to those in your network who may be interested. 💛〽️ Join us! 👉 jobs.sciencecareers.org/job/680440/ass…  #FacultyJobs #Pharmacology #TenureTrack 🧪🔵🧠
Aerial view of the University of Minnesota’s medical campus along the Mississippi River, with autumn-colored trees lining the riverbank and the downtown Minneapolis skyline in the distance beneath a clear blue sky.
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Jo VanEvery @jovanevery.bsky.social · 08/10/2026
Sabbatical goals
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Sarah Hird, PhD @sarahhird.bsky.social · 07/10/2026
That time I put almost all the chipmunk species in the western USA on one map. Did you know there’s 1 species of chipmunk in Asia, 1 in eastern USA & >20 in western USA? (I’m not the crazy one here. The chipmunks are the crazy ones.)
Map of the western USA with 20 overlapping chipmunk species distributions in different colors.
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Shawn Burgess @burgesslab.bsky.social · 07/10/2026
I feel seen www.instagram.com/reel/DeKIYa-...
instagram.com
Instagram
Create an account or log in to Instagram - Share what you're into with the people who get you.
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Shawn Burgess @burgesslab.bsky.social · 07/10/2026
Good morning
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