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Tamas Nagy

@tamasnagy.com
1.3K followers 295 following 154 posts

Cellular biophysicist. Microscopist. Urbanist. Working on cell fate decisions in collectives. Postdoc @UCLA with Tom Rando. Prev: PhD @UCSF with Orion Weiner. tamasnagy.com

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Tamas Nagy @tamasnagy.com · 26/09/2026
This is one of my favorite recent uses of spatial transcriptomics…pseudotemporal ordering of niche remodeling www.cell.com/cell/fulltex...
cell.com
Oncogenic and tumor-suppressive forces converge on a progenitor niche at the benign-to-malignant transition
Opposing oncogenic and tumor-suppressive forces establish a progenitor-like state that builds a self-reinforcing niche to drive benign-to-malignant transition in pancreatic cancer models. Disruption o...
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Rikki Garner @rikkigarner.bsky.social · 16/09/2026
Excited to announce that the Rikki Garner lab has opened its doors in beautiful Austin, TX! Our interdisciplinary lab @utaustin.bsky.social MBS investigates tissue fluidity as a universal physical regulator of multicellular patterning in health and disease. www.rikkigarnerlab.org 1/n
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Tamas Nagy @tamasnagy.com · 16/09/2026
Congrats Rikki!!
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Tamas Nagy @tamasnagy.com · 06/09/2026
Even with all the advancements in automated cell tracking getting us to 90%+ accuracy...that's still a lot of broken tracks over long movies! Our brains are pretty good at this so I made Vizsla 🐕, a little @napari.org plugin, to help you fix your tracks manually. 👉 pypi.org/project/napa...
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Tamas Nagy @tamasnagy.com · 08/09/2026
Wowowow. This some spectacular imaging. Amazing watching the immune cells migrate on top of the epithelia!
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Tamas Nagy @tamasnagy.com · 06/09/2026
It's my first Python package after lots of Julia packages so I'm excited to see what kind of new bug reports I'll get 😅
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Tamas Nagy @tamasnagy.com · 06/09/2026
I'm also quite proud of my (non-AI) logo 😀. Vizslas are a famous hunting dog from Hungary known for their almost supernatural ability to follow animal tracks under the toughest circumstances...exactly the sidekick you want!
Vizsla logo has a vizsla dog following a cell track
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Tamas Nagy @tamasnagy.com · 06/09/2026
It takes Cell-Tracking-Challenge (CTC) output from awesome tracking programs like Trackastra (by @bengallusser.bsky.social) or Ultrack (by @jookuma.bsky.social) & autosaves to CTC output as you go! Made possible by the great @napari.org ecosystem and tracksdata from @loicaroyer.bsky.social's lab.
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Tamas Nagy @tamasnagy.com · 06/09/2026
Even with all the advancements in automated cell tracking getting us to 90%+ accuracy...that's still a lot of broken tracks over long movies! Our brains are pretty good at this so I made Vizsla 🐕, a little @napari.org plugin, to help you fix your tracks manually. 👉 pypi.org/project/napa...
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The New Republic @newrepublic.com · 03/09/2026
newrepublic.com/post/215117/...
newrepublic.com
Hegseth and Co. Are Trying to Steal Other Agencies’ Funds, Dems Say
House Democrats say the Pentagon is attempting to siphon crucial NIH funds.
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Tamas Nagy @tamasnagy.com · 03/09/2026
Interesting how similar this is to neutrophil/immune cell migration under confinement…huh.
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Tamas Nagy @tamasnagy.com · 16/08/2026
I've struggled to get nice, pixel-perfect borderless animations out of Napari for presentations, but I recently hacked up a nice script for it. I'm pretty happy with the results! More info 👇 tamasnagy.com/blog/2026/na...
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Tamas Nagy @tamasnagy.com · 16/08/2026
I've struggled to get nice, pixel-perfect borderless animations out of Napari for presentations, but I recently hacked up a nice script for it. I'm pretty happy with the results! More info 👇 tamasnagy.com/blog/2026/na...
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Tamas Nagy @tamasnagy.com · 10/08/2026
This is such a good point. Given that genAI reproduces large chunks of code verbatim from open source software without crediting the original author...suffice to say, it's probably doing the same exact thing when writing.
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Zeke Hausfather @zekehausfather.com · 02/08/2026
I'm not sure folks have realized just how crazy the second half of 2026 and 2027 will be for global temperatures – on the back of a record-smashing El Niño event. Here is my latest estimate of where both years will end up compared to global temperatures since 1850.
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UCLA Broad Stem Cell Research Center @uclastemcell.bsky.social · 29/07/2026
Watch a muscle fiber take shape. 🔬 This microscopic video captures a muscle cell fusing with a developing muscle fiber, with cell membranes visible in purple and yellow. The Rando Lab uses live-cell imaging to understand how cells coordinate muscle regeneration. Credit: Tamas Nagy/Rando Lab
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jared toettcher @toettch.bsky.social · 24/07/2026
New Toettchlab paper alert! Harrison Oatman just published his beautiful work combining software design for "smart" microscopy+optogenetics and some really beautiful work understanding EGFR-driven collective cell migration. www.cell.com/cell-systems...
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Tamas Nagy @tamasnagy.com · 24/07/2026
Woods Hole is the best! Glad you had a great time :) Now go sleep for a week 😆
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Tamas Nagy @tamasnagy.com · 21/07/2026
Interesting work that shows that frontier models are basically not improving in reliability despite them appearing to do better on benchmarks. Reliability is key to trust. Hard to imagine LLMs being trusted with critical operations until this is solved, *if* it can be. arxiv.org/pdf/2602.16666
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Paul Francois @pfrancois.bsky.social · 14/07/2026
New paper 🧵 What if the "landscape" that guides cell differentiation isn't fixed, but is sculpted, in real time, by the very cells moving through it? We call this a 'sandscape' : grains of sand that carve dunes as they move, while the dunes' shape simultaneously steers where the grains go next.
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Tamas Nagy @tamasnagy.com · 10/07/2026
No worries. There are so many things to test! The flipped polarity gradient is really cool, turns a bunch of cell biology on its head!
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Ankita Jha @ankita13jha.bsky.social · 07/07/2026
Excited to share our new paper, now published in Nature Cell Biology! 🎉 We asked a fundamental question in cell biology: How do cells maintain polarity while migrating? Especially how do cancer cells navigate confined spaces? www.nature.com/articles/s41556-026-01981-1
nature.com
CD44 restricts EGFR mobility to polarize cytoskeletal signalling modules driving bleb-based migration - Nature Cell Biology
Jha et al. show that the transmembrane protein CD44 restricts EGFR mobility to maintain an EGFR–PI3K–Rac gradient during bleb-based cell migration.
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Tamas Nagy @tamasnagy.com · 10/07/2026
Super cool to see the story in its final form! Congrats @ankita13jha.bsky.social ! Out of curiosity did you ever try inhibiting NHE1 in the leader blebs? At least in neutrophils, we found that it was activated downstream of PI3Ky…it might be playing a role here too!
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Tamas Nagy @tamasnagy.com · 01/07/2026
Even for the coding, LLM capabilities are vastly overstated. Science is immensely harder and there’s way less training data, hard to imagine LLMs being super useful. It would likely take a total different architecture built on physical rules to be useful for scientific research.
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Christophe 🔬 Leterrier @christlet.bsky.social · 24/06/2026
This is clearly top 1% quality data
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Henry De Belly @henrydebelly.bsky.social · 10/06/2026
Very excited to be sharing our new paper, just out in Nature Cell Biology! The big question we investigate: How do migrating cells put their front 🔴 and back 🔵 in the right place?
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Tamas Nagy @tamasnagy.com · 30/05/2026
Got to play around with Holotomographic imaging of muscle cells yesterday via the @uclastemcell.bsky.social imaging core and the results are pretty spectacular 🤩 You can see everything from mitochrondria to lamellipodia to macropinocytosis…with no labels!
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Tamas Nagy @tamasnagy.com · 29/05/2026
Yeah, but most of us don’t pretend to know how exactly we arrived at a conclusion. We expect LLMs to behave like deterministic computer programs where we can actually understand how an answer was given. Instead LLMs just make something up, maybe they should just saw “idk” when someone asks.
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Tamas Nagy @tamasnagy.com · 29/05/2026
It really is concerning how few people know that this is the case.
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Reese Richardson @reeserichardson.bsky.social · 28/05/2026
TL;DR: We've identified more than 100 cases of apparent manipulation in Thermo Fisher Scientific's antibody verification data. @sholtodavid.bsky.social @johanduchene.bsky.social reeserichardson.blog/2026/05/28/h...
reeserichardson.blog
How much of Thermo Fisher’s antibody data has been manipulated?
We’ve documented more than 100 instances of apparent data manipulation in Thermo’s catalog
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Tamas Nagy @tamasnagy.com · 22/05/2026
Amazing imaging! What tissue is this?
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Tamas Nagy @tamasnagy.com · 12/05/2026
Super cool stuff Julia! Especially the fact that the binding partner can be untagged, that's 🤯 territory. How well does TTM work for more spaghetti IDR-heavy proteins?
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Julia Lazzari-Dean @jlazzaridean.bsky.social · 12/05/2026
We invented “triplet tumbling microscopy” (TTM) to track protein-protein interactions in living cells! Tag your protein with GFP and see it interact with *untagged* binding partners www.biorxiv.org/content/10.6...
A cartoon overview of triplet tumbling microscopy, comparing data from bound and unbound samples.
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Tamas Nagy @tamasnagy.com · 12/05/2026
Thank you!
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Tamas Nagy @tamasnagy.com · 08/05/2026
My PhD work showed that resting neutrophil -> activated/prime neutrophil is a pretty big volume change needed for motility :) Super fast, only a couple minutes to swell so not like other slower changes elifesciences.org/articles/90551
elifesciences.org
Neutrophils actively swell to potentiate rapid migration
Actin-independent water influx complements actin-driven cytoskeletal forces to potentiate chemoattractant-induced migration in primary human neutrophils.
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Berna Devezer @devezer.bsky.social · 30/04/2026
📣 The difference between replicable and not replicable is not itself scientifically replicable. 📣 New work with Erkan Buzbas, showing that verdicts such as "X% of results replicated" are based on an inferential machinery that doesn't work. arxiv.org/abs/2604.26268
Screenshot of a paper's title page. Title: "The Difference Between 'Replicable' and 'Not replicable' is not Itself Scientifically Replicable". Authors: Berna Devezer and Erkan O. Buzbas, both at the University of Idaho — Devezer in the Department of Business and the Institute for Modeling Collaboration and Innovation, Buzbas in the Department of Mathematics and Statistical Science. Authors contributed equally. Corresponding author: bdevezer@uidaho.edu.
Abstract: Replication studies estimate the replicability rate of scientific results by aggregating binary verdicts of experiments. Exact replications are rarely attainable, so most replication sequences are non-exact. Experiments differ in ways that matter and do not share a single common data-generating process. We formalize two statistical interpretations of this non-exactness. In a shared latent rate model (benchmark), experiments are exchangeable and depend on a common random replicability rate. In a conditionally independent rates model (operational), each experiment has its own replicability rate drawn independently from a population distribution. Under the shared latent rate model, even small variability among replicability rates induces an irreducible variance floor on the estimated mean replicability rate that cannot be eliminated by adding more replications. Under the conditionally independent rates model, the degree of non-exactness is not identifiable from standard replication data, because one binary verdict per experiment contains no information about between-experiment heterogeneity. Researchers therefore cannot tell which precision regime they are operating in or whether high- and low-replicability sequences can be distinguished in principle. As a result, the usual data structure of one binary verdict per experiment cannot support reliable demarcation between "replicable" and "not replicable" results and systematically understates uncertainty, making high- and low-replicability sequences appear discrim…
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Tamas Nagy @tamasnagy.com · 22/04/2026
Trainees jump on this! Juan is an awesome human and he’s gonna do some amazing science ✨ Can’t wait to see what he gets up to!
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Tamas Nagy @tamasnagy.com · 22/04/2026
Wow amazing! You’ve had helluva of year!
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Evelyn Strickland @strickland-evelyn.bsky.social · 20/04/2026
What if you got to work with some of your best friends on a science project? I can't publish how fun this was, but I can show you the data (🧵)! Last week, we posted our second neutrophil swarming paper to bioRxiv and I wanted to post my favorite videos here~ www.biorxiv.org/content/10.6...
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Juan C. Landoni @jclandoni.bsky.social · 03/04/2026
Our paper is now out in Science! Super excited to share our discovery that #mitochondria #pearling is the elusive mechanism driving the regular distribution and inheritance of #mtDNA nucleoids 🧬 [1/6]
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John Trant @trantteam.bsky.social · 30/03/2026
For me, the most maddening thing is when AI boosters, or detractors, all seem to agree that AlphaFold is an unmitigated good and useful tool showing the power of AI. I disagree. It's hit and miss. And the misses are REALLY expensive. Especially when the conversation suggests it is ALL HIT.
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David Ho @davidho.bsky.social · 26/03/2026
I don't think people fully appreciate how apocalyptic things are for US science. I haven't had any new funding since 2024, but I'm still ok since typical grants are for three years. This means next year I will be completely out of funding and will have to fire everyone in the lab. It's not great.
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Kai Johnsson @kjohnsson.bsky.social · 26/03/2026
A high-affinity split-HaloTag for live-cell protein labeling. And much more. www.nature.com/articles/s41...
nature.com
A high-affinity split-HaloTag for live-cell protein labeling
Nature Communications - Lin and colleagues present high-affinity split-HaloTag pairs for protein tagging and multiplexed labelling. This versatile system allows protein visualisation with diverse...
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Tamas Nagy @tamasnagy.com · 17/03/2026
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Tamas Nagy @tamasnagy.com · 17/03/2026
So excited to be drowning in new "findings". Coming soon to a journal near you! 🫠 github.com/aiming-lab/A...
github.com
GitHub - aiming-lab/AutoResearchClaw: Fully autonomous & self-evolving research from idea to paper. Chat an Idea. Get a Paper. 🦞
Fully autonomous & self-evolving research from idea to paper. Chat an Idea. Get a Paper. 🦞 - aiming-lab/AutoResearchClaw
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Denis Wirtz @deniswirtz.bsky.social · 26/02/2026
Federal funding for US biomedical research is moribund. Since October 1 2025, NIH is -80% in new grants and -70% in values (total dollars). Labs are closing down and researchers are leaving science. To what end?
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Tamas Nagy @tamasnagy.com · 25/02/2026
Do folks have a preferred protocol for bleaching fluorescent proteins prior to doing Immunofluorescence? I tried a 3% H2O2 + 12mM HCl solution but I had severe cell detachment problems (despite everything being fixed).
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Di Jiang @dijiang319.bsky.social · 19/02/2026
@science.org Evolution of error correction through a need for speed | Science #evolution 🧬🔬 www.science.org/doi/10.1126/...
science.org
Evolution of error correction through a need for speed
Kinetic proofreading is a class of error-correcting mechanisms in biology that expend energy to avoid mistakes during replication, transcription, and translation. Proofreading is typically assumed to ...
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Tamas Nagy @tamasnagy.com · 16/02/2026
Insane that anyone can just unleash hundreds of glorified spam bots on the public internet and harass people, with little to no repercussions. The person who fired up the agent might not even know that it’s doing this! How are we as a society going to handle BS at this scale?
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Tamas Nagy @tamasnagy.com · 16/02/2026
Absolutely wild timeline we live in TLDR: An agentic AI bot writes a takedown blog post of a matplotlib maintainer after he rejects its pull request. @arstechnica.com screws up and use AI to write a piece about the incident which hallucinates quotes. 🤦 theshamblog.com/an-ai-agent-...
theshamblog.com
An AI Agent Published a Hit Piece on Me
Summary: An AI agent of unknown ownership autonomously wrote and published a personalized hit piece about me after I rejected its code, attempting to damage my reputation and shame me into acceptin…
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