Daniel Asarnow
@dabiophysicist.bsky.social
Postdoctoral scholar in Veesler Lab @ UWa.
Former UCSF & SFSU & UCSC student & Exploratorium Explainer. He/him.
I take tiny pictures, in 2 & 3 dimensions.
https://github.com/asarnow
Former UCSF & SFSU & UCSC student & Exploratorium Explainer. He/him.
I take tiny pictures, in 2 & 3 dimensions.
https://github.com/asarnow
Pinned
Reposted by Daniel Asarnow
priviliged to be witnessing these amazing cellular vistas! makes you wonder about all the unknownwhat biology is being captured here!
February 19, 2026 at 6:55 PM
priviliged to be witnessing these amazing cellular vistas! makes you wonder about all the unknownwhat biology is being captured here!
My god man what's happened to you
February 19, 2026 at 4:56 PM
My god man what's happened to you
Reposted by Daniel Asarnow
We posted a biorxiv preprint on structural bioinformatics, AlphaFold modeling & machine learning on predicting specificity of E3 ligase ring domains for different E2 enzymes. 1/4
Preprint: www.biorxiv.org/content/10.6...
Models/data (UbiqCore website): dunbrack.fccc.edu/ubiqcore
Preprint: www.biorxiv.org/content/10.6...
Models/data (UbiqCore website): dunbrack.fccc.edu/ubiqcore
February 17, 2026 at 5:03 AM
We posted a biorxiv preprint on structural bioinformatics, AlphaFold modeling & machine learning on predicting specificity of E3 ligase ring domains for different E2 enzymes. 1/4
Preprint: www.biorxiv.org/content/10.6...
Models/data (UbiqCore website): dunbrack.fccc.edu/ubiqcore
Preprint: www.biorxiv.org/content/10.6...
Models/data (UbiqCore website): dunbrack.fccc.edu/ubiqcore
Reposted by Daniel Asarnow
🧵 After years out of the field, I and my lab are again working on bacterial type IV pili. We have just posted our first preprints, and I'm excited to share what we have discovered.
This shows Neisseria gonorrheae bacteria infecting a human epithelical cell. Here, you can see the pili in red.
1/
This shows Neisseria gonorrheae bacteria infecting a human epithelical cell. Here, you can see the pili in red.
1/
February 16, 2026 at 8:22 PM
🧵 After years out of the field, I and my lab are again working on bacterial type IV pili. We have just posted our first preprints, and I'm excited to share what we have discovered.
This shows Neisseria gonorrheae bacteria infecting a human epithelical cell. Here, you can see the pili in red.
1/
This shows Neisseria gonorrheae bacteria infecting a human epithelical cell. Here, you can see the pili in red.
1/
Reposted by Daniel Asarnow
I had Claude make this as a mini-game for Relay's disconnect screen (like Chrome's dinosaur), but then pivoted to stand-alone. In this game, you have to find Euler angles matching the target projection, i.e. cosplay RELION. It can be pretty hard. Works on mobile too! warpem.github.io/euler-hunt/
Euler Hunt
Can you find the Euler angles of a cryo-EM projection?
warpem.github.io
February 16, 2026 at 3:13 AM
I had Claude make this as a mini-game for Relay's disconnect screen (like Chrome's dinosaur), but then pivoted to stand-alone. In this game, you have to find Euler angles matching the target projection, i.e. cosplay RELION. It can be pretty hard. Works on mobile too! warpem.github.io/euler-hunt/
Reposted by Daniel Asarnow
holy shit
PR from an ‘agent’ gets closed so it writes a blog post with a personal takedown
Some interesting comments from the maintainers too
Slop machine go brr, dead internet theory x1000
github.com/matplotlib/m...
PR from an ‘agent’ gets closed so it writes a blog post with a personal takedown
Some interesting comments from the maintainers too
Slop machine go brr, dead internet theory x1000
github.com/matplotlib/m...
[PERF] Replace np.column_stack with np.vstack().T by crabby-rathbun · Pull Request #31132 · matplotlib/matplotlib
This PR addresses issue #31130 by replacing specific safe occurrences of np.column_stack with np.vstack().T for better performance.
IMPORTANT: This is a more targeted fix than originally proposed. ...
github.com
February 12, 2026 at 12:18 PM
holy shit
PR from an ‘agent’ gets closed so it writes a blog post with a personal takedown
Some interesting comments from the maintainers too
Slop machine go brr, dead internet theory x1000
github.com/matplotlib/m...
PR from an ‘agent’ gets closed so it writes a blog post with a personal takedown
Some interesting comments from the maintainers too
Slop machine go brr, dead internet theory x1000
github.com/matplotlib/m...
The striped HSB Silverfish. Lives in the basement of UWMC on a diet of hematology journal backissues from the 1950s. Much faster than regular silverfish, and camouflaged to match the floor.
February 10, 2026 at 8:32 PM
The striped HSB Silverfish. Lives in the basement of UWMC on a diet of hematology journal backissues from the 1950s. Much faster than regular silverfish, and camouflaged to match the floor.
Reposted by Daniel Asarnow
As Fran was nice enough to highlight this, I thought I'd put up a brief thread. 3 in 10 proteins that our cells make are either embedded in membranes (ion channels, adhesion molecules, etc.) or secreted (insulin, antibodies). They move through the secretory pathway.
1/
1/
February 6, 2026 at 6:39 PM
As Fran was nice enough to highlight this, I thought I'd put up a brief thread. 3 in 10 proteins that our cells make are either embedded in membranes (ion channels, adhesion molecules, etc.) or secreted (insulin, antibodies). They move through the secretory pathway.
1/
1/
Alcatraz Coyote vs Alameda raccoon?
i've been watching the coyote on Alcatraz's progress with great interest. a week-ish ago, a coyote SWAM to Alcatraz for the first time and looked fuckin rough after the dangerous swim. but the coyote is doing fine now, gorging itself on unprepared birds & rats who are dealing with a sort of Godzilla
January 29, 2026 at 9:05 PM
Alcatraz Coyote vs Alameda raccoon?
The trainees when you're at the GRC:
NO PI OK
January 18, 2026 at 2:05 AM
The trainees when you're at the GRC:
Great video (and voice over)! Missing sound effects though 😉
Our new movie is online, highlighting the assembly, secretion and mechanism of action of bacterial Tc toxins. We hope you enjoy it and use it for teaching purposes or just for fun. Nature is fascinating!
www.youtube.com/watch?v=UfEf...
www.youtube.com/watch?v=UfEf...
How bacterial Tc toxins work: secretion, pore formation and host cell disruption.
YouTube video by Max Planck Institute of Molecular Physiology
www.youtube.com
January 16, 2026 at 10:22 PM
Great video (and voice over)! Missing sound effects though 😉
Quote with a movie that's 10/10?
Mitsuo Yanagimachi's "Who's Camus anyway?" (Kamyu nante shiranai)
doesn't even have a Wiki entry, but is as close to filmically perfect as anything
Mitsuo Yanagimachi's "Who's Camus anyway?" (Kamyu nante shiranai)
doesn't even have a Wiki entry, but is as close to filmically perfect as anything
January 16, 2026 at 7:22 PM
Quote with a movie that's 10/10?
Mitsuo Yanagimachi's "Who's Camus anyway?" (Kamyu nante shiranai)
doesn't even have a Wiki entry, but is as close to filmically perfect as anything
Mitsuo Yanagimachi's "Who's Camus anyway?" (Kamyu nante shiranai)
doesn't even have a Wiki entry, but is as close to filmically perfect as anything
Very much so, but for every kind of lysate!
Also start with most highly cited Abs (check citeab.com), more likely to work but if they don't at least you'll know which papers are affected...
Also start with most highly cited Abs (check citeab.com), more likely to work but if they don't at least you'll know which papers are affected...
Throwing this out there for those doing westerns on mouse embryo lysates: ALWAYS do a secondary only blot. No matter how "clean" your primary is, your secondary can (and will) cause problems - and Murphy's law ensures the crossreactivity will be the same size as your protein of interest 1/3 🧪 🤬
January 15, 2026 at 4:58 PM
Very much so, but for every kind of lysate!
Also start with most highly cited Abs (check citeab.com), more likely to work but if they don't at least you'll know which papers are affected...
Also start with most highly cited Abs (check citeab.com), more likely to work but if they don't at least you'll know which papers are affected...
The return of "water memory," ironically at one time a (partial) motivator of serious science...
"liquid water essentially loses the memory of persistent correlations in its structure within 50 fs."
"liquid water essentially loses the memory of persistent correlations in its structure within 50 fs."
January 11, 2026 at 8:51 PM
The return of "water memory," ironically at one time a (partial) motivator of serious science...
"liquid water essentially loses the memory of persistent correlations in its structure within 50 fs."
"liquid water essentially loses the memory of persistent correlations in its structure within 50 fs."
Reposted by Daniel Asarnow
NEW article by me!
We can now visualize pathogens down to atoms; design vaccines in weeks; manufacture them in microbial factories; engineer them more precise than ever before.
We're living through a golden age of vaccine development, but only if we continue to invest in them.
We can now visualize pathogens down to atoms; design vaccines in weeks; manufacture them in microbial factories; engineer them more precise than ever before.
We're living through a golden age of vaccine development, but only if we continue to invest in them.
The golden age of vaccine development - Works in Progress Magazine
The first vaccine was a lucky accident. Now we can design new vaccines in weeks, atom by atom.
worksinprogress.co
January 7, 2026 at 3:20 PM
NEW article by me!
We can now visualize pathogens down to atoms; design vaccines in weeks; manufacture them in microbial factories; engineer them more precise than ever before.
We're living through a golden age of vaccine development, but only if we continue to invest in them.
We can now visualize pathogens down to atoms; design vaccines in weeks; manufacture them in microbial factories; engineer them more precise than ever before.
We're living through a golden age of vaccine development, but only if we continue to invest in them.
My old Sherpa/Free Radical had been sitting around for a few years until my 2nd oldest friend and I tracked down possibly the last surviving kid-carrier hardware (thanks @xtracycle.bsky.social!) and now he's *safely* taking his kids everywhere with it 🤩
(1st oldest is his wife btw)
(1st oldest is his wife btw)
December 30, 2025 at 6:08 AM
My old Sherpa/Free Radical had been sitting around for a few years until my 2nd oldest friend and I tracked down possibly the last surviving kid-carrier hardware (thanks @xtracycle.bsky.social!) and now he's *safely* taking his kids everywhere with it 🤩
(1st oldest is his wife btw)
(1st oldest is his wife btw)
Reposted by Daniel Asarnow
I'm really excited to break up the holiday relaxation time with a new preprint that benchmarks AlphaFold3 (AF3)/“co-folding” methods with 2 new stringent performance tests.
Thread below - but first some links:
A longer take:
fraserlab.com/2025/12/29/k...
Preprint:
www.biorxiv.org/content/10.6...
Thread below - but first some links:
A longer take:
fraserlab.com/2025/12/29/k...
Preprint:
www.biorxiv.org/content/10.6...
Know when to co-fold'em
This is the official web page for the James Fraser Lab at UCSF.
fraserlab.com
December 29, 2025 at 10:25 PM
I'm really excited to break up the holiday relaxation time with a new preprint that benchmarks AlphaFold3 (AF3)/“co-folding” methods with 2 new stringent performance tests.
Thread below - but first some links:
A longer take:
fraserlab.com/2025/12/29/k...
Preprint:
www.biorxiv.org/content/10.6...
Thread below - but first some links:
A longer take:
fraserlab.com/2025/12/29/k...
Preprint:
www.biorxiv.org/content/10.6...
Sprained an ankle and broke my glasses, separate shows at 924 ❤️😈
December 28, 2025 at 3:26 AM
Sprained an ankle and broke my glasses, separate shows at 924 ❤️😈
Wildcat soap dispenser ("environmental powder") 🤔
December 19, 2025 at 4:26 AM
Wildcat soap dispenser ("environmental powder") 🤔
Reposted by Daniel Asarnow
Can't sleep, thinking about molecular puppetry again
December 11, 2025 at 7:22 AM
Can't sleep, thinking about molecular puppetry again
I could actually hear the sound garden today!
December 7, 2025 at 5:59 AM
I could actually hear the sound garden today!
Dans la plaine
naît un bruit.
C'est l'haleine
de la nuit.
Elle brame
comme une âme
qu'une flamme
toujours suit!
naît un bruit.
C'est l'haleine
de la nuit.
Elle brame
comme une âme
qu'une flamme
toujours suit!
Which lines of poetry live rent-free in your head?
December 7, 2025 at 5:41 AM
Dans la plaine
naît un bruit.
C'est l'haleine
de la nuit.
Elle brame
comme une âme
qu'une flamme
toujours suit!
naît un bruit.
C'est l'haleine
de la nuit.
Elle brame
comme une âme
qu'une flamme
toujours suit!
"so far as anything is wrong" 💀
November 30, 2025 at 6:59 AM
"so far as anything is wrong" 💀
What have we here?
November 28, 2025 at 6:53 AM
What have we here?
