Alex Naka
@gottapatchemall.bsky.social
ML & protein engineering at http://science.xyz | into papers, pens, plots, puppies, proteins
algorithmic.ink
https://x.com/gottapatchemall
algorithmic.ink
https://x.com/gottapatchemall
it's been seriously inspiring to watch the progress on this, E11 is kicking ass
E11 Bio is excited to unveil PRISM technology for mapping brain wiring with simple light microscopes. Today, brain mapping in humans and other mammals is bottlenecked by accurate neuron tracing. PRISM uses molecular ID codes and AI to help neurons trace themselves.
Read more: e11.bio/blog/prism
Read more: e11.bio/blog/prism
October 1, 2025 at 5:23 PM
it's been seriously inspiring to watch the progress on this, E11 is kicking ass
Reposted by Alex Naka
E11 Bio is excited to unveil PRISM technology for mapping brain wiring with simple light microscopes. Today, brain mapping in humans and other mammals is bottlenecked by accurate neuron tracing. PRISM uses molecular ID codes and AI to help neurons trace themselves.
Read more: e11.bio/blog/prism
Read more: e11.bio/blog/prism
October 1, 2025 at 2:16 PM
E11 Bio is excited to unveil PRISM technology for mapping brain wiring with simple light microscopes. Today, brain mapping in humans and other mammals is bottlenecked by accurate neuron tracing. PRISM uses molecular ID codes and AI to help neurons trace themselves.
Read more: e11.bio/blog/prism
Read more: e11.bio/blog/prism
Reposted by Alex Naka
I LOVE their curtain test!!
September 18, 2025 at 3:53 AM
I LOVE their curtain test!!
Reposted by Alex Naka
Really cool stuff! Engineered excitatory opsins responding to 15nW light
WAChRs are excitatory opsins sensitive to indoor lighting www.biorxiv.org/content/10.1...
September 18, 2025 at 4:23 AM
Really cool stuff! Engineered excitatory opsins responding to 15nW light
My group at Science has been running a big campaign to engineer new channelrhodopsins.
Excited to share the first results from it today: a suite of highly sensitive new opsins.
We call them "WAChRs".
Everyday indoor office lighting is enough to activate them pretty strongly.
Excited to share the first results from it today: a suite of highly sensitive new opsins.
We call them "WAChRs".
Everyday indoor office lighting is enough to activate them pretty strongly.
September 18, 2025 at 2:06 PM
My group at Science has been running a big campaign to engineer new channelrhodopsins.
Excited to share the first results from it today: a suite of highly sensitive new opsins.
We call them "WAChRs".
Everyday indoor office lighting is enough to activate them pretty strongly.
Excited to share the first results from it today: a suite of highly sensitive new opsins.
We call them "WAChRs".
Everyday indoor office lighting is enough to activate them pretty strongly.
Reposted by Alex Naka
Happy to share our new preprint on the red-shifted channelrhodopsin ChR024, recently discovered by Inoue Lab (biorxiv.org/content/10.1...
), highlighting its long-wavelength absorption and ion conductance:
biorxiv.org/content/10.1...
Many thanks to our wonderful lab members and collaborators!
), highlighting its long-wavelength absorption and ion conductance:
biorxiv.org/content/10.1...
Many thanks to our wonderful lab members and collaborators!
September 18, 2025 at 3:28 AM
Happy to share our new preprint on the red-shifted channelrhodopsin ChR024, recently discovered by Inoue Lab (biorxiv.org/content/10.1...
), highlighting its long-wavelength absorption and ion conductance:
biorxiv.org/content/10.1...
Many thanks to our wonderful lab members and collaborators!
), highlighting its long-wavelength absorption and ion conductance:
biorxiv.org/content/10.1...
Many thanks to our wonderful lab members and collaborators!
Reposted by Alex Naka
mac is here on this #makeaterriblecomicday2025 to school you all in THREAT MANAGEMENT SYSTEMS do not get caught off guard or Who Knows What Might Happen
June 24, 2025 at 2:41 PM
mac is here on this #makeaterriblecomicday2025 to school you all in THREAT MANAGEMENT SYSTEMS do not get caught off guard or Who Knows What Might Happen
Reposted by Alex Naka
Alexandra Buckle, contemporary printmaker known for her woodland scenes created via linocuts #WomensArt
May 25, 2025 at 5:11 AM
Alexandra Buckle, contemporary printmaker known for her woodland scenes created via linocuts #WomensArt
Reposted by Alex Naka
not sure how i can be expected to focus on anything else today now that i've seen the promo photo from the Madden movie with Christian Bale as Al Davis and Nicolas Cage as John Madden
May 14, 2025 at 5:33 PM
not sure how i can be expected to focus on anything else today now that i've seen the promo photo from the Madden movie with Christian Bale as Al Davis and Nicolas Cage as John Madden
Snake venom protection by a cocktail of varespladib and broadly neutralizing human antibodies
www.cell.com/cell/fulltex...
broad spectrum antivenom
www.cell.com/cell/fulltex...
broad spectrum antivenom
May 2, 2025 at 3:34 PM
Snake venom protection by a cocktail of varespladib and broadly neutralizing human antibodies
www.cell.com/cell/fulltex...
broad spectrum antivenom
www.cell.com/cell/fulltex...
broad spectrum antivenom
ATLAS: a rationally designed anterograde transsynaptic tracer
www.nature.com/articles/s41...
very cool
www.nature.com/articles/s41...
very cool
May 1, 2025 at 5:42 PM
ATLAS: a rationally designed anterograde transsynaptic tracer
www.nature.com/articles/s41...
very cool
www.nature.com/articles/s41...
very cool
Connectomics of predicted Sst transcriptomic types in mouse visual cortex
www.nature.com/articles/s41...
🥰🥰🥰
www.nature.com/articles/s41...
🥰🥰🥰
Connectomics of predicted Sst transcriptomic types in mouse visual cortex - Nature
The authors use Patch-seq and electron microscopy datasets to relate synaptic connectivity to the transcriptomic cell type of different types of inhibitory neuron.
www.nature.com
April 18, 2025 at 3:58 AM
Connectomics of predicted Sst transcriptomic types in mouse visual cortex
www.nature.com/articles/s41...
🥰🥰🥰
www.nature.com/articles/s41...
🥰🥰🥰
Reposted by Alex Naka
Run BioEmu in Colab - just click "Runtime → Run all"! Our notebook uses ColabFold to generate MSAs, BioEmu to predict trajectories, and Foldseek to cluster conformations.
Thanks @jjimenezluna.bsky.social for the help!
🌐 colab.research.google.com/github/sokry...
📄 www.biorxiv.org/content/10.1...
Thanks @jjimenezluna.bsky.social for the help!
🌐 colab.research.google.com/github/sokry...
📄 www.biorxiv.org/content/10.1...
Google Colab
colab.research.google.com
March 29, 2025 at 9:50 AM
Run BioEmu in Colab - just click "Runtime → Run all"! Our notebook uses ColabFold to generate MSAs, BioEmu to predict trajectories, and Foldseek to cluster conformations.
Thanks @jjimenezluna.bsky.social for the help!
🌐 colab.research.google.com/github/sokry...
📄 www.biorxiv.org/content/10.1...
Thanks @jjimenezluna.bsky.social for the help!
🌐 colab.research.google.com/github/sokry...
📄 www.biorxiv.org/content/10.1...
complete and total vindication
March 14, 2025 at 6:55 PM
complete and total vindication
Reposted by Alex Naka
PREPRINT OUT ✨ "hack" your microscope to work as a 3D printer! print micrometer sized features at cm scale. a method for easy and cheap microfabrication, with a focus on biological applications. THREAD ↓
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
February 23, 2025 at 2:06 PM
PREPRINT OUT ✨ "hack" your microscope to work as a 3D printer! print micrometer sized features at cm scale. a method for easy and cheap microfabrication, with a focus on biological applications. THREAD ↓
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Alex Naka
It’s easy to overfit if you try. How does machine learning practice get around it?
The Adaptivity Paradox
Test-set reuse: the problem that wasn't.
www.argmin.net
February 18, 2025 at 3:30 PM
It’s easy to overfit if you try. How does machine learning practice get around it?
Reposted by Alex Naka
What these nihilistic vandals are doing to dismantle science & medicine—generations of expertise & public service & life improving benefits—is cultural revolution level national self harm. No foreign foe could inflict such brutal damage & senseless suffering on US so fast & effectively & unresisted.
February 15, 2025 at 4:10 AM
What these nihilistic vandals are doing to dismantle science & medicine—generations of expertise & public service & life improving benefits—is cultural revolution level national self harm. No foreign foe could inflict such brutal damage & senseless suffering on US so fast & effectively & unresisted.
Reposted by Alex Naka
Termination notices going out this afternoon to more than 300 employees of the National Cancer Institute. Access likely ends today. Four weeks paid leave and that’s it.
Strong power move for Team Cancer.
Strong power move for Team Cancer.
February 14, 2025 at 7:01 PM
Termination notices going out this afternoon to more than 300 employees of the National Cancer Institute. Access likely ends today. Four weeks paid leave and that’s it.
Strong power move for Team Cancer.
Strong power move for Team Cancer.
this is cool
Rational multienzyme architecture design with iMARS
Rational multienzyme architecture design with iMARS
January 23, 2025 at 5:18 PM
this is cool
Rational multienzyme architecture design with iMARS
Rational multienzyme architecture design with iMARS
Reposted by Alex Naka
Somatostatin interneurons have been an obsession of mine during my postdoc with Bernardo Rudy. They have diverse morphological, molecular and connectivity features. Here: a Martinotti with axon going all the way up, and a non-Martinotti whose axon targets layer 4.
#neuroskyence
#neuroskyence
January 17, 2025 at 2:50 PM
Somatostatin interneurons have been an obsession of mine during my postdoc with Bernardo Rudy. They have diverse morphological, molecular and connectivity features. Here: a Martinotti with axon going all the way up, and a non-Martinotti whose axon targets layer 4.
#neuroskyence
#neuroskyence
we're hiring a neuroscientist - looking for people with in vivo rodent physiology experience
science.xyz/careers/neur...
science.xyz/careers/neur...
Neuroscientist | Science Corporation
Science Corporation is a clinical-stage medical technology company.
science.xyz
December 19, 2024 at 6:06 PM
we're hiring a neuroscientist - looking for people with in vivo rodent physiology experience
science.xyz/careers/neur...
science.xyz/careers/neur...
Reposted by Alex Naka
Bluetorial: Mentors III: The textbook author
I worked in Lubert Stryer's laboratory as a freshman in college. This experience and my relationship with Lubert would change my life.
I worked in Lubert Stryer's laboratory as a freshman in college. This experience and my relationship with Lubert would change my life.
a cartoon says hey everybody an old man 's talking while bart simpson looks on
ALT: a cartoon says hey everybody an old man 's talking while bart simpson looks on
media.tenor.com
December 16, 2024 at 9:13 PM
Bluetorial: Mentors III: The textbook author
I worked in Lubert Stryer's laboratory as a freshman in college. This experience and my relationship with Lubert would change my life.
I worked in Lubert Stryer's laboratory as a freshman in college. This experience and my relationship with Lubert would change my life.
Reposted by Alex Naka
Predicting absolute protein folding stability using generative models
@mcagiada.bsky.social @sokrypton.org & I used ESM-IF to predict ∆G for folding & conformational change
Paper, code and colab
📜 dx.doi.org/10.1002/pro....
💾 github.com/KULL-Centre/...
👩💻 colab.research.google.com/github/KULL-...
@mcagiada.bsky.social @sokrypton.org & I used ESM-IF to predict ∆G for folding & conformational change
Paper, code and colab
📜 dx.doi.org/10.1002/pro....
💾 github.com/KULL-Centre/...
👩💻 colab.research.google.com/github/KULL-...
December 14, 2024 at 2:58 PM
Predicting absolute protein folding stability using generative models
@mcagiada.bsky.social @sokrypton.org & I used ESM-IF to predict ∆G for folding & conformational change
Paper, code and colab
📜 dx.doi.org/10.1002/pro....
💾 github.com/KULL-Centre/...
👩💻 colab.research.google.com/github/KULL-...
@mcagiada.bsky.social @sokrypton.org & I used ESM-IF to predict ∆G for folding & conformational change
Paper, code and colab
📜 dx.doi.org/10.1002/pro....
💾 github.com/KULL-Centre/...
👩💻 colab.research.google.com/github/KULL-...