Alex Naka
ML & protein engineering at http://science.xyz | into papers, pens, plots, puppies, proteins
algorithmic.ink
x.com/gottapatchemall
- we're hiring! looking for a systems neuroscientist with extracellular ephys experience please share! link below, feel free to DM with questions
- Reposted by Alex NakaJust published my review of neuroscience in 2025, on The Spike. The 10th of these, would you believe? This year we have foundation models, breakthroughs in using light to understand the brain, a gene therapy, and more Enjoy! medium.com/the-spike/20...
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- it's been seriously inspiring to watch the progress on this, E11 is kicking ass
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- Reposted by Alex NakaReally cool stuff! Engineered excitatory opsins responding to 15nW light
- WAChRs are excitatory opsins sensitive to indoor lighting www.biorxiv.org/content/10.1...
- 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.
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- Snake venom protection by a cocktail of varespladib and broadly neutralizing human antibodies www.cell.com/cell/fulltex... broad spectrum antivenom
- ATLAS: a rationally designed anterograde transsynaptic tracer www.nature.com/articles/s41... very cool
- Connectomics of predicted Sst transcriptomic types in mouse visual cortex www.nature.com/articles/s41... 🥰🥰🥰
- Reposted by Alex NakaRun 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...
- complete and total vindication
- Reposted by Alex NakaPREPRINT 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...
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- Reposted by Alex NakaWhat 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.
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- 😭😭😭😭😭
- this is cool Rational multienzyme architecture design with iMARS
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- we're hiring a neuroscientist - looking for people with in vivo rodent physiology experience science.xyz/careers/neur...
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- Reposted by Alex Naka🧪 E11 Bio is excited to share a major step towards brain mapping at 100x lower cost, making whole-brain connectomics at human & mouse scale feasible (🧠→🔬→💻). Critical for curing brain disorders, building human-like AI systems, and even simulating human brains. Read more: e11.bio/news/roadmap
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- Reposted by Alex NakaThree BioML starter packs now! Pack 1: go.bsky.app/2VWBcCd Pack 2: go.bsky.app/Bw84Hmc Pack 3: go.bsky.app/NAKYUok DM if you want to be included (or nominate people who should be!)at://did:plc:vcfu4zw4mstjnpvqb7yqby32/app.bsky.graph.starterpack/3lapi2tgwmz2y
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- A muddy fall hike with Lily and puppy QWERTY From Nov 2022
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- Reposted by Alex NakaI had an idea way back in college which I've long thought could be, in many ways, the ultimate BCI technology. What if instead of using electrodes, we used biological neurons embedded in electronics to communicate with the brain? Enter biohybrid neural interfaces: science.xyz/news/biohybr...
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- Reposted by Alex Naka🌟 Cai Lab Nature (@natureportfolio.bsky.social) paper alert! In work led by Joe Zaki, we find that rest periods after learning not only stabilize new memories BUT ALSO integrate new memories with older ones from days past! (1/10) Read it here: www.nature.com/articles/s41...
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- from may 2021
- Age-Normalized Testosterone Peaks at Series B for Male Startup Founders www.biorxiv.org/content/10.1... what's going on here
- Another old plot, from november 2020
- Reposted by Alex NakaThrilled to announce Boltz-1, the first open-source and commercially available model to achieve AlphaFold3-level accuracy on biomolecular structure prediction! An exciting collaboration with Jeremy, Saro, and an amazing team at MIT and Genesis Therapeutics. A thread!
- Reposted by Alex NakaNew GPU-based MMseqs2: 20x faster searches on a single L40S (approx. as fast as a RTX 4090) vs. a 128-core CPU. This work enables to set up a very cost-efficient ColabFold MSA GPU server. 🧵🧵 📄 www.biorxiv.org/content/10.1... 💾 mmseqs.com 🗞️ developer.nvidia.com/blog/boost-a...
- time to revisit some of my older pen plotter work - this is from #genuary 2021 I believe
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- wow this directory of starter packs is very helpful blueskydirectory.com/starter-pack...
