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...
- Reposted by Alex NakaPrima 2.2 companion device to restore vision for blindness caused by dry macular degeneration!! Created by @science.xyz !!!! Tera looks like a cartoon! Love it!!!!!! And optogenetics with ambient light by Amanda Tose and @gottapatchemall.bsky.social
- 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
- Reposted by Alex NakaE11 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
- Reposted by Alex NakaI LOVE their curtain test!!
- 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.
- Preprint here www.biorxiv.org/content/10.... Short thread below
- We used the K+ selective opsin WiChR as a starting point pmc.ncbi.nlm.nih.gov/articles/PM... WiChR is a strong, sensitive optogenetic silencer. We applied a mutation that breaks K+ selectivity, which converts it into an excitatory channel. We call this mutant WAChR (pronounced "watcher").
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View full threadTremendous effort by some very talented people: Amanda Tose, Alberto Nava, Sara McGrath, and @mardinly, among many others This lowercase science is brought to you by uppercase Science science.xyz/news/new-fr...
- Reposted by Alex NakaHappy 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!
- Reposted by Alex Nakamac 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 NakaAlexandra Buckle, contemporary printmaker known for her woodland scenes created via linocuts #WomensArt
- Reposted by Alex Nakanot 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
- 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...
- Reposted by Alex NakaIt’s easy to overfit if you try. How does machine learning practice get around it?
- 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.
- Reposted by Alex NakaTermination 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.
- 😭😭😭😭😭
- this is cool Rational multienzyme architecture design with iMARS
- Reposted by Alex NakaSomatostatin 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
- we're hiring a neuroscientist - looking for people with in vivo rodent physiology experience science.xyz/careers/neur...
- Reposted by Alex NakaBluetorial: 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.
- Reposted by Alex NakaPredicting 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-...
- Reposted by Alex NakaWe've now got a project page for our NeurIPS paper "Cost-aware Bayesian Optimization via the Pandora's Box Gittins Index" - link below! This paper proposes a cost-aware acquisition function design principle for Bayesian optimization. Check it out! papers.avt.im/pandoras-box...
- 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
- Reposted by Alex NakaNew blog post (and uh, new blog!) If you use observation-level random effects (e.g., for over-dispersed counts), your predictive checks are probably wrong. Here's how to do it the right way in both #brms and #PyMC. tl;dr: you need to sample new levels of the OLRE to avoid a false goodness-of-fit
- 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
- Reposted by Alex NakaNew blogpost: The ABCs of Alphafold 3, Boltz and Chai-1 blog.booleanbiotech.com/alphafold3-b...
- Reposted by Alex NakaWe’re excited to release a major update to the Boltz repo: v0.3.0. This release contains several important new features, including our confidence model and memory-efficient inference. Give it a try! github.com/jwohlwend/bo...
- Reposted by Alex NakaBacteriorhodopsin is a membrane-bound light-driven proton pump. Using neural networks, it's possible to redesign it so that it's soluble but retains its photocycle! @ivangushchin.bsky.social www.biorxiv.org/content/10.1...
- Reposted by Alex Naka[This post could not be retrieved]
- A muddy fall hike with Lily and puppy QWERTY From Nov 2022
- Reposted by Alex NakaYet more evidence that transfer learning of sequence-only PLMs does not benefit from scale beyond 650M params 🧵
- Reposted by Alex NakaI think many people really underestimate how likely a new pandemic is to occur in the next four years. Even if you think of a pandemic as a once-in-a-century event, that's a 4% chance over the next four years. And I think in the world we live in a pandemic is far from a once-in-100 years event. 🧪
- Reposted by Alex NakaOut yesterday in Neuron, the final print version of our paper on voltage imaging with ASAP5, "A fast and responsive voltage indicator with enhanced sensitivity for unitary synaptic events" www.cell.com/neuron/fullt...
- Reposted by Alex Nakaso excited to finally announce this to the world! what’s a probe that can get anywhere in the brain, without destroying any tissue in the way, wiring up to existing structure to extract and inject information? sounds like a neuron :) #neuroscience #bci 🧪👩🔬🧠
- I 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...
- 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...
- Reposted by Alex NakaTwo BioML starter packs now: Pack 1: go.bsky.app/2VWBcCd Pack 2: go.bsky.app/Bw84Hmc DM if you want to be included (or nominate people who should be!)
- I tried to make a bioml starter pack. DM if you want me to add or remove you? go.bsky.app/2VWBcCd
- Reposted by Alex Nakadear cornell I AM HERE see you tomorrow
- Reposted by Alex NakaHello numerous people who joined and followed! I want to hear your neuroscience takes, but not the same old debates. There's so much we can discuss that's truly new. Here I'll start: -The brain: too big, or not big enough -Most overrated region of cortex -manifolds: isn't just one fold sufficient
- Reposted by Alex NakaPack 2 is now up to 90/150. Get in while I can still keep up!
- Two BioML starter packs now: Pack 1: go.bsky.app/2VWBcCd Pack 2: go.bsky.app/Bw84Hmc DM if you want to be included (or nominate people who should be!)
- 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...
- Reposted by Alex NakaThis is clever. Because uv supports explicit indexes you can in fact switch pytorch versions based on environment markers. docs.astral.sh/uv/guides/in...
- 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
- unless i'm misunderstanding there are n=2 people in their series B bin
- 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
- Reposted by Alex NakaInterPLM: Discovering Interpretable Features in Protein Language Models via Sparse Autoencoders www.biorxiv.org/cont... --- #proteomics #prot-preprint
- Reposted by Alex NakaReposting because of the great influx of people here. Long story short: like inhibitory DREADDs but with light and switchable.
- Reposted by Alex NakaLooking for a tag to localise fluorescent proteins to the plasma membrane? Unsure which tag might work in your species? We generated a toolkit of 11 membrane-localising tags, which can be screened rapidly by microinjecting mRNA in your species of interest. 1/4 www.biorxiv.org/content/10.1...
- wow this directory of starter packs is very helpful blueskydirectory.com/starter-pack...
