Neil Thomas

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Neil Thomas

Neil Thomas

@countablyfinite

Building AI for biological design @evoscaleai / @officialbiohub 🧬 Formerly: @Theteamatx 🌘 PhD @UCBerkeley 🙈

Act V, Scene II Katılım Kasım 2015
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Kevin K. Yang 楊凱筌
Kevin K. Yang 楊凱筌@KevinKaichuang·
We made FLIP2, a protein fitness benchmark spanning seven new datasets, including enzymes, protein-protein interactions, and light-sensitive proteins, as well as splits that measure generalization relevant to real-world protein engineering campaigns.
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chetan mishra
chetan mishra@chetanfs·
Rhizome AI is in the Y Combinator W26 batch! We help 18 organizations understand FDA expectations (and the EMA, MHRA, etc.) and it's just the beginning! Appreciate those who believed in us early and those who continue to champion us.
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Neil Thomas
Neil Thomas@countablyfinite·
Excited about AI for Biology? At NeurIPS? Come say hi to the Biohub (née EvolutionaryScale) folks in the exhibit hall! Keep me company: Tue 12-3 Wed 3-6 Or stop by any time for a chance to meet my incredible colleagues: @ebetica @proteinrosh @MariusWiggert @rsm_ai @awfderry
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Gabriel Rocklin
Gabriel Rocklin@grocklin·
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
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Yun S. Song
Yun S. Song@yun_s_song·
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics. biorxiv.org/content/10.110… (1/n)
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Clara Fannjiang
Clara Fannjiang@clara_fannjiang·
✨ new work with @jiwoncpark #icml2025! a zoo of algos exists for designing new proteins & molecules w/ AI🧬🧪how do you pick which one to use? our method selects design algos that will achieve user-specified, population-level success criteria w/ high-prob guarantees.👇
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The Align Foundation
The Align Foundation@Align_Bio·
1/4 🚀 Announcing the 2025 Protein Engineering Tournament. This year’s challenge: design PETase enzymes, which degrade the type of plastic in bottles. Can AI-guided protein design help solve the climate crisis? Let’s find out! ⬇️ #AIforBiology #ClimateTech #ProteinEngineering #OpenScience
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EvolutionaryScale
EvolutionaryScale@EvoscaleAI·
We're sponsoring the use of ESM3 and EMSC to help researchers engineer improved PETase enzymes in the @AlignBio 2025 Protein Engineering Tournament. Get started using ESMC to predict protein function and ESM3 to generate new enzymes here: github.com/evolutionarysc…
The Align Foundation@Align_Bio

1/4 🚀 Announcing the 2025 Protein Engineering Tournament. This year’s challenge: design PETase enzymes, which degrade the type of plastic in bottles. Can AI-guided protein design help solve the climate crisis? Let’s find out! ⬇️ #AIforBiology #ClimateTech #ProteinEngineering #OpenScience

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Yun S. Song
Yun S. Song@yun_s_song·
Thrilled to see my digital art on the cover of @TrendsGenetics! The two binary strings represent reverse-complementary DNA sequences (00=A, 01=C, 10=G, 11=T) and the connecting rectangles represent “embeddings” learned by DNA language models. Our article: doi.org/10.1016/j.tig.…
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Romero lab
Romero lab@romerolab1·
Happy Sunday to all! This morning, we are excited to share Chase’s work developing a simple, scalable method to assemble 100s-1000s of custom genes from oligo pools using standard lab tools! (Small 🧵 below)
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Kevin K. Yang 楊凱筌
Kevin K. Yang 楊凱筌@KevinKaichuang·
Gene synthesis is often the most expensive part of protein engineering with generative models. Happy to have played a small part in this work, where Chase developed a method for precision library construction at scale, with per-gene costs as low as $1.50. @romerolab1
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Romero lab@romerolab1

Happy Sunday to all! This morning, we are excited to share Chase’s work developing a simple, scalable method to assemble 100s-1000s of custom genes from oligo pools using standard lab tools! (Small 🧵 below)

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Gina El Nesr
Gina El Nesr@ginaelnesr·
Protein function often depends on protein dynamics. To design proteins that function like natural ones, how do we predict their dynamics? @HWaymentSteele and I are thrilled to share the first big, experimental datasets on protein dynamics and our new model: Dyna-1! 🧵
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Anthony Gitter
Anthony Gitter@anthonygitter·
"Engineering of highly active and diverse nuclease enzymes by combining machine learning and ultra-high-throughput screening" from @countablyfinite @LucyColwell37 and team looks amazing. They compare directed evolution, hit recombination, and ML-guided design of NucB.
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Keşfet

@alexgolding_ @ebetica @proteinrosh @MariusWiggert @rsm_ai @awfderry @Masa_Uehara_1 @hla_michael