Jeff Nivala
@jeffnivala
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technomolecularfabulous. Assist. Professor at the University of Washington. @uwcse @UWMolES co-director @datamolecules
Seattle, WA
Joined November 2017
Announcing the Molecular Programming Decadal Flightplan! July 21–23 2025 | Seattle, WA We’re organizing a field-wide, community-driven conference to chart a 10-year strategic vision for molecular programming and we need you to help us lead it. Apply Now:
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great @naturemethods article: Is single-molecule protein sequencing here yet? spoiler alert: no. my more nuanced take: it depends.. https://t.co/tYaYldbcqe
nature.com
Nature Methods - As instruments and approaches emerge for single-molecule protein analysis, some developers and early users share their first impressions.
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Did we find Bigfoot? You’ll have to read the paper to find out..
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We searched for Bigfoot using CRISPR. DNA storage meets CRISPR search: AI maps the data, Cas9 slices it, nanopores read it. Multiplexed molecular search with semantic retrieval across a database of DNA-encoded images. Off-targets = a feature, not a bug.
nature.com
Nature Communications - CRISPR-Cas9 has potential as an efficient tool for information retrieval in DNA data storage. Here the authors present a Cas9-based random access and similarity search...
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Hybridization-encoded DNA tags with paper-based readout for anti-forgery raw material tracking | Nature Communications
nature.com
Nature Communications - Tracking raw materials is critical for securing global supply chains, but traditional tags lack in traceability and anticounterfeiting. The authors present a DNATag-based...
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What to agument your favourite protein with new functionalities? We've got a #biodesign workflow to help with that! In work led by Georgie Hau Sørensen we present SIMPLIFE that blends biophyscial and #ML models to extend biology in useful ways. #synbio
https://t.co/YvF3W9Wwbz
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Open to researchers at all levels, any country, across academia, industry, and government. If you self-identify as a molecular programmer and you’re excited about helping define the next decade of MP (challenges, breakthroughs, and community) we want you to join us!
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NSF program officers will be actively participating in the conference to engage with our discussions and help inform future priorities based on the community’s vision. Travel reimbursement available ($640/person).
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The Flightplan is an NSF-funded project structured around expert-led committees planning a comprehensive vision for accelerating molecular programming (from self-assembly and molecular circuits to medicine, materials, data storage, and novel massive collaborative structures)
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Do you work with recombinases?🛠️🧬In the latest from my lab, Veronica Greco shows how @nanopore sequencing paired with automated liquid handling provides the perfect platform for characterising these systems at scale! #synbio
https://t.co/xzrWPKpfpz
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Just a few months ago, the Baker and Garcia labs released con-concurrent preprints with incredible results. They designed de novo miniproteins that bound specific peptides presented in MHC-I. Now let me show how you can use BindCraft at @AriaxBio to do the same thing.
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Looking for a PhD ? I have a fully funded one for UK nationals on engineering gene circuits in probiotic microbes. Will bring together a lot of existing stands of #synbio research in my group and push towards some exciting applications! Start date will be Sept 2025. Pls RT
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Emerging protein sequencing technologies: proteomics without Mass spectrometry?: Expert Review of Proteomics:
tandfonline.com
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been a leading method for proteomics for 30 years. Advantages provided by LC-MS/MS are offset by significant disadvantages, including c...
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Had a great time on the @Agents_of_Tech podcast! Dreaming about 'data forests' of the future reminds me that biology is technology
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Genomics postdocs- deadline to submit to our April 15 symposium in Santa Cruz, CA, is NEXT SATURDAY (2/15)! Travel expenses covered for selected applicants ✈️😎🏖 Tag a colleague who is doing amazing research 🥼 Apply here: https://t.co/f1PzfZ4ORv
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Six new retrons just dropped! See how we isolated these cool bacterial immune systems from the wild in our latest preprint. From soil to sequence, we uncover the operons of these novel retrons and their phage defense properties. As a bonus, we repurpose them for genome editing 🧬
We just posted a new preprint where we found retrons in bacteria out in the real world, in dirt and water. We describe the first retrons in a handful of new species, show how they defend against phages, and use them to edit genomes. Read about it here: https://t.co/DiZmZOWCGs
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Oh dear.
New preprint claims that most existing DNA language models perform just as well with random weights, suggesting that pretraining does nothing (Mistral & DNABERT-2 look like exceptions). We need better DNA language models.
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This rate of validation suggests that antibodies should be considered non-specific until proven otherwise: 357 validated out of 1,124 tested. .
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We’re excited to announce our first speaker of London Calling 2025 @jeffnivala will share their groundbreaking ‘proof-of-concept' method showcasing the capability of #nanopore sequencing to read #polypeptide strands – a major step forward in protein analysis.
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We did gene therapies like this in our garage almost 10 years ago Tbh my Netflix special, Unnatural Selection, was better Also, the company in prospera is the same scam company in my Netflix special
Watched the @bryan_johnson documentary DONT DIE last night. Go give it a watch!!! The trip to Prospera for gene therapy is very eye-opening. What if the follistatin gene Tx Bryan takes increases muscle mass and is safe? Is that a trillion dollar product? It's crazy that
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