This year's UO iGEM team is building a histamine-responsive probiotic to help tame mast cell flares in MCAD. Help us get more students to the iGEM Jamboree in Paris this October (gifts via UO Foundation may be tax-deductible): duckfunder.uoregon.edu/project/46947

Our BioE dept at @uoknightcampus.bsky.social has an open rank search for two complementary tenure-track faculty positions in Neuroengineering focused on: 1) Experimental & Translational Neuroengineering and 2) Computational & Data-Science Neuroengineering. careers.uoregon.edu/en-us/job/53... ...1/n

WORK! I currently have 5 (!) open positions for postdocs/PhD students in our CDlab for projects: - Nanopore protein sequencing - Archaeal CDV cell division - Microfluidics for synthetic cells - Nuclear Pore Complex - Origami mimics of peroxisomes Please apply! ceesdekkerlab.nl/come-join-us/ RT=👍

Our new Science Advances paper is out! 🎉 The Plesa Lab's first, it builds on DropSynth technology as a proof of concept for large-scale synthetic gene libraries, showcasing a synthetic metagenomics approach to studying antibiotic resistance at scale. 👉 www.science.org/doi/10.1126/...

CAGT was fun! Thanks @carldeboer.bsky.social @sudpinglay.bsky.social and the de Boer lab for organizing! Folks from Seattle, Oregon, and other places. Great community. Arman gave a usual super talk, and Sanchit and Dayag won poster prizes☺️

Amazing PhD defense by Dr. Natanya Villegas! She pioneered CRISPR-Cas9 and RNA work in our lab and drove multiple tech-dev projects. She is looking for opportunities in the PNW so reach out -> @trienetoscience.bsky.social

Huge congrats to Dr. Andrew Holston on a successful PhD defense!! Andrew has been working on the large-scale characterization and engineering of chimeric receptor histidine kinases. He’s looking for roles in biotech/academia, let’s connect if you’re hiring! -> @hkalltheway.bsky.social

Join us today, May 27, for @trienetoscience.bsky.social's PhD thesis defense. Natanya is a graduate student in @calin.bsky.social's lab, where her research has focused on innovations in programmable nucleic acid libraries and CRISPR enrichment for molecular biology applications. 🧬

Join us tomorrow, May 23, for Andrew Holston’s PhD thesis defense. Andrew is a graduate student in @calin.bsky.social’s lab, where his research has focused on the large-scale engineering of chimeric histidine kinases. 🧪

Have we hit a "scaling wall" for protein language models? 🤔 Our latest ProteinGym v1.3 release suggests that for zero-shot fitness prediction, simply making pLMs bigger isn't better beyond 1-4B parameters. The winning strategy? Combining MSAs & structure in multimodal models!

Preprint from the lab🚨 Have you ever engineered proteins to be more stable and were unhappy about your predictor's success rate? We got you covered with BoostMut! Great work led by @kerlenkorbeld.bsky.social now online at www.biorxiv.org/content/10.1... A thread 🧵

We unlock breakthrough insights by delivering the best training sets in biology—at unprecedented scale. youtu.be/KuCaJTPHM2o

Join us June 19-20, 2025 in Vancouver BC for the Cascadia Advanced Genomic Technologies meeting! Featuring Keynote speaker Calin Plesa @calin.bsky.social Abstract deadline April 30🔔, but registration is capped so don't wait! 😱 de-boer-lab.github.io/CAGT_meeting/

New preprint! We carried out the largest complementation and inhibition study for diverse homologs in a single protein family (DHFR) to date. Highlights thread follows... 1/n 🧵

Great article. That last quote from Zhu sums it up: “The devil is in the details, and there are a lot of devils.”

Let's talk about how close we are to a cell-free mirror image central dogma in a tube, aka Mirror-PURE! This topic has been getting a lot of attention due to the recent @science.org letter (www.science.org/doi/10.1126/...) outlining the threats posed by mirror life. 1/n

Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent antibody response against a pathogen. Could lead to topical vaccines that are applied in a cream. @djenetbousbaine.bsky.social led the charge... @natureportfolio.bsky.social 1/55

Congrats to Knight Campus assistant professor @calin.bsky.social on his grant from the MJ Murdock Charitable Trust through its Commercialization Initiation Program! The award includes matching funds from the #KnightCampus and @universityoforegon.bsky.social Research: bit.ly/49hs1LI

An update on our engineered PPI prediction challenge originally posted on the other platform... www.dickinsonlab.uchicago.edu/ppi-challenge We got many submissions. Interestingly, most approaches were able to get ~25% accurate (meaning the #1 predicted interaction was the real one) 1/n

Need long-read sequencing? We just completed the first ever run on @uoregon.bsky.social GC3F core’s new @pacbio.bsky.social Revio instrument! Perfect for amplicons too long for Illumina, and with Kinnex, you can get >10x more data. Great pricing, no queue, try it: gc3f.uoregon.edu/pacbio-seque...

There are just 2️⃣ days until the registration deadline for #NGSB24, the upcoming #synbio conference featuring 29 top researchers from academia & industry. Don't miss out & join your (future) colleagues here: vibbio.tech/3OlPFND 🎤Keynotes: Petra Schwille, @calin.bsky.social, Chris Barnes & Tobias Erb

Starter pack for researchers at the University of Oregon. I was expecting a bunch more, to be frank. People might not be listing their affiliations, so please do let me know if you would like to be added. go.bsky.app/HNkp5Uq

On to Part 2 of the Synthetic Biology (SynBio) starter pack. Part 1: bsky.app/starter-pack... Part 2: bsky.app/starter-pack... Reply or DM to add/nominate.

As part of a multi-year hiring plan for up to 16 positions, the @uoregon.bsky.social #KnightCampus Dept. of BioE is hiring 3 tenure-track faculty members. Now Seeking experts in Biomedical Data Science, Synthetic Biology, Neural Engineering & Immune Engineering: bit.ly/4935cLS

Every day a new foundation model drops, and as an experimentalist, I just skim the preprint and go back to my pipettes. Foundation model fatigue. The bar for adoption is high and requires experimental validation.

We have an AI-designed antibodies challenge! 🔥 Nature: www.nature.com/articles/s41... Website: www.aintibody.org (Co-authored with approximately everyone, haha. 🌟) The challenge is primarily around CDR design, with the submitted sequences tested in vitro. 🧪 Come give it a go :)

Left: Experimentally validated PPIs Right: AF3-predicted PPIs Coevolution is all we've got Source: threadreaderapp.com/thread/18564...

3M is discontinuing manufacturing of both Novec HFE-7500 and Fluorinert FC-40 in the next few months. These are the major diluents currently used in most emulsion fluorous oils (combined with fluorinated surfactants). Has anyone been looking for or testing alternatives?

I tried to make a bioml starter pack. DM if you want me to add or remove you? go.bsky.app/2VWBcCd

1/AlphaFold 3 code now available, following researcher criticism for not providing it with the initial publication. www.nature.com/articles/d41...

Started creating a synthetic biology starter pack. Still missing many so reply here if I forgot you or someone else. go.bsky.app/SjfpxTK #synbio

Story time! Introducing the first of several new flavors of DropSynth gene synthesis we have been working on, cooked up by @hkalltheway.bsky.social and Sam Hinton. TLDR: We show multiple gene variants assembled per barcoded droplet and 1 kbp lengths. 1/n www.biorxiv.org/content/10.1...

We (UOregon Knight Campus) are hiring 1-2 tenure track faculty positions at any level. Focus is on data-enabled approaches to improve human health with applications in regenerative medicine, immunoengineering, synthetic biology, biosensors, human performance, or aging. Deadline is October 16. 1/2