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Calin Plesa

@calin.bsky.social

1.4K followers 930 following 170 posts

Assistant Prof. @uoknightcampus.bsky.social. Cofounder @synplexity.bsky.social. Gene synthesis, synbio, protein engineering, nanopores, multiplex assays. Opinions my own. www.plesalab.org

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Calin Plesa @calin.bsky.social · Jan 28

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 🧵

bioRxivpreprint @biorxivpreprint.bsky.social · Jan 25

Exploring Antibiotic Resistance in Diverse Homologs of the Dihydrofolate Reductase Protein Family through Broad Mutational Scanning https://www.biorxiv.org/content/10.1101/2025.01.23.634126v1

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Calin Plesa @calin.bsky.social · 23d

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

iGEM 2025

Help University of Oregon raise $6,000 for the project: iGEM 2025. Your gift will make a difference!

duckfunder.uoregon.edu

Calin Plesa @calin.bsky.social · 29d

The BioE dept in the Knight Campus is a great place to work and is unique in many ways! We are expanding over the next few years with our second building opening in 2026. Come join us, applications begin review on October 15. ...4/n

Calin Plesa @calin.bsky.social · 29d

Computational & Data-Science Neuroengineering: neural signal processing and analytics, closed-loop behavior tracking, neuromorphic computing and brain-inspired AI, spatial multi-omics analysis ...3/n

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Calin Plesa @calin.bsky.social · 29d

Experimental & Translational Neuroengineering: neural interfaces, neurophotonics for brain stimulation/recording/imaging, pre-clinical bioelectric medicine or brain injury repair models, brain organoid technology, disease models ...2/n

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Calin Plesa @calin.bsky.social · 29d

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

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Reposted by Calin Plesa

Cees Dekker @ceesdekker.bsky.social · Aug 13

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=👍

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Reposted by Calin Plesa

Karl Romanowicz @kroman.bsky.social · Aug 16

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/...

Exploring antibiotic resistance in diverse homologs of the dihydrofolate reductase protein family through broad mutational scanning

DropSynth technology enables scalable and cost-effective exploration of antibiotic resistance across the DHFR protein family.

www.science.org

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Reposted by Calin Plesa

Nozomu Yachie @nzmyachie.bsky.social · Jun 20

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☺️

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Calin Plesa @calin.bsky.social · May 29

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

Calin Plesa @calin.bsky.social · May 27

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

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Reposted by Calin Plesa

The Knight Campus at the University of Oregon @uoknightcampus.bsky.social · May 27

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. 🧬

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Reposted by Calin Plesa

The Knight Campus at the University of Oregon @uoknightcampus.bsky.social · May 22

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. 🧪

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Reposted by Calin Plesa

Pascal Notin @pascalnotin.bsky.social · May 8

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!

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Reposted by Calin Plesa

Max Fürst @maxfus.bsky.social · May 7

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 🧵

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Calin Plesa @calin.bsky.social · Mar 28

Added!

Reposted by Calin Plesa

SynPlexity @synplexity.bsky.social · Mar 26

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

Save 90% on DNA variant libraries today

YouTube video by IndieBio

youtu.be

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Reposted by Calin Plesa

Carl de Boer @carldeboer.bsky.social · Mar 26

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/

CAGT: Cascadia Advanced Genomic Technologies

June 19-20 2025, Vancouver, BC, Canada

de-boer-lab.github.io

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Calin Plesa @calin.bsky.social · Jan 28

We’d love to hear your comments and feedback! Disclosure: I’m a co-founder and equity holder in @synplexity.bsky.social, which is commercializing DropSynth to empower other researchers to perform similar studies at scale. 13/n

Calin Plesa @calin.bsky.social · Jan 28

Computational: There is a huge amount of data here and we have only started scratching the surface in its analysis. We’ve already started playing around with ML models for prediction and generation. 12/n

Calin Plesa @calin.bsky.social · Jan 28

Experimental: this study was only an initial pilot. We’re assembling a library 10x as large and with continuing improvements in NGS, the amount of functional data that can be collected will be incredible. 11/n

Calin Plesa @calin.bsky.social · Jan 28

There is a lot more discussed in the preprint, but I’ll wrap up with some thoughts about the future. 10/n
www.biorxiv.org/content/10.1...

Exploring Antibiotic Resistance in Diverse Homologs of the Dihydrofolate Reductase Protein Family through Broad Mutational Scanning

Current antibiotic resistance studies often focus on individual protein variants, neglecting broader protein family dynamics. Dihydrofolate reductase (DHFR), a key antibiotic target, has been extensiv...

www.biorxiv.org

Calin Plesa @calin.bsky.social · Jan 28

Zooming in: Each homolog typically has ~30 mutants. This granular view lets us see not just overall trends but also some of the individual mutations driving resistance or loss of function. 9/n

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Calin Plesa @calin.bsky.social · Jan 28

Next, we turned to Trimethoprim resistance. We examined how each homolog behaved across 6 concentrations, with only a few still surviving at the highest concentration tested. 8/n

Calin Plesa @calin.bsky.social · Jan 28

Patterns in gain-of-function mutants pointed to specific regions critical for restoring function. In DHFR many factors contribute to fitness: catalytic activity, expression level, folding, metabolic flux, coupling to thymidylate synthase, PPIs, … 7/n

Calin Plesa @calin.bsky.social · Jan 28

The silver lining: gain-of-function mutants. Many poorly complementing homologs gained function with minor changes. Including mutants up to 3 a.a. away increases the fraction of complementing homologs to 91%. 6/n