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Calin Plesa

@calin.bsky.social
1.4K followers 941 following 193 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 · 05/08/2026
Cool preprint. Rather than engineering TdT around reversible terminators, they use the natural sugar specificity of an RNA polymerase to achieve terminator-free, template-free single-nucleotide addition. www.researchsquare.com/article/rs-9...
researchsquare.com
A 3′ terminal sugar-specific polymerase for terminator-free single-nucleotide extension of RNA oligonucleotides
Extant single-nucleotide extension (SNE) methods for oligonucleotide synthesis rely on terminator-modified substrates, which require complex nucleotide synthesis and induce side reactions that comprom...
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Calin Plesa @calin.bsky.social · 15/06/2026
Looking for a synthetic biology faculty position? Come talk to me at SEED 2026 about upcoming opportunities at @uoknightcampus.bsky.social #synbio #SEED
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Calin Plesa @calin.bsky.social · 02/06/2026
We just preprinted DropSynth-Gold where we replaced PCA with Golden Gate Assembly (GGA) inside emulsion droplets, extending multiplexed gene synthesis to ~3 kb constructs assembled from up to 12 fragments while preserving the scalability of DropSynth. 1/n
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Alison Tebo @agtebo.bsky.social · 17/02/2026
We’re excited to announce the next Fluorescent Proteins & Biological Sensors conference! Abstract submissions are now open—hope to see you there. www.janelia.org/you-janelia/...
janelia.org
Fluorescent Proteins and Biological Sensors VIII
Organizers Eric Schreiter, HHMI/Janelia Research Campus Alison Tebo, HHMI/Janelia Research Campus Invited Participants Xiaolu Cambronne, University of Texas at Austin Katharine Diehl, University of
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Addgene @addgene.bsky.social · 04/03/2026
Just released! Fluorescent Protein Libraries from the Plesa Lab. Benchmarking protein expression, developing imaging tools, fluorescent protein engineering, and more. www.addgene.org/pooled-libra...
addgene.org
Addgene: Fluorescent Protein Libraries
Use to benchmark protein expression, develop imaging tools, or to serve as a starting point for fluorescent protein engineering.
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Calin Plesa @calin.bsky.social · 03/03/2026
New lab preprint: if ML struggles with extrapolation, let's expand the diversity of training data with gene synth, DNA shuffling, and ML gen.... also lots of #FluorescentProteins #ProteinEngineering #MachineLearning #SyntheticBiology 1/n
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Calin Plesa @calin.bsky.social · 16/09/2025
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
duckfunder.uoregon.edu
iGEM 2025
Help University of Oregon raise $6,000 for the project: iGEM 2025. Your gift will make a difference!
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Calin Plesa @calin.bsky.social · 09/09/2025
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
Knight Campus buildings
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Cees Dekker @ceesdekker.bsky.social · 13/08/2025
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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Karl Romanowicz @kroman.bsky.social · 16/08/2025
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/...
science.org
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.
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Nozomu Yachie @nzmyachie.bsky.social · 20/06/2025
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 · 29/05/2025
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
Dr. Natanya Villegas PhD defense
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Calin Plesa @calin.bsky.social · 28/05/2025
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
Dr. Andrew Holston PhD defense
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The Knight Campus at the University of Oregon @uoknightcampus.bsky.social · 27/05/2025
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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The Knight Campus at the University of Oregon @uoknightcampus.bsky.social · 22/05/2025
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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Pascal Notin @pascalnotin.bsky.social · 08/05/2025
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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Max Fürst @maxfus.bsky.social · 07/05/2025
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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SynPlexity @synplexity.bsky.social · 26/03/2025
We unlock breakthrough insights by delivering the best training sets in biology—at unprecedented scale. youtu.be/KuCaJTPHM2o
youtu.be
Save 90% on DNA variant libraries today
YouTube video by IndieBio
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Carl de Boer @carldeboer.bsky.social · 26/03/2025
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/
de-boer-lab.github.io
CAGT: Cascadia Advanced Genomic Technologies
June 19-20 2025, Vancouver, BC, Canada
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Calin Plesa @calin.bsky.social · 28/01/2025
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 🧵
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Calin Plesa @calin.bsky.social · 22/12/2024
Great article. That last quote from Zhu sums it up: “The devil is in the details, and there are a lot of devils.”
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Calin Plesa @calin.bsky.social · 22/12/2024
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
media.tenor.com
a man in a black coat stands next to another man in a dark room with a green screen that says dr80
ALT: a man in a black coat stands next to another man in a dark room with a green screen that says dr80
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Michael Fischbach @mfgrp.bsky.social · 11/12/2024
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
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The Knight Campus at the University of Oregon @uoknightcampus.bsky.social · 03/12/2024
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
Calin Plesa in the laboratory
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Bryan Dickinson @chembiobryan.bsky.social · 25/11/2024
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
dickinsonlab.uchicago.edu
PPI Challenge 1 | dickinson-group
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Calin Plesa @calin.bsky.social · 25/11/2024
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...
PacBio instrument showing inside, with a green background light.PacBio instrument with a green light.Price table
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VIB Training & Conferences @vibtrainconf.bsky.social · 25/11/2024
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
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Patrick Phillips @patrickphillips.bsky.social · 25/11/2024
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
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Calin Plesa @calin.bsky.social · 23/11/2024
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.
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The Knight Campus at the University of Oregon @uoknightcampus.bsky.social · 20/11/2024
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
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Calin Plesa @calin.bsky.social · 19/11/2024
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.
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Patrick Kidger @patrickkidger.bsky.social · 13/11/2024
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 :)
nature.com
AIntibody: an experimentally validated in silico antibody discovery design challenge - Nature Biotechnology
Nature Biotechnology - AIntibody: an experimentally validated in silico antibody discovery design challenge
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Diego del Alamo @delalamo.xyz · 13/11/2024
Left: Experimentally validated PPIs Right: AF3-predicted PPIs Coevolution is all we've got Source: threadreaderapp.com/thread/18564...
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Calin Plesa @calin.bsky.social · 12/11/2024
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?
Microscope picture of emulsion droplets.
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 11/11/2024
I tried to make a bioml starter pack. DM if you want me to add or remove you? go.bsky.app/2VWBcCd
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Michael Hoffman @michaelhoffman.bsky.social · 11/11/2024
1/AlphaFold 3 code now available, following researcher criticism for not providing it with the initial publication. www.nature.com/articles/d41...
nature.com
AI protein-prediction tool AlphaFold3 is now open source
The code underlying the Nobel-prize-winning tool for modelling protein structures can now be downloaded by academics.
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Calin Plesa @calin.bsky.social · 12/11/2024
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
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Calin Plesa @calin.bsky.social · 12/12/2023
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...
biorxiv.org
Degenerate DropSynth for Simultaneous Assembly of Diverse Gene Libraries and Local Designed Mutants
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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Calin Plesa @calin.bsky.social · 05/09/2023
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
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