Calin Plesa
@calin.bsky.social
Assistant Prof. @uoknightcampus.bsky.social. Cofounder @synplexity.bsky.social. Gene synthesis, synbio, protein engineering, nanopores, multiplex assays. Opinions my own. www.plesalab.org
Pinned
Calin Plesa
@calin.bsky.social
· Jan 28
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
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 🧵
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
September 16, 2025 at 1:34 AM
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
careers.uoregon.edu/en-us/job/53... ...1/n
September 9, 2025 at 5:32 PM
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
careers.uoregon.edu/en-us/job/53... ...1/n
Reposted by Calin Plesa
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=👍
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=👍
August 13, 2025 at 1:30 PM
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=👍
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=👍
Reposted by Calin Plesa
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
August 16, 2025 at 6:30 AM
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/...
Reposted by Calin Plesa
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☺️
June 20, 2025 at 10:17 PM
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
May 29, 2025 at 5:36 PM
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
May 27, 2025 at 11:32 PM
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
Reposted by Calin Plesa
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. 🧬
May 27, 2025 at 4:39 PM
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. 🧬
Reposted by Calin Plesa
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. 🧪
May 22, 2025 at 10:37 PM
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. 🧪
Reposted by Calin Plesa
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!
May 8, 2025 at 12:29 AM
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!
Reposted by Calin Plesa
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 🧵
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 🧵
May 7, 2025 at 5:04 PM
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 🧵
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 🧵
Reposted by Calin Plesa
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
March 26, 2025 at 9:48 PM
We unlock breakthrough insights by delivering the best training sets in biology—at unprecedented scale. youtu.be/KuCaJTPHM2o
Reposted by Calin Plesa
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_meeting/
CAGT: Cascadia Advanced Genomic Technologies
June 19-20 2025, Vancouver, BC, Canada
de-boer-lab.github.io
March 26, 2025 at 4:47 PM
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_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 🧵
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
January 28, 2025 at 1:27 AM
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.”
Good thread. I recently wrote an overview of Zhu's work here. A "cell-free central dogma" is a nice way of putting it for how close we are to the basic components. And that's still a HUGE way off anything genuinely lifelike.
nautil.us/mirror-image...
nautil.us/mirror-image...
December 22, 2024 at 10:00 PM
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
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
media.tenor.com
December 22, 2024 at 7:24 PM
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
Reposted by Calin Plesa
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
December 11, 2024 at 4:29 PM
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
Reposted by Calin Plesa
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
December 3, 2024 at 12:54 AM
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
Reposted by Calin Plesa
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
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
PPI Challenge 1 | dickinson-group
www.dickinsonlab.uchicago.edu
November 25, 2024 at 4:03 PM
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
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...
@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...
November 25, 2024 at 2:53 PM
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.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...
Reposted by Calin Plesa
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
🎤Keynotes: Petra Schwille, @calin.bsky.social, Chris Barnes & Tobias Erb
November 25, 2024 at 9:19 AM
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
🎤Keynotes: Petra Schwille, @calin.bsky.social, Chris Barnes & Tobias Erb
Reposted by Calin Plesa
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
November 25, 2024 at 2:36 AM
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.
Part 1: bsky.app/starter-pack...
Part 2: bsky.app/starter-pack...
Reply or DM to add/nominate.
November 23, 2024 at 4:31 PM
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.
Part 1: bsky.app/starter-pack...
Part 2: bsky.app/starter-pack...
Reply or DM to add/nominate.
Reposted by Calin Plesa
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
November 20, 2024 at 11:33 PM
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.
November 19, 2024 at 5:31 PM
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.