Sean Johnson
@trichomedoctor.bsky.social
Protein ML. Synbio. Enzyme discovery and engineering. Glandular trichomes. Proud Washington State alum.
Reposted by Sean Johnson
Reposted by Sean Johnson
⭐ NAR Breakthrough! ⭐
🔬 New study by Betancurt et al. uses #PacBio single-molecule sequencing to build a long-read fidelity assay that reveals how different #DNApolymerase families make distinct errors.
🧬 Read more: doi.org/10.1093/nar/...
@nebiolabs.bsky.social @pasteur.fr
#NARBreakthrough
🔬 New study by Betancurt et al. uses #PacBio single-molecule sequencing to build a long-read fidelity assay that reveals how different #DNApolymerase families make distinct errors.
🧬 Read more: doi.org/10.1093/nar/...
@nebiolabs.bsky.social @pasteur.fr
#NARBreakthrough
November 21, 2025 at 6:18 PM
⭐ NAR Breakthrough! ⭐
🔬 New study by Betancurt et al. uses #PacBio single-molecule sequencing to build a long-read fidelity assay that reveals how different #DNApolymerase families make distinct errors.
🧬 Read more: doi.org/10.1093/nar/...
@nebiolabs.bsky.social @pasteur.fr
#NARBreakthrough
🔬 New study by Betancurt et al. uses #PacBio single-molecule sequencing to build a long-read fidelity assay that reveals how different #DNApolymerase families make distinct errors.
🧬 Read more: doi.org/10.1093/nar/...
@nebiolabs.bsky.social @pasteur.fr
#NARBreakthrough
Reposted by Sean Johnson
A few py2Dmol updates 🧬
py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)
py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)
November 19, 2025 at 8:15 AM
A few py2Dmol updates 🧬
py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)
py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)
Great postdoc opportunity to work on protein engineering with some of the best in the business.
Looking for a #postdoc in applied protein science and engineering? Check out the IPI Springer-Lu Postdoctoral Fellowship. Applications are open until Jan. 20! buff.ly/ko7q2QE
#PostDocJobs #PostdocPosition #PhDChat #ScienceJobs #PostdoctoralFellow #STEMCareers
#PostDocJobs #PostdocPosition #PhDChat #ScienceJobs #PostdoctoralFellow #STEMCareers
Springer-Lu Postdoctoral Fellowship
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buff.ly
November 5, 2025 at 7:17 PM
Great postdoc opportunity to work on protein engineering with some of the best in the business.
Reposted by Sean Johnson
So happy to share our new study
“A Bait-and-Switch strategy links phenotypes to genes coding for Polymer-Degrading Enzymes in Intact Microbiomes.”
In this work, we discovered novel chitinases directly on microbiome; a study brilliantly led by Dr. Colleen Yancey
www.biorxiv.org/content/10.1...
“A Bait-and-Switch strategy links phenotypes to genes coding for Polymer-Degrading Enzymes in Intact Microbiomes.”
In this work, we discovered novel chitinases directly on microbiome; a study brilliantly led by Dr. Colleen Yancey
www.biorxiv.org/content/10.1...
October 13, 2025 at 10:50 PM
So happy to share our new study
“A Bait-and-Switch strategy links phenotypes to genes coding for Polymer-Degrading Enzymes in Intact Microbiomes.”
In this work, we discovered novel chitinases directly on microbiome; a study brilliantly led by Dr. Colleen Yancey
www.biorxiv.org/content/10.1...
“A Bait-and-Switch strategy links phenotypes to genes coding for Polymer-Degrading Enzymes in Intact Microbiomes.”
In this work, we discovered novel chitinases directly on microbiome; a study brilliantly led by Dr. Colleen Yancey
www.biorxiv.org/content/10.1...
Reposted by Sean Johnson
The posting is unfortunately not super clear on this, but please apply if you want to do BioML research, especially around machine learning for molecular biology and bioengineering!
I get sad if there are no applicants with this profile in the pool!
I get sad if there are no applicants with this profile in the pool!
If you're an undergrad and want to intern with me, this is where you need to apply!
The Microsoft Research Undergraduate Internship Program offers 12-week internships in our Redmond, NYC, or New England labs for rising juniors and seniors who are passionate about technology. Apply by October 6: msft.it/6015scgSJ
September 15, 2025 at 1:58 PM
The posting is unfortunately not super clear on this, but please apply if you want to do BioML research, especially around machine learning for molecular biology and bioengineering!
I get sad if there are no applicants with this profile in the pool!
I get sad if there are no applicants with this profile in the pool!
Reposted by Sean Johnson
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 27, 2025 at 4:14 PM
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Sean Johnson
So I am absolutely going to host a Flower Design symposium in 2030. This is a formal call for designers. We have @nickdesnoyer.bsky.social with his beautiful Arabidopsis roses, and I'm likely giving my life to my Alice Petunia...but we need more people. Where you at?!
SHOW US YOUR BLOOM PLANS
SHOW US YOUR BLOOM PLANS
a man in a suit standing in a greenhouse
ALT: a man in a suit standing in a greenhouse
media.tenor.com
August 22, 2025 at 7:19 PM
So I am absolutely going to host a Flower Design symposium in 2030. This is a formal call for designers. We have @nickdesnoyer.bsky.social with his beautiful Arabidopsis roses, and I'm likely giving my life to my Alice Petunia...but we need more people. Where you at?!
SHOW US YOUR BLOOM PLANS
SHOW US YOUR BLOOM PLANS
Reposted by Sean Johnson
(1/7)
Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3)
[https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)
Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3)
[https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)
Accelerating Biomolecular Modeling with AtomWorks and RF3
Deep learning methods trained on protein structure databases have revolutionized biomolecular structure prediction, but developing and training new models remains a considerable challenge. To facilita...
www.biorxiv.org
August 15, 2025 at 5:17 PM
(1/7)
Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3)
[https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)
Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3)
[https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)
Reposted by Sean Johnson
I keep seeing heartbreaking stories about people who spend years in grad school, apply to jobs, and only then learn that their dream job needs a skill they didn’t learn during grad school.
Looking at job ads *now*, years before you’re applying, can help identify skills to develop.
🧪🌎🦑🐠
Looking at job ads *now*, years before you’re applying, can help identify skills to develop.
🧪🌎🦑🐠
Here’s what I teach my students about finding jobs in marine biology and conservation
Our field is competitive, some job postings are confusing, and some career advice is contradictory or wrong. Here’s an exercise I have my students perform that I hope can help you. Graphic vi…
www.southernfriedscience.com
April 10, 2025 at 11:02 AM
I keep seeing heartbreaking stories about people who spend years in grad school, apply to jobs, and only then learn that their dream job needs a skill they didn’t learn during grad school.
Looking at job ads *now*, years before you’re applying, can help identify skills to develop.
🧪🌎🦑🐠
Looking at job ads *now*, years before you’re applying, can help identify skills to develop.
🧪🌎🦑🐠
Reposted by Sean Johnson
🚨We've updated our preprint "Frustration, Dynamics, and Catalysis" ✨ We appreciate RT ☺️
A short 🧵1/8: We expanded the conceptual connection between the energy landscapes theory and catalysis, added new figures, and clarified how local frustration shapes enzyme function.
arxiv.org/pdf/2505.00600
A short 🧵1/8: We expanded the conceptual connection between the energy landscapes theory and catalysis, added new figures, and clarified how local frustration shapes enzyme function.
arxiv.org/pdf/2505.00600
July 9, 2025 at 9:17 AM
🚨We've updated our preprint "Frustration, Dynamics, and Catalysis" ✨ We appreciate RT ☺️
A short 🧵1/8: We expanded the conceptual connection between the energy landscapes theory and catalysis, added new figures, and clarified how local frustration shapes enzyme function.
arxiv.org/pdf/2505.00600
A short 🧵1/8: We expanded the conceptual connection between the energy landscapes theory and catalysis, added new figures, and clarified how local frustration shapes enzyme function.
arxiv.org/pdf/2505.00600
The Research Bioinformatics Group (www.neb.com/en-us/resear...) at New England Biolabs is hiring a bioinformatics scientist with NGS expertise.
Come work with us on a wide variety of applied- and basic research projects.
neb.wd5.myworkdayjobs.com/en-US/NEB_Ca...
Come work with us on a wide variety of applied- and basic research projects.
neb.wd5.myworkdayjobs.com/en-US/NEB_Ca...
June 17, 2025 at 6:28 PM
The Research Bioinformatics Group (www.neb.com/en-us/resear...) at New England Biolabs is hiring a bioinformatics scientist with NGS expertise.
Come work with us on a wide variety of applied- and basic research projects.
neb.wd5.myworkdayjobs.com/en-US/NEB_Ca...
Come work with us on a wide variety of applied- and basic research projects.
neb.wd5.myworkdayjobs.com/en-US/NEB_Ca...
Reposted by Sean Johnson
NEB remains undefeated. Truly the GOAT of biotech. Wait time for live chat was mere seconds near EOD on a friday. Sorted my order in less than 3 mins. Why would I buy from anywhere else?
June 13, 2025 at 10:10 PM
NEB remains undefeated. Truly the GOAT of biotech. Wait time for live chat was mere seconds near EOD on a friday. Sorted my order in less than 3 mins. Why would I buy from anywhere else?
Reposted by Sean Johnson
My father worked in a tire factory in Appalachia. Friends and family in the military. Used to vote Republican. Got into college on a diversity program for the underprivileged. Ended up a Harvard professor. And now my funding is terminated because we're trying to stick it to the elites.
May 28, 2025 at 3:07 PM
My father worked in a tire factory in Appalachia. Friends and family in the military. Used to vote Republican. Got into college on a diversity program for the underprivileged. Ended up a Harvard professor. And now my funding is terminated because we're trying to stick it to the elites.
Reposted by Sean Johnson
The war on science in the US is already having an effect on private sector research like AlphaFold. Bears repeating but the private sector builds on top of things created by academic research for the public good. This hurts everyone.
May 28, 2025 at 10:18 AM
The war on science in the US is already having an effect on private sector research like AlphaFold. Bears repeating but the private sector builds on top of things created by academic research for the public good. This hurts everyone.
Reposted by Sean Johnson
🧵5 Top Free Alternatives to BioRender for Scientific Illustrations!
These five websites offer free scientific illustrations for biologists. Great for presentations, research papers and other research communication needs.
Save and share the post!
These five websites offer free scientific illustrations for biologists. Great for presentations, research papers and other research communication needs.
Save and share the post!
May 13, 2025 at 7:55 PM
🧵5 Top Free Alternatives to BioRender for Scientific Illustrations!
These five websites offer free scientific illustrations for biologists. Great for presentations, research papers and other research communication needs.
Save and share the post!
These five websites offer free scientific illustrations for biologists. Great for presentations, research papers and other research communication needs.
Save and share the post!
Reposted by Sean Johnson
📢 Our new preprint is out on bioRxiv! We introduce RAG-ESM, a retrieval-augmented framework that improves pretrained protein language models like ESM2 by making them homology-aware with minimal additional training costs.
🔗 doi.org/10.1101/2025...
💻 github.com/Bitbol-Lab/r...
1/7
🔗 doi.org/10.1101/2025...
💻 github.com/Bitbol-Lab/r...
1/7
April 11, 2025 at 2:47 PM
📢 Our new preprint is out on bioRxiv! We introduce RAG-ESM, a retrieval-augmented framework that improves pretrained protein language models like ESM2 by making them homology-aware with minimal additional training costs.
🔗 doi.org/10.1101/2025...
💻 github.com/Bitbol-Lab/r...
1/7
🔗 doi.org/10.1101/2025...
💻 github.com/Bitbol-Lab/r...
1/7
My colleagues discovered four RNA modifications not previously seen in archaeal mRNA, and identified an enzyme responsible for m7G in modification of 23S rRNA.
Comprehensive nucleoside analysis of archaeal RNA modification profiles reveals an m7G in the conserved P loop of 23S rRNA
Comprehensive nucleoside analysis of archaeal RNA modification profiles reveals an m7G in the conserved P loop of 23S rRNA
Tsai et al. describe comprehensive nucleoside profiles of archaeal RNAs and identify temperature-responsive modifications using LC-MS/MS. They establish a workflow for RNA-modifying enzyme discovery by associating enzyme predictions with global nucleoside profiles. This approach reveals a methyltransferase responsible for installing an m7G in the peptidyl transferase center of 23S rRNA.
dlvr.it
March 26, 2025 at 6:26 PM
My colleagues discovered four RNA modifications not previously seen in archaeal mRNA, and identified an enzyme responsible for m7G in modification of 23S rRNA.
Reposted by Sean Johnson
Gene synthesis is often the most expensive part of protein engineering with generative models.
Happy to have played a small part in this work, where Chase developed a method for precision library construction at scale, with per-gene costs as low as $1.50.
@philromero.bsky.social
Happy to have played a small part in this work, where Chase developed a method for precision library construction at scale, with per-gene costs as low as $1.50.
@philromero.bsky.social
March 24, 2025 at 5:24 PM
Gene synthesis is often the most expensive part of protein engineering with generative models.
Happy to have played a small part in this work, where Chase developed a method for precision library construction at scale, with per-gene costs as low as $1.50.
@philromero.bsky.social
Happy to have played a small part in this work, where Chase developed a method for precision library construction at scale, with per-gene costs as low as $1.50.
@philromero.bsky.social
Reposted by Sean Johnson
NEB will be hosting a scientific symposium on Environmental DNA and Metagenomics on April 9th in Cambridge. Please join us for this exciting event if you are in the Boston area!
go.neb.com/DecodingtheB...
go.neb.com/DecodingtheB...
Interested in learning more about custom product options, large volume purchases, lyophilized products or GMP-grade* products?
go.neb.com
March 18, 2025 at 7:34 PM
NEB will be hosting a scientific symposium on Environmental DNA and Metagenomics on April 9th in Cambridge. Please join us for this exciting event if you are in the Boston area!
go.neb.com/DecodingtheB...
go.neb.com/DecodingtheB...
Reposted by Sean Johnson
USAID matters. I've often disagreed with their strategy and choices, but their work saves more lives than any philanthropy can. It's a rounding error in the federal budget, and one of the best things we do as a country. To see it destroyed overnight by one unelected man is an unmitigated horror.
February 3, 2025 at 10:15 PM
USAID matters. I've often disagreed with their strategy and choices, but their work saves more lives than any philanthropy can. It's a rounding error in the federal budget, and one of the best things we do as a country. To see it destroyed overnight by one unelected man is an unmitigated horror.
Reposted by Sean Johnson
How can any of us feel anything other than intensely ashamed to be associated with this? Just incredible cruelty and indifference. www.nytimes.com/2025/01/31/w...
January 31, 2025 at 12:37 PM
How can any of us feel anything other than intensely ashamed to be associated with this? Just incredible cruelty and indifference. www.nytimes.com/2025/01/31/w...
Reposted by Sean Johnson
Engineering FPs is not new & not hard. There are better embeddings for protein engineering, eg using ancestral reconstruction. You don’t need billions of params in your model!
www.sciencedirect.com/science/arti...
www.nature.com/articles/s42...
www.sciencedirect.com/science/arti...
www.nature.com/articles/s42...
Ancestral sequence reconstruction for protein engineers
In addition to its value in the study of molecular evolution, ancestral sequence reconstruction (ASR) has emerged as a useful methodology for engineer…
www.sciencedirect.com
January 17, 2025 at 11:58 AM
Engineering FPs is not new & not hard. There are better embeddings for protein engineering, eg using ancestral reconstruction. You don’t need billions of params in your model!
www.sciencedirect.com/science/arti...
www.nature.com/articles/s42...
www.sciencedirect.com/science/arti...
www.nature.com/articles/s42...
Reposted by Sean Johnson
We’re hiring! IPI is searching for a principal scientist with strong skills in #lightmicroscopyimaging of neuronal cells and tissues. Help us develop new protein tools for neuroscience applications! 🧬🧶#molecularneuroscience #proteinscience #proteintools
Institute for Protein Innovation - Principal Scientist / Neuroscience Group
Purpose The Neuroscience group at IPI leverages antibody panels from IPI's antibody platform for specialized neuroscience applications, serving as a bridge to the neuroscience research community. The…
buff.ly
January 15, 2025 at 4:00 PM
We’re hiring! IPI is searching for a principal scientist with strong skills in #lightmicroscopyimaging of neuronal cells and tissues. Help us develop new protein tools for neuroscience applications! 🧬🧶#molecularneuroscience #proteinscience #proteintools
Reposted by Sean Johnson
Excited to share that we have just released genomenotebook 1.0 together with @trichomedoctor.bsky.social ! If you like to analyze genomics data in Jupyter notebooks this is for you. You can get beautiful genome browsers directly in your notebooks: dbikard.github.io/genomenotebo...
genomenotebook
A genome browser in your Jupyter notebook
dbikard.github.io
December 13, 2024 at 4:48 PM
Excited to share that we have just released genomenotebook 1.0 together with @trichomedoctor.bsky.social ! If you like to analyze genomics data in Jupyter notebooks this is for you. You can get beautiful genome browsers directly in your notebooks: dbikard.github.io/genomenotebo...