iiinova — where your digital self keeps evolving

Reposted by Sean Johnson

Danial @danialgh.bsky.social · 05/07/2026

Excited to share our latest paper: Prot2Prop! A parameter-efficient multitask protein language model that jointly predicts six developability properties from sequence using lightweight adapters. 📄 doi.org/10.64898/202... 💻 github.com/NeurosnapInc...

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Sean Johnson @trichomedoctor.bsky.social · 28/06/2026

seanrjohnson.github.io/circletheaar... I made this game a long time ago. It was written in MonkeyX, a weird old game programming language. Now, through the magic of agentic AI, it has been translated to TypeScript and deployed to GitHub pages for all to enjoy in perpetuity.

seanrjohnson.github.io

Circle the Aardvark in the Back of the Pickup Truck

Circle the aardvarks in pickup trucks, but do not circle Otto von Bismarck.

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Sean Johnson @trichomedoctor.bsky.social · 10/06/2026

It was a privilege to make a small contribution to this work by the Trachman lab. A multidisciplinary effort including beautiful cryo-EM structures and creative mass spec analysis to unravel the mechanism of a bacterial defense system.

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Sean Johnson @trichomedoctor.bsky.social · 20/04/2026

Incredible work by an incredible team, developing a powerful new strategy for 5mC mapping.

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Sean Johnson @trichomedoctor.bsky.social · 14/04/2026

FAMSA is great. It's fast, accurate, easy to run, and works on huge lists of proteins.

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Reposted by Sean Johnson

New England Biolabs @nebiolabs.bsky.social · 22/02/2026

Ready for #AGBTGM! Come visit us in Sarasota Suite 🦋

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Reposted by Sean Johnson

Milot Mirdita @milot.bsky.social · 20/01/2026

My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring! mirdita.org

mirdita.org

Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning

Mirdita Lab builds scalable bioinformatics methods.

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Sean Johnson @trichomedoctor.bsky.social · 15/12/2025

I used github copilot to port Aggregscan3D from python 2 to python 3. I wasn't able to test/debug the parts relying on proprietary software like FoldX, but the basic functionality works. github.com/seanrjohnson...

github.com

GitHub - seanrjohnson/aggrescan3d_py3: Python 3 port of Aggrescan3d

Python 3 port of Aggrescan3d. Contribute to seanrjohnson/aggrescan3d_py3 development by creating an account on GitHub.

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Reposted by Sean Johnson

Janani Durairaj (Jay) @ninjani.bsky.social · 01/12/2025

Been excited about this one for a while! What would you do with a new alphabet and the wealth of protein sequence bioinformatics at your disposal? We're also around at #EMBOComp3D Heidelberg and MLSB Copenhagen this week to discuss

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Reposted by Sean Johnson

Nucleic Acids Research @narjournal.bsky.social · 21/11/2025

⭐ 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

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Reposted by Sean Johnson

Sergey Ovchinnikov @sokrypton.org · 19/11/2025

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)

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Sean Johnson @trichomedoctor.bsky.social · 05/11/2025

Great postdoc opportunity to work on protein engineering with some of the best in the business.

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Reposted by Sean Johnson

Laurence Ettwiller @ettwiller.bsky.social · 13/10/2025

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...

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Reposted by Sean Johnson

Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 15/09/2025

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!

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Reposted by Sean Johnson

Martin Pacesa @martinpacesa.bsky.social · 27/08/2025

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...

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Reposted by Sean Johnson

Sebastian S. Cocioba @atinygreencell.bsky.social · 22/08/2025

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

media.tenor.com

a man in a suit standing in a greenhouse

ALT: a man in a suit standing in a greenhouse

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Reposted by Sean Johnson

David Shiffman, Ph.D. 🦈 @whysharksmatter.bsky.social · 10/04/2025

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. 🧪🌎🦑🐠

southernfriedscience.com

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…

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Reposted by Sean Johnson

Gonzalo Parra @gonzaparra.bsky.social · 09/07/2025

🚨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

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Sean Johnson @trichomedoctor.bsky.social · 17/06/2025

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...

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Reposted by Sean Johnson

Sebastian S. Cocioba @atinygreencell.bsky.social · 13/06/2025

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?

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Reposted by Sean Johnson

David Pfau @davidpfau.com · 28/05/2025

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.

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Reposted by Sean Johnson

Rafeeque Mavoor @rafeequemavoor.bsky.social · 13/05/2025

🧵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!

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Reposted by Sean Johnson

Damiano Sgarbossa @damianosg.bsky.social · 11/04/2025

📢 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

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Sean Johnson @trichomedoctor.bsky.social · 26/03/2025

My colleagues discovered four RNA modifications not previously seen in archaeal mRNA, and identified an enzyme responsible for m7G in modification of 23S rRNA.

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Reposted by Sean Johnson

Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 24/03/2025

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

Oligo-based Multiplexed Efficient Gene Assembly (OMEGA)

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Reposted by Sean Johnson

evarney22.bsky.social @evarney22.bsky.social · 18/03/2025

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

Interested in learning more about custom product options, large volume purchases, lyophilized products or GMP-grade* products?

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Reposted by Sean Johnson

John Green @johngreensbluesky.bsky.social · 03/02/2025

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.

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Reposted by Sean Johnson

Jameel Jaffer @jameeljaffer.bsky.social · 31/01/2025

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...

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Reposted by Sean Johnson

Howard Salis @hsalis.bsky.social · 17/01/2025

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...

sciencedirect.com

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…

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Reposted by Sean Johnson

David Bikard @dbikard.bsky.social · 13/12/2024

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...

dbikard.github.io

genomenotebook

A genome browser in your Jupyter notebook

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Sean Johnson @trichomedoctor.bsky.social · 09/12/2024

Peter, Zhiyi, myself, and the rest of the team are happy to share our newest work. Domainator, a flexible software suite for domain-based annotation and neighborhood analysis, identifies proteins involved in antiviral systems. academic.oup.com/nar/advance-... GitHub: github.com/nebiolabs/do...

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Sean Johnson @trichomedoctor.bsky.social · 09/12/2024

A major advancement in DNA methylation mapping technology! Congratulations to Weiwei, YJ, Peter, Laurence, and the rest of the team.

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Reposted by Sean Johnson

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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