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

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

In the before-times, I spent a couple weekends sketching out circular DNA sequences and thinking of all the edge cases related to annotating around the origin and across intron boundaries. It was fun. Kind of sad to think that the next generation won't have that same joy. But that's progress I guess

If you're not already using pyhmmer and the other python wrappers by Martin Larralde, you should. They are amazing. github.com/althonos

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

Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning Mirdita Lab builds scalable bioinformatics methods.

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

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.

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...

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

I taught an octopus piano (It took 6 months) YouTube video by Mattias Krantz

m.youtube.com/watch?v=PcWn...

⭐ 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

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)

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

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...

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!

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...

a man in a suit standing in a greenhouse ALT: a man in a suit standing in a greenhouse

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

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...

(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)

[www.biorxiv.org/content/10.1101/2025.08....

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…

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.

🧪🌎🦑🐠

🚨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

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...

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?

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.

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.

🧵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!

RAG-ESM logo

📢 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...

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You know it's an elegant model when instead of having a github link, they give a full implementation in a single page of supplemental data.

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

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

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...

It is only a tiny fraction of the number of proteins that exist in nature. It is only most of the proteins that existed in one database at the time of the work. Nature and biological diversity are vast!