thecodingbiologist
@codingbiologist
Creating tools and tutorials to make lab life a little easier.
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Excited that our work on transcription-coupled DNA repair is now published @CellCellPress! We recapitulated TC-NER in Xenopus egg extract and identified STK19 as a core repair factor that couples stalled Pol II to TFIIH. 🧬🐸 ➡️ cell.com/cell/fulltext/…
Make publication ready figures from your #AlphaFold PAE files. Works on multimer and AlphaFold 3 files. Customize colors and export as an SVG for editing in illustrator! thecodingbiologist.com/tools/pae.html
Excited to share that our new preprint is out! We used #AlphaFold multimer to screen 7000+ nuclear proteins to find new nucleosome acidic patch binders. Great collaboration between @FrogWalterLab and @LucasFarnung. biorxiv.org/content/10.110…
Riding the #AlphaFold3 wave with a new analysis tool. It’s super new/unpolished, but would love to get community feedback! Extract and filter residue level interaction data from your AF3 server prediction zip files! Try it here: predictomes.org/tools/af3/
So excited to share the first work from our lab. Led by @StevePilley with help from lots of amazing collaborators. A special shout out to @LyssiotisLab and @BKennedy_aging and their labs!
Introducing the SPECTRA python package! github.com/mims-harvard/S… This package implements the spectral framework for model evaluation. All you need to get started is (1) a model, (2) a dataset, and (3) a definition of sample to sample similarity!
It is no secret there exists a generalizability problem in AI for biology. Despite all the advances in ML methods, the way we evaluate generalizability in ML models has not changed. How well does your ML model generalize across the entire spectrum of possible dataset splits?…
I just posted the first of what will be several chapters about transformers, which in the last year has been the most requested topic for the channel. youtu.be/wjZofJX0v4M
youtube.com
YouTube
Transformers, the tech behind LLMs | Deep Learning Chapter 5
couldn’t agree more about the need for more computational biologists. More importantly, we must ensure they receive the recognition and support they deserve. Their work should never be dismissed as merely “just service”. Additionally, I’d like to remind everyone of the excellent…
WE NEED COMPUTATIONAL PEOPLE IN BIOLOGY. WE NEED THEM IN DRUG DISCOVERY AND MULTI OMICS. WE NEED HARDWARE PEOPLE TO BUILD SPECIFIC AND PORTABLE DEVICES. BUT MOST IMPORTANTLY WE NEED DEVS. WE NEED TO MAKE OPEN ACCESS DATA AS ACCESSIBLE AS POSSIBLE. WE NEED COMPUTE GRANTS. GIVE
Check out this massive study led by @GygiLab member Jonathan Van Vranken and lab alumnus @dschweppe1 to learn how thermal stability measurements and small molecule screening can be used together to tease apart the compounds' direct and indirect effects!
We quantified 1.498 million thermal stability measurements in cells and crude extracts treated with small molecule therapeutics and tool compounds! We interrogated on- and off-target effects to dissect direct ligand binding and indirect effects.biorxiv.org/content/10.110…
Our essay in Nat Cell Bio: "Bringing computation to biology by bridging the last mile" We argue to shift resources/rewards towards creating user-friendly software to bridge computation and biology-it yields huge returns! @shantanuXsingh Free author link: rdcu.be/dv82F
A higher power
Stringz: A GUI based string manipulation tool producthunt.com/posts/stringz via @producthunt
Analyze strings, reveal hidden characters, visualize character indices and more: thecodingbiologist.com/tools/chartool…
Drop an #AlphaFold PDB file, select the chain and or region you want to analyze, and export the pLDDT values. It's that easy: thecodingbiologist.com/tools/plddt.ht…
I’m looking for a postdoc who wants to work with me and Andrew Kruse to design and characterize new protein sensors! If you’re interested or have any leads, let me know!
I had a great time working with the @GygiLab team on this story! GoDig is an amazing new tool that allows for rapid targeted proteomics assay development. Congrats to Qing and everyone involved. Check it out ⬇️ nature.com/articles/s4146…
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