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Out now nature we report the structural basis of Gabija defense and how the anti-defense phage protein Gad1 wraps around Gabija in an octameric web for immune evasion! 🐙🕸 rdcu.be/drLOR #b3d #MolecularNodes Brady Johnston

Really happy to have this officially published! Thanks to Shen Lab, Simonetta Gribaldo, and Najwa for their amazing support! Give it a read if you’re interested in bacterial cell division, spore formation, and the evolution of PG synthases that drive them: nature.com/articles/s4146…

B. subtilis 🤝 literal sauna

How does a progenitor cell differentially express genes in daughter cells after asymmetric division? @Sylvia_Char 's fancy microscopy in her paper PNASNews says the division machinery itself positions a transcription activator asymmetrically! pnas.org/doi/10.1073/pn…

Predictomes: A classifier-curated database of AlphaFold-modeled protein-protein interactions biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

Impressive work on a classifier to distinguish likely true AF-multimer predictions from false positives. A bacterial classifier next please!

Bacillus subtilis uses the SigM signaling pathway to prioritize the use of its lipid carrier for cell wall synthesis PLOS Biology by Ian Roney and David Rudner journals.plos.org/plosbiology/ar…

Super excited to be releasing AlphaFold 3 today, developed by Isomorphic Labs and Google DeepMind: our next generation AI model for predicting the biomolecular structures and interactions of proteins, DNA, RNA, small molecules, and more: bit.ly/44yfaCw 1/

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/

another great year for Boston Bacterial Meeting (BBM)! huge shoutout to all of the presenters, the OC, and to Laurent Dubois and Molly Sargen for running the whole show (& for incredible crisis management when BBM went dark)

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 Johannes Walter and Lucas Farnung. biorxiv.org/content/10.110…

Interactively browse all the predicted structures here: predictomes.org/view/acidicpat…

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

I had a lovely time getting to hear some fantastic talks and share my own work at the John Innes Centre yesterday! So much exciting microbiology happening.

The Bartlett Lab is open for business at the Wadsworth Center! We study pathogens with "unusual" shapes (balls & corkscrews) to find vulnerabilities in their growth plans, and learn how bacterial shape impacts infection. We are hiring... join us! wadsworth.org/research/labor…

Stem cell-like states confer poor outcomes in blood cancer—but what mechanisms drive this and how can they be therapeutically targeted? In our new preprint, we show how a single TF represses one enhancer to maintain a subset of high-risk leukemias: 🧵👇 biorxiv.org/content/10.110…

Angelika Gründling’s work from her sabbatical in the Bernhardt-Rudner labs is out! She came with the goal of finding the missing G+ phosphatidylglycerol phosphate phosphatase and found it with time to spare. I can also highly recommend her as a bay mate! pnas.org/doi/10.1073/pn…

SAVE THE DATE ‼️ 📆 📢 BBM 2025 will be held on June 9-10th at the Harvard Science Center feat. the one and only Dr. Petra Levin as keynote! We can't wait to see you there. Registration and scholarship applications open next week.

Very excited to share that my thesis work is out in Molecular Cell! We trained a Structure and Omics informed Classifier (SPOC) to score binary AlphaFold multimer (AF-M) predictions by structural quality and consistency with experimental omics datasets. cell.com/molecular-cell…