#AF3 is amazing but the webserver does not display all scores needed to evaluate a model. Our Colab-based AlphaFold3 score visualizer helps! Check it out at colab.research.google.com/drive/1YB2378j… Thanks to Robin Schaeper!

I'm happy to share that out paper on Phantasus, a web-application for visual and interactive gene expression analysis, got out in eLife - the journal elifesciences.org/articles/85722 Here, I'm using it to analyze a random GEO dataset, including basic QC to filter outliers, in under 100 seconds! 1/n

OpenFold developed by Gustaf Ahdritz, Nazim Bouatta, and Mohammed AlQuraishi is a trainable, open-source implementation of AlphaFold2. It is fast and memory efficient, and the code and training data are available under a permissive license.
nature.com/articles/s4159…

Spatial mapping of hepatic ER and mitochondria architecture reveals zonated remodeling in fasting and #obesity Nature Communications nature.com/articles/s4146…

#Sleep fragmentation induces #heartfailure in a hypertrophic cardiomyopathy mouse model by altering redox #metabolism
sciencedirect.com/science/articl…

Carbonyl adducts generating by alterations in nucleobase, carbonyl, and reactive oxygen species metabolic pathways are MR1-presented self-antigens recognized by T cells Science Immunology
science.org/doi/10.1126/sc…

Congrats ⁦Jonathan Schertzer (SchertzerLab)⁩ Intermittent fasting influences immunity and metabolism: Trends in Endocrinology & Metabolism cell.com/trends/endocri…

Assessing #phage -host population dynamics by reintroducing virulent viruses. Emma Allen-Vercoe shows colony isolation removes virulent viruses from gut #bacteria . Reintroducing virulent #virome to bacteria has specific impacts on community & prophages cell.com/cell-host-micr…

While AlphaFold3 improves upon the previous version, it still can't handle conformational changes during binding like our NeuralPlexer does.
Paper: nature.com/articles/s4225…
Summary: nature.com/articles/s4159…
'NeuralPLexer can predict both apo and bound forms of proteins and can

Happy to share the first preprint from the lab! We describe how extracellular lipid availability regulates a polyunsaturated fatty acid trafficking pathway in cancer cells that influences ferroptosis sensitivity. Check it out! 👇
biorxiv.org/content/10.110…

Thrilled to share our characterization of the human tyrosine kinome.
Try out the public website: kinase-library.mit.edu/home
Wonderful collaboration with Cantley Lab Turk Lab YaffeLab. Many years of work led by Jared Johnson!

nature.com/articles/s4158…

Who remembers these?

Surely it's time to expand HCM genetic testing beyond sarcomeric genes?

JPH2 - 3% of cases in 🇫🇮 #5 gene (at least)
FHOD3 - 6% of cases in 🇸🇮 🇧🇦 #3 gene
CSRP3 / TRIM63 - 4.5% of cases in 🇪🇬 #5/6 genes
ALPK3 - 1.5% of cases in 🇪🇺 but maybe ~5-6% in 🇮🇳/🇵🇰?
etc.

Here are the ligands that Alphafold3 supports if anyone was wondering.

Featured Article: Microbiota metabolism of amino acids
Gut microbes &metabolic genes deplete amino acids, affecting host AA homeostasis. ie, #microbiota genes in branched-chain amino acid & tryptophan depletion regulate glucose tolerance CJ
cell.com/cell-host-micr…

Here's a free online course on AlphaFold you can take at your leisure:

ebi.ac.uk/training/onlin…

A randomized, controlled, double-blind trial of patients w HFrEF evaluated ketone ester (KE) beyond acute treatment & found favorable CV effects achieved on top of optimal #HF therapy @bborlaugmd Kristian Christensen Bertil Ladefoged @Gnigopan @krisberghansen ahajournals.org/doi/10.1161/CI…

LHI Lecture May 15, noon: Zoltan P. Arany, M.D., Ph.D. “Human Cardiac Metabolism.” 1-101 Microbiology Research Facility | More info: buff.ly/4cD0eXj | Webcast: buff.ly/4cIssQI #UMNresearch #UMNheart

Preprint alert 🔥🔥🔥

This has been a long but super-fun journey together with INRAE TIM

We found some really cool stuff about intermittent #fasting , #transcription_factors and #chromatin

A short thread 🧵 👇

biorxiv.org/content/10.110…

Online now! Systematic analysis of NDUFAF6 in complex I assembly and mitochondrial disease dlvr.it/T6dHG3