GMHI-webtool: a user-friendly browser application for assessing health through metagenomic gut microbiome profiling biorxiv.org/cgi/content/sh… #bioRxiv

Imagine gut microbiome testing as part of our routine health checks. Soon, we'll be able to non-invasively and longitudinally track health, just by screening for gut microbes in 💩. Presenting the 2nd iteration of our stool metagenome health indicator: biorxiv.org/content/10.110…

New paper in BMC Medicine: We report #GutMicrobiome results from a phase I clinical trial on the potential of kefir (a fermented dairy drink rich in probiotics) to improve #GutHealth in critically ill patients in the #IntensiveCareUnit (ICU). #ICUResearch bmcmedicine.biomedcentral.com/articles/10.11…

📢New from Jordan Cahoon Charleston Chiang & co 📰Imputation accuracy across global human populations cell.com/ajhg/abstract/…

How to pick a problem. Today in Cell. 1/53 cell.com/cell/fulltext/…

On knowing a gene: Distributional hypothesis of gene function Just as words derive meanings from context, genes can switch their roles with biological surroundings. Traditional gene annotations miss this Advances in transformers suggest a new perspective: gene functions as

There's been amazing coverage of our new paper nature nature.com/articles/s4158… but I wanted to put together a walk-through (and make this accessible as possible). It's a bit long so get a cup of tea! The full version is open access so pls do have a read if you are interested...

📽️ New 4 hour (lol) video lecture on YouTube: "Let’s reproduce GPT-2 (124M)" youtu.be/l8pRSuU81PU The video ended up so long because it is... comprehensive: we start with empty file and end up with a GPT-2 (124M) model: - first we build the GPT-2 network - then we optimize

Excited to share the Smillie Lab's first paper! We discovered distinct lineages of the gut microbiota that are exquisitely adapted to inflammatory disease. This was a monumental effort led by Adarsh Kumbhari @mgh_ri Harvard Medical School Broad Institute More: doi.org/10.1016/j.chom…

I'm making an open offer to any compbio grad students/postdocs who are aiming for faculty positions. If you have strong impactful research but no glam pubs & need someone to advocate for you, please get in touch. I promise u, I & a bunch of other faculty will strongly support u.

Excited to share our new paper on Contextual AI models for context-specific prediction in biology in @NatureMethods led by stellar Michelle M. Li (李敏蕊) rdcu.be/dOxQ7 Understanding how proteins work and developing new therapies requires knowing which cell types proteins act

Sharing our latest work with KenWarringtonMD in Annals of the Rheumatic Diseases! We used SomaLogic proteomics to identify blood protein patterns in active and inactive Giant Cell Arteritis. Sights are now set to develop and validate ML-based multiplex biomarker panels for GCA!🚀 ard.bmj.com/content/early/…

Our latest tool, the Gut Microbiome Wellness Index2, is now out in Nature Communications. Fantastic work led by Daniel Chang & vinod gupta! GMWI2 is a disease-agnostic indicator of gut health that quantifies disease likelihood from a gut microbiome sample. nature.com/articles/s4146…

Should you ask your HCP for a gut #microbiome wellness profile? GMWI2 represents a timely, pivotal resource for evaluating health using an individual’s unique gut microbial composition Nature Communications nature.com/articles/s4146…

Mayo Clinic researchers have developed an innovative computational tool that analyzes the gut microbiome, a complex ecosystem of trillions of bacteria, fungi, viruses and other microorganisms, to provide insights into overall well-being. Learn more: mayocl.in/4e9FLcQ

biorxiv.org/content/10.110… Nice benchmark of single cell "foundation models" (scGPT, scFoundation) and GEARS (a GNN model) further hyped as "virtual cell models" against linear baselines on perturbation prediction. Long-story short: they can't beat the linear baselines. 1/

In the latest issue! Mining human microbiomes reveals an untapped source of peptide antibiotics dlvr.it/TDWzpm