Nick Youngblut

swimming in data 🐟🐟🐟

@strnr So the tree of life no longer includes archaea?

Genomic divergence across the tree of life pnas.org/doi/10.1073/pn… 🧬🖥️🧪

@bycloudai Normalize by API price and the chart will look very different

the grok-3 benchmark is pretty useful in comparing base models, so I added GPT-4.5

Revealed: the millions of dollars in time wasted making papers fit journal guidelines nature.com/articles/d4158…

@mruehlemann @pam_ferretti @PLOSCompBiol Thanks! The proportion of misassemblies is highest for the longest and the shortest contigs. See Fig D in the supplemental

Excited to share our latest article published in @ploscompbiol: journals.plos.org/ploscompbiol/a… #ploscompbiolauthor ResMiCo accurately identifies misassemblies, which seem to be quite prevalent in MAG datasets (~7% of contigs misassembled).

If you assemble metagenomes or are interested in deep learning methods applied to metagenome data, check this paper out

ResMiCo is easy to install and use. Check out the code at github.com/leylabmpi/ResM…

Our deep learning model was trained/tested on 210 Gbps of sequence data! We validated on simulated, mock, and real-world metagenomes. Our testing showed that ResMiCo is accurate & generalizes well to novel data.

Now @emily_fogarty11's pre-print is officially out (🎉), I'd like to tell you more about one of the most curious things we (or at least me, my ignorant self) stumbled upon in the human gut microbiome. This is about a cryptic plasmid, called pBI143. biorxiv.org/content/10.110…

@ArmitageDW Check out the Rephrase task at elicit.org

An extraordinary effort with @bbuchfink, @Haim_Ashkenazy, Klaus Reuter & John Kennedy 👉 with fantastic support by @PlantEvolution, @MPI_for_DB & @maxplanckpress. With DIAMOND DeepClust protein clustering is up to 13x faster than MMSeqs Linclust or 82x faster than CD-hit.

Need to interpret ML models for microbiome or other (biological) data? Interested in methanogens (archaea) in the human gut? For either: check out the endoR manuscript, now published at PLOS Comp Bio dx.plos.org/10.1371/journa…

🦠+🧠=⚠️ New #preprint that we are super excited about: #archaea in #human gut #microbiome linked to #Parkinson’s disease pathogenesis. @uni_lu @lcsb_uni_lu @ResearchLux Funded by @ERC_Research @FnrLux @MichaelJFoxOrg @ParkinsonDotOrg @Rotary #Luxembourg researchsquare.com/article/rs-182…

We developed a new deep learning model for predicting misassemblies in metagenome assemblies, with much better performance than existing methods ResMiCo: increasing the quality of metagenome-assembled genomes with deep learning biorxiv.org/content/10.110…

Our paper published today @nature describes an ancient epidemic that occurred in central Eurasia in the years 1338-1339. We find that the epidemic was caused by plague (Y. pestis) and that it was associated with the beginnings of the Black Death. nature.com/articles/s4158…

The human microbiome: there is much left to do @Nature Perspective piece by @RuthLeyMicro on the 10th anniversary of the Human Microbiome Project on where we go next. nature.com/articles/d4158…

I am thrilled to announce that I will be starting as an Assistant Professor at Arizona State University on January 1st, 2023 🌵 This is a joint position between the College of Health Solutions and Biodesign Center for Health Through Microbiomes. 1/2

Our story of horizontal gene transfer in nematodes has made the cover story in Molecular Evolution and Biology. Thanks to Daphne Welter for her fantastic illustration. Link to the article: academic.oup.com/mbe/article/39…

The developing infant gut #microbiome: A strain-level view. @HagayEnav @BackhedLab @RuthLeyMicro review recent studies on #infant #gutmicrobiome, moving from broad taxonomic studies to strain level analyses & shedding new light on colonization & maturation cell.com/cell-host-micr…