Nick Youngblut

Working on computational biology at the Arc Institute

[Nick Youngblut @nick_youngblut]

@delafuentelab @bbuchfink Not “AlltheArchaea (and bacteria)”?

[Nick Youngblut @nick_youngblut]

@ClaudeDevs Radio, cool.
How about the >10k open issues in the claude-code github repo?

[Nick Youngblut @nick_youngblut]

swimming in data 🐟🐟🐟

[Nick Youngblut @nick_youngblut]

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

[Nick Youngblut @nick_youngblut]

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

[John F. Cryan @jfcryan]

Revealed: the millions of dollars in time wasted making papers fit journal guidelines https://t.co/FMFdbTDSp2

[Nick Youngblut @nick_youngblut]

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

[Nick Youngblut @nick_youngblut]

Excited to share our latest article published in @ploscompbiol: https://t.co/i8qLfzsPGr #ploscompbiolauthor

ResMiCo accurately identifies misassemblies, which seem to be quite prevalent in MAG datasets (~7% of contigs misassembled).

[Nick Youngblut @nick_youngblut]

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

[Metagenomics Papers @metagenomic_lit]

ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning https://t.co/CTMqZkGuAu

[Nick Youngblut @nick_youngblut]

ResMiCo is easy to install and use.
Check out the code at https://t.co/s1xgMj5iPU

[Nick Youngblut @nick_youngblut]

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.

[A. Murat Eren (Meren) @merenbey]

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.

https://t.co/VT4ZuxCPra

[Nick Youngblut @nick_youngblut]

@ArmitageDW Check out the Rephrase task at https://t.co/otdxMl2Vac

[Hajk-Georg Drost @HajkDrost]

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.

[Nick Youngblut @nick_youngblut]

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
https://t.co/QnteD8Hejf

[wilmeslab @wilmeslab]

🦠+🧠=⚠️ 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
https://t.co/iswg7DVMMy

[Nick Youngblut @nick_youngblut]

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 https://t.co/t1t3zDLvfU

[Maria Spyrou @ma_spyrou]

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. https://t.co/nWzObniTT3

[Host-Microbe Interactions @HostMicrobeLit]

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.

https://t.co/gxGIMyIr1w

[Taichi Suzuki @Taichi_A_Suzuki]

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