Mehrbod Estaki

We've got ISSUES. Literally.

We scraped >100k special issues & over 1 million articles to bring you a PISS-poor paper. We quantify just how many excess papers are published by guest editors abusing special issues to boost their CVs. How bad is it & what can we do?

arxiv.org/abs/2601.07563

A 🧵 1/n

TIR: Legendre, Fortin, Borcard 2015 on why the Mantel test, which is often used to test spatial autocorrelation in measured data, doesn’t actually not actually do that.

You probably want dbMEM analysis instead!

https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12425

A conversation about the human gut microbiome Still working on my next post, so I thought I’d share a recent conversation with Dr.

This week's #substack is a recent podcast conversation, where we chat about the human microbiome, health, and some new work from the lab that involves predicting diet from poop DNA. gibbological.substack.com/p/a-conversa...

I wrote a short letter to the editor of The Missoulian, my hometown newspaper in Montana, about the importance of science funding. I'm posting here in a thread, in case others want a template for writing home to their red state papers.

Disclaimer: these are my own personal opinions/views.

🧵 1/9

Metagenomic estimation of dietary intake from human stool - Nature Metabolism Diener et al. present a method that allows the estimation of dietary intake from human stool by detecting food-derived DNA in faecal metagenomes.

Happy to announce that MEDI, our method to quantify dietary intake through metagenomics is out now. 🧬 🧪🧫🦠 www.nature.com/articles/s42...

#metagenomics #microbiome #microbiomesky

So what is MEDI? A combination of two things:

TEMPTED: time-informed dimensionality reduction for longitudinal microbiome studies - Genome Biology Longitudinal studies are crucial for understanding complex microbiome dynamics and their link to health. We introduce TEMPoral TEnsor Decomposition (TEMPTED), a time-informed dimensionality reduction ...

New tensor factorization paper out today — a fun collaboration with Pixu Shi, Liat Shenhav, Rob Knight, & Anru_Zhang! 🎉 Check it out here: genomebiology.biomedcentral.com/articles/10....

Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent antibody response against a pathogen. Could lead to topical vaccines that are applied in a cream. @djenetbousbaine.bsky.social led the charge... @natureportfolio.bsky.social 1/55

Woo! Congrats Sean and Christian! Well deserved and cannot wait to see all the amazing work that will inevitably be coming out of that lab,

January 31, 2024 General microbiome Finding Candida auris in public metagenomic repositories - Mario-Vasquez et al. - PLOS One Pregnancy and early life A pilot study of fecal pH and redox as functional markers in the ...

Todays's #microbiome digest

microbiomedigest.com/2024/01/30/j...

#MicrobiomeSky 🦠

@elisabethbik.bsky.social