So, Poore et al. analyzed both Cancer Genome Atlas data
and cell-free blood nucleic acids. TCGA is under miserable
data restrictions, so I reanalyzed their plasma samples....

By reanalzed, I mean metagenomic assembly, of course!
I was able to assemble and bin several bacterial genomes from these samples.

The dominant genomes in the samples are a mix of common contaminants, but also very interestingly, highly divergent novel ultrasmall bacteria: novel CPR and chlamydiae (see prior tree)

So, the original analysis was with Kraken and Shogun.

My experience, which is a common one, is that when you pass DNA from novel genomes to these sorts of software, their specificity trends to 0: kraken will tell you a CPR genome is just about everything. Hence why I do not recommend the use of these programs in microbial ecology.

So of course these highly novel bacteria result in tons of reported microbial species that do not actually exist in the samples, and those are of course the features that end up being analyzed. This is how you get lines like this in Poore et al:

"for LIHC tumours, the Orthohepadnavirus genus was the second most important feature (after the hepatotoxic Microcystis genus37)."

(Sorry, there are definitely not hepatoxic Cyanobacteria in your tumours!)

Fascinatingly, these ultratiny bacteria are only found in the human samples, not in the negative controls (I commend Poore et al. on doing these controls!). However, across cohorts, I assemble pretty much nearly identical bacterial genomes, implausible that they are actually in unrelated patients.

So, I suspect that these ultratiny bacteria are introduced via some equipment for actual plasma collection that isn't used in the controls.

So, in the end, Poore et al. ended up doing machine learning on a bunch of reported microbial species that were not actually there. It is unlikely that their reported results will be robust for future prediction, or are biological in nature.

I don't fault the authors much, really! The use of these faulty computational approaches is common in our field.

These tools neglect the only law of metagenomics: what is in your sample isn't in the database. 😀

A good oral history here. It was during a break while filming the movie, a benefit concert for their choreographer Loyce Holton.

loudersound.com/features/purpl…

Purple Rain by Prince: the story behind the song

Prince's Purple Rain was the epic ballad that reclaimed rock for black musicians, enjoying airplay everywhere from country to rock radio

^{Nick Hasted (Louder)}

I am sad that the game which intrigues me most is on the $60 version and not the $10.

A ttrpg called TOMBS: Toot On My Boner, Skeleton. About horny revenants who have been post-life so long they've forgotten how sex works, and are left to improvise.

Odin project facing economical troubles, If I understood correctly.
amateurgods.substack.com/p/the…
Besides, low quality materials and worst, i.e E. Coli in Starter Kit and others are not proper E. Coli supposed to be.

Odin is so closed to G. Church, and George Church for sure is someone to be suspicious about. No consideration in tech assessment, only progress no matter what the costs. He is also one of the milking people of the Crispr Technology patent I suppose.

If you need free wetware for free give a chance to Free Genes Project
stanford.freegenes.org/

Or community spaces around you if any (hackerspaces, biohackerspaces, and others)

Communities / people ?
Hackteria, OpenWetWare, Hackuarium, etc, ect.

We also can supply and provide some equipment, materials, kits somehow

@danwchan can also maybe share some highlights and answers about DIY Genetic Engineering

The death of SynthBio companies and my other predictions for Biotech in 2023

The death of the synthetic biology company and the rise of consumer biotech. I’ma be honest, I’ve been pushing on the consumer biotech thing before everyone else thought it was cool.

^{Jo Zayner, PhD (Biohack the Planet)}

It would be nice to view global resources consuming plan. I have read that US consumes about 40% resources.

If China and India will make their level of life comparable we can enter great resource crisis of the Earth scale

More important issue is the global plan for human populatioon to survive for the next 100-200 years minimum. We are not ready to return to Middle Ages tech

@zorrobandito “Earth's human population recently reached 8 billion people.”

“Here's where they live.”

At this point, I thought we were heading for planetary-scale doxxing 😀