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Reposted by Silas Kieser

Tim Straub @timothystraub.com · Aug 29

This looks really promising! It’s a step in the right direction to drill down to a more function based microbiome analysis while still maintaining taxonomic information.

Silas Kieser @silask.bsky.social · Aug 29

New paper out: Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research.

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Silas Kieser @silask.bsky.social · Aug 29

Link: silask.github.io/publication/...

Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research | Silas Kieser

Tričković et al. develop a comprehensive genomic human gut microbiota subspecies catalog by defining operational subspecies units (OSUs) in an unbiased, cohort-independent manner. Panhashome, a sketch...

silask.github.io

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Silas Kieser @silask.bsky.social · Aug 29

Because our subspecies are genome-based, we can identify specific genes or mutations that explain differential associations. This provides a direct path to mechanistic understanding.

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Silas Kieser @silask.bsky.social · Aug 29

We found many cases where only one subspecies associates with disease while sibling-subspecies don't. Sometimes no association is detected at species level because opposing subspecies associations cancel each other out.

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Silas Kieser @silask.bsky.social · Aug 29

Why it matters: Subspecies explain disease associations invisible at the species level. For example, in colorectal cancer, subspecies-based ML models consistently outperformed species-level ones.

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Silas Kieser @silask.bsky.social · Aug 29

We created a sourmash-based method for fast & accurate subspecies quantification, enabling large-scale analysis across entire datasets, e.g., the whole SRA.

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Silas Kieser @silask.bsky.social · Aug 29

We built HuMSub: the most comprehensive catalog of human gut microbiota subspecies (5,361 OSUs across 977 species).
We found that 1/3 of species in the human gut have subspecies, most of which we knew nothing about.

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Silas Kieser @silask.bsky.social · Aug 29

Going down to the strain-level isn't useful for most comparative studies, because everyone has person-specific strains for most of their microbes!
We need an intermediate level: Subspecies.

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Silas Kieser @silask.bsky.social · Aug 29

Most microbiome studies stop at the species level. But strains within a species can differ dramatically in function. This obscures associations and limits reproducibility.

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Silas Kieser @silask.bsky.social · Aug 29

New paper out: Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research.

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Silas Kieser @silask.bsky.social · May 20

What do you think about our latest pre-print?

1/3 of human microbioal species have, mostly neglected, subspecies.

Human gut microbiota subspecies carry implicit information for in-depth microbiome research
doi.org/10.1101/2025...

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Silas Kieser @silask.bsky.social · Feb 14

My supervisor finally agreed to post a preprint, but he said I should not publicize it on social media.. sad it is revolutionary...

Silas Kieser @silask.bsky.social · Dec 17

Google voice typing needed 2y to be on the same level as Whisper, but it still cannot distinguish if I speak french or english ,🙄

Silas Kieser @silask.bsky.social · Dec 4

That will be the future?

Magda Grabowska @mmgrabow.bsky.social · Dec 4

I worry less about AI taking my job and more about how much of my job becomes 1) verifying AI-generated claims and 2) figuring out where the AI went wrong and fixing it.

Dr. Damien P. Williams Wants A Better Sociotechnical Paradigm @wolvendamien.bsky.social · Jun 15

First Sundar Pichai, now Tim Cook, both admitting that generative "AI," by dint of its very foundations (cf. "Bias Optimizers"), will not and cannot stop bullshitting (cf. "On Bullshit Engines").

futurism.com/the-byte/tim...

Reposted by Silas Kieser

Magda Grabowska @mmgrabow.bsky.social · Dec 4

I worry less about AI taking my job and more about how much of my job becomes 1) verifying AI-generated claims and 2) figuring out where the AI went wrong and fixing it.

Dr. Damien P. Williams Wants A Better Sociotechnical Paradigm @wolvendamien.bsky.social · Jun 15

First Sundar Pichai, now Tim Cook, both admitting that generative "AI," by dint of its very foundations (cf. "Bias Optimizers"), will not and cannot stop bullshitting (cf. "On Bullshit Engines").

futurism.com/the-byte/tim...

Tim Cook Admits Apple May Never Be Able to Make Its AI Stop Lying

In a new Washington Post interview, Apple CEO Tim Cook admitted that he's not "100 percent" sure the company's AI will stop lying.

futurism.com

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Reposted by Silas Kieser

Dr. Lucky Tran @luckytran.com · Dec 1

10 INCREDIBLE ways to BOOST your immune system:

The Measles vaccine
The Mumps vaccine
The Rubella vaccine
The Tetanus vaccine
The Diphtheria vaccine
The Polio vaccine
The HPV vaccine
The Pneumonia vaccine
The Hepatitis B vaccine
The Covid-19 vaccine

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Reposted by Silas Kieser

Antti Karkman @anttikarkman.bsky.social · Nov 19

There’s an open postdoc position in our EIC funded project FIBRE-MATCH at the University of Helsinki, Finland. Further information in the ad.
jobs.helsinki.fi/job-invite/3...

Postdoctoral Researcher in Bioinformatics of the Human Gut Microbiome

jobs.helsinki.fi

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Reposted by Silas Kieser

Blaise Reymondin @reymondin.bsky.social · Nov 24

J’ai regroupé dans ce stack les outils #IA que j’utilise ou que je trouve dignes d’intérêt. 🤖

Cette liste est vouée à évoluer chaque semaine, vu les évolutions incessantes dans le domaine. N'hésitez pas à me dire s'il manque quelque chose 🙂

reymondin.notion.site/144643c1f676...

Notion – The all-in-one workspace for your notes, tasks, wikis, and databases.

A new tool that blends your everyday work apps into one. It's the all-in-one workspace for you and your team

reymondin.notion.site

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Reposted by Silas Kieser

Willem van Schaik @wvschaik.bsky.social · Nov 28

Vaccines work.

JAMA @jama.com · Nov 28

Cervical cancer mortality in US women younger than 25 years significantly declined between 2016 and 2021, likely due to the widespread adoption of HPV vaccination.

ja.ma/4i9ghPC

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Silas Kieser @silask.bsky.social · Nov 28

Yes, the church leaders acepted heliocentrism once the evidence convinced them that's better for calculating dates. I don't think any evidence could convince RFK Jr

Silas Kieser @silask.bsky.social · Nov 20

I find surprising that CLR is not helpful for the associations, rather it is counterproductive.

But then they didn't used the multiplicative replacement for zero-imputing.

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Silas Kieser @silask.bsky.social · Nov 20

I didn't know ncbi actually made a CLI to download genomes and gene sets github.com/ncbi/datasets

GitHub - ncbi/datasets: NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.

NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. - ncbi/datasets

github.com

Reposted by Silas Kieser

Luis Pedro Coelho @luispedrocoelho.bsky.social · Nov 19

Reading "A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies" from our friends in Berlin and in Leiden

Quotes are from the paper (minor edits for space), non quoted text is me

link.springer.com/article/10.1...

A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies - Genome Biology

Background In microbiome disease association studies, it is a fundamental task to test which microbes differ in their abundance between groups. Yet, consensus on suitable or optimal statistical method...

link.springer.com

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Silas Kieser @silask.bsky.social · Nov 20

Maybe its even too much asked from a supervisor. Be a at top of the biology as well as the bioinformatics

Silas Kieser @silask.bsky.social · Nov 11

Google doc is the hit.

Would you do it even though MS office is offered by the institution? Do you use a personal Foogle doc account?

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