Silas Kieser

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.

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...

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

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.

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.

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.

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

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.

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.

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

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

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...

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

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

That will be the future?

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.

10 INCREDIBLE ways to BOOST your immune system:

The Measles vaccine
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The Polio vaccine
The HPV vaccine
The Pneumonia vaccine
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The Covid-19 vaccine

Postdoctoral Researcher in Bioinformatics of the Human Gut Microbiome Postdoctoral Researcher in Bioinformatics of the Human Gut Microbiome

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...

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

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...

Vaccines work.

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

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.

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

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

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...

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...

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

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?

Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon Synonymous codons translate into chemically identical amino acids. Once considered inconsequential to the formation of the protein product, there is evidence to suggest that codon usage affects co-tra...

This explains this controversed finding www.ncbi.nlm.nih.gov/pmc/articles...

Should we use blastocystis as probiotic?

African elephants address one another with individually specific name-like calls - Nature Ecology & Evolution Machine learning analyses and playback experiments in wild African elephants suggest that individuals address conspecifics with name-like calls that do not rely on imitation of the receiver.

African elephants address one another with individually specific name-like calls www.nature.com/articles/s41...

And in theory the full proposal inc milestones should be useful for the doing the project once the grant is awarded.

Do grant proposal texts matter for funding decisions? A field experiment - Scientometrics Scientists and funding agencies invest considerable resources in writing and evaluating grant proposals. But do grant proposal texts noticeably change panel decisions in single blind review? We report...

"A random half of panelists were shown a CV and only a one-paragraph summary of the proposed research, while the other half were shown a CV and a full proposal. We find that withholding proposal texts from panelists did not detectibly impact their proposal rankings"
link.springer.com/article/10.1...