Silas Kieser
@silask.bsky.social
Microbiome researcher, co-leader of a family of soon five, Developer of metagenome-atlas.
silask.github.io
silask.github.io
@garymarcus.bsky.social
If the AI models hallucinate is it a good idea to let robots run free?
www.perplexity.ai/page/study-f...
If the AI models hallucinate is it a good idea to let robots run free?
www.perplexity.ai/page/study-f...
Perplexity
Perplexity is a free AI-powered answer engine that provides accurate, trusted, and real-time answers to any question.
www.perplexity.ai
November 11, 2025 at 9:37 AM
@garymarcus.bsky.social
If the AI models hallucinate is it a good idea to let robots run free?
www.perplexity.ai/page/study-f...
If the AI models hallucinate is it a good idea to let robots run free?
www.perplexity.ai/page/study-f...
Reposted by Silas Kieser
New #MicrobiomeDigest is OUT microbiomedigest.com/2025/09/04/s...
• subspecies of the human gut microbiota / @silask.bsky.social
• red grouse microbiota / @microbes4ever.bsky.social
• "Biopolis – into the microbiome" podcast
• invitation for the next week #GloMiNe2025
& more.
Happy Friday!
• subspecies of the human gut microbiota / @silask.bsky.social
• red grouse microbiota / @microbes4ever.bsky.social
• "Biopolis – into the microbiome" podcast
• invitation for the next week #GloMiNe2025
& more.
Happy Friday!
September 5, 2025
See you next week at #GloMiNe2025! Gut microbiome Gut fungi are associated with human genetic variation and disease risk – Emily P. Van Syoc – Plos Biology The resident gut microbiome modulates the…
microbiomedigest.com
September 5, 2025 at 5:42 AM
New #MicrobiomeDigest is OUT microbiomedigest.com/2025/09/04/s...
• subspecies of the human gut microbiota / @silask.bsky.social
• red grouse microbiota / @microbes4ever.bsky.social
• "Biopolis – into the microbiome" podcast
• invitation for the next week #GloMiNe2025
& more.
Happy Friday!
• subspecies of the human gut microbiota / @silask.bsky.social
• red grouse microbiota / @microbes4ever.bsky.social
• "Biopolis – into the microbiome" podcast
• invitation for the next week #GloMiNe2025
& more.
Happy Friday!
Reposted by Silas Kieser
There are two recent papers that use sourmash in creative ways - and it gladdens my heart! pubmed.ncbi.nlm.nih.gov/40812187/ by @silask.bsky.social et al looks cleverly at human gut subspecies. www.biorxiv.org/content/10.1... by @rayanchikhi.bsky.social et al counts billions of k-mers. Super neat!
Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research - PubMed
Microbial strains within a single species can exhibit distinct functional characteristics due to variations in gene content and often show individual specificity, which can obscure unbiased associatio...
pubmed.ncbi.nlm.nih.gov
September 8, 2025 at 1:49 PM
There are two recent papers that use sourmash in creative ways - and it gladdens my heart! pubmed.ncbi.nlm.nih.gov/40812187/ by @silask.bsky.social et al looks cleverly at human gut subspecies. www.biorxiv.org/content/10.1... by @rayanchikhi.bsky.social et al counts billions of k-mers. Super neat!
Reposted by 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.
New paper out: Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research.
August 29, 2025 at 10:03 PM
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.
New paper out: Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research.
August 29, 2025 at 10:06 AM
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...
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...
May 20, 2025 at 8:42 PM
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...
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...
February 14, 2025 at 6:17 PM
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 ,🙄
December 17, 2024 at 11:33 AM
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.
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...
futurism.com/the-byte/tim...
December 4, 2024 at 9:17 PM
That will be the future?
Reposted by Silas Kieser
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.
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...
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
December 4, 2024 at 3:40 PM
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.
Reposted by Silas Kieser
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
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
December 1, 2024 at 9:19 PM
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
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
Reposted by Silas Kieser
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...
jobs.helsinki.fi/job-invite/3...
Postdoctoral Researcher in Bioinformatics of the Human Gut Microbiome
Postdoctoral Researcher in Bioinformatics of the Human Gut Microbiome
jobs.helsinki.fi
November 19, 2024 at 3:12 PM
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...
jobs.helsinki.fi/job-invite/3...
Reposted by Silas Kieser
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...
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
November 24, 2024 at 5:45 PM
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...
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...
Reposted by Silas Kieser
Vaccines work.
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
ja.ma/4i9ghPC
November 28, 2024 at 8:26 AM
Vaccines work.
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
November 20, 2024 at 8:11 AM
I didn't know ncbi actually made a CLI to download genomes and gene sets github.com/ncbi/datasets
Reposted by Silas Kieser
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...
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
November 19, 2024 at 7:09 AM
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...
Quotes are from the paper (minor edits for space), non quoted text is me
link.springer.com/article/10.1...
Reposted by Silas Kieser
African elephants address one another with individually specific name-like calls www.nature.com/articles/s41...
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.
www.nature.com
June 13, 2024 at 3:27 PM
African elephants address one another with individually specific name-like calls www.nature.com/articles/s41...
Reposted by Silas Kieser
"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...
link.springer.com/article/10.1...
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...
link.springer.com
June 3, 2024 at 9:26 PM
"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...
link.springer.com/article/10.1...
Who had thought that something as basic as sequence alignment can still be improved www.research-collection.ethz.ch/handle/20.50...
May 3, 2024 at 6:38 AM
Who had thought that something as basic as sequence alignment can still be improved www.research-collection.ethz.ch/handle/20.50...
And I complain, when my ssh connection is delayed for halve a second. What about coding with 22h delay blogs.nasa.gov/voyager/2024...
April 23, 2024 at 5:33 AM
And I complain, when my ssh connection is delayed for halve a second. What about coding with 22h delay blogs.nasa.gov/voyager/2024...
Reposted by Silas Kieser
Now published: "Phage predation, disease severity, and pathogen genetic diversity in cholera patients"
www.science.org/doi/10.1126/...
Check out the podcast to hear co-senior author Eric Nelson talk about the twists and turns of our study (around 18:25):
www.science.org/content/podc...
www.science.org/doi/10.1126/...
Check out the podcast to hear co-senior author Eric Nelson talk about the twists and turns of our study (around 18:25):
www.science.org/content/podc...
April 19, 2024 at 7:28 PM
Now published: "Phage predation, disease severity, and pathogen genetic diversity in cholera patients"
www.science.org/doi/10.1126/...
Check out the podcast to hear co-senior author Eric Nelson talk about the twists and turns of our study (around 18:25):
www.science.org/content/podc...
www.science.org/doi/10.1126/...
Check out the podcast to hear co-senior author Eric Nelson talk about the twists and turns of our study (around 18:25):
www.science.org/content/podc...
Inspiring! German state ditches Microsoft for Linux and LibreOffice
April 7, 2024 at 1:27 PM
Inspiring! German state ditches Microsoft for Linux and LibreOffice
Reposted by Silas Kieser
Some exciting GLP-1 drug new randomized trial evidence for potential disease-modifying impact on Parkinson's disease (there are none).
No progression of motor disability in the Rx group for 12 months.
nejm.org/doi/full/10....
No progression of motor disability in the Rx group for 12 months.
nejm.org/doi/full/10....
April 3, 2024 at 9:09 PM
Some exciting GLP-1 drug new randomized trial evidence for potential disease-modifying impact on Parkinson's disease (there are none).
No progression of motor disability in the Rx group for 12 months.
nejm.org/doi/full/10....
No progression of motor disability in the Rx group for 12 months.
nejm.org/doi/full/10....
Reposted by Silas Kieser
Excited to share our latest preprint on a novel computational tool to predict fecal microbial load solely from relative species profiles! Our study revealed that fecal microbial load is a substantial confounder in microbiome-disease association studies.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
March 19, 2024 at 11:41 AM
Excited to share our latest preprint on a novel computational tool to predict fecal microbial load solely from relative species profiles! Our study revealed that fecal microbial load is a substantial confounder in microbiome-disease association studies.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...