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Silas Kieser

@silask.bsky.social
97 followers 97 following 41 posts

Microbiome researcher, co-leader of a family of soon five, Developer of metagenome-atlas. silask.github.io

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Silas Kieser @silask.bsky.social · 09/12/2025
www.linkedin.com/posts/silas-...
linkedin.com
#phd #pancreaticcancer #bioinformatics #metagenomics #researchopportunity #universityofoulu #cancerresearch #translationalresearch #ngs | Silas Kieser
PhD Candidate Position in Pancreatic Cancer Metagenomics We're looking for a talented and motivated PhD candidate to join our translational research team at the University of Oulu! **The Opportunity...
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Silas Kieser @silask.bsky.social · 09/12/2025
New job opening in my previous lab: www.linkedin.com/feed/update/... What we are looking for • Strong interest in bioinformatics and disease mechanisms • Programming experience and familiarity with Unix • Diploma/MSc degree for PhD applicants or PhD degree for postdoc applicants
linkedin.com
PhD_postdoc_bioinformatics | Matija Trickovic
Our group at the University of Geneva is looking for a new PhD student and/or postdoctoral researcher in bioinformatics to join our work on the microbiome, metabolism and cancer. The person will take ...
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Silas Kieser @silask.bsky.social · 11/11/2025
@garymarcus.bsky.social If the AI models hallucinate is it a good idea to let robots run free? www.perplexity.ai/page/study-f...
perplexity.ai
Perplexity
Perplexity is a free AI-powered answer engine that provides accurate, trusted, and real-time answers to any question.
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Svetlana Ugarcina Perovic @svetlanaup.bsky.social · 05/09/2025
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!
microbiomedigest.com
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…
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Titus Brown @titus.idyll.org · 08/09/2025
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!
pubmed.ncbi.nlm.nih.gov
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...
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Tim Straub @timothystraub.com · 29/08/2025
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.
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Silas Kieser @silask.bsky.social · 29/08/2025
Link: silask.github.io/publication/...
silask.github.io
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...
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Silas Kieser @silask.bsky.social · 29/08/2025
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 · 29/08/2025
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 · 29/08/2025
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 · 29/08/2025
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 · 29/08/2025
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 · 29/08/2025
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 · 29/08/2025
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 · 29/08/2025
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 · 20/05/2025
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 · 14/02/2025
My supervisor finally agreed to post a preprint, but he said I should not publicize it on social media.. sad it is revolutionary...
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Silas Kieser @silask.bsky.social · 17/12/2024
Google voice typing needed 2y to be on the same level as Whisper, but it still cannot distinguish if I speak french or english ,🙄
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Silas Kieser @silask.bsky.social · 04/12/2024
That will be the future?
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Magda Grabowska @mmgrabow.bsky.social · 04/12/2024
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.
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Dr. Lucky Tran @luckytran.com · 01/12/2024
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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Antti Karkman @anttikarkman.bsky.social · 19/11/2024
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
Postdoctoral Researcher in Bioinformatics of the Human Gut Microbiome
Postdoctoral Researcher in Bioinformatics of the Human Gut Microbiome
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Blaise Reymondin @reymondin.bsky.social · 24/11/2024
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...
reymondin.notion.site
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
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Willem van Schaik @wvschaik.bsky.social · 28/11/2024
Vaccines work.
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Silas Kieser @silask.bsky.social · 28/11/2024
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
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Silas Kieser @silask.bsky.social · 20/11/2024
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 · 20/11/2024
I didn't know ncbi actually made a CLI to download genomes and gene sets github.com/ncbi/datasets
github.com
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
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Luis Pedro Coelho @luispedrocoelho.bsky.social · 19/11/2024
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...
link.springer.com
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...
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Silas Kieser @silask.bsky.social · 20/11/2024
Maybe its even too much asked from a supervisor. Be a at top of the biology as well as the bioinformatics
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Silas Kieser @silask.bsky.social · 11/11/2024
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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Silas Kieser @silask.bsky.social · 20/07/2024
This explains this controversed finding www.ncbi.nlm.nih.gov/pmc/articles...
ncbi.nlm.nih.gov
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...
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Silas Kieser @silask.bsky.social · 16/07/2024
Should we use blastocystis as probiotic?
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Stephen Turner @stephenturner.us · 13/06/2024
African elephants address one another with individually specific name-like calls www.nature.com/articles/s41...
nature.com
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.
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Silas Kieser @silask.bsky.social · 06/06/2024
And in theory the full proposal inc milestones should be useful for the doing the project once the grant is awarded.
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Christopher Madan @engra.me · 03/06/2024
"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
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...
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Silas Kieser @silask.bsky.social · 03/06/2024
Someone tried threads?
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Silas Kieser @silask.bsky.social · 29/05/2024
Ask chatgpt to be a tutor for german - dutch .
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Silas Kieser @silask.bsky.social · 18/05/2024
www.nature.com/articles/d41...
nature.com
Gut microbes linked to fatty diet drive tumour growth
Scientists know there is a link between obesity and some cancers. A study in mice and people suggests why that might be. Scientists know there is a link between obesity and some cancers. A study in mi...
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Silas Kieser @silask.bsky.social · 03/05/2024
The author meant that almost all allongement algorithms in bioinformatics could be made more precise (not necessarily faster).
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Silas Kieser @silask.bsky.social · 03/05/2024
Who had thought that something as basic as sequence alignment can still be improved www.research-collection.ethz.ch/handle/20.50...
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Silas Kieser @silask.bsky.social · 23/04/2024
And I complain, when my ssh connection is delayed for halve a second. What about coding with 22h delay blogs.nasa.gov/voyager/2024...
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Silas Kieser @silask.bsky.social · 22/04/2024
Bonjour, si je comprends bien. on risque des grosses pertes agricoles à cause de gel après les plantes ont déjà débourré?
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Silas Kieser @silask.bsky.social · 20/04/2024
What about (high-)Throughput Evaluation of bacTeRIal Survivability T,R,I from bacterial
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Silas Kieser @silask.bsky.social · 20/04/2024
www.science.org/podcasts?sta...
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Jesse Shapiro @bjesseshapiro.bsky.social · 19/04/2024
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...
science.org
Phage predation, disease severity, and pathogen genetic diversity in cholera patients
Despite an increasingly detailed picture of the molecular mechanisms of bacteriophage (phage)–bacterial interactions, we lack an understanding of how these interactions evolve and impact disease withi...
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Silas Kieser @silask.bsky.social · 07/04/2024
Inspiring! German state ditches Microsoft for Linux and LibreOffice
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Eric Topol @erictopol.bsky.social · 03/04/2024
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....
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Suguru Nishijima @suguru-nishijima.bsky.social · 19/03/2024
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...
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Matt Olm @mattolm.bsky.social · 14/03/2024
A fantastic postdoc position in bioinformatic microbiome research is available in Justin Sonnenburg's lab at Stanford! I'm leaving after 4 great years to start my lab at Boulder, and Justin is looking to fill my position. DM me or email Justin (Admin_Sonnenburg@stanford.edu) for questions
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 15/03/2024
Expanding the human gut microbiome atlas of Africa www.biorxiv.org/content/10.1101/202…
biorxiv.org
Expanding the human gut microbiome atlas of Africa https://www.biorxiv.org/content/10.1101/2024.03.13.584859v1
Population studies are crucial in understanding the complex interplay between the gut microbiome and
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