Silas Kieser
@silask.bsky.social
Microbiome researcher, co-leader of a family of soon five, Developer of metagenome-atlas. silask.github.io
www.linkedin.com/posts/silas-...
#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...
linkedin.com
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
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 ...
linkedin.com
@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
Perplexity is a free AI-powered answer engine that provides accurate, trusted, and real-time answers to any question.
perplexity.ai
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!
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
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
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 · 12mo agoNew paper out: Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research.
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 ,🙄
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 is just… so tired.@wolven.blacksky.app · 2y agoFirst 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...
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
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
Postdoctoral Researcher in Bioinformatics of the Human Gut Microbiome
jobs.helsinki.fi
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
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
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
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.
nature.com
"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...
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
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...
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...
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...
science.org
Jesse Shapiro@bjesseshapiro.bsky.social · 3y agoRevised preprint: Phage predation is a biomarker for disease severity and shapes pathogen genetic diversity in cholera patients. To support major conclusions, we repeated key analyses using qPCR instead of metagenomics to quantify phage ICP1 and V. cholerae www.biorxiv.org/content/10.1...
Inspiring! German state ditches Microsoft for Linux and LibreOffice
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....
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...
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
Expanding the human gut microbiome atlas of Africa https://www.biorxiv.org/content/10.1101/2024.03.13.584859v1
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
biorxiv.org
I thought the Biodynamic farm at EPFL was as low as it gets @skepteis.bsky.social www.science.org/doi/abs/10.1...
Teach Indigenous knowledge alongside science
Evidence supports the teaching of Indigenous knowledge alongside sciences in the classroom
science.org
