Silas Kieser

Silas Kieser

Metagenome researcher

Developer of Metagenome-Atlas

About me

I’m fascinated by the microbiome and search for ways to harness it to make us healthier.

When I first learned about metagenomics, I found the idea of sequencing thousand of microbial genomes at once mind-boggling. I’m happy to be part of this endeavor to resolve these enormous puzzles and recover genomes from metagenomes. Besides microbiome analysis at the computer, I’m also hands-on involved by changing the diapers of my two children.

Interests
  • Metagenomics
  • Human gut microbiota
  • Apologetics
Education

  • PhD, 2021

    Université de Genève

  • Bioengineer, 2017

    École polytechnique fédérale de Lausanne

Recent Posts

HPC Server: The tricks you need to know
Connecting to a high-performance computing (HPC) server might seem daunting at first. However, with the right tools and guidance, it can be a straightforward process. This blog post aims to demystify the connection process, making it accessible to both novices and seasoned users.
Silas Kieser
7. Nov 2023 5 min read Bioinformatics, Bash
HPC Server: The tricks you need to know
Science et foi: Union insensée?
Note : Ce blog est adapté d’une présentation donnée aux Big Questions 2022. Mon point de vue a évolué depuis sur certains détails. Table of Contents 1. La religion fournit le cadre conceptuel dans lequel la science peut s’épanouir.
7. Nov 2023 10 min read Français, apologetics
Binning with more than one Sample
Recent years we saw an explosion of genomes beeing assembled from megagenomes. Most of the studies assemble and bin each sample individually, because this is the most scalable. Maybe it’s time to think if this approach is really the best?
Silas Kieser
11. Aug 2023 3 min read Binning, Metagenomics
Try out Quarto
Quarto Quarto and Hugo Quarto Quarto is the successor to R-markdown. Drawing heavily from tools like Pandoc, it not only supports R but also allows the inclusion and execution of Python code, even through a Jupyter interface.
Silas Kieser
Last updated on 11. Aug 2023 2 min read Website, Coding
3 ways to improve genome catalogs
Metagenomics has revoluzionized microbiology. This sequencing technology enables researchers to gain insight into the composition and functional potential of a microbial community in situ. Even though it is called metagenomics, the sequenced reads were not analyzed on a genome level due to technical limitations, especially the lack of reference genomes for many microbiomes.
Last updated on 12. Apr 2022 6 min read
3 ways to improve genome catalogs
See all posts

Recent & Upcoming Talks

ESA Planetary Protection Workshop
Speaking at the ESA Planetary Protection Workshop on Assessing metagenomic methods for their inclusion in ESA standards.
3. Oct 2023 00:00 — 4. Oct 2023 23:59 ESTEC, Noordwijk, The Netherlands
Silas Kieser
Project
Tutorial at the ISMB 2023
A Tutorial about Metagenome-Atlas at the ISMB/ECCB conference
17. Jul 2023 — 18. Jul 2023 Remote
Silas Kieser
Code Project Register
Tutorial at the ISMB 2023
Talk at the Lausanne Comp Bio Meeting
Talk title: Decoding the Microbial Universe: Large-Scale Metagenomics at the Sub-Species Level
14. Jun 2023 10:00 — 12:30 University of Lausanne
Silas Kieser
Project
Lecture at the Functional genomics center 2023
Content In preparation. Already have a look at the course from last year
30. Mar 2023 13:00 Zurich
Silas Kieser
Project
Invited talk at the Swedish University of Agricultural Science
Prof. Samuel Flores, dean of Students for MedBioInfo, the Swedish National Research School in Medical Bioinformatics, invited me to give a talk on metagenomics. This was a fantastic opportunity to discuss how metagenomics can be used in a variety of research projects.
30. Nov 2022 Swedish University of Agricultural Science
Project
Invited talk at the Swedish University of Agricultural Science
See all events

Experience

 
 
 
 
 
Nestlé Health Sciences
Microbiome data specialist
Nestlé Health Sciences
Sep 2022 – Aug 2023
  • Automation of microbiome analysis for clinical trials using R-markdown
  • Strain-analysis of the airways-microbiome
  • Publications
 
 
 
 
 
University of Geneva
PhD
University of Geneva
May 2017 – Aug 2021
 
 
 
 
 
École polytechnique fédérale de Lausanne
Master in Bioengineering
École polytechnique fédérale de Lausanne
Sep 2011 – Mar 2017
Minor in Biocomputing
Courses include: Machine learning, Genomics and genetics, and Entrepreneurship
Grade: 5.12/6

Popular Topics

apologetics Binning Bioinformatics ESA Genome-resolved metagenomics human gut microbiota Metagenome-assembled genomes metagenome-atlas metagenomics Nestlé phages PhD PhD thsis Snakemake subspecies teaching Virus

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