Silas Kieser

Silas Kieser

Metagenome researcher

University of Geneva

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.

I’m finishing my PhD at the University of Geneva in the lab of Prof. Mirko Trajkovski, co-supervised by Prof. Evgeny Zdobnov. 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 & Upcoming Talks

Lecture at the Functional genomics center
Slides Content: A brief hisotry of genome-resolved metagenomics See the introduction of my thesis. Metagenome-atlas Compositional data analysis See Ch. 5 of my thesis. Genome catalogs For direct use of the mouse or human genome catalog see github.
7. Apr 2022 10:30 Zurich
Silas Kieser
Project Reactions
3-day course on Metagenome-atlas
Metagenome-atlas Three commands to start analysing your metagenome data
3. Sep 2021 22:50 — 4. Oct 2021 17:00 virtual
Silas Kieser
Project Reactions
3-day course on Metagenome-atlas
My PhD defence
I will soon graduate. I would love you to be part of this event in one way or another. Please register.
3. Sep 2021 16:30
My PhD defence

Recent Posts

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
3 ways to improve genome catalogs
Der Booster der keiner ist
Die Entwicklung der Corona-Impfung war vielleicht doch etwas zu rasch. Warum ich mich trotzdem boostern lasse.
Silas Kieser
Last updated on 17. Jan 2022
It is finished!
I finished writing my PhD Thesis with the title: Computational approaches for a healthier microbiome You can peak inside here. I made a small graphic how many words I wrote over time.
Silas Kieser
12. May 2021 PhD
It is finished!

Experience

 
 
 
 
 
University of Geneva
PhD
University of Geneva
May 2017 – Present
 
 
 
 
 
Nestlé Health Sciences
Microbiome data analyst
Nestlé Health Sciences
Apr 2016 – Mar 2017
Relating microbiota data to human health (See Publications)
 
 
 
 
 
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

Featured Publications

Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart
Mouse is the most used model for studying the impact of microbiota on its host, but the rep- ertoire of species from the mouse gut …
Silas Kieser, Evgeny M. Zdobnov, Mirko Trajkovski
Code Dataset Project DOI
Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart
Warmth Prevents Bone Loss Through the Gut Microbiota
Warmth exposure (34°C) protects against ovariectomy-induced bone loss in adult female, as well as in young male mice. Transplantation of the warm-adapted microbiota phenocopies the warmth-induced bone effects.
Chevalier Claire, Silas Kieser, Melis Çolakoğlu, Noushin Hadadi, Julia Brun, Dorothée Rigo, Nicolas Suárez-Zamorano, Martina Spiljar, Salvatore Fabbiano, Björn Busse, Julijana Ivanišević, Andrew Macpherson, Nicolas Bonnet, Mirko Trajkovski
Video DOI
Warmth Prevents Bone Loss Through the Gut Microbiota
Bangladeshi children with acute diarrhoea show faecal microbiomes with increased Streptococcus abundance, irrespective of diarrhoea aetiology
We report streptococcal dysbiosis in acute diarrhoea irrespective of aetiology. Compared with 20 healthy local controls, 71 Bangladeshi …
Silas Kieser, Shafiqul A. Sarker, Olga Sakwinska, FrancisFoata, Shamima Sultana, Zeenat Khan, Shoheb Islam, Nadine Porta, Séverine Combremont, Bertrand Betrisey, Coralie Fournier, Aline Charpagne, Patrick Descombes, Annick Mercenier, Bernard Berger, Brüssow Harald
Project DOI
Bangladeshi children with acute diarrhoea show faecal microbiomes with increased Streptococcus abundance, irrespective of diarrhoea aetiology
Antibiotic Treatment Leads to Fecal Escherichia coli and Coliphage Expansion in Severely Malnourished Diarrhea Patients
Malnutrition predisposes to diarrhea and diarrhea adversely affects the nutritional status creating a vicious cycle. The role of the …
Silas Kieser, Shafiqul A. Sarker, Bernard Berger, Shamima Sultana, Mohammed J. Chisti, Shoeb B. Islam, Francis Foata, Nadine Porta, Bertrand Betrisey, Coralie Fournier, Patrick Descombes, Annick Mercenier, Olga Sakwinska, Harald Brüssow
Project DOI
Antibiotic Treatment Leads to Fecal Escherichia coli and Coliphage Expansion in Severely Malnourished Diarrhea Patients

Popular Topics

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

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