Silas Kieser

Embedded Bioinformatician and PhD candidate

University of Geneva

Biography

I’m studying the link between alterations in the gut microbiota and the glucose homeostasis in mice using metagenomics and other omics-approaches. An internship at Nestlé research center allowed me to learn from experts about children gut microbiota and to realize my first publications. Now, I’m doing a PhD at University of Geneva in the lab of Prof. Mirko Trajkovski and are co-supervised by Prof. Evgeny Zdobnov. I like to cook with my wife and to dance Salsa, but not both on the same time.

Interests

Metagenomics
Human gut microbiota
Apologetics

Education

Bioengineer, 2017

École polytechnique fédérale de Lausanne

Featured Publications

Silas Kieser, Joseph Brown, Evgeny M. Zdobnov, Mirko Trajkovski, Lee Ann McCue

October 2019 bioRxiv bioinformatics

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

ATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome and metatranscriptome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas.

Project DOI

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

December 2017 CMGH human gut microbiota

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. 1 The role of the gut microbiome in malnutrition is an active research area. 2 Parenteral antibiotics are recommended by the World Health Organization in hospitalized pediatric patients with severe acute malnutrition (SAM) presenting signs of infections.3 Stool microbiota data for such patients are, however, lacking. To fill this gap, we studied the stool microbiota in 19 SAM patients from Bangladesh hospitalized with acute diarrhea (AD) and compared it with that of matched 20 healthy control subjects (HC).