Author

Silas Kieser

University of GenevaORCID 0000-0002-5935-9734Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:metagenomics· 4 Research Focus:benchmarking· 3 Research Focus:database / resource· 2 Research Focus:differential expression· 2 Approach:experimental assay· 2 Organism:human· 2 Research Focus:software / tool· 2 Approach:statistical model· 2

Frequent Co-Authors

Mirko TrajkovskiiD· 3 shared Evgeny M. ZdobnoviD· 2 shared Aaron E. DarlingiD· 1 shared Adrian FritziD· 1 shared Alessio MilaneseiD· 1 shared Alexandru Cristian· 1 shared Alexey A. GurevichiD· 1 shared Andrew S. WarreniD· 1 shared

Activity by Year

2020-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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3 shared papersBioinformatics

Mirko TrajkovskiORCID

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Author profile →

4 papers

Recent·Most cited

Shared species, strains and resistome between humans and pigs: A metagenomic analysis

Simeon Streit, Nadezda Kryuchkova-Mostacci, Julia Moor, Anne Oppliger, Silas Kieser, Markus Hilty

This study uses metagenomics to analyze microbial and resistome sharing between pigs and farmers, finding shared species and resistome signatures but no evidence of strain or mobile genetic element transmission.

bioRxiv · Sep 10, 2026 · PreprintMicrobiology

Human gut microbiota subspecies carry implicit information for in-depth microbiome research

Matija Tričković, Silas Kieser, Evgeny M. Zdobnov, Mirko Trajkovski

This paper defines human gut microbiota at subspecies resolution, identifies disease-associated subspecies, and shows that subspecies-level analysis improves CRC diagnosis compared to species-level methods.

Cell Host & Microbe · Aug 1, 2025Peer-reviewedBioinformatics

Critical Assessment of Metagenome Interpretation - the second round of challenges

Fernando Meyer, Adrian Fritz, Zhi-Luo Deng, David Koslicki, Till Robin Lesker, Alexey A. Gurevich, Gary Robertson, Mohammed Alser, Dmitry Antipov, Francesco Beghini, Denis Bertrand, Jaqueline Brito, C. Titus Brown, Jan P. Buchmann, Aydın Buluç, , Till Strowig

The paper evaluates metagenomic software tools using realistic datasets, highlighting improvements in assembly and taxon profiling while identifying remaining challenges in virus/archaea detection and reproducibility.

Nature Methods · Apr 1, 2022Peer-reviewedBioinformatics

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

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

ATLAS is a Snakemake workflow for processing metagenome data to assemble, annotate, and bin sequences into genomes and functional annotations.

BMC Bioinformatics · Jun 22, 2020Peer-reviewedBioinformatics