Author

Fabienne Estermann

University of BaselORCID 0000-0002-9629-4386Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Organism:bacteria (other)· 1 Research Focus:batch correction / integration· 1 Assay:bulk RNA-seq· 1 Research Focus:cell type annotation· 1 Organism:E. coli· 1 Approach:experimental assay· 1 Research Focus:host-pathogen & immune response· 1 Organism:human· 1

Frequent Co-Authors

Adrian EgliiD· 1 shared Aisylu ShaidullinaiD· 1 shared Alejandro Tejada-ArranziD· 1 shared Alexander HarmsiD· 1 shared Alexia FerrandiD· 1 shared Aline Amani Loriol· 1 shared Aline CuénodiD· 1 shared Anne-Kathrin WoischnigiD· 1 shared

Activity by Year

2022-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 16 mutual co-author links

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1 shared paperMicrobiology

Adrian EgliORCID

Mutual co-authors in cluster

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3 papers

Recent·Most cited

Microgeography of staphyloccoci in human tissue explains antibiotic failure

Vishwachi Tripathi, Benedict Morin, Minia Antelo-Varela, Aline Amani Loriol, Kristiina Kurg, Sandro Jakonia, Asvin Ehsan, Sébastien Herbert, Alexia Ferrand, Loïc Sauteur, Florian C Marro, Noemi Henselmann, Jasmin Künnecke, Fabienne Estermann, Kerstin Strenger, , Dirk Bumann

The paper maps Staphylococcus aureus microgeography in human tissue using AI-guided imaging and finds antibiotic failure is linked to intracellular bacterial persistence and metabolic constraints.

bioRxiv · Sep 12, 2025 · PreprintMicrobiology

Completing the BASEL phage collection to unlock hidden diversity for systematic exploration of phage-host interactions

Dorentina Humolli, Damien Piel, Enea Maffei, Yannik Heyer, Elia Agustoni, Aisylu Shaidullina, Luc Willi, Patrick Imwinkelried, Fabienne Estermann, Aline Cuénod, Dominik P. Buser, Carola Alampi, Mohamed Chami, Adrian Egli, Sebastian Hiller, , Alexander Harms

The paper completes the BASEL phage collection by overcoming host limitations to isolate new phages, revealing insights into viral host recognition and bacterial immunity.

PLoS Biology · Apr 7, 2025Peer-reviewedMicrobiology

reComBat: Batch effect removal in large-scale, multi-source omics data integration

Michael F. Adamer, Sarah C. Brüningk, Alejandro Tejada-Arranz, Fabienne Estermann, Marek Basler, Karsten Michael Borgwardt

reComBat removes batch effects from large-scale, multi-source omics data while preserving biological variation, outperforming existing methods for public gene expression data of Pseudomonas aeruginosa.

Bioinformatics Advances · Jan 1, 2022Peer-reviewedBioinformatics