Author

Jochen Singer

SIB Swiss Institute of BioinformaticsORCID 0000-0003-0001-8625Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1 Genomics· 1 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Organism:human· 2 Approach:statistical model· 2 Research Focus:variant calling· 2 Approach:Bayesian inference· 1 Assay:bulk RNA-seq· 1 Research Focus:differential expression· 1 Organism:non-human primate· 1 Research Focus:phylogenetics / evolution· 1

Frequent Co-Authors

Jack KuipersiD· 2 shared Niko BeerenwinkeliD· 2 shared Eloïse HudryiD· 1 shared Fumiaki AiharaiD· 1 shared Karine Bigot· 1 shared Katharina JahniD· 1 shared Keith Mansfield· 1 shared Mathew Mardo· 1 shared

Activity by Year

2018-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 24 mutual co-author links

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2 shared papersGenomics

Jack KuipersORCID

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3 papers

Recent·Most cited

Molecular BiologyMolecular Therapy — Methods & Clinical DevelopmentPeer-reviewedOct 17, 2025

Transcriptional changes in non-human primate tissues after intrathecal delivery of serotype 9 adeno-associated viral vector: insights into organ toxicities

Fumiaki Aihara, Mathew Mardo, Vera M. Ruda…·Eloïse Hudry

This study examines transcriptional changes in non-human primate tissues after AAV9 vector delivery, finding significant immune-related gene upregulation in liver and DRG.

1 citation

non-human primatebulk RNA-seq

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GenomicsBioinformaticsPeer-reviewedAug 24, 2022

Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence

Jack Kuipers, Jochen Singer, Niko Beerenwinkel

This paper presents a Bayesian method to call mutations and reconstruct phylogenetic trees from single-cell tumour sequencing data, accounting for mutational loss and recurrence.

14 citations

humanwhole-genome sequencing

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BioinformaticsNature CommunicationsPeer-reviewedNov 28, 2018

SCIΦ: Single-cell mutation identification via phylogenetic inference

Jochen Singer, Jack Kuipers, Katharina Jahn, Niko Beerenwinkel

SCIΦ identifies mutations in single-cell tumor data by inferring phylogenetic relationships, outperforming existing methods on simulated and real datasets.

95 citations

humanwhole-exome sequencing

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