Author

Arianne M. Brandsma

Oncode InstituteORCID 0000-0002-7969-4046Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:whole-genome sequencing· 3 Organism:human· 2 Approach:statistical model· 2 Research Focus:variant calling· 2 Research Focus:benchmarking· 1 Approach:machine learning (classical)· 1 Approach:simulation· 1 Research Focus:software / tool· 1

Frequent Co-Authors

Mark VerheuliD· 3 shared Markus J. van RoosmaleniD· 3 shared Ruben van BoxteliD· 3 shared Eline J.M. BertrumsiD· 2 shared Freek MandersiD· 2 shared Laurianne TrabutiD· 2 shared Lucca L. M. DerksiD· 2 shared Sjors MiddelkampiD· 2 shared

Activity by Year

2022-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 39 mutual co-author links

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3 shared papersGenomics

Mark VerheulORCID

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3 papers

Recent·Most cited

Somatic variant detection using an individual-specific pangenome reference: a case study of a pediatric acute myeloid leukemia patient

Elizaveta Kulaeva, Eline J.M. Bertrums, Markus J. van Roosmalen, Rico Hagelaar, Lucca L. M. Derks, Laurianne Trabut, Arianne M. Brandsma, Mark Verheul, Matteo Boretto, Sjors Middelkamp, Pjotr Prins, Ruben van Boxtel, Andrea Guarracino

This study evaluates the impact of an individual-specific pangenome on somatic variant calling in a pediatric AML patient, finding reduced false positives and altered phylogenetic branching.

bioRxiv · Oct 30, 2026 · PreprintGenomics

Comprehensive single-cell genome analysis at nucleotide resolution using the PTA Analysis Toolbox

Sjors Middelkamp, Freek Manders, Flavia Peci, Markus J. van Roosmalen, Diego Montiel González, Eline J.M. Bertrums, Inge M. van der Werf, Lucca L. M. Derks, Niels M. Groenen, Mark Verheul, Laurianne Trabut, Cayetano Pleguezuelos‐Manzano, Arianne M. Brandsma, Evangelia Antoniou, Dirk Reinhardt, , Ruben van Boxtel

The paper introduces PTATO, a bioinformatic workflow for detecting somatic mutations in single-cell WGS data using PTA, achieving high sensitivity for base substitutions and indels.

Cell Genomics · Aug 23, 2023Peer-reviewedGenomics

MutationalPatterns: The one stop shop for the analysis of mutational processes

Freek Manders, Arianne M. Brandsma, Jurrian K. de Kanter, Mark Verheul, Rurika Oka, Markus J. van Roosmalen, Bastiaan R. Van der Roest, Arne van Hoeck, Edwin P. J. G. Cuppen, Ruben van Boxtel

The paper introduces an updated R/Bioconductor package for analyzing mutational patterns, demonstrating its ability to detect mutational signatures and their biological implications using simulated and real data.

BMC Genomics · Feb 15, 2022Peer-reviewedGenomics