Author

Freek Manders

Oncode InstituteORCID 0000-0001-6197-347XUnclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Organism:human· 2 Approach:statistical model· 2 Assay:whole-genome sequencing· 2 Research Focus:benchmarking· 1 Assay:ChIP-seq· 1 Research Focus:gene regulatory network inference· 1 Approach:machine learning (classical)· 1 Research Focus:software / tool· 1

Frequent Co-Authors

Arianne M. BrandsmaiD· 2 shared Mark VerheuliD· 2 shared Markus J. van RoosmaleniD· 2 shared Ruben van BoxteliD· 2 shared Arne van HoeckiD· 1 shared Bastiaan R. Van der RoestiD· 1 shared Cayetano Pleguezuelos‐ManzanoiD· 1 shared Cheng WangiD· 1 shared

Activity by Year

2019-2023 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 25 mutual co-author links

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2 shared papersGenomics

Arianne M. BrandsmaORCID

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3 papers

Recent·Most cited

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

The CTCF Anatomy of Topologically Associating Domains

Luca Nanni, Cheng Wang, Freek Manders, Laszlo A. Groh, Paula Haro, Roel Oldenkamp, Stefano Ceri, Colin Logie

The paper investigates how CTCF site orientation relates to TAD structure by analyzing 4C data and spatial CTCF patterns, finding divergent sites at TAD boundaries and convergent sites within TADs.

bioRxiv · Sep 1, 2019 · PreprintGenomics