Author

Ben Berkhout

Amsterdam University Medical CentersORCID 0000-0002-1905-8486Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1 Immunology· 1 Microbiology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 3 Research Focus:cell type annotation· 2 Research Focus:gene regulatory network inference· 2 Organism:human· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:cell-cell communication· 1 Research Focus:differential expression· 1

Frequent Co-Authors

Aldo Jongejaan· 1 shared Alexander GabeliD· 1 shared Alexander O. PasternakiD· 1 shared Alexandra VujkoviciD· 1 shared Annabelle J. GourlayiD· 1 shared Ard van SighemiD· 1 shared Asimenia Vlachou· 1 shared Astrid GalliD· 1 shared

Activity by Year

2018-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 12 mutual co-author links

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1 shared paperImmunology

Aldo Jongejaan

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3 papers

Recent·Most cited

HIV-2 evades restriction by ZAP through adaptations in the U3 LTR region despite increased CpG levels

Dorota Kmieć, Rayhane Nchioua, Alexander Gabel, Asimenia Vlachou, Sabina Ganskih, Sümeyye Erdemci-Evin, Stacey A. Lapp, Diane G. Carnathan, Steven E. Bosinger, Ben Berkhout, Atze T. Das, Mathias Munschauer, Frank Kirchhoff

This study identifies that HIV-2 evades ZAP restriction through adaptations in the U3 LTR region despite having higher CpG levels compared to HIV-1 and SIVsmm.

Nucleic Acids Research · Aug 7, 2025Peer-reviewedMicrobiology

Pure CD32+ CD4+ Cells Are Cytotoxic Memory CD4+ T Lymphocytes Highly Enriched for HIV-1 DNA

Philipp Adams, Elena Herrera-Carrillo, Alexandra Vujkovic, Aldo Jongejaan, Perry D. Moerland, Majdouline El Moussaoui, Gilles Darcis, Ben Berkhout, Alexander O. Pasternak

The paper identifies CD32+ CD4+ T cells as a rare, cytotoxic memory subset enriched for HIV-1 DNA in treated patients.

bioRxiv · Jul 9, 2025 · PreprintImmunology

Easy and Accurate Reconstruction of Whole HIV Genomes from Short-Read Sequence Data

Chris Wymant, François Blanquart, Tanya Golubchik, Astrid Gall, Margreet E. Bakker, Daniela Bezemer, Nicholas J. Croucher, Matthew D. Hall, M Hillebregt, Swee Hoe Ong, Oliver Ratmann, Jan Albert, Norbert Bannert, Jacques Fellay, Katrien Fransen, , Christophe Fraser

The paper develops a tool to accurately reconstruct whole HIV genomes from short-read data by using tailored references, showing improved accuracy over standard references.

Virus Evolution · Jan 1, 2018Peer-reviewedBioinformatics