Author

Salim S. Abdool Karim

University of Cape TownORCID 0000-0002-4986-2133Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:bulk RNA-seq· 2 Assay:DNA methylation· 2 Organism:human· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Research Focus:clustering· 1 Research Focus:database / resource· 1

Frequent Co-Authors

Nigel GarrettiD· 2 shared Alash’le AbimikuiD· 1 shared Aminu Musa· 1 shared Amy Sondgeroth· 1 shared Anna WintersiD· 1 shared Anna YsseliD· 1 shared Carolyn E. WilliamsoniD· 1 shared Chenfeng XiongiD· 1 shared

Activity by Year

2024-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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2 shared papersGenomics

Nigel GarrettORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

Cell-free RNA reveals host and microbial correlates of broadly neutralizing antibody development against HIV

Mark Kowarsky, Mercedes Dalman, Mira N. Moufarrej, Jennifer Okamoto, Yike Xie, Norma F Neff, Salim S. Abdool Karim, Nigel Garrett, Penny L. Moore, Joan Camuñas-Soler, Stephen R. Quake

The paper uses cfDNA/cfRNA sequencing to identify molecular correlates of bNAb development in HIV patients, finding an MHC class I activation signature and microbial changes associated with bNAb production.

PLoS Pathogens · Apr 9, 2026Peer-reviewedGenomics

HIV-1 Rebound Virus Consists of a Small Number of Lineages That Entered the Reservoir Close to ART Initiation

Lynn Tyers, Matthew Moeser, Jean Felistas Ntuli, Shuntai Zhou, E. Spielvogel, Amy Sondgeroth, Craig H. Adams, Ruwayhida Thebus, Anna Yssel, Salim S. Abdool Karim, Nigel Garrett, Sergei L. Kosakovsky Pond, Carolyn E. Williamson, Ronald I. Swanstrom, Melissa-Rose Abrahams, Sarah Joseph

The paper identifies that HIV-1 rebound virus primarily originates from a small number of lineages that entered the reservoir near ART initiation, despite the reservoir containing older sequences.

bioRxiv · Jan 29, 2025 · PreprintMicrobiology

Craft: A Machine Learning Approach to Dengue Subtyping

Daniel J. van Zyl, Marcel Dunaiski, Houriiyah Tegally, Cheryl Baxter, Túlio de Oliveira, Joicymara Santos Xavier, Christina Riley, Anna Winters, Vivek Naranbhai, Felix Made, Salim S. Abdool Karim, Kennedy Otwombe, Alash’le Abimiku, Sophia Osawe, James Ezenwa Onyemata, , Xin Wu

Craft is a machine learning framework for dengue subtyping that achieves high accuracy and speed, outperforming existing tools in classification efficiency.

Bioinformatics Advances · Dec 26, 2024Peer-reviewedGenomics