Author

Bassem Ben Cheikh

Akoya Biosciences (United States)

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Genomics· 2 Cancer Biology· 1 Immunology· 1 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 3 Research Focus:cell-cell communication· 2 Research Focus:differential expression· 2 Organism:human· 2 Assay:proteomics· 2 Assay:scRNA-seq· 2 Approach:statistical model· 2 Approach:experimental assay· 1

Frequent Co-Authors

Nadya NikulinaiD· 2 shared Oliver BraubachiD· 2 shared Simon KnottiD· 2 shared Aatish ThennavaniD· 1 shared Alastair Mark ThompsoniD· 1 shared Alexey SergushicheviD· 1 shared Amisha Dhawan· 1 shared Andrew John Li· 1 shared

Activity by Year

2018-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 14 mutual co-author links

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2 shared papersGenomics

Nadya NikulinaORCID

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Author profile →

5 papers

Recent·Most cited

Immune Checkpoint Therapy Drives Maturation of a Cellular Neighborhood Nucleated by T Cell-APC Triads Enabling Spatially Compartmentalized Tumor Immunity

Ruan F.V. Medrano, Vladimir Sukhov, Kevin Hoffer-Hawlik, Bar Rozenman, Cora D. Arthur, Fei Han, Bassem Ben Cheikh, Hussein Sultan, Yoshiko Takeuchi, Samuel Ameh, Derek J. Theisen, Yuang Song, Heather N. Kohlmiller, J. Michael White, Alexey Sergushichev, , Robert D. Schreiber

The paper uses multiplex imaging to track the development of T cell-APC triad neighborhoods during immune checkpoint therapy, showing their role in spatially organizing tumor immunity.

bioRxiv · Apr 12, 2026 · PreprintImmunology

The mutational landscape defines the proteome and spatial organization of tumor, stroma and immune cells in ovarian cancer

Kruttika Dabke, Nicole Gull, Simion D. Kreimer, Pei-Chen Peng, Michael Diaz, Bassem Ben Cheikh, Amisha Dhawan, Katrina Evans, Nathan D. Ng, Xioapu Yuan, B.J. Rimel, Andrew John Li, Beth Y. Karlan, Simon Knott, Simon A. Gayther, , Michelle R. Jones

This study profiles the proteome of ovarian cancer tumors before and after chemotherapy, revealing how HRD status affects immune pathways and identifies potential therapeutic targets.

bioRxiv · Jun 1, 2025 · PreprintCancer Biology

A Machine Learning One-Class Logistic Regression Model to Predict Stemness in Single Cell Transcriptomics and Spatial Omics Datasets

Felipe Segato Dezem, Maycon Marção, Bassem Ben Cheikh, Nadya Nikulina, Ayodele J. Omotoso, Destiny B. Burnett, Priscila Campos dos Santos Coelho, Simone Badal, Judith Hurley, Carmen Gómez, Tien Phan-Everson, Giang Ong, Luciano Gastón Martelotto, Zachary R. Lewis, Sophia George, , Jasmine Plummer

The paper applies a one-class logistic regression model to predict stemness in single-cell and spatial omics datasets without requiring cell annotation.

BMC Genomics · Nov 28, 2023Peer-reviewedGenomics

A spatially resolved single cell genomic atlas of the adult human breast

Tapsi Kumar, Kevin Nee, Runmin Wei, Siyuan He, Quy Nguyen, Shanshan Bai, Kerrigan Blake, Maren Pein, Yanwen Gong, Emi Sei, Min Shan Hu, Tod D. Casasent, Aatish Thennavan, Jianzhuo Li, Tuan Tran, , Nicholas E. Navin

This paper constructs a comprehensive spatially resolved single-cell genomic atlas of the adult human breast, identifying 11 major cell types and revealing diverse immune and epithelial cell populations.

Nature · Jun 28, 2023Peer-reviewedGenomics

SmartCodes : functionalized barcodes that enable targeted retrieval of clonal lineages from a heterogeneous population

Clare A. Rebbeck, Florian Raths, Bassem Ben Cheikh, Kenneth H. Gouin, Gregory J. Hannon, Simon Knott

This paper introduces SmartCodes, functionalized barcodes that allow targeted retrieval and manipulation of clonal lineages in heterogeneous populations using CRISPR-based readers.

bioRxiv · Jun 20, 2018 · PreprintMolecular Biology