Researcher profile · Semantic Scholar

J. Samir

h-index: 11
Works: 28
Citations: 932

Most-cited papers

VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium
Dmitry V. Bagaev, R. Vroomans, J. Samir, U. Stervbo +14 more
2019Nucleic Acids Res.407 citations Open access
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VDJdb in the pandemic era: a compendium of T cell receptors specific for SARS-CoV-2
Mikhail Goncharov, Dmitry V. Bagaev, Dmitrii S. Shcherbinin, I. Zvyagin +22 more
2022Nature Methods207 citations Open access
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B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle
Simone Rizzetto, David Koppstein, J. Samir, Mandeep Singh +6 more
2017bioRxiv92 citations Open access
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Global and cell type-specific immunological hallmarks of severe dengue progression identified via a systems immunology approach
L. Ghita, Zhi-Yuan Yao, Yike Xie, Verónica Durán +20 more
2023bioRxiv48 citations
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Newborn and child-like molecular signatures in older adults stem from TCR shifts across human lifespan
C. E. van de Sandt, Thi H. O. Nguyen, N. Gherardin, J. Crawford +32 more
2023Nature Immunology40 citations Open access
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CAR+ and CAR− T cells share a differentiation trajectory into an NK-like subset after CD19 CAR T cell infusion in patients with B cell malignancies
R. Louie, C. Cai, J. Samir, Mandeep Singh +14 more
2023Nature Communications36 citations Open access
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Identification of human progenitors of exhausted CD8+ T cells associated with elevated IFN-γ response in early phase of viral infection
C. Cai, J. Samir, Mehdi R. Pirozyan, T. Adikari +16 more
2022Nature Communications28 citations Open access
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Natural killer cell receptors regulate responses of HLA-E–restricted T cells
L. Sullivan, Thi H. O. Nguyen, Christopher M. Harpur, S. Stanković +16 more
2021Science immunology22 citations
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Exploring and analysing single cell multi-omics data with VDJView
J. Samir, Simone Rizzetto, Money Gupta, F. Luciani
2019BMC Medical Genomics17 citations Open access
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Human CD8 T‐stem cell memory subsets phenotypic and functional characterization are defined by expression of CD122 or CXCR3
Yan-Ran Zhao, C. Cai, J. Samir, J. Palgen +6 more
2021European Journal of Immunology14 citations Open access
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Expanded T cell clones with lymphoma driver somatic mutations accumulate in refractory celiac disease.
Mandeep Singh, R. Louie, J. Samir, M. Field +27 more
2025Science Translational Medicine13 citations
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Central memory T cells with key TCR repertoires and gene expression profiles dominate influenza CD8+ T cell pools across the human lifespan
Tejas Menon, H. McQuilten, J. Samir, Thi H. O. Nguyen +14 more
2025Proceedings of the National Academy of Sciences of the United States of America4 citations Open access
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Single-Cell Transcriptome Analysis of T Cells.
Willem Van Der Byl, Simone Rizzetto, J. Samir, C. Cai +2 more
2019Methods in molecular biology4 citations
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Expanded T cell clones with lymphoma driver somatic mutations in refractory celiac disease
M. Singh, R. Louie, J. Samir, M. Field +25 more
2024medRxiv2 citations Open access
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Exploring and analysing immune single cell multi-omics data with VDJView
J. Samir, Simone Rizzetto, Money Gupta, F. Luciani
2019bioRxiv1 citations Open access
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Single-cell multi-omics maps clonal IEL expansion and epithelial remodelling in refractory coeliac disease
Michael Li, Arman Safavi, J. Samir, R. Louie +23 more
2026bioRxiv0 citations Open access
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Detecting Somatic Mutations in Rare Clones using Single Cell Multi-Omics
R. Gillman, S. Dudka, J. Samir, Raymond J. Louie +4 more
2025bioRxiv0 citations Open access
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Human axillary lymph node T follicular helper (Tfh) and Precursor‐Tfh cells exhibit functional flexibility following seasonal influenza vaccination
H. Law, R. Louie, O. Faridani, Alexandra Carey Hoppé +9 more
2025Clinical & Translational Immunology0 citations Open access
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Progenitor effects and unique transcriptomic signatures linked to differentiation phenotype in clonally expanded antigen-specific CD8 T memory stem cells.
Yan-Ran Zhao, J. Samir, Elizabeth Keoshkerian, Hui Li +4 more
2025Journal of Immunology0 citations Open access
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Discovery of a monoclonal, high‐affinity CD8+ T‐cell clone following natural hepatitis C virus infection
C. Cai, Elizabeth Keoshkerian, K. Wing, J. Samir +6 more
2024Immunology and Cell Biology0 citations Open access
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Identification of clonally expanded γδ T‐cell populations during CAR‐T cell therapy
Arman Safavi, J. Samir, Mandeep Singh, M. Bonomi +3 more
2024Immunology and Cell Biology0 citations
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Abstract 882: Harnessing single cell multi-omics data to identify predictors of clinical outcome in CD19 CAR T cell therapy
R. Louie, J. Samir, C. Cai, Helen M. McGuire +14 more
2024Cancer Research0 citations
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CAR +and CAR −T cells differentiate into an NK-like subset that is associated with increased inflammatory cytokines following infusion
F. Luciani, R. Louie, C. Cai, Mandeep Singh +12 more
2023Journal of Immunology0 citations Open access
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CAR+ and CAR- T cells differentiate into an NK-like subset that is associated with increased inflammatory cytokines following infusion
R. Louie, C. Cai, M. Singh, I. Deveson +12 more
2022medRxiv0 citations Open access
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The functional and molecular determinants of HCV-specific CD8 T cell responses during early infection
C. Cai, J. Samir, T. Adikari, Tim Peters +1 more
2022Journal of Immunology0 citations
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Author response for "Human CD8 T stem cell memory subsets phenotypic and functional characterisation are defined by expression of CD122 or CXCR3"
Yan-Ran Zhao, C. Cai, J. Samir, J. Palgen +6 more
20210 citations Open access
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Single cell multi-omics reveals early elevated function and multiple fates within human progenitor exhausted CD8+ T cells
C. Cai, J. Samir, Mehdi R. Pirozyan, T. Adikari +16 more
20210 citations Open access
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Single cell multi-modal analysis with VDJPuzzle identifies clonality and gene expression profiles of T and B cells
J. Samir, Simone Rizzetto, Money Gupta, Mandeep Singh +7 more
20190 citations
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Elizabeth Keoshkerian×6

Auda A. Eltahla×5

Money Gupta×5