| VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium DV Bagaev, RMA Vroomans, J Samir, U Stervbo, C Rius, G Dolton, ... Nucleic acids research 48 (D1), D1057-D1062, 2020 | 354 | 2020 |
| VDJdb in the pandemic era: a compendium of T cell receptors specific for SARS-CoV-2 M Goncharov, D Bagaev, D Shcherbinin, I Zvyagin, D Bolotin, PG Thomas, ... Nature methods 19 (9), 1017-1019, 2022 | 107 | 2022 |
| B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle S Rizzetto, DNP Koppstein, J Samir, M Singh, JH Reed, CH Cai, AR Lloyd, ... Bioinformatics 34 (16), 2846-2847, 2018 | 107 | 2018 |
| Natural killer cell receptors regulate responses of HLA-E–restricted T cells LC Sullivan, THO Nguyen, CM Harpur, S Stankovic, AR Kanagarajah, ... Science immunology 6 (58), eabe9057, 2021 | 23 | 2021 |
| Exploring and analysing single cell multi-omics data with VDJView J Samir, S Rizzetto, M Gupta, F Luciani BMC medical genomics 13, 1-9, 2020 | 19 | 2020 |
| Global and cell type-specific immunological hallmarks of severe dengue progression identified via a systems immunology approach L Ghita, Z Yao, Y Xie, V Duran, HB Cagirici, J Samir, I Osman, ... Nature immunology 24 (12), 2150-2163, 2023 | 13 | 2023 |
| 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, MR Pirozyan, TN Adikari, M Gupta, P Leung, B Hughes, ... Nature communications 13 (1), 7543, 2022 | 11 | 2022 |
| 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 RHY Louie, C Cai, J Samir, M Singh, IW Deveson, JM Ferguson, TG Amos, ... Nature Communications 14 (1), 7767, 2023 | 10 | 2023 |
| Newborn and child-like molecular signatures in older adults stem from TCR shifts across human lifespan CE van de Sandt, THO Nguyen, NA Gherardin, JC Crawford, J Samir, ... Nature immunology 24 (11), 1890-1907, 2023 | 10 | 2023 |
| Human CD8 T‐stem cell memory subsets phenotypic and functional characterization are defined by expression of CD122 or CXCR3 Y Zhao, C Cai, J Samir, JL Palgen, E Keoshkerian, H Li, RA Bull, ... European Journal of Immunology 51 (7), 1732-1747, 2021 | 10 | 2021 |
| Single-cell transcriptome analysis of T cells W Van Der Byl, S Rizzetto, J Samir, C Cai, AA Eltahla, F Luciani In Vitro Differentiation of T-Cells: Methods and Protocols, 155-205, 2019 | 4 | 2019 |
| Expanded T cell clones with lymphoma driver somatic mutations in refractory celiac disease M Singh, RHY Louie, J Samir, MA Field, C Milthorpe, T Aldiriki, J Mackie, ... medRxiv, 2024.03. 17.24304320, 2024 | 1 | 2024 |
| Global and cell type-specific immunological hallmarks of severe dengue progression L Ghita, Z Yao, Y Xie, V Duran, HB Cagirici, J Samir, I Osman, ... Biorxiv, 2022.12. 11.519930, 2022 | 1 | 2022 |
| Identification of clonally expanded γδ T‐cell populations during CAR‐T cell therapy A Safavi, J Samir, M Singh, M Bonomi, RY Louie, K Micklethwaite, ... Immunology and Cell Biology, 2024 | | 2024 |
| Identification of clonally expanded Tγδ populations during CAR-T cell therapy A Safavi, J Samir, M Singh, M Bonomi, RHY Louie, K Micklethwaite, ... | | 2024 |
| Discovery of a monoclonal, high‐affinity CD8+ T‐cell clone following natural hepatitis C virus infection C Cai, E Keoshkerian, K Wing, J Samir, M Effenberger, K Schober, ... Immunology and Cell Biology, 2024 | | 2024 |
| Harnessing single cell multi-omics data to identify predictors of clinical outcome in CD19 CAR T cell therapy RY Louie, J Samir, C Cai, H McGuire, T Amos, J Fergsuson, I Deveson, ... Cancer Research 84 (6_Supplement), 882-882, 2024 | | 2024 |
| The development of bioinformatics workflows to explore single-cell multi-omics data from T and B lymphocytes J Samir UNSW Sydney, 2023 | | 2023 |
| The functional and molecular determinants of HCV-specific CD8 T cell responses during early infection C Cai, J Samir, T Adikari, T Peters, F Luciani The Journal of Immunology 208 (1_Supplement), 169.12-169.12, 2022 | | 2022 |
| CAR+ and CAR- T cells differentiate into an NK-like subset that is associated with increased inflammatory cytokines following infusion RHY Louie, C Cai, M Singh, I Deveson, J Ferguson, TG Amos, ... medRxiv, 2022.03. 29.22273013, 2022 | | 2022 |
