By Dr Jerome Samir

Journal articles

Louie RY; Samir J; Cai C; McGuire H; Amos T; Fergsuson J; Deveson I; Adikari T; Bonomi M; Bishop D; Mason CE; Balderas R; Ruella M; Singh M; Gottlieb D; Blyth E; Micklethwaite K; Luciani F, 2024, 'Abstract 882: Harnessing single cell multi-omics data to identify predictors of clinical outcome in CD19 CAR T cell therapy', Cancer Research, 84, pp. 882 - 882, http://dx.doi.org/10.1158/1538-7445.am2024-882

Louie RHY; Cai C; Samir J; Singh M; Deveson IW; Ferguson JM; Amos TG; McGuire HM; Gowrishankar K; Adikari T; Balderas R; Bonomi M; Ruella M; Bishop D; Gottlieb D; Blyth E; Micklethwaite K; Luciani F, 2023, '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', Nature Communications, 14, http://dx.doi.org/10.1038/s41467-023-43656-7

Ghita L; Yao Z; Xie Y; Duran V; Cagirici HB; Samir J; Osman I; Rebellón-Sánchez DE; Agudelo-Rojas OL; Sanz AM; Sahoo MK; Robinson ML; Gelvez-Ramirez RM; Bueno N; Luciani F; Pinsky BA; Montoya JG; Estupiñan-Cardenas MI; Villar-Centeno LA; Rojas-Garrido EM; Rosso F; Quake SR; Zanini F; Einav S, 2023, 'Global and cell type-specific immunological hallmarks of severe dengue progression identified via a systems immunology approach', Nature Immunology, 24, pp. 2150 - 2163, http://dx.doi.org/10.1038/s41590-023-01654-3

van de Sandt CE; Nguyen THO; Gherardin NA; Crawford JC; Samir J; Minervina AA; Pogorelyy MV; Rizzetto S; Szeto C; Kaur J; Ranson N; Sonda S; Harper A; Redmond SJ; McQuilten HA; Menon T; Sant S; Jia X; Pedrina K; Karapanagiotidis T; Cain N; Nicholson S; Chen Z; Lim R; Clemens EB; Eltahla A; La Gruta NL; Crowe J; Lappas M; Rossjohn J; Godfrey DI; Thomas PG; Gras S; Flanagan KL; Luciani F; Kedzierska K, 2023, 'Newborn and child-like molecular signatures in older adults stem from TCR shifts across human lifespan', Nature Immunology, 24, pp. 1890 - 1907, http://dx.doi.org/10.1038/s41590-023-01633-8

Luciani F; Louie RY; Cai C; Singh M; Deveson I; Ferguson J; Amos T; McGuire H; Samir J; Gowrishankar K; Adikari T; Balderas R; Bishop D; Gottileb D; Blyth E; Micklethwaite K, 2023, 'CAR +and CAR −T cells differentiate into an NK-like subset that is associated with increased inflammatory cytokines following infusion', The Journal of Immunology, 210, pp. 159.15 - 159.15, http://dx.doi.org/10.4049/jimmunol.210.supp.159.15

Cai C; Samir J; Pirozyan MR; Adikari TN; Gupta M; Leung P; Hughes B; Van der Byl W; Rizzetto S; Elthala A; Keoshkerian E; Palgen JL; Peters T; Nguyen THO; Louie R; Kedzierska K; Gaudieri S; Bull RA; Lloyd AR; Luciani F, 2022, 'Identification of human progenitors of exhausted CD8⁺ T cells associated with elevated IFN-γ response in early phase of viral infection', Nature Communications, 13, http://dx.doi.org/10.1038/s41467-022-35281-7

Cai C; Samir J; Adikari T; Peters T; Luciani F, 2022, 'The functional and molecular determinants of HCV-specific CD8 T cell responses during early infection', The Journal of Immunology, 208, pp. 169.12 - 169.12, http://dx.doi.org/10.4049/jimmunol.208.supp.169.12

Goncharov M; Bagaev D; Shcherbinin D; Zvyagin I; Bolotin D; Thomas PG; Minervina AA; Pogorelyy MV; Ladell K; McLaren JE; Price DA; Nguyen THO; Rowntree LC; Clemens EB; Kedzierska K; Dolton G; Rius CR; Sewell A; Samir J; Luciani F; Zornikova KV; Khmelevskaya AA; Sheetikov SA; Efimov GA; Chudakov D; Shugay M, 2022, 'VDJdb in the pandemic era: a compendium of T cell receptors specific for SARS-CoV-2', Nature Methods, http://dx.doi.org/10.1038/s41592-022-01578-0

Zhao Y; Cai C; Samir J; Palgen JL; Keoshkerian E; Li H; Bull RA; Luciani F; An H; Lloyd AR, 2021, 'Human CD8 T-stem cell memory subsets phenotypic and functional characterization are defined by expression of CD122 or CXCR3', European Journal of Immunology, 51, pp. 1732 - 1747, http://dx.doi.org/10.1002/eji.202049057

Sullivan LC; Nguyen THO; Harpur CM; Stankovic S; Kanagarajah AR; Koutsakos M; Saunders PM; Cai Z; Gray JA; Widjaja JML; Lin J; Pietra G; Mingari MC; Moretta L; Samir J; Luciani F; Westall GP; Malmberg KJ; Kedzierska K; Brooks AG, 2021, 'Natural killer cell receptors regulate responses of HLA-E-restricted T cells', Science Immunology, 6, http://dx.doi.org/10.1126/sciimmunol.abe9057

Samir J; Rizzetto S; Gupta M; Luciani F, 2020, 'Exploring and analysing single cell multi-omics data with VDJView', BMC Medical Genomics, 13, http://dx.doi.org/10.1186/s12920-020-0696-z

Bagaev DV; Vroomans RMA; Samir J; Stervbo U; Rius C; Dolton G; Greenshields-Watson A; Attaf M; Egorov ES; Zvyagin IV; Babel N; Cole DK; Godkin AJ; Sewell AK; Kesmir C; Chudakov DM; Luciani F; Shugay M, 2020, 'VDJdb in 2019: Database extension, new analysis infrastructure and a T-cell receptor motif compendium', Nucleic Acids Research, 48, pp. D1057 - D1062, http://dx.doi.org/10.1093/nar/gkz874

Rizzetto S; Koppstein DNP; Samir J; Singh M; Reed JH; Cai CH; Lloyd AR; Eltahla AA; Goodnow CC; Luciani F, 2018, 'B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle', Bioinformatics, 34, pp. 2846 - 2847, http://dx.doi.org/10.1093/BIOINFORMATICS/BTY171

Rizzetto S; Koppstein DNP; Samir J; Singh M; Reed J; Cai C; Lloyd A; Eltahla A; Goodnow C; Luciani F, 2017, 'B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle', , http://dx.doi.org/10.1101/181156

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