Dr Jerome Samir

Dr Jerome Samir

Research Associate

2017 - Bachelor of Bioinformatics Engineering (Hons)
2022 - PhD (Bioinformatics)

Medicine & Health
School of Biomedical Sciences

Jerome is a bioinformatician currently working to apply network theory, machine learning and artificial intelligence techniques to single cell RNA sequencing data from adaptive immune cells specific to cancer and autoimmune disease. Having studied Bioinformatics, he comes from a largely computational background, and completed his PhD under Associate Professor Fabio Luciani. During his studies, he utilised large T and B cell multi-omics datasets to explore antigen specificity and cross-reactivity, and predict phenotype and cellular function in viral infection and cancer. His area of interest is T cells, and more specifically TCR specificity prediction, and T cell functional and phenotypic analyses.

 

  • Book Chapters | 2019
    Van Der Byl W; Rizzetto S; Samir J; Cai C; Eltahla AA; Luciani F, 2019, 'Single-Cell Transcriptome Analysis of T Cells', in Methods in Molecular Biology, pp. 155 - 205, http://dx.doi.org/10.1007/978-1-4939-9728-2_16
  • Journal articles | 2023
    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
    Journal articles | 2023
    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
    Journal articles | 2023
    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
    Journal articles | 2023
    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
    Journal articles | 2022
    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
    Journal articles | 2022
    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
    Journal articles | 2022
    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
    Journal articles | 2021
    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
    Journal articles | 2021
    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
    Journal articles | 2020
    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
    Journal articles | 2020
    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
    Journal articles | 2018
    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
    Journal articles | 2017
    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
  • Preprints | 2022
    Ghita L; Yao Z; Xie Y; Duran V; Cagirici HB; Samir J; Osman I; Agudelo Rojas OL; Sanz AM; Sahoo MK; Robinson ML; Gelvez 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, 2022, Global and cell type-specific immunological hallmarks of severe dengue progression, , http://dx.doi.org/10.1101/2022.12.11.519930
    Preprints | 2022
    Louie R; Cai C; Singh M; Deveson I; Ferguson J; Amos T; McGuire H; Samir J; Gowrishankar K; Adikari T; Balderas R; Bishop D; Gottlieb D; Blyth E; Micklethwaite K; Luciani F, 2022, CAR+ and CAR- T cells differentiate into an NK-like subset that is associated with increased inflammatory cytokines following infusion, , http://dx.doi.org/10.21203/rs.3.rs-1495587/v1
    Preprints | 2022
    Louie RHY; Cai C; Singh M; Deveson I; Ferguson J; Amos T; McGuire HM; Samir J; Gowrishankar K; Adikari T; Balderas R; Bishop D; Gottlieb D; Blyth E; Micklethwaite K; Luciani F, 2022, CAR+ and CAR- T cells differentiate into an NK-like subset that is associated with increased inflammatory cytokines following infusion, , http://dx.doi.org/10.1101/2022.03.29.22273013
    Preprints | 2021
    Cai C; Samir J; Pirozyan M; Adikari T; Gupta M; Leung P; Hughes B; Van der Byl W; Rizzetto S; Elthala A; Keoshkerian E; Palgen J-L; Peters T; Nguyen T; Louie R; Kedzierska K; Gaudieri S; Bull R; Lloyd A; Luciani F, 2021, Single cell multi-omics reveals early elevated function and multiple fates within human progenitor exhausted CD8+ T cells, , http://dx.doi.org/10.1101/2021.09.09.459584
    Preprints | 2020
    Samir J; Rizzetto S; Gupta M; Luciani F, 2020, Exploring and analysing single cell multi-omics data with VDJView, , http://dx.doi.org/10.21203/rs.2.14949/v3
    Preprints | 2020
    Samir J; Rizzetto S; Gupta M; Luciani F, 2020, Exploring and analysing single cell multi-omics data with VDJView, , http://dx.doi.org/10.21203/rs.2.14949/v4
    Preprints | 2019
    Samir J; Rizzetto S; Gupta M; Luciani F, 2019, Exploring and analysing immune single cell multi-omics data with VDJView, , http://dx.doi.org/10.1101/613083
    Preprints | 2019
    Samir J; Rizzetto S; Gupta M; Luciani F, 2019, Exploring and analysing single cell multi-omics data with VDJView, , http://dx.doi.org/10.21203/rs.2.14949/v1
    Preprints | 2019
    Samir J; Rizzetto S; Gupta M; Luciani F, 2019, Exploring and analysing single cell multi-omics data with VDJView, , http://dx.doi.org/10.21203/rs.2.14949/v2