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VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements.
Toby IT, Levin MK, Salinas EA, Christley S, Bhattacharya S, Breden F, Buntzman A, Corrie B, Fonner J, Gupta NT, Hershberg U, Marthandan N, Rosenfeld A, Rounds W, Rubelt F, Scarborough W, Scott JK, Uduman M, Vander Heiden JA, Scheuermann RH, Monson N, Kleinstein SH, Cowell LG. Toby IT, et al. Among authors: gupta nt. BMC Bioinformatics. 2016 Oct 6;17(Suppl 13):333. doi: 10.1186/s12859-016-1214-3. BMC Bioinformatics. 2016. PMID: 27766961 Free PMC article.
Neutralizing antibodies against West Nile virus identified directly from human B cells by single-cell analysis and next generation sequencing.
Tsioris K, Gupta NT, Ogunniyi AO, Zimnisky RM, Qian F, Yao Y, Wang X, Stern JN, Chari R, Briggs AW, Clouser CR, Vigneault F, Church GM, Garcia MN, Murray KO, Montgomery RR, Kleinstein SH, Love JC. Tsioris K, et al. Among authors: gupta nt. Integr Biol (Camb). 2015 Dec;7(12):1587-97. doi: 10.1039/c5ib00169b. Epub 2015 Oct 20. Integr Biol (Camb). 2015. PMID: 26481611 Free PMC article.
Molecular assessment of intratumoral immune cell subsets and potential mechanisms of resistance to odronextamab, a CD20×CD3 bispecific antibody, in patients with relapsed/refractory B-cell non-Hodgkin lymphoma.
Brouwer-Visser J, Fiaschi N, Deering RP, Cygan KJ, Scott D, Jeong S, Boucher L, Gupta NT, Gupta S, Adler C, Topp MS, Bannerji R, Duell J, Advani RH, Flink DM, Chaudhry A, Thurston G, Ambati SR, Jankovic V. Brouwer-Visser J, et al. Among authors: gupta nt. J Immunother Cancer. 2024 Mar 21;12(3):e008338. doi: 10.1136/jitc-2023-008338. J Immunother Cancer. 2024. PMID: 38519055 Free PMC article.
Intratumoral dendritic cell-CD4+ T helper cell niches enable CD8+ T cell differentiation following PD-1 blockade in hepatocellular carcinoma.
Magen A, Hamon P, Fiaschi N, Soong BY, Park MD, Mattiuz R, Humblin E, Troncoso L, D'souza D, Dawson T, Kim J, Hamel S, Buckup M, Chang C, Tabachnikova A, Schwartz H, Malissen N, Lavin Y, Soares-Schanoski A, Giotti B, Hegde S, Ioannou G, Gonzalez-Kozlova E, Hennequin C, Le Berichel J, Zhao Z, Ward SC, Fiel I, Kou B, Dobosz M, Li L, Adler C, Ni M, Wei Y, Wang W, Atwal GS, Kundu K, Cygan KJ, Tsankov AM, Rahman A, Price C, Fernandez N, He J, Gupta NT, Kim-Schulze S, Gnjatic S, Kenigsberg E, Deering RP, Schwartz M, Marron TU, Thurston G, Kamphorst AO, Merad M. Magen A, et al. Among authors: gupta nt. Nat Med. 2023 Jun;29(6):1389-1399. doi: 10.1038/s41591-023-02345-0. Epub 2023 Jun 15. Nat Med. 2023. PMID: 37322116
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