|Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data|
NT Gupta, JA Vander Heiden, M Uduman, D Gadala-Maria, G Yaari, ...
Bioinformatics 31 (20), 3356-3358, 2015
|Models of somatic hypermutation targeting and substitution based on synonymous mutations from high-throughput immunoglobulin sequencing data|
G Yaari, JA Vander Heiden, M Uduman, D Gadala-Maria, N Gupta, ...
Frontiers in immunology 4, 2013
|Salmonella infection drives promiscuous B cell activation followed by extrafollicular affinity maturation|
R Di Niro, SJ Lee, JA Vander Heiden, RA Elsner, N Trivedi, JM Bannock, ...
Immunity 43 (1), 120-131, 2015
|Interleukin-10 from CD4+ follicular regulatory T cells promotes the germinal center response|
BJ Laidlaw, Y Lu, RA Amezquita, JS Weinstein, JA Vander Heiden, ...
Sci Immunol 2 (16), eaan4767, 2017
|Hierarchical Clustering Can Identify B Cell Clones with High Confidence in Ig Repertoire Sequencing Data|
NT Gupta, KD Adams, AW Briggs, SC Timberlake, F Vigneault, ...
The Journal of Immunology 198 (6), 2489-2499, 2017
|Neutralizing antibodies against West Nile virus identified directly from human B cells by single-cell analysis and next generation sequencing|
K Tsioris, NT Gupta, AO Ogunniyi, RM Zimnisky, F Qian, Y Yao, X Wang, ...
Integrative Biology 7 (12), 1587-1597, 2015
|Responsive population dynamics and wide seeding into the duodenal lamina propria of transglutaminase-2-specific plasma cells in celiac disease|
R Di Niro, O Snir, K Kaukinen, G Yaari, KEA Lundin, NT Gupta, ...
Mucosal immunology 9 (1), 254-264, 2016
|Neoadjuvant cemiplimab for resectable hepatocellular carcinoma: a single-arm, open-label, phase 2 trial|
TU Marron, MI Fiel, P Hamon, N Fiaschi, E Kim, SC Ward, Z Zhao, J Kim, ...
The Lancet Gastroenterology & Hepatology 7 (3), 219-229, 2022
|A framework for highly multiplexed dextramer mapping and prediction of T cell receptor sequences to antigen specificity|
W Zhang, PG Hawkins, J He, NT Gupta, J Liu, G Choonoo, SW Jeong, ...
Science Advances 7 (20), eabf5835, 2021
|Endogenous retroviral proteins provide an immunodominant but not requisite antigen in a murine immunotherapy tumor model|
X Ye, JC Waite, A Dhanik, N Gupta, M Zhong, C Adler, E Malahias, M Ni, ...
Oncoimmunology 9 (1), 1758602, 2020
|VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements|
IT Toby, MK Levin, EA Salinas, S Christley, S Bhattacharya, F Breden, ...
BMC bioinformatics 17 (13), 5-14, 2016
|Graded vector representations of immunoglobulins produced in response to west Nile virus|
T Cohen, D Widdows, JAV Heiden, NT Gupta, SH Kleinstein
International Symposium on Quantum Interaction, 135-148, 2016
|Absence of central tolerance in Aire-deficient mice synergizes with immune-checkpoint inhibition to enhance antitumor responses|
AA Benitez, S Khalil-Agüero, A Nandakumar, NT Gupta, W Zhang, ...
Communications biology 3 (1), 1-13, 2020
|Systems and Methods for Sequencing T Cell Receptors and Uses Thereof|
W Zhang, B Wang, N Gupta
US Patent App. 17/591,355, 2022
|Systems and methods for sequencing T cell receptors and uses thereof|
W Zhang, B Wang, N Gupta
US Patent 11,274,342, 2022
|Intratumoral mregDC and CXCL13 T helper niches enable local differentiation of CD8 T cells following PD-1 blockade|
A Magen, P Hamon, N Fiaschi, L Troncoso, E Humblin, D D’souza, ...
|Methods and systems for analysis of receptor interaction|
W Zhang, J He, N Gupta, GS Atwal, P Hawkins
US Patent App. 17/236,998, 2021
|Shazam: Tuning clonal assignment thresholds with nearest neighbor distances|
N Gupta, S Marquez, N Nouri, JQ Zhou
N Nouri, SH Kleinstein, NT Gupta
|Absence of central tolerance as a sculpting mechanism of immune-checkpoint therapy.|
AA Benitez, S Khalil-Aguero, A Nandakumar, N Gupta, W Zhang, ...
CANCER IMMUNOLOGY RESEARCH 8 (3), 51-51, 2020