Search Results - "Gupta, Namita T."

Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data by Gupta, Namita T, Vander Heiden, Jason A, Uduman, Mohamed, Gadala-Maria, Daniel, Yaari, Gur, Kleinstein, Steven H

“…Advances in high-throughput sequencing technologies now allow for large-scale characterization of B cell immunoglobulin (Ig) repertoires. The high germline and…”
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Salmonella Infection Drives Promiscuous B Cell Activation Followed by Extrafollicular Affinity Maturation by Di Niro, Roberto, Lee, Seung-Joo, Vander Heiden, Jason A., Elsner, Rebecca A., Trivedi, Nikita, Bannock, Jason M., Gupta, Namita T., Kleinstein, Steven H., Vigneault, Francois, Gilbert, Tamara J., Meffre, Eric, McSorley, Stephen J., Shlomchik, Mark J.

“…The B cell response to Salmonella typhimurium (STm) occurs massively at extrafollicular sites, without notable germinal centers (GCs). Little is known in terms…”
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Designing meaningful continuous representations of T cell receptor sequences with deep generative models by Leary, Allen Y., Scott, Darius, Gupta, Namita T., Waite, Janelle C., Skokos, Dimitris, Atwal, Gurinder S., Hawkins, Peter G.

“…T Cell Receptor (TCR) antigen binding underlies a key mechanism of the adaptive immune response yet the vast diversity of TCRs and the complexity of protein…”
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Rapid TCR:Epitope Ranker (RAPTER): a primary human T cell reactivity screening assay pairing epitope and TCR at single cell resolution by Deering, Raquel P., Blumenberg, Lili, Li, Lianjie, Dhanik, Ankur, Jeong, Se, Pourpe, Stephane, Song, Hang, Boucher, Lauren, Ragunathan, Shoba, Li, Yanxia, Zhong, Maggie, Kuhnert, Jessica, Adler, Christina, Hawkins, Peter, Gupta, Namita T., Moore, Michael, Ni, Min, Hansen, Johanna, Wei, Yi, Thurston, Gavin

“…Identifying epitopes that T cells respond to is critical for understanding T cell-mediated immunity. Traditional multimer and other single cell assays often…”
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Neutralizing antibodies against West Nile virus identified directly from human B cells by single-cell analysis and next generation sequencing by Tsioris, Konstantinos, Gupta, Namita T, Ogunniyi, Adebola O, Zimnisky, Ross M, Qian, Feng, Yao, Yi, Wang, Xiaomei, Stern, Joel N H, Chari, Raj, Briggs, Adrian W, Clouser, Christopher R, Vigneault, Francois, Church, George M, Garcia, Melissa N, Murray, Kristy O, Montgomery, Ruth R, Kleinstein, Steven H, Love, J Christopher

“…West Nile virus (WNV) infection is an emerging mosquito-borne disease that can lead to severe neurological illness and currently has no available treatment or…”
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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 by Brouwer-Visser, Jurriaan, Fiaschi, Nathalie, Deering, Raquel P, Cygan, Kamil J, Scott, Darius, Jeong, Se, Boucher, Lauren, Gupta, Namita T, Gupta, Suraj, Adler, Christina, Topp, Max S, Bannerji, Rajat, Duell, Johannes, Advani, Ranjana H, Flink, Dina M, Chaudhry, Aafia, Thurston, Gavin, Ambati, Srikanth R, Jankovic, Vladimir

“…BackgroundPatients with relapsed/refractory B-cell non-Hodgkin lymphoma (R/R B-NHL) have a significant need for effective treatment options. Odronextamab is an…”
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Hierarchical Clustering Can Identify B Cell Clones with High Confidence in Ig Repertoire Sequencing Data by Gupta, Namita T, Adams, Kristofor D, Briggs, Adrian W, Timberlake, Sonia C, Vigneault, Francois, Kleinstein, Steven H

“…Adaptive immunity is driven by the expansion, somatic hypermutation, and selection of B cell clones. Each clone is the progeny of a single B cell responding to…”
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Intratumoral dendritic cell–CD4+ T helper cell niches enable CD8+ T cell differentiation following PD-1 blockade in hepatocellular carcinoma by Magen, Assaf, Hamon, Pauline, Fiaschi, Nathalie, Soong, Brian Y., Park, Matthew D., Mattiuz, Raphaël, Humblin, Etienne, Troncoso, Leanna, D’souza, Darwin, Dawson, Travis, Kim, Joel, Hamel, Steven, Buckup, Mark, Chang, Christie, Tabachnikova, Alexandra, Schwartz, Hara, Malissen, Nausicaa, Lavin, Yonit, Soares-Schanoski, Alessandra, Giotti, Bruno, Hegde, Samarth, Ioannou, Giorgio, Gonzalez-Kozlova, Edgar, Hennequin, Clotilde, Le Berichel, Jessica, Zhao, Zhen, Ward, Stephen C., Fiel, Isabel, Kou, Baijun, Dobosz, Michael, Li, Lianjie, Adler, Christina, Ni, Min, Wei, Yi, Wang, Wei, Atwal, Gurinder S., Kundu, Kunal, Cygan, Kamil J., Tsankov, Alexander M., Rahman, Adeeb, Price, Colles, Fernandez, Nicolas, He, Jiang, Gupta, Namita T., Kim-Schulze, Seunghee, Gnjatic, Sacha, Kenigsberg, Ephraim, Deering, Raquel P., Schwartz, Myron, Marron, Thomas U., Thurston, Gavin, Kamphorst, Alice O., Merad, Miriam

“…Despite no apparent defects in T cell priming and recruitment to tumors, a large subset of T cell rich tumors fail to respond to immune checkpoint blockade…”
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LTβR Agonism Promotes Anti-Tumor Immune Responses via Modulation of the Tumor Microenvironment by An, Disi, Chen, Guoying, Cheng, Wei-Yi, Mohrs, Katja, Adler, Christina, Gupta, Namita T, Atwal, Gurinder S, DiLillo, David J, Daly, Christopher, Lin, John C, Kuhnert, Frank

“…The presence of high endothelial venules (HEV) and tertiary lymphoid structures (TLS) in solid tumors is correlated with favorable prognosis and better…”
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Neoadjuvant cemiplimab for resectable hepatocellular carcinoma: a single-arm, open-label, phase 2 trial by Marron, Thomas U, Fiel, Maria Isabel, Hamon, Pauline, Fiaschi, Nathalie, Kim, Edward, Ward, Stephen C, Zhao, Zhen, Kim, Joel, Kennedy, Paul, Gunasekaran, Ganesh, Tabrizian, Parissa, Doroshow, Deborah, Legg, Meredith, Hammad, Ashley, Magen, Assaf, Kamphorst, Alice O, Shareef, Muhammed, Gupta, Namita T, Deering, Raquel, Wang, Wei, Wang, Fang, Thanigaimani, Pradeep, Mani, Jayakumar, Troncoso, Leanna, Tabachnikova, Alexandra, Chang, Christie, Akturk, Guray, Buckup, Mark, Hamel, Steven, Ioannou, Giorgio, Hennequin, Clotilde, Jamal, Hajra, Brown, Haley, Bonaccorso, Antoinette, Labow, Daniel, Sarpel, Umut, Rosenbloom, Talia, Sung, Max W, Kou, Baijun, Li, Siyu, Jankovic, Vladimir, James, Nicola, Hamon, Sara C, Cheung, Hung Kam, Sims, Jennifer S, Miller, Elizabeth, Bhardwaj, Nina, Thurston, Gavin, Lowy, Israel, Gnjatic, Sacha, Taouli, Bachir, Schwartz, Myron E, Merad, Miriam

“…Surgical resection of early stage hepatocellular carcinoma is standard clinical practice; however, most tumours recur despite surgery, and no perioperative…”
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Cancer cell-derived type I interferons instruct tumor monocyte polarization by Kwart, Dylan, He, Jing, Srivatsan, Subhashini, Lett, Clarissa, Golubov, Jacquelynn, Oswald, Erin M., Poon, Patrick, Ye, Xuan, Waite, Janelle, Zaretsky, Arielle Glatman, Haxhinasto, Sokol, Au-Yeung, Elsa, Gupta, Namita T., Chiu, Joyce, Adler, Christina, Cherravuru, Samvitha, Malahias, Evangelia, Negron, Nicole, Lanza, Kathryn, Coppola, Angel, Ni, Min, Song, Hang, Wei, Yi, Atwal, Gurinder S., Macdonald, Lynn, Oristian, Nicole Stokes, Poueymirou, William, Jankovic, Vladimir, Fury, Matthew, Lowy, Israel, Murphy, Andrew J., Sleeman, Matthew A., Wang, Bei, Skokos, Dimitris

“…Monocytes are highly plastic immune cells that modulate antitumor immunity. Therefore, identifying factors that regulate tumor monocyte functions is critical…”
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A framework for highly multiplexed dextramer mapping and prediction of T cell receptor sequences to antigen specificity by Zhang, Wen, Hawkins, Peter G, He, Jing, Gupta, Namita T, Liu, Jinrui, Choonoo, Gabrielle, Jeong, Se W, Chen, Calvin R, Dhanik, Ankur, Dillon, Myles, Deering, Raquel, Macdonald, Lynn E, Thurston, Gavin, Atwal, Gurinder S

“…T cell receptor (TCR) antigen-specific recognition is essential for the adaptive immune system. However, building a TCR-antigen interaction map has been…”
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VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements by Toby, Inimary T, Levin, Mikhail K, Salinas, Edward A, Christley, Scott, Bhattacharya, Sanchita, Breden, Felix, Buntzman, Adam, Corrie, Brian, Fonner, John, Gupta, Namita T, Hershberg, Uri, Marthandan, Nishanth, Rosenfeld, Aaron, Rounds, William, Rubelt, Florian, Scarborough, Walter, Scott, Jamie K, Uduman, Mohamed, Vander Heiden, Jason A, Scheuermann, Richard H, Monson, Nancy, Kleinstein, Steven H, Cowell, Lindsay G

“…The genes that produce antibodies and the immune receptors expressed on lymphocytes are not germline encoded; rather, they are somatically generated in each…”
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Absence of central tolerance in Aire-deficient mice synergizes with immune-checkpoint inhibition to enhance antitumor responses by Benitez, Asiel A., Khalil-Agüero, Sara, Nandakumar, Anjali, Gupta, Namita T., Zhang, Wen, Atwal, Gurinder S., Murphy, Andrew J., Sleeman, Matthew A., Haxhinasto, Sokol

“…The endogenous anti-tumor responses are limited in part by the absence of tumor-reactive T cells, an inevitable consequence of thymic central tolerance…”
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Hierarchical clustering can identify B cell clones with high confidence in Ig repertoire sequencing data1 by Gupta, Namita T., Adams, Kristofor D., Briggs, Adrian W., Timberlake, Sonia C., Vigneault, Francois, Kleinstein, Steven H.

“…Adaptive immunity is driven by the expansion, somatic hypermutation, and selection of B cell clones. Each clone is the progeny of a single B cell responding to…”
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Neutralizing antibodies against West Nile virus identified directly from human B cells by single-cell analysis and next generation sequencingElectronic supplementary information (ESI) available. See DOI: 10.1039/c5ib00169b by Tsioris, Konstantinos, Gupta, Namita T, Ogunniyi, Adebola O, Zimnisky, Ross M, Qian, Feng, Yao, Yi, Wang, Xiaomei, Stern, Joel N. H, Chari, Raj, Briggs, Adrian W, Clouser, Christopher R, Vigneault, Francois, Church, George M, Garcia, Melissa N, Murray, Kristy O, Montgomery, Ruth R, Kleinstein, Steven H, Love, J. Christopher

“…West Nile virus (WNV) infection is an emerging mosquito-borne disease that can lead to severe neurological illness and currently has no available treatment or…”
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