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Published in Nature biotechnology (01.01.2020)
Published in Nature biotechnology (01.01.2020)
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T cell receptor repertoires of mice and humans are clustered in similarity networks around conserved public CDR3 sequences
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Published in eLife (21.07.2017)
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Molecular constraints on CDR3 for thymic selection of MHC-restricted TCRs from a random pre-selection repertoire
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Published in Nature communications (04.03.2019)
Published in Nature communications (04.03.2019)
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A functional map of HIV-host interactions in primary human T cells
Hiatt, Joseph, Hultquist, Judd F., McGregor, Michael J., Bouhaddou, Mehdi, Leenay, Ryan T., Simons, Lacy M., Young, Janet M., Haas, Paige, Roth, Theodore L., Tobin, Victoria, Wojcechowskyj, Jason A., Woo, Jonathan M., Rathore, Ujjwal, Cavero, Devin A., Shifrut, Eric, Nguyen, Thong T., Haas, Kelsey M., Malik, Harmit S., Doudna, Jennifer A., May, Andrew P., Marson, Alexander, Krogan, Nevan J.
Published in Nature communications (01.04.2022)
Published in Nature communications (01.04.2022)
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CNS-specific immunity at the choroid plexus shifts toward destructive Th2 inflammation in brain aging
Baruch, Kuti, Ron-Harel, Noga, Gal, Hilah, Deczkowska, Aleksandra, Shifrut, Eric, Ndifon, Wilfred, Mirlas-Neisberg, Nataly, Cardon, Michal, Vaknin, Ilan, Cahalon, Liora, Berkutzki, Tamara, Mattson, Mark P., Gomez-Pinilla, Fernando, Friedman, Nir, Schwartz, Michal
Published in Proceedings of the National Academy of Sciences - PNAS (05.02.2013)
Published in Proceedings of the National Academy of Sciences - PNAS (05.02.2013)
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Functional CRISPR dissection of gene networks controlling human regulatory T cell identity
Schumann, Kathrin, Raju, Siddharth S., Lauber, Michael, Kolb, Saskia, Shifrut, Eric, Cortez, Jessica T., Skartsis, Nikolaos, Nguyen, Vinh Q., Woo, Jonathan M., Roth, Theodore L., Yu, Ruby, Nguyen, Michelle L. T., Simeonov, Dimitre R., Nguyen, David N., Targ, Sasha, Gate, Rachel E., Tang, Qizhi, Bluestone, Jeffrey A., Spitzer, Matthew H., Ye, Chun Jimmie, Marson, Alexander
Published in Nature immunology (01.11.2020)
Published in Nature immunology (01.11.2020)
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Feature selection using a one dimensional naïve Bayes' classifier increases the accuracy of support vector machine classification of CDR3 repertoires
Cinelli, Mattia, Sun, Yuxin, Best, Katharine, Heather, James M, Reich-Zeliger, Shlomit, Shifrut, Eric, Friedman, Nir, Shawe-Taylor, John, Chain, Benny
Published in Bioinformatics (Oxford, England) (01.04.2017)
Published in Bioinformatics (Oxford, England) (01.04.2017)
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Crosslinking of Ly6a metabolically reprograms CD8 T cells for cancer immunotherapy
Maliah, Avishai, Santana-Magal, Nadine, Parikh, Shivang, Gordon, Sagi, Reshef, Keren, Sade, Yuval, Khateeb, Aseel, Richter, Alon, Gutwillig, Amit, Parikh, Roma, Golan, Tamar, Krissi, Matan, Na, Manho, Binshtok, Gal, Manich, Paulee, Elkoshi, Nadav, Grisaru-Tal, Sharon, Zemser-Werner, Valentina, Brenner, Ronen, Vaknine, Hananya, Nizri, Eran, Moyal, Lilach, Amitay-Laish, Iris, Rosemberg, Luiza, Munitz, Ariel, Kronfeld-Schor, Noga, Shifrut, Eric, Kobiler, Oren, Madi, Asaf, Geiger, Tamar, Carmi, Yaron, Levy, Carmit
Published in Nature communications (27.09.2024)
Published in Nature communications (27.09.2024)
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Chromatin conformation governs T-cell receptor Jβ gene segment usage
Ndifon, Wilfred, Gal, Hilah, Shifrut, Eric, Aharoni, Rina, Yissachar, Nissan, Waysbort, Nir, Reich-Zeliger, Shlomit, Arnon, Ruth, Friedman, Nir
Published in Proceedings of the National Academy of Sciences - PNAS (25.09.2012)
Published in Proceedings of the National Academy of Sciences - PNAS (25.09.2012)
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Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition
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Published in PloS one (06.11.2018)
Published in PloS one (06.11.2018)
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XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment
Lee, Youjin, Bogdanoff, Derek, Wang, Yutong, Hartoularos, George C, Woo, Jonathan M, Mowery, Cody T, Nisonoff, Hunter M, Lee, David S, Sun, Yang, Lee, James, Mehdizadeh, Sadaf, Cantlon, Joshua, Shifrut, Eric, Ngyuen, David N, Roth, Theodore L, Song, Yun S, Marson, Alexander, Chow, Eric D, Ye, Chun Jimmie
Published in Science advances (01.04.2021)
Published in Science advances (01.04.2021)
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TIM-3, LAG-3, or 2B4 gene disruptions increase the anti-tumor response of engineered T cells
Cianciotti, Beatrice Claudia, Magnani, Zulma Irene, Ugolini, Alessia, Camisa, Barbara, Merelli, Ivan, Vavassori, Valentina, Potenza, Alessia, Imparato, Antonio, Manfredi, Francesco, Abbati, Danilo, Perani, Laura, Spinelli, Antonello, Shifrut, Eric, Ciceri, Fabio, Vago, Luca, Di Micco, Raffaella, Naldini, Luigi, Genovese, Pietro, Ruggiero, Eliana, Bonini, Chiara
Published in Frontiers in immunology (29.02.2024)
Published in Frontiers in immunology (29.02.2024)
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McPAS-TCR: a manually curated catalogue of pathology-associated T cell receptor sequences
Tickotsky, Nili, Sagiv, Tal, Prilusky, Jaime, Shifrut, Eric, Friedman, Nir
Published in Bioinformatics (Oxford, England) (15.09.2017)
Published in Bioinformatics (Oxford, England) (15.09.2017)
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Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function
Shifrut, Eric, Carnevale, Julia, Tobin, Victoria, Roth, Theodore L., Woo, Jonathan M., Bui, Christina T., Li, P. Jonathan, Diolaiti, Morgan E., Ashworth, Alan, Marson, Alexander
Published in Cell (13.12.2018)
Published in Cell (13.12.2018)
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Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence
Belk, Julia A., Yao, Winnie, Ly, Nghi, Freitas, Katherine A., Chen, Yan-Ting, Shi, Quanming, Valencia, Alfredo M., Shifrut, Eric, Kale, Nupura, Yost, Kathryn E., Duffy, Connor V., Daniel, Bence, Hwee, Madeline A., Miao, Zhuang, Ashworth, Alan, Mackall, Crystal L., Marson, Alexander, Carnevale, Julia, Vardhana, Santosh A., Satpathy, Ansuman T.
Published in Cancer cell (11.07.2022)
Published in Cancer cell (11.07.2022)
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T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity
Madi, Asaf, Shifrut, Eric, Reich-Zeliger, Shlomit, Gal, Hilah, Best, Katharine, Ndifon, Wilfred, Chain, Benjamin, Cohen, Irun R, Friedman, Nir
Published in Genome research (01.10.2014)
Published in Genome research (01.10.2014)
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Reprogramming human T cell function and specificity with non-viral genome targeting
Roth, Theodore L., Puig-Saus, Cristina, Yu, Ruby, Shifrut, Eric, Carnevale, Julia, Li, P. Jonathan, Hiatt, Joseph, Saco, Justin, Krystofinski, Paige, Li, Han, Tobin, Victoria, Nguyen, David N., Lee, Michael R., Putnam, Amy L., Ferris, Andrea L., Chen, Jeff W., Schickel, Jean-Nicolas, Pellerin, Laurence, Carmody, David, Alkorta-Aranburu, Gorka, del Gaudio, Daniela, Matsumoto, Hiroyuki, Morell, Montse, Mao, Ying, Cho, Min, Quadros, Rolen M., Gurumurthy, Channabasavaiah B., Smith, Baz, Haugwitz, Michael, Hughes, Stephen H., Weissman, Jonathan S., Schumann, Kathrin, Esensten, Jonathan H., May, Andrew P., Ashworth, Alan, Kupfer, Gary M., Greeley, Siri Atma W., Bacchetta, Rosa, Meffre, Eric, Roncarolo, Maria Grazia, Romberg, Neil, Herold, Kevan C., Ribas, Antoni, Leonetti, Manuel D., Marson, Alexander
Published in Nature (London) (01.07.2018)
Published in Nature (London) (01.07.2018)
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Pooled Knockin Targeting for Genome Engineering of Cellular Immunotherapies
Roth, Theodore L., Li, P. Jonathan, Blaeschke, Franziska, Nies, Jasper F., Apathy, Ryan, Mowery, Cody, Yu, Ruby, Nguyen, Michelle L.T., Lee, Youjin, Truong, Anna, Hiatt, Joseph, Wu, David, Nguyen, David N., Goodman, Daniel, Bluestone, Jeffrey A., Ye, Chun Jimmie, Roybal, Kole, Shifrut, Eric, Marson, Alexander
Published in Cell (30.04.2020)
Published in Cell (30.04.2020)
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CRISPR screen in regulatory T cells reveals modulators of Foxp3
Cortez, Jessica T., Montauti, Elena, Shifrut, Eric, Gatchalian, Jovylyn, Zhang, Yusi, Shaked, Oren, Xu, Yuanming, Roth, Theodore L., Simeonov, Dimitre R., Zhang, Yana, Chen, Siqi, Li, Zhongmei, Woo, Jonathan M., Ho, Josephine, Vogel, Ian A., Prator, Grace Y., Zhang, Bin, Lee, Youjin, Sun, Zhaolin, Ifergan, Igal, Van Gool, Frédéric, Hargreaves, Diana C., Bluestone, Jeffrey A., Marson, Alexander, Fang, Deyu
Published in Nature (London) (18.06.2020)
Published in Nature (London) (18.06.2020)
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High-yield genome engineering in primary cells using a hybrid ssDNA repair template and small-molecule cocktails
Shy, Brian R., Vykunta, Vivasvan S., Ha, Alvin, Talbot, Alexis, Roth, Theodore L., Nguyen, David N., Pfeifer, Wolfgang G., Chen, Yan Yi, Blaeschke, Franziska, Shifrut, Eric, Vedova, Shane, Mamedov, Murad R., Chung, Jing-Yi Jing, Li, Hong, Yu, Ruby, Wu, David, Wolf, Jeffrey, Martin, Thomas G., Castro, Carlos E., Ye, Lumeng, Esensten, Jonathan H., Eyquem, Justin, Marson, Alexander
Published in Nature biotechnology (01.04.2023)
Published in Nature biotechnology (01.04.2023)
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