Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors
Villani, Alexandra-Chloé, Satija, Rahul, Reynolds, Gary, Sarkizova, Siranush, Shekhar, Karthik, Fletcher, James, Griesbeck, Morgane, Butler, Andrew, Zheng, Shiwei, Lazo, Suzan, Jardine, Laura, Dixon, David, Stephenson, Emily, Nilsson, Emil, Grundberg, Ida, McDonald, David, Filby, Andrew, Li, Weibo, De Jager, Philip L., Rozenblatt-Rosen, Orit, Lane, Andrew A., Haniffa, Muzlifah, Regev, Aviv, Hacohen, Nir
Published in Science (American Association for the Advancement of Science) (21.04.2017)
Published in Science (American Association for the Advancement of Science) (21.04.2017)
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Journal Article
A large peptidome dataset improves HLA class I epitope prediction across most of the human population
Sarkizova, Siranush, Klaeger, Susan, Le, Phuong M., Li, Letitia W., Oliveira, Giacomo, Keshishian, Hasmik, Hartigan, Christina R., Zhang, Wandi, Braun, David A., Ligon, Keith L., Bachireddy, Pavan, Zervantonakis, Ioannis K., Rosenbluth, Jennifer M., Ouspenskaia, Tamara, Law, Travis, Justesen, Sune, Stevens, Jonathan, Lane, William J., Eisenhaure, Thomas, Lan Zhang, Guang, Clauser, Karl R., Hacohen, Nir, Carr, Steven A., Wu, Catherine J., Keskin, Derin B.
Published in Nature biotechnology (01.02.2020)
Published in Nature biotechnology (01.02.2020)
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Journal Article
Personal neoantigen vaccines induce persistent memory T cell responses and epitope spreading in patients with melanoma
Hu, Zhuting, Leet, Donna E., Allesøe, Rosa L., Oliveira, Giacomo, Li, Shuqiang, Luoma, Adrienne M., Liu, Jinyan, Forman, Juliet, Huang, Teddy, Iorgulescu, J. Bryan, Holden, Rebecca, Sarkizova, Siranush, Gohil, Satyen H., Redd, Robert A., Sun, Jing, Elagina, Liudmila, Giobbie-Hurder, Anita, Zhang, Wandi, Peter, Lauren, Ciantra, Zoe, Rodig, Scott, Olive, Oriol, Shetty, Keerthi, Pyrdol, Jason, Uduman, Mohamed, Lee, Patrick C., Bachireddy, Pavan, Buchbinder, Elizabeth I., Yoon, Charles H., Neuberg, Donna, Pentelute, Bradley L., Hacohen, Nir, Livak, Kenneth J., Shukla, Sachet A., Olsen, Lars Rønn, Barouch, Dan H., Wucherpfennig, Kai W., Fritsch, Edward F., Keskin, Derin B., Wu, Catherine J., Ott, Patrick A.
Published in Nature medicine (01.03.2021)
Published in Nature medicine (01.03.2021)
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Journal Article
Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer
Ouspenskaia, Tamara, Law, Travis, Clauser, Karl R., Klaeger, Susan, Sarkizova, Siranush, Aguet, François, Li, Bo, Christian, Elena, Knisbacher, Binyamin A., Le, Phuong M., Hartigan, Christina R., Keshishian, Hasmik, Apffel, Annie, Oliveira, Giacomo, Zhang, Wandi, Chen, Sarah, Chow, Yuen Ting, Ji, Zhe, Jungreis, Irwin, Shukla, Sachet A., Justesen, Sune, Bachireddy, Pavan, Kellis, Manolis, Getz, Gad, Hacohen, Nir, Keskin, Derin B., Carr, Steven A., Wu, Catherine J., Regev, Aviv
Published in Nature biotechnology (01.02.2022)
Published in Nature biotechnology (01.02.2022)
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Journal Article
Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction
Abelin, Jennifer G., Keskin, Derin B., Sarkizova, Siranush, Hartigan, Christina R., Zhang, Wandi, Sidney, John, Stevens, Jonathan, Lane, William, Zhang, Guang Lan, Eisenhaure, Thomas M., Clauser, Karl R., Hacohen, Nir, Rooney, Michael S., Carr, Steven A., Wu, Catherine J.
Published in Immunity (Cambridge, Mass.) (21.02.2017)
Published in Immunity (Cambridge, Mass.) (21.02.2017)
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Journal Article
Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq
Li, Bo, Gould, Joshua, Yang, Yiming, Sarkizova, Siranush, Tabaka, Marcin, Ashenberg, Orr, Rosen, Yanay, Slyper, Michal, Kowalczyk, Monika S., Villani, Alexandra-Chloé, Tickle, Timothy, Hacohen, Nir, Rozenblatt-Rosen, Orit, Regev, Aviv
Published in Nature methods (01.08.2020)
Published in Nature methods (01.08.2020)
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Journal Article
Two distinct colonic CD14+ subsets characterized by single-cell RNA profiling in Crohn’s disease
Chapuy, Laurence, Bsat, Marwa, Sarkizova, Siranush, Rubio, Manuel, Therrien, Amélie, Wassef, Evelyne, Bouin, Mickael, Orlicka, Katarzina, Weber, Audrey, Hacohen, Nir, Villani, Alexandra-Chloé, Sarfati, Marika
Published in Mucosal immunology (01.05.2019)
Published in Mucosal immunology (01.05.2019)
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Journal Article
Disabled Homolog 2 Controls Prometastatic Activity of Tumor-Associated Macrophages
Marigo, Ilaria, Trovato, Rosalinda, Hofer, Francesca, Ingangi, Vincenzo, Desantis, Giacomo, Leone, Kevin, De Sanctis, Francesco, Ugel, Stefano, Canè, Stefania, Simonelli, Anna, Lamolinara, Alessia, Iezzi, Manuela, Fassan, Matteo, Rugge, Massimo, Boschi, Federico, Borile, Giulia, Eisenhaure, Thomas, Sarkizova, Siranush, Lieb, David, Hacohen, Nir, Azzolin, Luca, Piccolo, Stefano, Lawlor, Rita, Scarpa, Aldo, Carbognin, Luisa, Bria, Emilio, Bicciato, Silvio, Murray, Peter J., Bronte, Vincenzo
Published in Cancer discovery (01.11.2020)
Published in Cancer discovery (01.11.2020)
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Journal Article
The HLA-II immunopeptidome of SARS-CoV-2
Weingarten-Gabbay, Shira, Chen, Da-Yuan, Sarkizova, Siranush, Taylor, Hannah B., Gentili, Matteo, Hernandez, Gabrielle M., Pearlman, Leah R., Bauer, Matthew R., Rice, Charles M., Clauser, Karl R., Hacohen, Nir, Carr, Steven A., Abelin, Jennifer G., Saeed, Mohsan, Sabeti, Pardis C.
Published in Cell reports (Cambridge) (23.01.2024)
Published in Cell reports (Cambridge) (23.01.2024)
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Journal Article
ERAP2 Increases the Abundance of a Peptide Submotif Highly Selective for the Birdshot Uveitis-Associated HLA-A29
Venema, Wouter J, Hiddingh, Sanne, de Boer, Joke H, Claas, Frans H J, Mulder, Arend, den Hollander, Anneke I, Stratikos, Efstratios, Sarkizova, Siranush, van der Veken, Lars T, Janssen, George M C, van Veelen, Peter A, Kuiper, Jonas J W
Published in Frontiers in immunology (25.02.2021)
Published in Frontiers in immunology (25.02.2021)
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Journal Article
Correction: Two distinct colonic CD14+ subsets characterized by single-cell RNA profiling in Crohn’s disease
Chapuy, Laurence, Bsat, Marwa, Sarkizova, Siranush, Rubio, Manuel, Therrien, Amélie, Wassef, Evelyne, Bouin, Mickael, Orlicka, Katarzina, Weber, Audrey, Hacohen, Nir, Villani, Alexandra-Chloé, Sarfati, Marika
Published in Mucosal immunology (01.03.2020)
Published in Mucosal immunology (01.03.2020)
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Journal Article
Systems Immunology: Learning the Rules of the Immune System
Villani, Alexandra-Chloé, Sarkizova, Siranush, Hacohen, Nir
Published in Annual review of immunology (26.04.2018)
Published in Annual review of immunology (26.04.2018)
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Journal Article
Aryl Hydrocarbon Receptor Controls Monocyte Differentiation into Dendritic Cells versus Macrophages
Goudot, Christel, Coillard, Alice, Villani, Alexandra-Chloé, Gueguen, Paul, Cros, Adeline, Sarkizova, Siranush, Tang-Huau, Tsing-Lee, Bohec, Mylène, Baulande, Sylvain, Hacohen, Nir, Amigorena, Sebastian, Segura, Elodie
Published in Immunity (Cambridge, Mass.) (19.09.2017)
Published in Immunity (Cambridge, Mass.) (19.09.2017)
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Journal Article
High-throughput RNA isoform sequencing using programmed cDNA concatenation
Al’Khafaji, Aziz M., Smith, Jonathan T., Garimella, Kiran V., Babadi, Mehrtash, Popic, Victoria, Sade-Feldman, Moshe, Gatzen, Michael, Sarkizova, Siranush, Schwartz, Marc A., Blaum, Emily M., Day, Allyson, Costello, Maura, Bowers, Tera, Gabriel, Stacey, Banks, Eric, Philippakis, Anthony A., Boland, Genevieve M., Blainey, Paul C., Hacohen, Nir
Published in Nature biotechnology (01.04.2024)
Published in Nature biotechnology (01.04.2024)
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Journal Article
Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps
Chen, Bob, Scurrah, Cherie’ R., McKinley, Eliot T., Simmons, Alan J., Ramirez-Solano, Marisol A., Zhu, Xiangzhu, Markham, Nicholas O., Heiser, Cody N., Vega, Paige N., Rolong, Andrea, Kim, Hyeyon, Sheng, Quanhu, Drewes, Julia L., Zhou, Yuan, Southard-Smith, Austin N., Xu, Yanwen, Ro, James, Jones, Angela L., Revetta, Frank, Berry, Lynne D., Niitsu, Hiroaki, Islam, Mirazul, Pelka, Karin, Hofree, Matan, Chen, Jonathan H., Sarkizova, Siranush, Ng, Kimmie, Giannakis, Marios, Boland, Genevieve M., Aguirre, Andrew J., Anderson, Ana C., Rozenblatt-Rosen, Orit, Regev, Aviv, Hacohen, Nir, Kawasaki, Kenta, Sato, Toshiro, Goettel, Jeremy A., Grady, William M., Zheng, Wei, Washington, M. Kay, Cai, Qiuyin, Sears, Cynthia L., Goldenring, James R., Franklin, Jeffrey L., Su, Timothy, Huh, Won Jae, Vandekar, Simon, Roland, Joseph T., Liu, Qi, Coffey, Robert J., Shrubsole, Martha J., Lau, Ken S.
Published in Cell (22.12.2021)
Published in Cell (22.12.2021)
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Journal Article
Optimized Liquid and Gas Phase Fractionation Increases HLA-Peptidome Coverage for Primary Cell and Tissue Samples
Klaeger, Susan, Apffel, Annie, Clauser, Karl R., Sarkizova, Siranush, Oliveira, Giacomo, Rachimi, Suzanna, Le, Phuong M., Tarren, Anna, Chea, Vipheaviny, Abelin, Jennifer G., Braun, David A., Ott, Patrick A., Keshishian, Hasmik, Hacohen, Nir, Keskin, Derin B., Wu, Catherine J., Carr, Steven A.
Published in Molecular & cellular proteomics (2021)
Published in Molecular & cellular proteomics (2021)
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Journal Article
Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy
Chen, Jonathan H., Nieman, Linda T., Spurrell, Maxwell, Jorgji, Vjola, Elmelech, Liad, Richieri, Peter, Xu, Katherine H., Madhu, Roopa, Parikh, Milan, Zamora, Izabella, Mehta, Arnav, Nabel, Christopher S., Freeman, Samuel S., Pirl, Joshua D., Lu, Chenyue, Meador, Catherine B., Barth, Jaimie L., Sakhi, Mustafa, Tang, Alexander L., Sarkizova, Siranush, Price, Colles, Fernandez, Nicolas F., Emanuel, George, He, Jiang, Van Raay, Katrina, Reeves, Jason W., Yizhak, Keren, Hofree, Matan, Shih, Angela, Sade-Feldman, Moshe, Boland, Genevieve M., Pelka, Karin, Aryee, Martin J., Mino-Kenudson, Mari, Gainor, Justin F., Korsunsky, Ilya, Hacohen, Nir
Published in Nature immunology (01.04.2024)
Published in Nature immunology (01.04.2024)
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Journal Article
MS-Based HLA-II Peptidomics Combined With Multiomics Will Aid the Development of Future Immunotherapies
Taylor, Hannah B., Klaeger, Susan, Clauser, Karl R., Sarkizova, Siranush, Weingarten-Gabbay, Shira, Graham, Daniel B., Carr, Steven A., Abelin, Jennifer G.
Published in Molecular & cellular proteomics (01.01.2021)
Published in Molecular & cellular proteomics (01.01.2021)
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