Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis von Levine, Jacob H., Simonds, Erin F., Bendall, Sean C., Davis, Kara L., Amir, El-ad D., Tadmor, Michelle D., Litvin, Oren, Fienberg, Harris G., Jager, Astraea, Zunder, Eli R., Finck, Rachel, Gedman, Amanda L., Radtke, Ina, Downing, James R., Pe’er, Dana, Nolan, Garry P.

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Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development von Bendall, Sean C., Davis, Kara L., Amir, El-ad David, Tadmor, Michelle D., Simonds, Erin F., Chen, Tiffany J., Shenfeld, Daniel K., Nolan, Garry P., Pe’er, Dana

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Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses von Lavin, Yonit, Kobayashi, Soma, Leader, Andrew, Amir, El-ad David, Elefant, Naama, Bigenwald, Camille, Remark, Romain, Sweeney, Robert, Becker, Christian D., Levine, Jacob H., Meinhof, Klaus, Chow, Andrew, Kim-Shulze, Seunghee, Wolf, Andrea, Medaglia, Chiara, Li, Hanjie, Rytlewski, Julie A., Emerson, Ryan O., Solovyov, Alexander, Greenbaum, Benjamin D., Sanders, Catherine, Vignali, Marissa, Beasley, Mary Beth, Flores, Raja, Gnjatic, Sacha, Pe’er, Dana, Rahman, Adeeb, Amit, Ido, Merad, Miriam

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Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum von Bendall, Sean C., Simonds, Erin F., Qiu, Peng, Amir, El-ad D., Krutzik, Peter O., Finck, Rachel, Bruggner, Robert V., Melamed, Rachel, Trejo, Angelica, Ornatsky, Olga I., Balderas, Robert S., Plevritis, Sylvia K., Sachs, Karen, Pe'er, Dana, Tanner, Scott D., Nolan, Garry P.

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Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm von Zunder, Eli R, Finck, Rachel, Behbehani, Gregory K, Amir, El-ad D, Krishnaswamy, Smita, Gonzalez, Veronica D, Lorang, Cynthia G, Bjornson, Zach, Spitzer, Matthew H, Bodenmiller, Bernd, Fantl, Wendy J, Pe'er, Dana, Nolan, Garry P

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Single-cell immune landscape of human atherosclerotic plaques von Fernandez, Dawn M., Rahman, Adeeb H., Fernandez, Nicolas F., Chudnovskiy, Aleksey, Amir, El-ad David, Amadori, Letizia, Khan, Nayaab S., Wong, Christine K., Shamailova, Roza, Hill, Christopher A., Wang, Zichen, Remark, Romain, Li, Jennifer R., Pina, Christian, Faries, Christopher, Awad, Ahmed J., Moss, Noah, Bjorkegren, Johan L. M., Kim-Schulze, Seunghee, Gnjatic, Sacha, Ma’ayan, Avi, Mocco, J, Faries, Peter, Merad, Miriam, Giannarelli, Chiara

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Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy von Hartmann, Felix J., Babdor, Joel, Gherardini, Pier Federico, Amir, El-Ad D., Jones, Kyle, Sahaf, Bita, Marquez, Diana M., Krutzik, Peter, O’Donnell, Erika, Sigal, Natalia, Maecker, Holden T., Meyer, Everett, Spitzer, Matthew H., Bendall, Sean C.

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Full spectrum flow cytometry and mass cytometry: A 32‐marker panel comparison von Jaimes, Maria C., Leipold, Michael, Kraker, Geoffrey, Amir, El‐ad, Maecker, Holden, Lannigan, Joanne

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viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia von Amir, El-ad David, Davis, Kara L, Tadmor, Michelle D, Simonds, Erin F, Levine, Jacob H, Bendall, Sean C, Shenfeld, Daniel K, Krishnaswamy, Smita, Nolan, Garry P, Pe'er, Dana

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Highly multiplexed profiling of single-cell effector functions reveals deep functional heterogeneity in response to pathogenic ligands von Lu, Yao, Xue, Qiong, Eisele, Markus R., Sulistijo, Endah S., Brower, Kara, Han, Lin, Amir, El-ad David, Pe’er, Dana, Miller-Jensen, Kathryn, Fan, Rong

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Host-Protozoan Interactions Protect from Mucosal Infections through Activation of the Inflammasome von Chudnovskiy, Aleksey, Mortha, Arthur, Kana, Veronika, Kennard, Andrea, Ramirez, Juan David, Rahman, Adeeb, Remark, Romain, Mogno, Ilaria, Ng, Ruby, Gnjatic, Sasha, Amir, El-ad David, Solovyov, Alexander, Greenbaum, Benjamin, Clemente, Jose, Faith, Jeremiah, Belkaid, Yasmine, Grigg, Michael E., Merad, Miriam

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An integrated framework using high‐dimensional mass cytometry and fluorescent flow cytometry identifies discrete B cell subsets in patients with red meat allergy von Cox, Kelly M., Commins, Scott P., Capaldo, Brian J., Workman, Lisa J., Platts‐Mills, Thomas A. E., Amir, El‐ad D., Lannigan, Josephine A., Schuyler, Alexander J., Erickson, Loren D.

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Development of a Comprehensive Antibody Staining Database Using a Standardized Analytics Pipeline von Amir, El-Ad David, Lee, Brian, Badoual, Paul, Gordon, Martin, Guo, Xinzheng V, Merad, Miriam, Rahman, Adeeb H

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A Modified Injector and Sample Acquisition Protocol Can Improve Data Quality and Reduce Inter‐Instrument Variability of the Helios Mass Cytometer von Lee, Brian H., Kelly, Geoffrey, Bradford, Shermineh, Davila, Melanie, Guo, Xinzheng V., Amir, El‐Ad David, Thrash, Emily M., Solga, Michael D., Lannigan, Joanne, Sellers, Brian, Candia, Julian, Tsang, John, Montgomery, Ruth R., Tamaki, Stanley J., Sigdel, Tara K., Sarwal, Minnie M., Lanier, Lewis L., Tian, Yuan, Kim, Cheryl, Hinz, Denise, Peters, Bjoern, Sette, Alessandro, Rahman, Adeeb H.

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Comprehensive innate immune profiling of chikungunya virus infection in pediatric cases von Michlmayr, Daniela, Pak, Theodore R, Rahman, Adeeb H, Amir, El‐Ad David, Kim, Eun‐Young, Kim‐Schulze, Seunghee, Suprun, Maria, Stewart, Michael G, Thomas, Guajira P, Balmaseda, Angel, Wang, Li, Zhu, Jun, Suaréz‐Fariñas, Mayte, Wolinsky, Steven M, Kasarskis, Andrew, Harris, Eva

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Protein Barcodes Enable High-Dimensional Single-Cell CRISPR Screens von Wroblewska, Aleksandra, Dhainaut, Maxime, Ben-Zvi, Benjamin, Rose, Samuel A., Park, Eun Sook, Amir, El-Ad David, Bektesevic, Anela, Baccarini, Alessia, Merad, Miriam, Rahman, Adeeb H., Brown, Brian D.

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High-dimensional CyTOF analysis of dengue virus-infected human DCs reveals distinct viral signatures von Hamlin, Rebecca E, Rahman, Adeeb, Pak, Theodore R, Maringer, Kevin, Mena, Ignacio, Bernal-Rubio, Dabeiba, Potla, Uma, Maestre, Ana M, Fredericks, Anthony C, Amir, El-Ad D, Kasarskis, Andrew, Ramos, Irene, Merad, Miriam, Fernandez-Sesma, Ana

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Multimodal Mapping of the Tumor and Peripheral Blood Immune Landscape in Human Pancreatic Cancer von Steele, Nina G, Carpenter, Eileen S, Kemp, Samantha B, Sirihorachai, Veerin R, The, Stephanie, Delrosario, Lawrence, Lazarus, Jenny, Amir, El-Ad David, Gunchick, Valerie, Espinoza, Carlos, Bell, Samantha, Harris, Lindsey, Lima, Fatima, Irizarry-Negron, Valerie, Paglia, Daniel, Macchia, Justin, Chu, Angel Ka Yan, Schofield, Heather, Wamsteker, Erik-Jan, Kwon, Richard, Schulman, Allison, Prabhu, Anoop, Law, Ryan, Sondhi, Arjun, Yu, Jessica, Patel, Arpan, Donahue, Katelyn, Nathan, Hari, Cho, Clifford, Anderson, Michelle A, Sahai, Vaibhav, Lyssiotis, Costas A, Zou, Weiping, Allen, Benjamin L, Rao, Arvind, Crawford, Howard C, Bednar, Filip, Frankel, Timothy L, Pasca di Magliano, Marina

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Differentiable, multi-dimensional, knowledge-based energy terms for torsion angle probabilities and propensities von Amir, El-Ad David, Kalisman, Nir, Keasar, Chen

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KinSNP software for homozygosity mapping of disease genes using SNP microarrays von Amir, El-Ad David, Bartal, Ofer, Morad, Efrat, Nagar, Tal, Sheynin, Jony, Parvari, Ruti, Chalifa-Caspi, Vered

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