Inhibitory CD161 receptor identified in glioma-infiltrating T cells by single-cell analysis

Authors: Mathewson, Nathan D., Ashenberg, Orr, Tirosh, Itay, Gritsch, Simon, Perez, Elizabeth M., Marx, Sascha, Jerby-Arnon, Livnat, Chanoch-Myers, Rony, Hara, Toshiro, Richman, Alyssa R., Ito, Yoshinaga, Pyrdol, Jason, Friedrich, Mirco, Schumann, Kathrin, Poitras, Michael J., Gokhale, Prafulla C., Gonzalez Castro, L. Nicolas, Shore, Marni E., Hebert, Christine M., Shaw, Brian, Cahill, Heather L., Drummond, Matthew, Zhang, Wubing, Olawoyin, Olamide, Wakimoto, Hiroaki, Rozenblatt-Rosen, Orit, Brastianos, Priscilla K., Liu, X. Shirley, Jones, Pamela S., Cahill, Daniel P., Frosch, Matthew P., Louis, David N., Freeman, Gordon J., Ligon, Keith L., Marson, Alexander, Chiocca, E. Antonio, Reardon, David A., Regev, Aviv, Suvà, Mario L., Wucherpfennig, Kai W.

Source: In Cell 4 March 2021 184(5):1281-1298

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade

Authors: Jerby-Arnon, Livnat, Shah, Parin, Cuoco, Michael S., Rodman, Christopher, Su, Mei-Ju, Melms, Johannes C., Leeson, Rachel, Kanodia, Abhay, Mei, Shaolin, Lin, Jia-Ren, Wang, Shu, Rabasha, Bokang, Liu, David, Zhang, Gao, Margolais, Claire, Ashenberg, Orr, Ott, Patrick A., Buchbinder, Elizabeth I., Haq, Rizwan, Hodi, F. Stephen, Boland, Genevieve M., Sullivan, Ryan J., Frederick, Dennie T., Miao, Benchun, Moll, Tabea, Flaherty, Keith T., Herlyn, Meenhard, Jenkins, Russell W., Thummalapalli, Rohit, Kowalczyk, Monika S., Cañadas, Israel, Schilling, Bastian, Cartwright, Adam N.R., Luoma, Adrienne M., Malu, Shruti, Hwu, Patrick, Bernatchez, Chantale, Forget, Marie-Andrée, Barbie, David A., Shalek, Alex K., Tirosh, Itay, Sorger, Peter K., Wucherpfennig, Kai, Van Allen, Eliezer M., Schadendorf, Dirk, Johnson, Bruce E., Rotem, Asaf, Rozenblatt-Rosen, Orit, Garraway, Levi A., Yoon, Charles H., Izar, Benjamin, Regev, Aviv

Source: In Cell 1 November 2018 175(4):984-997

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

Authors: Dixit, Atray, Parnas, Oren, Li, Biyu, Chen, Jenny, Fulco, Charles P., Jerby-Arnon, Livnat, Marjanovic, Nemanja D., Dionne, Danielle, Burks, Tyler, Raychowdhury, Raktima, Adamson, Britt, Norman, Thomas M., Lander, Eric S., Weissman, Jonathan S., Friedman, Nir, Regev, Aviv

Source: In Cell 15 December 2016 167(7):1853-1866

Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality

Authors: Jerby-Arnon, Livnat, Pfetzer, Nadja, Waldman, Yedael Y., McGarry, Lynn, James, Daniel, Shanks, Emma, Seashore-Ludlow, Brinton, Weinstock, Adam, Geiger, Tamar, Clemons, Paul A., Gottlieb, Eyal, Ruppin, Eytan

Source: In Cell 28 August 2014 158(5):1199-1209

DIALOGUE maps multicellular programs in tissue from single-cell or spatial transcriptomics data.

Authors: Jerby-Arnon, Livnat^1,2,3 (AUTHOR) ljerby@stanford.edu, Regev, Aviv^3,4,5 (AUTHOR) aviv.regev.sc@gmail.com

Source: Nature Biotechnology. Oct2022, Vol. 40 Issue 10, p1467-1477. 11p.

IL-33 Signaling Alters Regulatory T Cell Diversity in Support of Tumor Development

Authors: Li, Amy ^{1, 2, 3, 10}, Herbst, Rebecca H. ^{3, 4, 10}, Canner, David ^{1, 2, 10}, Schenkel, Jason M. ^{1, 5}, Smith, Olivia C. ¹, Kim, Jonathan Y. ¹, Hillman, Michelle ¹, Bhutkar, Arjun ¹, Cuoco, Michael S. ⁴, Rappazzo, C. Garrett ^{1, 9}, Rogers, Patricia ⁴, Dang, Celeste ¹, Jerby-Arnon, Livnat ⁴, Rozenblatt-Rosen, Orit ⁴, Cong, Le ^{6, 7}, Birnbaum, Michael ^{1, 9}, Regev, Aviv ^{1, 2, 4, 8, ∗}, Jacks, Tyler ^{1, 2, 8, 11, ∗∗}

Source: In Cell Reports 3 December 2019 29(10):2998-3008

Massively parallel phenotyping of coding variants in cancer with Perturb-seq.

Authors: Ursu, Oana, Neal, James T., Shea, Emily, Thakore, Pratiksha I., Jerby-Arnon, Livnat, Nguyen, Lan, Dionne, Danielle, Diaz, Celeste, Bauman, Julia, Mosaad, Mariam Mounir, Fagre, Christian, Lo, April, McSharry, Maria, Giacomelli, Andrew O., Ly, Seav Huong, Rozenblatt-Rosen, Orit, Hahn, William C., Aguirre, Andrew J., Berger, Alice H., Regev, Aviv

Source: Nature Biotechnology; Jun2022, Vol. 40 Issue 6, p896-905, 10p

Inter-cellular CRISPR screens reveal regulators of cancer cell phagocytosis.

Authors: Kamber, Roarke A., Nishiga, Yoko, Morton, Bhek, Banuelos, Allison M., Barkal, Amira A., Vences-Catalán, Felipe, Gu, Mingxin, Fernandez, Daniel, Seoane, Jose A., Yao, David, Liu, Katherine, Lin, Sijie, Spees, Kaitlyn, Curtis, Christina, Jerby-Arnon, Livnat, Weissman, Irving L., Sage, Julien, Bassik, Michael C.

Source: Nature; 9/23/2021, Vol. 597 Issue 7877, p549-554, 6p

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Opposing Immune and Genetic Mechanisms Shape Oncogenic Programs in Synovial Sarcoma

Authors: Jerby-Arnon, Livnat, Neftel, Cyril, Shore, Marni E., Weisman, Hannah R., Mathewson, Nathan, McBride, Matthew J., Haas, Brian, Izar, Benjamin, Volorio, Angela, Boulay, Gaylor, Cironi, Luisa, Richman, Alyssa R., Broye, Liliane C., Gurski, Joseph M., Luo, Christina, Mylvaganam, Ravindra, Nguyen, Lan, Mei, Shaolin, Melms, Johannes, Georgescu, Christophe, Cohen, Ofir, Buendia Buendia, Jorge Eduardo, Segerstolpe, Asa, Sud, Malika, Cuoco, Michael, Labes, Danny, Zollinger, Daniel R., Ortogero, Nicole, Beechem, Joseph M., Nielsen, G. Petur, Chebib, Ivan, Nguyen-Ngoc, Tu, Montemurro, Michael, Cote, Gregory, Choy, Edwin, Letovanec, Igor, Cherix, Stéphane, Wagle, Nikhil, Sorger, Peter, Haynes, Alex, Mullen, John, Stamenkovic, Ivan, Rivera, Miguel, Kadoch, Cigall, Wucherpfennig, Kai, Rozenblatt-Rosen, Orit, Suvà, Mario L., Riggi, Nicolò, Regev, Aviv

Source: Jerby-Arnon, Livnat, Cyril Neftel, Marni E Shore, Hannah R Weisman, Nathan D Mathewson, Matthew J McBride, Brian Haas, et al. 2021. “Opposing Immune and Genetic Mechanisms Shape Oncogenic Programs in Synovial Sarcoma.” Nature Medicine 27 (2): 289–300.

File Description: application/pdf

Relation: Nature Medicine

Access URL: https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37375080

Harnessing synthetic lethality to predict the response to cancer treatment.

Authors: Joo Sang Lee, Das, Avinash, Jerby-Arnon, Livnat, Arafeh, Rand, Auslander, Noam, Davidson, Matthew, McGarry, Lynn, James, Daniel, Amzallag, Arnaud, Seung Gu Park, Kuoyuan Cheng, Robinson, Welles, Atias, Dikla, Stossel, Chani, Buzhor, Ella, Stein, Gidi, Waterfall, Joshua J., Meltzer, Paul S., Golan, Talia, Hannenhalli, Sridhar

Source: Nature Communications; 6/29/2018, Vol. 9 Issue 1, p1-12, 12p

Subject Terms: CANCER treatment, DRUG efficacy, SYNTHETIC biology, ISLANDS

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

Authors: Slyper, Michal, Porter, Caroline, Ashenberg, Orr, Waldman, Julia, Drokhlyansky, Eugene, Wakiro, Isaac, Smilie, Christopher, Smith-Rosario, Gabriela, Wu, Jingyi, Dionne, Danielle, Vigneau, Sebastien, Jane-Valbuena, Judit, Tickle, Timothy, Napolitano, Sara, Su, Mei-Ju, Patel, Anand, Karlstrom, Asa, Gristch, Simon, Nomura, Masashi, Waghray, Avinash, Gohil, Satyen, Tsankov, Alexander, Jerby-Arnon, Livnat, Cohen, Ofir, Klughammer, Johanna, Rosen, Yanay, Gould, Joshua, Nguyen, Lan, Hofree, Matan, Tramontozzi, Peter, Levy, Rachel, Li, Bo, Wu, Catherine, Izar, Benjamin, Haq, Rizwan, Hodi, Stephen, Yoon, Charles, Hata, Aaron, Baker, Suzanne, Suva, Mario, Bueno, Raphael, Stover, Elizabeth, Clay, Michael, Dyer, M Aiven, Collins, Natalie, Matulonis, Ursula, Wagle, Nikhil, Johnson, Bruce, Rotem, Asaf, Rozenblatt-Rosen, Orit, Regev, Aviv

Source: Slyper, Michal, Caroline Porter, Orr Ashenberg, Julia Waldman, Eugene Drokhlyansky, Isaac Wakiro, Christopher Smilie et al. "A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors." Nat Med 26, no. 5 (2020): 792-802. DOI: 10.1038/s41591-020-0844-1

Subject Terms: General Biochemistry, Genetics and Molecular Biology, General Medicine

File Description: application/pdf

Relation: Nature Medicine; Nat Med

Access URL: https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37377135

Author Correction: Massively parallel phenotyping of coding variants in cancer with Perturb-seq.

Authors: Ursu, Oana, Neal, James T., Shea, Emily, Thakore, Pratiksha I., Jerby-Arnon, Livnat, Nguyen, Lan, Dionne, Danielle, Diaz, Celeste, Bauman, Julia, Mosaad, Mariam Mounir, Fagre, Christian, Lo, April, McSharry, Maria, Giacomelli, Andrew O., Ly, Seav Huong, Rozenblatt-Rosen, Orit, Hahn, William C., Aguirre, Andrew J., Berger, Alice H., Regev, Aviv

Source: Nature Biotechnology; Nov2022, Vol. 40 Issue 11, p1691-1691, 1p

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Genome‐wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy.

Authors: Park, Seung Gu, Sahu, Avinash Das, Ponomarova, Olga, Jerby‐Arnon, Livnat, Wagner, Allon, Miao, Benchun, Friedman, Adam A, Amzallag, Arnaud, Moll, Tabea, Kasumova, Gyulnara, Greninger, Patricia, Egan, Regina K, Damon, Leah J, Frederick, Dennie T, Boland, Genevieve, Benes, Cyril, Flaherty, Keith, Cheng, Kuoyuan, Robinson, Welles, Hannenhalli, Sridhar

Source: Molecular Systems Biology; Mar2019, Vol. 15 Issue 3, pN.PAG-N.PAG, 1p

Subject Terms: PHARMACOGENOMICS, CANCER, DRUG resistance, IMMUNOTHERAPY, DATA analysis