Decoupling epithelial-mesenchymal transitions from stromal profiles by integrative expression analysis von Tyler, Michael, Tirosh, Itay

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Two strategies for gene regulation by promoter nucleosomes von Tirosh, Itay, Barkai, Naama

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Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action von McFarland, James M., Paolella, Brenton R., Warren, Allison, Geiger-Schuller, Kathryn, Shibue, Tsukasa, Rothberg, Michael, Kuksenko, Olena, Colgan, William N., Jones, Andrew, Chambers, Emily, Dionne, Danielle, Bender, Samantha, Wolpin, Brian M., Ghandi, Mahmoud, Tirosh, Itay, Rozenblatt-Rosen, Orit, Roth, Jennifer A., Golub, Todd R., Regev, Aviv, Aguirre, Andrew J., Vazquez, Francisca, Tsherniak, Aviad

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Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer von Puram, Sidharth V., Tirosh, Itay, Parikh, Anuraag S., Patel, Anoop P., Yizhak, Keren, Gillespie, Shawn, Rodman, Christopher, Luo, Christina L., Mroz, Edmund A., Emerick, Kevin S., Deschler, Daniel G., Varvares, Mark A., Mylvaganam, Ravi, Rozenblatt-Rosen, Orit, Rocco, James W., Faquin, William C., Lin, Derrick T., Regev, Aviv, Bernstein, Bradley E.

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Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells von Kowalczyk, Monika S, Tirosh, Itay, Heckl, Dirk, Rao, Tata Nageswara, Dixit, Atray, Haas, Brian J, Schneider, Rebekka K, Wagers, Amy J, Ebert, Benjamin L, Regev, Aviv

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Interactions between cancer cells and immune cells drive transitions to mesenchymal-like states in glioblastoma von Hara, Toshiro, Chanoch-Myers, Rony, Mathewson, Nathan D., Myskiw, Chad, Atta, Lyla, Bussema, Lillian, Eichhorn, Stephen W., Greenwald, Alissa C., Kinker, Gabriela S., Rodman, Christopher, Gonzalez Castro, L. Nicolas, Wakimoto, Hiroaki, Rozenblatt-Rosen, Orit, Zhuang, Xiaowei, Fan, Jean, Hunter, Tony, Verma, Inder M., Wucherpfennig, Kai W., Regev, Aviv, Suvà, Mario L., Tirosh, Itay

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Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets von Macosko, Evan Z., Basu, Anindita, Satija, Rahul, Nemesh, James, Shekhar, Karthik, Goldman, Melissa, Tirosh, Itay, Bialas, Allison R., Kamitaki, Nolan, Martersteck, Emily M., Trombetta, John J., Weitz, David A., Sanes, Joshua R., Shalek, Alex K., Regev, Aviv, McCarroll, Steven A.

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Challenges and emerging directions in single-cell analysis von Yuan, Guo-Cheng, Cai, Long, Elowitz, Michael, Enver, Tariq, Fan, Guoping, Guo, Guoji, Irizarry, Rafael, Kharchenko, Peter, Kim, Junhyong, Orkin, Stuart, Quackenbush, John, Saadatpour, Assieh, Schroeder, Timm, Shivdasani, Ramesh, Tirosh, Itay

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Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma von Patel, Anoop P., Tirosh, Itay, Trombetta, John J., Shalek, Alex K., Gillespie, Shawn M., Wakimoto, Hiroaki, Cahill, Daniel P., Nahed, Brian V., Curry, William T., Martuza, Robert L., Louis, David N., Rozenblatt-Rosen, Orit, Suvà, Mario L., Regev, Aviv, Bernstein, Bradley E.

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Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq von Tirosh, Itay, Izar, Benjamin, Prakadan, Sanjay M., Wadsworth, Marc H., Treacy, Daniel, Trombetta, John J., Rotem, Asaf, Rodman, Christopher, Lian, Christine, Murphy, George, Fallahi-Sichani, Mohammad, Dutton-Regester, Ken, Lin, Jia-Ren, Cohen, Ofir, Shah, Parin, Lu, Diana, Genshaft, Alex S., Hughes, Travis K., Ziegler, Carly G. K., Kazer, Samuel W., Gaillard, Aleth, Kolb, Kellie E., Villani, Alexandra-Chloé, Johannessen, Cory M., Andreev, Aleksandr Y., Van Allen, Eliezer M., Bertagnolli, Monica, Sorger, Peter K., Sullivan, Ryan J., Flaherty, Keith T., Frederick, Dennie T., Jané-Valbuena, Judit, Yoon, Charles H., Rozenblatt-Rosen, Orit, Shalek, Alex K., Regev, Aviv, Garraway, Levi A.

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A single-cell landscape of high-grade serous ovarian cancer von Izar, Benjamin, Tirosh, Itay, Stover, Elizabeth H., Wakiro, Isaac, Cuoco, Michael S., Alter, Idan, Rodman, Christopher, Leeson, Rachel, Su, Mei-Ju, Shah, Parin, Iwanicki, Marcin, Walker, Sarah R., Kanodia, Abhay, Melms, Johannes C., Mei, Shaolin, Lin, Jia-Ren, Porter, Caroline B. M., Slyper, Michal, Waldman, Julia, Jerby-Arnon, Livnat, Ashenberg, Orr, Brinker, Titus J., Mills, Caitlin, Rogava, Meri, Vigneau, Sébastien, Sorger, Peter K., Garraway, Levi A., Konstantinopoulos, Panagiotis A., Liu, Joyce F., Matulonis, Ursula, Johnson, Bruce E., Rozenblatt-Rosen, Orit, Rotem, Asaf, Regev, Aviv

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Evaluation of RNAi and CRISPR technologies by large-scale gene expression profiling in the Connectivity Map von Smith, Ian, Greenside, Peyton G, Natoli, Ted, Lahr, David L, Wadden, David, Tirosh, Itay, Narayan, Rajiv, Root, David E, Golub, Todd R, Subramanian, Aravind, Doench, John G

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Genome-wide CRISPR screen identifies PRC2 and KMT2D-COMPASS as regulators of distinct EMT trajectories that contribute differentially to metastasis von Zhang, Yun, Donaher, Joana Liu, Das, Sunny, Li, Xin, Reinhardt, Ferenc, Krall, Jordan A., Lambert, Arthur W., Thiru, Prathapan, Keys, Heather R., Khan, Mehreen, Hofree, Matan, Wilson, Molly M., Yedier-Bayram, Ozlem, Lack, Nathan A., Onder, Tamer T., Bagci-Onder, Tugba, Tyler, Michael, Tirosh, Itay, Regev, Aviv, Lees, Jacqueline A., Weinberg, Robert A.

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A genetic signature of interspecies variations in gene expression von Barkai, Naama, Tirosh, Itay, Weinberger, Adina, Carmi, Miri

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Coupled evolution of transcription and mRNA degradation von Dori-Bachash, Mally, Shema, Efrat, Tirosh, Itay

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High-throughput Phenotyping of Lung Cancer Somatic Mutations von Berger, Alice H., Brooks, Angela N., Wu, Xiaoyun, Shrestha, Yashaswi, Chouinard, Candace, Piccioni, Federica, Bagul, Mukta, Kamburov, Atanas, Imielinski, Marcin, Hogstrom, Larson, Zhu, Cong, Yang, Xiaoping, Pantel, Sasha, Sakai, Ryo, Watson, Jacqueline, Kaplan, Nathan, Campbell, Joshua D., Singh, Shantanu, Root, David E., Narayan, Rajiv, Natoli, Ted, Lahr, David L., Tirosh, Itay, Tamayo, Pablo, Getz, Gad, Wong, Bang, Doench, John, Subramanian, Aravind, Golub, Todd R., Meyerson, Matthew, Boehm, Jesse S.

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Stochastic transitions as a major source of cancer heterogeneity von Tirosh, Itay

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Elucidating the diversity of malignant mesenchymal states in glioblastoma by integrative analysis von Chanoch-Myers, Rony, Wider, Adi, Suva, Mario L, Tirosh, Itay

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An activation to memory differentiation trajectory of tumor-infiltrating lymphocytes informs metastatic melanoma outcomes von Jaiswal, Abhinav, Verma, Akanksha, Dannenfelser, Ruth, Melssen, Marit, Tirosh, Itay, Izar, Benjamin, Kim, Tae-Gyun, Nirschl, Christopher J., Devi, K. Sanjana P., Olson, Walter C., Slingluff, Craig L., Engelhard, Victor H., Garraway, Levi, Regev, Aviv, Minkis, Kira, Yoon, Charles H., Troyanskaya, Olga, Elemento, Olivier, Suárez-Fariñas, Mayte, Anandasabapathy, Niroshana

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Correction: Elucidating the diversity of malignant mesenchymal states in glioblastoma by integrative analysis von Chanoch-Myers, Rony, Wider, Adi, Suva, Mario L, Tirosh, Itay

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