Single-Cell Profiles of Retinal Ganglion Cells Differing in Resilience to Injury Reveal Neuroprotective Genes von Tran, Nicholas M., Shekhar, Karthik, Whitney, Irene E., Jacobi, Anne, Benhar, Inbal, Hong, Guosong, Yan, Wenjun, Adiconis, Xian, Arnold, McKinzie E., Lee, Jung Min, Levin, Joshua Z., Lin, Dingchang, Wang, Chen, Lieber, Charles M., Regev, Aviv, He, Zhigang, Sanes, Joshua R.

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Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics von Shekhar, Karthik, Lapan, Sylvain W., Whitney, Irene E., Tran, Nicholas M., Macosko, Evan Z., Kowalczyk, Monika, Adiconis, Xian, Levin, Joshua Z., Nemesh, James, Goldman, Melissa, McCarroll, Steven A., Cepko, Constance L., Regev, Aviv, Sanes, Joshua R.

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Individual brain organoids reproducibly form cell diversity of the human cerebral cortex von Velasco, Silvia, Kedaigle, Amanda J., Simmons, Sean K., Nash, Allison, Rocha, Marina, Quadrato, Giorgia, Paulsen, Bruna, Nguyen, Lan, Adiconis, Xian, Regev, Aviv, Levin, Joshua Z., Arlotta, Paola

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RIPK1 mediates a disease-associated microglial response in Alzheimer’s disease von Ofengeim, Dimitry, Mazzitelli, Sonia, Ito, Yasushi, DeWitt, Judy Park, Mifflin, Lauren, Zou, Chengyu, Das, Sudeshna, Adiconis, Xian, Chen, Hongbo, Zhu, Hong, Kelliher, Michelle A., Levin, Joshua Z., Yuan, Junying

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Massively parallel sequencing of human urinary exosome/microvesicle RNA reveals a predominance of non-coding RNA von Miranda, Kevin C, Bond, Daniel T, Levin, Joshua Z, Adiconis, Xian, Sivachenko, Andrey, Russ, Carsten, Brown, Dennis, Nusbaum, Chad, Russo, Leileata M

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Systematic comparison of single-cell and single-nucleus RNA-sequencing methods von Ding, Jiarui, Adiconis, Xian, Simmons, Sean K., Kowalczyk, Monika S., Hession, Cynthia C., Marjanovic, Nemanja D., Hughes, Travis K., Wadsworth, Marc H., Burks, Tyler, Nguyen, Lan T., Kwon, John Y. H., Barak, Boaz, Ge, William, Kedaigle, Amanda J., Carroll, Shaina, Li, Shuqiang, Hacohen, Nir, Rozenblatt-Rosen, Orit, Shalek, Alex K., Villani, Alexandra-Chloé, Regev, Aviv, Levin, Joshua Z.

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Comprehensive comparative analysis of strand-specific RNA sequencing methods von Levin, Joshua Z, Regev, Aviv, Yassour, Moran, Adiconis, Xian, Nusbaum, Chad, Thompson, Dawn Anne, Friedman, Nir, Gnirke, Andreas

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RNA-SeQC: RNA-seq metrics for quality control and process optimization von DELUCA, David S, LEVIN, Joshua Z, SIVACHENKO, Andrey, FENNELL, Timothy, NAZAIRE, Marc-Danie, WILLIAMS, Chris, REICH, Michael, WINCKLER, Wendy, GETZ, Gad

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Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells von Shalek, Alex K., Satija, Rahul, Adiconis, Xian, Gertner, Rona S., Gaublomme, Jellert T., Raychowdhury, Raktima, Schwartz, Schraga, Yosef, Nir, Malboeuf, Christine, Lu, Diana, Trombetta, John J., Gennert, Dave, Gnirke, Andreas, Goren, Alon, Hacohen, Nir, Levin, Joshua Z., Park, Hongkun, Regev, Aviv

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Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex von Uzquiano, Ana, Kedaigle, Amanda J, Pigoni, Martina, Paulsen, Bruna, Adiconis, Xian, Kim, Kwanho, Faits, Tyler, Nagaraja, Surya, Antón-Bolaños, Noelia, Gerhardinger, Chiara, Tucewicz, Ashley, Murray, Evan, Jin, Xin, Buenrostro, Jason, Chen, Fei, Velasco, Silvia, Regev, Aviv, Levin, Joshua Z, Arlotta, Paola

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Pyramidal neuron subtype diversity governs microglia states in the neocortex von Stogsdill, Jeffrey A., Kim, Kwanho, Binan, Loïc, Farhi, Samouil L., Levin, Joshua Z., Arlotta, Paola

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Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis von Pauli, Andrea, Valen, Eivind, Lin, Michael F, Garber, Manuel, Vastenhouw, Nadine L, Levin, Joshua Z, Fan, Lin, Sandelin, Albin, Rinn, John L, Regev, Aviv, Schier, Alexander F

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Single-cell transcriptomic profiling of the aging mouse brain von Ximerakis, Methodios, Lipnick, Scott L., Innes, Brendan T., Simmons, Sean K., Adiconis, Xian, Dionne, Danielle, Mayweather, Brittany A., Nguyen, Lan, Niziolek, Zachary, Ozek, Ceren, Butty, Vincent L., Isserlin, Ruth, Buchanan, Sean M., Levine, Stuart S., Regev, Aviv, Bader, Gary D., Levin, Joshua Z., Rubin, Lee L.

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Peptidomic discovery of short open reading frame–encoded peptides in human cells von Slavoff, Sarah A, Mitchell, Andrew J, Schwaid, Adam G, Cabili, Moran N, Ma, Jiao, Levin, Joshua Z, Karger, Amir D, Budnik, Bogdan A, Rinn, John L, Saghatelian, Alan

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De novo assembly of highly diverse viral populations von Yang, Xiao, Charlebois, Patrick, Gnerre, Sante, Coole, Matthew G, Lennon, Niall J, Levin, Joshua Z, Qu, James, Ryan, Elizabeth M, Zody, Michael C, Henn, Matthew R

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Comparative analysis of RNA sequencing methods for degraded or low-input samples von Adiconis, Xian, Borges-Rivera, Diego, Satija, Rahul, DeLuca, David S, Busby, Michele A, Berlin, Aaron M, Sivachenko, Andrey, Thompson, Dawn Anne, Wysoker, Alec, Fennell, Timothy, Gnirke, Andreas, Pochet, Nathalie, Regev, Aviv, Levin, Joshua Z

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Full-length transcriptome assembly from RNA-Seq data without a reference genome von Friedman, Nir, Regev, Aviv, Grabherr, Manfred G, Haas, Brian J, Yassour, Moran, Levin, Joshua Z, Thompson, Dawn A, Amit, Ido, Adiconis, Xian, Fan, Lin, Raychowdhury, Raktima, Zeng, Qiandong, Chen, Zehua, Mauceli, Evan, Hacohen, Nir, Gnirke, Andreas, Rhind, Nicholas, di Palma, Federica, Birren, Bruce W, Nusbaum, Chad, Lindblad-Toh, Kerstin

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The evolution, evolvability and engineering of gene regulatory DNA von Vaishnav, Eeshit Dhaval, de Boer, Carl G., Molinet, Jennifer, Yassour, Moran, Fan, Lin, Adiconis, Xian, Thompson, Dawn A., Levin, Joshua Z., Cubillos, Francisco A., Regev, Aviv

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In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes von Jin, Xin, Simmons, Sean K, Guo, Amy, Shetty, Ashwin S, Ko, Michelle, Nguyen, Lan, Jokhi, Vahbiz, Robinson, Elise, Oyler, Paul, Curry, Nathan, Deangeli, Giulio, Lodato, Simona, Levin, Joshua Z, Regev, Aviv, Zhang, Feng, Arlotta, Paola

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Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs von Guttman, Mitchell, Garber, Manuel, Regev, Aviv, Levin, Joshua Z, Donaghey, Julie, Robinson, James, Adiconis, Xian, Fan, Lin, Koziol, Magdalena J, Gnirke, Andreas, Nusbaum, Chad, Rinn, John L, Lander, Eric S

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