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.

Volltext

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.

Volltext

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

Volltext

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.

Volltext

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

Volltext

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

Volltext

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

Volltext

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

Volltext

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

Volltext

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

Volltext

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

Volltext

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

Volltext

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

Volltext

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

Volltext

Distinct subnetworks of the thalamic reticular nucleus von Li, Yinqing, Lopez-Huerta, Violeta G., Adiconis, Xian, Levandowski, Kirsten, Choi, Soonwook, Simmons, Sean K., Arias-Garcia, Mario A., Guo, Baolin, Yao, Annie Y., Blosser, Timothy R., Wimmer, Ralf D., Aida, Tomomi, Atamian, Alexander, Naik, Tina, Sun, Xuyun, Bi, Dasheng, Malhotra, Diya, Hession, Cynthia C., Shema, Reut, Gomes, Marcos, Li, Taibo, Hwang, Eunjin, Krol, Alexandra, Kowalczyk, Monika, Peça, João, Pan, Gang, Halassa, Michael M., Levin, Joshua Z., Fu, Zhanyan, Feng, Guoping

Volltext

Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia von Wang, Lili, Brooks, Angela N., Fan, Jean, Wan, Youzhong, Gambe, Rutendo, Li, Shuqiang, Hergert, Sarah, Yin, Shanye, Freeman, Samuel S., Levin, Joshua Z., Fan, Lin, Seiler, Michael, Buonamici, Silvia, Smith, Peter G., Chau, Kevin F., Cibulskis, Carrie L., Zhang, Wandi, Rassenti, Laura Z., Ghia, Emanuela M., Kipps, Thomas J., Fernandes, Stacey, Bloch, Donald B., Kotliar, Dylan, Landau, Dan A., Shukla, Sachet A., Aster, Jon C., Reed, Robin, DeLuca, David S., Brown, Jennifer R., Neuberg, Donna, Getz, Gad, Livak, Kenneth J., Meyerson, Matthew M., Kharchenko, Peter V., Wu, Catherine J.

Volltext

The effect of background noise and its removal on the analysis of single-cell expression data von Janssen, Philipp, Kliesmete, Zane, Vieth, Beate, Adiconis, Xian, Simmons, Sean, Marshall, Jamie, McCabe, Cristin, Heyn, Holger, Levin, Joshua Z, Enard, Wolfgang, Hellmann, Ines

Volltext

Comprehensive comparative analysis of 5′-end RNA-sequencing methods von Adiconis, Xian, Haber, Adam L., Simmons, Sean K., Levy Moonshine, Ami, Ji, Zhe, Busby, Michele A., Shi, Xi, Jacques, Justin, Lancaster, Madeline A., Pan, Jen Q., Regev, Aviv, Levin, Joshua Z.

Volltext

Comparative Analysis Highlights Variable Genome Content of Wheat Rusts and Divergence of the Mating Loci von Cuomo, Christina A, Bakkeren, Guus, Khalil, Hala Badr, Panwar, Vinay, Joly, David, Linning, Rob, Sakthikumar, Sharadha, Song, Xiao, Adiconis, Xian, Fan, Lin, Goldberg, Jonathan M, Levin, Joshua Z, Young, Sarah, Zeng, Qiandong, Anikster, Yehoshua, Bruce, Myron, Wang, Meinan, Yin, Chuntao, McCallum, Brent, Szabo, Les J, Hulbert, Scot, Chen, Xianming, Fellers, John P

Volltext

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes von Giannoukos, Georgia, Ciulla, Dawn M, Huang, Katherine, Haas, Brian J, Izard, Jacques, Levin, Joshua Z, Livny, Jonathan, Earl, Ashlee M, Gevers, Dirk, Ward, Doyle V, Nusbaum, Chad, Birren, Bruce W, Gnirke, Andreas

Volltext