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

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Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species od Yassour, Moran, Pfiffner, Jenna, Levin, Joshua Z., Adiconis, Xian, Gnirke, Andreas, Nusbaum, Chad, Thompson, Dawn-Anne, Friedman, Nir, Regev, Aviv, Yassour, Moran

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Development and evaluation of RNA-seq methods od Levin, Joshua Z., Adiconis, Xian, Yassour, Moran, Thompson, Dawn, Guttman, Mitchell, Berger, Michael F., Fan, Lin, Friedman, Nir, Nusbaum, Chad, Gnirke, Andreas, Regev, Aviv

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Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells od Rabani, Michal, Levin, Joshua Z., Fan, Lin, Adiconis, Xian, Raychowdhury, Raktima, Garber, Manuel, Gnirke, Andreas, Nusbaum, Chad, Hacohen, Nir, Friedman, Nir, Amit, Ido, Regev, Aviv

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The evolution, evolvability and engineering of gene regulatory DNA od 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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Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis od Lin, Michael F., Regev, Aviv, Pauli, Andrea, Valen, Eivind, Garber, Manuel, Vastenhouw, Nadine L., Levin, Joshua Z., Fan, Lin, Sandelin, Albin, Rinn, John L., Schier, Alexander F.

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Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs od Guttman, Mitchell, Garber, Manuel, Levin, Joshua Z., Donaghey, Julie, Robinson, James, Adiconis, Xian, Fan, Lin, Koziol, Magdalena J., Gnirke, Andreas, Nusbaum, Chad, Rinn, John L., Regev, Aviv, Lander, Eric Steven

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Reduction of mNAT1/hNAT2 contributes to cerebral endothelial necroptosis and Aβ accumulation in alzheimer's disease od Zou, Chengyu, Mifflin, Lauren, Hu, Zhirui, Zhang, Tian, Shan, Bing, Wang, Huibing, Xing, Xin, Zhu, Hong, Adiconis, Xian, Levin, Joshua Z., Li, Fupeng, Liu, Chuan-Fa, Liu, Jun S., Yuan, Junying

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In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes od 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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In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes od 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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Comparative analysis of RNA sequencing methods for degraded or low-input samples od 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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Comparative analysis of RNA sequencing methods for degraded or low-input samples od 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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Mostly natural sequencing-by-synthesis for scRNA-seq using Ultima sequencing od Simmons, Sean K, Lithwick-Yanai, Gila, Adiconis, Xian, Oberstrass, Florian, Iremadze, Nika, Geiger-Schuller, Kathryn, Thakore, Pratiksha I, Frangieh, Chris J, Barad, Omer, Almogy, Gilad, Rozenblatt-Rosen, Orit, Regev, Aviv, Lipson, Doron, Levin, Joshua Z

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Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics od 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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Effects of 3D culturing conditions on the transcriptomic profile of stem-cell-derived neurons od Tekin, Halil, Simmons, Sean, Cummings, Beryl, Gao, Linyi, Adiconis, Xian, Hession, Cynthia C., Ghoshal, Ayan, Dionne, Danielle, Choudhury, Sourav, Yesilyurt, Volkan, Sanjana, Neville E, Shi, Xi, Lu, Congyi, Heidenreich, Matthias, Pan, Jen Q., Levin, Joshua Z., Zhang, Feng

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

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Single-Cell Profiles of Retinal Ganglion Cells Differing in Resilience to Injury Reveal Neuroprotective Genes od 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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Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells od Shalek, Alex K., Satija, Rahul, Adiconis, Xian, Gertner, Rona S., Gaublomme, Jellert T., Raychowdhury, Raktima, Schwartz, Schraga, Yosef, Nir, Malboeuf, Christine, Trombetta, John J., Gennert, David, Gnirke, Andreas, Goren, Alon, Hacohen, Nir, Levin, Joshua Z., Park, Hongkun, Regev, Aviv, Lu, Diana, Ph. D. Massachusetts Institute of Technology

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Autism genes converge on asynchronous development of shared neuron classes od Paulsen, Bruna, Velasco, Silvia, Kedaigle, Amanda J, Pigoni, Martina, Quadrato, Giorgia, Deo, Anthony J, Adiconis, Xian, Uzquiano, Ana, Sartore, Rafaela, Yang, Sung Min, Simmons, Sean K, Symvoulidis, Panagiotis, Kim, Kwanho, Tsafou, Kalliopi, Podury, Archana, Abbate, Catherine, Tucewicz, Ashley, Smith, Samantha N, Albanese, Alexandre, Barrett, Lindy, Sanjana, Neville E, Shi, Xi, Chung, Kwanghun, Lage, Kasper, Boyden, Edward S, Regev, Aviv, Levin, Joshua Z, Arlotta, Paola

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Integrative analysis of the melanoma transcriptome od Berger, Michael F., Levin, Joshua Z., Vijayendran, Krishna, Sivachenko, Andrey, Adiconis, Xian, Maguire, Jared, Johnson, Laura A., Robinson, James, Verhaak, Roel G., Sougnez, Carrie, Onofrio, Robert, Ziaugra, Liuda, Cibulskis, Kristian, Laine, Elisabeth, Barretina, Jordi, Winckler, Wendy, Fisher, David E., Getz, Gad, Meyerson, Matthew L., Jaffe, David B., Gabriel, Stacey B., Dummer, Reinhard, Gnirke, Andreas, Nusbaum, Chad, Garraway, Levi A., Lander, Eric Steven

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