Comprehensive comparative analysis of strand-specific RNA sequencing methods Yazar: 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 Yazar: 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 Yazar: 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 Yazar: 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 Yazar: 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 Yazar: 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 Yazar: 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 Yazar: 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 Yazar: 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 Yazar: 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 Yazar: 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 Yazar: 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 Yazar: 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 Yazar: 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 Yazar: 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 Yazar: 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 Yazar: 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 Yazar: 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 Yazar: 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 Yazar: 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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