Comprehensive comparative analysis of strand-specific RNA sequencing methods door 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 door 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 door 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 door 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 door 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 door 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 door 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 door 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 door 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 door 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 door 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 door 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 door 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 door 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 door 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 door 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 door 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 door 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 door 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 door 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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