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