MERFISHing for spatial context by Satija, Rahul, Shalek, Alexander K

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Spatial reconstruction of single-cell gene expression data by Satija, Rahul, Farrell, Jeffrey A, Gennert, David, Schier, Alexander F, Regev, Aviv

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A Generic and Cell-Type-Specific Wound Response Precedes Regeneration in Planarians by Wurtzel, Omri, Poirier, Amber, Satija, Rahul, Cote, Lauren Esther, Regev, Aviv, Reddien, Peter

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Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing by Trombetta, John J., Gennert, David, Satija, Rahul, Shalek, Alex K., Regev, Aviv, Lu, Diana, Ph. D. Massachusetts Institute of Technology

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Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput by Bryson, Bryan D, Butler, Andrew, Satija, Rahul, Fortune, Sarah, Love, J Christopher, Gierahn, Todd Michael, Wadsworth, Marc Havens, Hughes, Travis K., Shalek, Alexander K

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Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses by Avraham, Roi, Brown, Douglas, Penaranda, Cristina, Jijon, Humberto B., Trombetta, John J., Satija, Rahul, Xavier, Ramnik J., Hung, Deborah T., Haseley, Nathan Scott, Shalek, Alexander K, Regev, Aviv

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Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity by Gaublomme, Jellert T., Yosef, Nir, Lee, Youjin, Gertner, Rona S., Yang, Li V., Wu, Chuan, Pandolfi, Pier Paolo, Mak, Tak, Satija, Rahul, Kuchroo, Vijay K., Park, Hongkun, Regev, Aviv, Shalek, Alexander K

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Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA by Schwartz, Schraga, Bernstein, Douglas A., Mumbach, Maxwell R., Jovanovic, Marko, Herbst, Rebecca H., León-Ricardo, Brian X., Guttman, Mitchell, Satija, Rahul, Fink, Gerald, Engreitz, Jesse Michael, Lander, Eric Steven, Regev, Aviv

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High-Resolution Mapping Reveals a Conserved, Widespread, Dynamic mRNA Methylation Program in Yeast Meiosis by Schwartz, Schraga, Mumbach, Maxwell R., Jovanovic, Marko, Mertins, Philipp, Shishkin, Alexander, Tabach, Yuval, Mikkelsen, Tarjei S., Satija, Rahul, Ruvkun, Gary, Carr, Steven A., Regev, Aviv, Agarwala, Sudeep, Lander, Eric Steven, Fink, Gerald R.

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Comparative analysis of RNA sequencing methods for degraded or low-input samples by 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 by 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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Deconstructing transcriptional heterogeneity in pluripotent stem cells by Kumar, Roshan M., Cahan, Patrick, Shalek, Alex K., Satija, Rahul, DaleyKeyser, AJay, Li, Hu, Zhang, Jin, Pardee, Keith, Gennert, David, Trombetta, John J., Ferrante, Thomas C., Regev, Aviv, Daley, George Q., Collins, James J.

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A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks by Parnas, Oren, Jovanovic, Marko, Eisenhaure, Thomas M., Herbst, Rebecca H., Ye, Chun Jimmie, Przybylski, Dariusz, Tirosh, Itay, Satija, Rahul, Raychowdhury, Raktima, Mertins, Philipp, Carr, Steven A., Hacohen, Nir, Regev, Aviv, Dixit, Atray C., Platt, Randall Jeffrey, Sanjana, Neville E, Shalem, Ophir, Zhang, Feng

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Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets by Macosko, Evan Z., Satija, Rahul, Nemesh, James, Shekhar, Karthik, Goldman, Melissa, Tirosh, Itay, Bialas, Allison R., Kamitaki, Nolan, Martersteck, Emily M., Trombetta, John J., Weitz, David A., Sanes, Joshua R., McCarroll, Steven A., Shalek, Alexander K, Regev, Aviv, Basu, Anindita, 1978-

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Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells by 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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Perturbation of m6A Writers Reveals Two Distinct Classes of mRNA Methylation at Internal and 5′ Sites by Schwartz, Schraga, Mumbach, Maxwell R., Jovanovic, Marko, Wang, Tim, Maciag, Karolina, Bushkin, G. Guy, Mertins, Philipp, Ter-Ovanesyan, Dmitry, Habib, Naomi, Cacchiarelli, Davide, Sanjana, Neville E., Freinkman, Elizaveta, Pacold, Michael E., Satija, Rahul, Hacohen, Nir, Zhang, Feng, Regev, Aviv, Mikkelsen, Tarjei Sigurd, 1978-, Carr, Steven A, Lander, Eric Steven

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Dynamic regulatory network controlling TH17 cell differentiation by Yosef, Nir, Shalek, Alex K., Gaublomme, Jellert T., Jin, Hulin, Lee, Youjin, Awasthi, Amit, Wu, Chuan, Karwacz, Katarzyna, Xiao, Sheng, Jorgolli, Marsela, Gennert, David, Satija, Rahul, Shakya, Arvind, Trombetta, John J., Pillai, Meenu R., Ratcliffe, Peter J., Coleman, Mathew L., Bix, Mark, Tantin, Dean, Park, Hongkun, Kuchroo, Vijay K., Regev, Aviv, Lu, Diana

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Single-cell RNA-seq reveals dynamic paracrine control of cellular variation by Satija, Rahul, Shuga, Joe, Trombetta, John J., Gennert, David, Chen, Peilin, Gertner, Rona S., Gaublomme, Jellert T., Yosef, Nir, Schwartz, Schraga, Fowler, Brian, Weaver, Suzanne, Wang, Jing, Wang, Xiaohui, Ding, Ruihua, Raychowdhury, Raktima, Friedman, Nir, Hacohen, Nir, Park, Hongkun, May, Andrew P., Regev, Aviv, Shalek, Alex K., Lu, Diana, Ph. D. Massachusetts Institute of Technology

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Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors by Villani, Alexandra-Chloé, Satija, Rahul, Reynolds, Gary, Sarkizova, Siranush, Shekhar, Karthik, Fletcher, James, Griesbeck, Morgane, Butler, Andrew, Zheng, Shiwei, Lazo, Suzan, Jardine, Laura, Dixon, David, Stephenson, Emily, Nilsson, Emil, Grundberg, Ida, McDonald, David, Filby, Andrew, Li, Weibo, De Jager, Philip L., Rozenblatt-Rosen, Orit, Lane, Andrew A., Haniffa, Muzlifah, Regev, Aviv, Hacohen, Nir

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Landscape of X chromosome inactivation across human tissues by Tukiainen, Taru, Villani, Alexandra-Chloé, Rivas, Manuel A., Marshall, Jamie L., Satija, Rahul, Aguirre, Matt, Gauthier, Laura, Fleharty, Mark, Kirby, Andrew, Cummings, Beryl B., Castel, Stephane E., Karczewski, Konrad J., Aguet, François, Byrnes, Andrea, Aguet, François, Ardlie, Kristin G., Cummings, Beryl B., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Karczewski, Konrad J., Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Yen, Angela, Regev, Aviv

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