MERFISHing for spatial context

by Satija, Rahul, Shalek, Alexander K
Published 2018

Spatial reconstruction of single-cell gene expression data

by Satija, Rahul, Farrell, Jeffrey A, Gennert, David, Schier, Alexander F, Regev, Aviv
Published 2016

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
Published 2017

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
Published 2015

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
Published 2018

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
Published 2016

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
Published 2016

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
Published 2017

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.
Published 2017

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.
Published 2014

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.
Published 2014

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.
Published 2015

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
Published 2017

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-
Published 2017

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
Published 2014

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
Published 2015

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
Published 2013

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
Published 2015

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
Published 2018