Strategies to discover regulatory circuits of the mammalian immune system by Amit, Ido, Regev, Aviv, Hacohen, Nir

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A cell-free nanobody engineering platform rapidly generates SARS-CoV-2 neutralizing nanobodies by Chen, Xun, Gentili, Matteo, Hacohen, Nir, Regev, Aviv

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Targeting individual cells by barcode in pooled sequence libraries by Villani, Alexandra-Chloé, Blainey, Paul C, Ranu, Navpreet Singh, Hacohen, Nir

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MAUDE: inferring expression changes in sorting-based CRISPR screens by de Boer, Carl G., Ray, John P, Hacohen, Nir, Regev, Aviv

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Dnase2a Deficiency Uncovers Lysosomal Clearance of Damaged Nuclear DNA via Autophagy by Lan, Yuk Yuen, Bouley, Richard, Rooney, Michael S., Hacohen, Nir, Londono, Diana, Rooney, Michael S.

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Positional specificity of different transcription factor classes within enhancers by Engreitz, Jesse, Ray, John P., Nguyen, Tung H., Hacohen, Nir, Grossman, Sharon Rachel, Lander, Eric Steven

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Multiplexed enrichment and genomic profiling of peripheral blood cells reveal subset-specific immune signatures by Vickers, Dwayne, Billman, Kianna, Eisenhaure, Thomas, Hoover, Paul, Browne, Edward P., Rao, Deepak A., Hacohen, Nir, Reyes, Miguel, Blainey, Paul C

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Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli by Gat-Viks, Irit, Chevrier, Nicolas, Wilentzik, Roni, Eisenhaure, Thomas, Raychowdhury, Raktima, Steuerman, Yael, Shalek, Alex K., Hacohen, Nir, Amit, Ido, Regev, Aviv

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Lysosomal Trafficking, Antigen Presentation, and Microbial Killing Are Controlled by the Arf-like GTPase Arl8b by Garg, Salil, Sharma, Mahak, Ung, Cindy, Tuli, Amit, Barral, Duarte C., Hava, David L., Veerapen, Natacha, Besra, Gurdyal S., Hacohen, Nir, Brenner, Michael B.

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Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells by 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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High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies by Raychowdhury, Raktima, Jovanovic, Marko, Stumpo, Deborah J., Pauli, Andrea, Hacohen, Nir, Schier, Alexander F., Blackshear, Perry J., Friedman, Nir, Amit, Ido, Rabani, Michal, Rooney, Michael Steven, Regev, Aviv

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An immune-cell signature of bacterial sepsis by Reyes, Miguel, Filbin, Michael R., Bhattacharyya, Roby P., Billman, Kianna, Eisenhaure, Thomas, Hung, Deborah T., Levy, Bruce D., Baron, Rebecca M., Blainey, Paul C, Goldberg, Marcia B., Hacohen, Nir

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A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation by Fields, Alexander P., Rodriguez, Edwin H., Jovanovic, Marko, Stern-Ginossar, Noam, Haas, Brian J., Mertins, Philipp, Raychowdhury, Raktima, Hacohen, Nir, Carr, Steven A., Ingolia, Nicholas T., Regev, Aviv, Weissman, Jonathan S.

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Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq by Li, Bo, Gould, Joshua, Yang, Yiming, Sarkizova, Siranush, Tabaka, Marcin, Ashenberg, Orr, Rosen, Yanay, Slyper, Michal, Kowalczyk, Monika S, Villani, Alexandra-Chloé, Tickle, Timothy, Hacohen, Nir, Rozenblatt-Rosen, Orit, Regev, Aviv

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An Integrative Framework Reveals Signaling-to-Transcription Events in Toll-like Receptor Signaling by Yosef, Nir, Qiao, Jana, Raychowdhury, Raktima, Maritzen, Tanja, Haucke, Volker, Satoh, Takashi, Akira, Shizuo, Mertins, Philipp, Przybylski, Dariusz, Eisenhaure, Thomas, Carr, Steven A, Regev, Aviv, Hacohen, Nir, Chevrier, Nicolas, Clauser, Karl R.

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Streamlined Protocol for Deep Proteomic Profiling of FAC-sorted Cells and Its Application to Freshly Isolated Murine Immune Cells* by Myers, Samuel A, Rhoads, Andrew, Cocco, Alexandra R, Peckner, Ryan, Haber, Adam L, Schweitzer, Lawrence D, Krug, Karsten, Mani, DR, Clauser, Karl R, Rozenblatt-Rosen, Orit, Hacohen, Nir, Regev, Aviv, Carr, Steven A

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Automated Flow Synthesis of Tumor Neoantigen Peptides for Personalized Immunotherapy by Truex, Nicholas, Holden, Rebecca Lynn, Wang, Bin-You, Chen, Pu-Guang, Hanna, Stephanie, Hu, Zhuting, Shetty, Keerthi, Olive, Oriol, Neuberg, Donna, Hacohen, Nir, Keskin, Derin B., Ott, Patrick A., Wu, Catherine J., Pentelute, Bradley L.

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A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection by Shapira, Sagi D., Gat-Viks, Irit, Shum, Bennett O. V., Dricot, Amelie, DeGrace, Marciela M., Wu, Liguo, Gupta, Piyush, Hao, Tong, Silver, Serena J., Root, David E., Hill, David E., Regev, Aviv, Hacohen, Nir

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Nanowire-Mediated Delivery Enables Functional Interrogation of Primary Immune Cells: Application to the Analysis of Chronic Lymphocytic Leukemia by Shalek, Alex K., Gaublomme, Jellert T., Wang, Lili, Yosef, Nir, Chevrier, Nicolas, Andersen, Mette S., Robinson, Jacob T., Pochet, Nathalie, Neuberg, Donna S., Gertner, Rona S., Amit, Ido, Brown, Jennifer R., Hacohen, Nir, Regev, Aviv, Wu, Catherine J., Park, Hongkun

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Semiconductor-based DNA sequencing of histone modification states by Cheng, Christine S., Rai, Kunal, Garber, Manuel, Hollinger, Andrew, Robbins, Dana, Anderson, Scott, Macbeth, Alyssa, Tzou, Austin, Carneiro, Mauricio O., Raychowdhury, Raktima, Russ, Carsten, Hacohen, Nir, Gershenwald, Jeffrey E., Lennon, Niall, Nusbaum, Chad, Chin, Lynda, Regev, Aviv, Amit, Ido

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