Systematic comparison of single-cell and single-nucleus RNA-sequencing methods von Ding, Jiarui, Adiconis, Xian, Simmons, Sean K., Kowalczyk, Monika S., Hession, Cynthia C., Marjanovic, Nemanja D., Hughes, Travis K., Wadsworth, Marc H., Burks, Tyler, Nguyen, Lan T., Kwon, John Y. H., Barak, Boaz, Ge, William, Kedaigle, Amanda J., Carroll, Shaina, Li, Shuqiang, Hacohen, Nir, Rozenblatt-Rosen, Orit, Shalek, Alex K., Villani, Alexandra-Chloé, Regev, Aviv, Levin, Joshua Z.

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Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors von 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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The evolving landscape of immune‐related adverse events that follow immune checkpoint immunotherapy in cancer patients von Villani, Alexandra‐Chloé

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Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq von 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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The Incidence, Causes, and Risk Factors of Acute Kidney Injury in Patients Receiving Immune Checkpoint Inhibitors von Seethapathy, Harish, Zhao, Sophia, Chute, Donald F, Zubiri, Leyre, Oppong, Yaa, Strohbehn, Ian, Cortazar, Frank B, Leaf, David E, Mooradian, Meghan J, Villani, Alexandra-Chloé, Sullivan, Ryan J, Reynolds, Kerry, Sise, Meghan E

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Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis von Smillie, Christopher S., Biton, Moshe, Ordovas-Montanes, Jose, Sullivan, Keri M., Burgin, Grace, Graham, Daniel B., Herbst, Rebecca H., Rogel, Noga, Slyper, Michal, Waldman, Julia, Sud, Malika, Andrews, Elizabeth, Velonias, Gabriella, Haber, Adam L., Jagadeesh, Karthik, Vickovic, Sanja, Yao, Junmei, Stevens, Christine, Dionne, Danielle, Nguyen, Lan T., Villani, Alexandra-Chloé, Hofree, Matan, Creasey, Elizabeth A., Huang, Hailiang, Rozenblatt-Rosen, Orit, Garber, John J., Khalili, Hamed, Desch, A. Nicole, Daly, Mark J., Ananthakrishnan, Ashwin N., Shalek, Alex K., Xavier, Ramnik J., Regev, Aviv

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The activation trajectory of plasmacytoid dendritic cells in vivo during a viral infection von Abbas, Abdenour, Vu Manh, Thien-Phong, Valente, Michael, Collinet, Nils, Attaf, Noudjoud, Dong, Chuang, Naciri, Karima, Chelbi, Rabie, Brelurut, Geoffray, Cervera-Marzal, Inaki, Rauwel, Benjamin, Davignon, Jean-Luc, Bessou, Gilles, Thomas-Chollier, Morgane, Thieffry, Denis, Villani, Alexandra-Chloé, Milpied, Pierre, Dalod, Marc, Tomasello, Elena

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Decoding human fetal liver haematopoiesis von Popescu, Dorin-Mirel, Botting, Rachel A., Stephenson, Emily, Green, Kile, Webb, Simone, Jardine, Laura, Calderbank, Emily F., Polanski, Krzysztof, Goh, Issac, Efremova, Mirjana, Acres, Meghan, Maunder, Daniel, Vegh, Peter, Gitton, Yorick, Park, Jong-Eun, Vento-Tormo, Roser, Miao, Zhichao, Dixon, David, Rowell, Rachel, McDonald, David, Fletcher, James, Poyner, Elizabeth, Reynolds, Gary, Mather, Michael, Moldovan, Corina, Mamanova, Lira, Greig, Frankie, Young, Matthew D., Meyer, Kerstin B., Lisgo, Steven, Bacardit, Jaume, Fuller, Andrew, Millar, Ben, Innes, Barbara, Lindsay, Susan, Stubbington, Michael J. T., Kowalczyk, Monika S., Li, Bo, Ashenberg, Orr, Tabaka, Marcin, Dionne, Danielle, Tickle, Timothy L., Slyper, Michal, Rozenblatt-Rosen, Orit, Filby, Andrew, Carey, Peter, Villani, Alexandra-Chloé, Roy, Anindita, Regev, Aviv, Chédotal, Alain, Roberts, Irene, Göttgens, Berthold, Behjati, Sam, Laurenti, Elisa, Teichmann, Sarah A., Haniffa, Muzlifah

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Common Genetic Variants Modulate Pathogen-Sensing Responses in Human Dendritic Cells von Lee, Mark N., Ye, Chun, Villani, Alexandra-Chloé, Raj, Towfique, Li, Weibo, Eisenhaure, Thomas M., Imboywa, Selina H., Chipendo, Portia I., Ran, F. Ann, Slowikowski, Kamil, Ward, Lucas D., Raddassi, Khadir, McCabe, Cristin, Lee, Michelle H., Frohlich, Irene Y., Hafler, David A., Kellis, Manolis, Raychaudhuri, Soumya, Zhang, Feng, Stranger, Barbara E., Benoist, Christophe O., De Jager, Philip L., Regev, Aviv, Hacohen, Nir

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Genetic Risk Factors for Post-Infectious Irritable Bowel Syndrome Following a Waterborne Outbreak of Gastroenteritis von Villani, Alexandra–Chloé, Lemire, Mathieu, Thabane, Marroon, Belisle, Alexandre, Geneau, Geneviève, Garg, Amit X, Clark, William F, Moayyedi, Paul, Collins, Stephen M, Franchimont, Denis, Marshall, John K

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Widespread haploid-biased gene expression enables sperm-level natural selection von Bhutani, Kunal, Stansifer, Katherine, Ticau, Simina, Bojic, Lazar, Villani, Alexandra-Chloé, Slisz, Joanna, Cremers, Claudia M, Roy, Christian, Donovan, Jerry, Fiske, Brian, Friedman, Robin C

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Two distinct colonic CD14+ subsets characterized by single-cell RNA profiling in Crohn’s disease von Chapuy, Laurence, Bsat, Marwa, Sarkizova, Siranush, Rubio, Manuel, Therrien, Amélie, Wassef, Evelyne, Bouin, Mickael, Orlicka, Katarzina, Weber, Audrey, Hacohen, Nir, Villani, Alexandra-Chloé, Sarfati, Marika

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Common variants in the NLRP3 region contribute to Crohn's disease susceptibility von Baba, Nobuyasu, Villani, Alexandra-Chloé, Belaiche, Jacques, Rutgeerts, Paul, Louis, Edouard, Fortin, Paul R, Silverberg, Mark S, Gaudet, Daniel, Bitton, Alain, Libioulle, Cécile, Langelier, Diane, Vermeire, Severine, Lemire, Mathieu, Fortin, Geneviève, Sarfati, Marika, Cohen, Albert, Collette, Catherine, Franchimont, Denis, Wither, Joan E, Hudson, Thomas J, Rioux, John D

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Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection von Ye, Chun Jimmie, Chen, Jenny, Villani, Alexandra-Chloé, Gate, Rachel E, Subramaniam, Meena, Bhangale, Tushar, Lee, Mark N, Raj, Towfique, Raychowdhury, Raktima, Li, Weibo, Rogel, Noga, Simmons, Sean, Imboywa, Selina H, Chipendo, Portia I, McCabe, Cristin, Lee, Michelle H, Frohlich, Irene Y, Stranger, Barbara E, De Jager, Philip L, Regev, Aviv, Behrens, Tim, Hacohen, Nir

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Identification of regulators of the innate immune response to cytosolic DNA and retroviral infection by an integrative approach von Lee, Mark N, Roy, Matthew, Ong, Shao-En, Mertins, Philipp, Villani, Alexandra-Chloé, Li, Weibo, Dotiwala, Farokh, Sen, Jayita, Doench, John G, Orzalli, Megan H, Kramnik, Igor, Knipe, David M, Lieberman, Judy, Carr, Steven A, Hacohen, Nir

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Single-cell transcriptomic analyses reveal distinct immune cell contributions to epithelial barrier dysfunction in checkpoint inhibitor colitis von Thomas, Molly Fisher, Slowikowski, Kamil, Manakongtreecheep, Kasidet, Sen, Pritha, Samanta, Nandini, Tantivit, Jessica, Nasrallah, Mazen, Zubiri, Leyre, Smith, Neal P., Tirard, Alice, Ramesh, Swetha, Arnold, Benjamin Y., Nieman, Linda T., Chen, Jonathan H., Eisenhaure, Thomas, Pelka, Karin, Song, Yuhui, Xu, Katherine H., Jorgji, Vjola, Pinto, Christopher J., Sharova, Tatyana, Glasser, Rachel, Chan, PuiYee, Sullivan, Ryan J., Khalili, Hamed, Juric, Dejan, Boland, Genevieve M., Dougan, Michael, Hacohen, Nir, Li, Bo, Reynolds, Kerry L., Villani, Alexandra-Chloé

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Association between serum lactate dehydrogenase and cutaneous immune-related adverse events among patients on immune checkpoint inhibitors for advanced melanoma von Asdourian, Maria S., Otto, Tracey S., Jacoby, Ted V., Shah, Nishi, Thompson, Leah L., Blum, Steven M., Reynolds, Kerry L., Semenov, Yevgeniy R., Lawrence, Donald P., Sullivan, Ryan J., Boland, Genevieve M., Villani, Alexandra-Chloé, Chen, Steven T.

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IL-32 Supports the Survival of Malignant T Cells in Cutaneous T-cell Lymphoma von Yu, Kenneth K., Smith, Neal P., Essien, Sernah V., Teague, Jessica E., Vieyra-Garcia, Pablo, Gehad, Ahmed, Zhan, Qian, Crouch, Jack D., Gerard, Nega, Larocca, Cecilia, Wolf, Peter, LeBoeuf, Nicole R., Tawa, Marianne, Kupper, Thomas S., Villani, Alexandra-Chloé, Clark, Rachael A.

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Antigen Presenting Cells Link the Female Genital Tract Microbiome to Mucosal Inflammation, With Hormonal Contraception as an Additional Modulator of Inflammatory Signatures von Byrne, Elizabeth H., Farcasanu, Mara, Bloom, Seth M., Xulu, Nondumiso, Xu, Jiawu, Hykes, Barry L., Mafunda, Nomfuneko A., Hayward, Matthew R., Dong, Mary, Dong, Krista L., Gumbi, Thandeka, Ceasar, Fransisca Xolisile, Ismail, Nasreen, Ndung’u, Thumbi, Gosmann, Christina, Ghebremichael, Musie S., Handley, Scott A., Mitchell, Caroline M., Villani, Alexandra-Chloé, Kwon, Douglas S.

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Longitudinal characterization of circulating neutrophils uncovers phenotypes associated with severity in hospitalized COVID-19 patients von LaSalle, Thomas J, Gonye, Anna L K, Freeman, Samuel S, Kaplonek, Paulina, Gushterova, Irena, Kays, Kyle R, Manakongtreecheep, Kasidet, Tantivit, Jessica, Rojas-Lopez, Maricarmen, Russo, Brian C, Sharma, Nihaarika, Thomas, Molly F, Lavin-Parsons, Kendall M, Lilly, Brendan M, Mckaig, Brenna N, Charland, Nicole C, Khanna, Hargun K, Lodenstein, Carl L, Margolin, Justin D, Blaum, Emily M, Lirofonis, Paola B, Revach, Or-Yam, Mehta, Arnav, Sonny, Abraham, Bhattacharyya, Roby P, Parry, Blair Alden, Goldberg, Marcia B, Alter, Galit, Filbin, Michael R, Villani, Alexandra-Chloé, Hacohen, Nir, Sade-Feldman, Moshe

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