MARS-seq2.0: an experimental and analytical pipeline for indexed sorting combined with single-cell RNA sequencing von Keren-Shaul, Hadas, Kenigsberg, Ephraim, Jaitin, Diego Adhemar, David, Eyal, Paul, Franziska, Tanay, Amos, Amit, Ido

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Serum Amyloid A Proteins Induce Pathogenic Th17 Cells and Promote Inflammatory Disease von Lee, June-Yong, Hall, Jason A., Kroehling, Lina, Wu, Lin, Najar, Tariq, Nguyen, Henry H., Lin, Woan-Yu, Yeung, Stephen T., Silva, Hernandez Moura, Li, Dayi, Hine, Ashley, Loke, P’ng, Hudesman, David, Martin, Jerome C., Kenigsberg, Ephraim, Merad, Miriam, Khanna, Kamal M., Littman, Dan R.

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A myeloid–stromal niche and gp130 rescue in NOD2-driven Crohn’s disease von Nayar, Shikha, Morrison, Joshua K., Giri, Mamta, Gettler, Kyle, Chuang, Ling-shiang, Walker, Laura A., Ko, Huaibin M., Kenigsberg, Ephraim, Kugathasan, Subra, Merad, Miriam, Chu, Jaime, Cho, Judy H.

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DNA methylation disruption reshapes the hematopoietic differentiation landscape von Izzo, Franco, Lee, Stanley C., Poran, Asaf, Chaligne, Ronan, Gaiti, Federico, Gross, Baptiste, Murali, Rekha R., Deochand, Sunil D., Ang, Chelston, Jones, Philippa Wyndham, Nam, Anna S., Kim, Kyu-Tae, Kothen-Hill, Steven, Schulman, Rafael C., Ki, Michelle, Lhoumaud, Priscillia, Skok, Jane A., Viny, Aaron D., Levine, Ross L., Kenigsberg, Ephraim, Abdel-Wahab, Omar, Landau, Dan A.

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Altering Sphingolipid Metabolism Attenuates Cell Death and Inflammatory Response After Myocardial Infarction von Hadas, Yoav, Vincek, Adam S., Youssef, Elias, Żak, Magdalena M., Chepurko, Elena, Sultana, Nishat, Sharkar, Mohammad Tofael Kabir, Guo, Ningning, Komargodski, Rinat, Kurian, Ann Anu, Kaur, Keerat, Magadum, Ajit, Fargnoli, Anthony, Katz, Michael G., Hossain, Nadia, Kenigsberg, Ephraim, Dubois, Nicole C., Schadt, Eric, Hajjar, Roger, Eliyahu, Efrat, Zangi, Lior

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Primate CpG Islands Are Maintained by Heterogeneous Evolutionary Regimes Involving Minimal Selection von Cohen, Netta Mendelson, Kenigsberg, Ephraim, Tanay, Amos

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The mutation spectrum in genomic late replication domains shapes mammalian GC content von Kenigsberg, Ephraim, Yehuda, Yishai, Marjavaara, Lisette, Keszthelyi, Andrea, Chabes, Andrei, Tanay, Amos, Simon, Itamar

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Drosophila functional elements are embedded in structurally constrained sequences von Kenigsberg, Ephraim, Tanay, Amos

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Single-cell profiling to transform immunotherapy usage and target discovery in immune-mediated inflammatory diseases von Chapelle, Nicolas, Fantou, Aurelie, Marron, Thomas, Kenigsberg, Ephraim, Merad, Miriam, Martin, Jerome C.

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Widespread compensatory evolution conserves DNA-encoded nucleosome organization in yeast von Kenigsberg, Ephraim, Bar, Amir, Segal, Eran, Tanay, Amos

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Prioritizing Crohn’s disease genes by integrating association signals with gene expression implicates monocyte subsets von Gettler, Kyle, Giri, Mamta, Kenigsberg, Ephraim, Martin, Jerome, Chuang, Ling-Shiang, Hsu, Nai-Yun, Denson, Lee A., Hyams, Jeffrey S., Griffiths, Anne, Noe, Joshua D., Crandall, Wallace V., Mack, David R., Kellermayer, Richard, Abraham, Clara, Hoffman, Gabriel, Kugathasan, Subra, Cho, Judy H.

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Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types von Jaitin, Diego Adhemar, Kenigsberg, Ephraim, Keren-Shaul, Hadas, Elefant, Naama, Paul, Franziska, Zaretsky, Irina, Mildner, Alexander, Cohen, Nadav, Jung, Steffen, Tanay, Amos, Amit, Ido

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Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome von Sexton, Tom, Yaffe, Eitan, Kenigsberg, Ephraim, Bantignies, Frédéric, Leblanc, Benjamin, Hoichman, Michael, Parrinello, Hugues, Tanay, Amos, Cavalli, Giacomo

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A conserved dendritic-cell regulatory program limits antitumour immunity von Maier, Barbara, Leader, Andrew M., Chen, Steven T., Tung, Navpreet, Chang, Christie, LeBerichel, Jessica, Chudnovskiy, Aleksey, Maskey, Shrisha, Walker, Laura, Finnigan, John P., Kirkling, Margaret E., Reizis, Boris, Ghosh, Sourav, D’Amore, Natalie Roy, Bhardwaj, Nina, Rothlin, Carla V., Wolf, Andrea, Flores, Raja, Marron, Thomas, Rahman, Adeeb H., Kenigsberg, Ephraim, Brown, Brian D., Merad, Miriam

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Tissue-resident macrophages provide a pro-tumorigenic niche to early NSCLC cells von Casanova-Acebes, María, Dalla, Erica, Leader, Andrew, Leberichel, Jessica, Nikolic, Jovan, Morales, Blanca, Brown, Markus, Chang, Christie, Troncoso, Leanna, Chen, Steven, Sastre-Perona, Ana, Park, Matthew, Tabachnikova, Alexandra, Dhainaut, Maxime, Hamon, Pauline, Maier, Barbara, Sawai, Catherine, Agulló-Pascual, Esperanza, Schober, Markus, Brown, Brian, Reizis, Boris, Marron, Thomas, Kenigsberg, Ephraim, Moussion, Christine, Benaroch, Philippe, Aguirre-Ghiso, Julio, Merad, Miriam

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Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors von Paul, Franziska, Arkin, Ya’ara, Giladi, Amir, Jaitin, Diego Adhemar, Kenigsberg, Ephraim, Keren-Shaul, Hadas, Winter, Deborah, Lara-Astiaso, David, Gury, Meital, Weiner, Assaf, David, Eyal, Cohen, Nadav, Lauridsen, Felicia Kathrine Bratt, Haas, Simon, Schlitzer, Andreas, Mildner, Alexander, Ginhoux, Florent, Jung, Steffen, Trumpp, Andreas, Porse, Bo Torben, Tanay, Amos, Amit, Ido

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Tissue-resident macrophages provide a pro-tumorigenic niche to early NSCLC cells von Casanova-Acebes, María, Dalla, Erica, Leader, Andrew M., LeBerichel, Jessica, Nikolic, Jovan, Morales, Blanca M., Brown, Markus, Chang, Christie, Troncoso, Leanna, Chen, Steven T., Sastre-Perona, Ana, Park, Matthew D., Tabachnikova, Alexandra, Dhainaut, Maxime, Hamon, Pauline, Maier, Barbara, Sawai, Catherine M., Agulló-Pascual, Esperanza, Schober, Markus, Brown, Brian D., Reizis, Boris, Marron, Thomas, Kenigsberg, Ephraim, Moussion, Christine, Benaroch, Philippe, Aguirre-Ghiso, Julio A., Merad, Miriam

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Immunology of COVID-19: Current State of the Science von Vabret, Nicolas, Britton, Graham J., Gruber, Conor, Hegde, Samarth, Kim, Joel, Kuksin, Maria, Levantovsky, Rachel, Malle, Louise, Moreira, Alvaro, Park, Matthew D., Pia, Luisanna, Risson, Emma, Saffern, Miriam, Salomé, Bérengère, Esai Selvan, Myvizhi, Spindler, Matthew P., Tan, Jessica, van der Heide, Verena, Gregory, Jill K., Alexandropoulos, Konstantina, Bhardwaj, Nina, Brown, Brian D., Greenbaum, Benjamin, Gümüş, Zeynep H., Homann, Dirk, Horowitz, Amir, Kamphorst, Alice O., Curotto de Lafaille, Maria A., Mehandru, Saurabh, Merad, Miriam, Samstein, Robert M., Agrawal, Manasi, Aleynick, Mark, Belabed, Meriem, Brown, Matthew, Casanova-Acebes, Maria, Catalan, Jovani, Centa, Monica, Charap, Andrew, Chan, Andrew, Chen, Steven T., Chung, Jonathan, Bozkus, Cansu Cimen, Cody, Evan, Cossarini, Francesca, Dalla, Erica, Fernandez, Nicolas, Grout, John, Ruan, Dan Fu, Hamon, Pauline, Humblin, Etienne, Jha, Divya, Kodysh, Julia, Leader, Andrew, Lin, Matthew, Lindblad, Katherine, Lozano-Ojalvo, Daniel, Lubitz, Gabrielle, Magen, Assaf, Mahmood, Zafar, Martinez-Delgado, Gustavo, Mateus-Tique, Jaime, Meritt, Elliot, Moon, Chang, Noel, Justine, O’Donnell, Tim, Ota, Miyo, Plitt, Tamar, Pothula, Venu, Redes, Jamie, Reyes Torres, Ivan, Roberto, Mark, Sanchez-Paulete, Alfonso R., Shang, Joan, Schanoski, Alessandra Soares, Suprun, Maria, Tran, Michelle, Vaninov, Natalie, Wilk, C. Matthias, Aguirre-Ghiso, Julio, Bogunovic, Dusan, Cho, Judy, Faith, Jeremiah, Grasset, Emilie, Heeger, Peter, Kenigsberg, Ephraim, Krammer, Florian, Laserson, Uri

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Single-Cell Analysis of Crohn’s Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy von Martin, Jerome C., Chang, Christie, Boschetti, Gilles, Ungaro, Ryan, Giri, Mamta, Grout, John A., Gettler, Kyle, Chuang, Ling-shiang, Nayar, Shikha, Greenstein, Alexander J., Dubinsky, Marla, Walker, Laura, Leader, Andrew, Fine, Jay S., Whitehurst, Charles E., Mbow, M Lamine, Kugathasan, Subra, Denson, Lee A., Hyams, Jeffrey S., Friedman, Joshua R., Desai, Prerak T., Ko, Huaibin M., Laface, Ilaria, Akturk, Guray, Schadt, Eric E., Salmon, Helene, Gnjatic, Sacha, Rahman, Adeeb H., Merad, Miriam, Cho, Judy H., Kenigsberg, Ephraim

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Single-cell analysis of human non-small cell lung cancer lesions refines tumor classification and patient stratification von Leader, Andrew M., Grout, John A., Maier, Barbara B., Nabet, Barzin Y., Park, Matthew D., Tabachnikova, Alexandra, Chang, Christie, Walker, Laura, Lansky, Alona, Le Berichel, Jessica, Troncoso, Leanna, Malissen, Nausicaa, Davila, Melanie, Martin, Jerome C., Magri, Giuliana, Tuballes, Kevin, Zhao, Zhen, Petralia, Francesca, Samstein, Robert, D’Amore, Natalie Roy, Thurston, Gavin, Kamphorst, Alice O., Wolf, Andrea, Flores, Raja, Wang, Pei, Müller, Sören, Mellman, Ira, Beasley, Mary Beth, Salmon, Hélène, Rahman, Adeeb H., Marron, Thomas U., Kenigsberg, Ephraim, Merad, Miriam

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