Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis von Farrell, Jeffrey A, Wang, Yiqun, Riesenfeld, Samantha J, Shekhar, Karthik, Regev, Aviv, Schier, Alexander F

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EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data von Lun, Aaron T L, Riesenfeld, Samantha, Andrews, Tallulah, Dao, The Phuong, Gomes, Tomas, Marioni, John C

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Calcitonin Gene-Related Peptide Negatively Regulates Alarmin-Driven Type 2 Innate Lymphoid Cell Responses von Wallrapp, Antonia, Burkett, Patrick R., Riesenfeld, Samantha J., Kim, Se-Jin, Christian, Elena, Abdulnour, Raja-Elie E., Thakore, Pratiksha I., Schnell, Alexandra, Lambden, Conner, Herbst, Rebecca H., Khan, Pavana, Tsujikawa, Kazutake, Xavier, Ramnik J., Chiu, Isaac M., Levy, Bruce D., Regev, Aviv, Kuchroo, Vijay K.

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Dissection and integration of bursty transcriptional dynamics for complex systems von Gao, Cheng Frank, Vaikuntanathan, Suriyanarayanan, Riesenfeld, Samantha J

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A cellular and spatial map of the choroid plexus across brain ventricles and ages von Dani, Neil, Herbst, Rebecca H., McCabe, Cristin, Green, Gilad S., Kaiser, Karol, Head, Joshua P., Cui, Jin, Shipley, Frederick B., Jang, Ahram, Dionne, Danielle, Nguyen, Lan, Rodman, Christopher, Riesenfeld, Samantha J., Prochazka, Jan, Prochazkova, Michaela, Sedlacek, Radislav, Zhang, Feng, Bryja, Vitezslav, Rozenblatt-Rosen, Orit, Habib, Naomi, Regev, Aviv, Lehtinen, Maria K.

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The neuropeptide NMU amplifies ILC2-driven allergic lung inflammation von Wallrapp, Antonia, Riesenfeld, Samantha J., Burkett, Patrick R., Abdulnour, Raja-Elie E., Nyman, Jackson, Dionne, Danielle, Hofree, Matan, Cuoco, Michael S., Rodman, Christopher, Farouq, Daneyal, Haas, Brian J., Tickle, Timothy L., Trombetta, John J., Baral, Pankaj, Klose, Christoph S. N., Mahlakõiv, Tanel, Artis, David, Rozenblatt-Rosen, Orit, Chiu, Isaac M., Levy, Bruce D., Kowalczyk, Monika S., Regev, Aviv, Kuchroo, Vijay K.

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Nociceptor neurons direct goblet cells via a CGRP-RAMP1 axis to drive mucus production and gut barrier protection von Yang, Daping, Jacobson, Amanda, Meerschaert, Kimberly A., Sifakis, Joseph Joy, Wu, Meng, Chen, Xi, Yang, Tiandi, Zhou, Youlian, Anekal, Praju Vikas, Rucker, Rachel A., Sharma, Deepika, Sontheimer-Phelps, Alexandra, Wu, Glendon S., Deng, Liwen, Anderson, Michael D., Choi, Samantha, Neel, Dylan, Lee, Nicole, Kasper, Dennis L., Jabri, Bana, Huh, Jun R., Johansson, Malin, Thiagarajah, Jay R., Riesenfeld, Samantha J., Chiu, Isaac M.

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Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide α-CGRP Modulates Group 2 Innate Lymphoid Cell Responses von Xu, Heping, Ding, Jiarui, Porter, Caroline B.M., Wallrapp, Antonia, Tabaka, Marcin, Ma, Sai, Fu, Shujie, Guo, Xuanxuan, Riesenfeld, Samantha J., Su, Chienwen, Dionne, Danielle, Nguyen, Lan T., Lefkovith, Ariel, Ashenberg, Orr, Burkett, Patrick R., Shi, Hai Ning, Rozenblatt-Rosen, Orit, Graham, Daniel B., Kuchroo, Vijay K., Regev, Aviv, Xavier, Ramnik J.

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Type 2 innate lymphoid cells in the induction and resolution of tissue inflammation von Wallrapp, Antonia, Riesenfeld, Samantha J., Burkett, Patrick R., Kuchroo, Vijay K.

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Skin-resident innate lymphoid cells converge on a pathogenic effector state von Bielecki, Piotr, Riesenfeld, Samantha J., Hütter, Jan-Christian, Torlai Triglia, Elena, Kowalczyk, Monika S., Ricardo-Gonzalez, Roberto R., Lian, Mi, Amezcua Vesely, Maria C., Kroehling, Lina, Xu, Hao, Slyper, Michal, Muus, Christoph, Ludwig, Leif S., Christian, Elena, Tao, Liming, Kedaigle, Amanda J., Steach, Holly R., York, Autumn G., Skadow, Mathias H., Yaghoubi, Parastou, Dionne, Danielle, Jarret, Abigail, McGee, Heather M., Porter, Caroline B. M., Licona-Limón, Paula, Bailis, Will, Jackson, Ruaidhrí, Gagliani, Nicola, Gasteiger, Georg, Locksley, Richard M., Regev, Aviv, Flavell, Richard A.

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Eomes expression identifies the early bone marrow precursor to classical NK cells von Liang, Zhitao, Anderson, Hope D., Locher, Veronica, O’Leary, Crystal, Riesenfeld, Samantha J., Jabri, Bana, McDonald, Benjamin D., Bendelac, Albert

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Immunotherapy-activated T cells recruit and skew late-stage activated M1-like macrophages that are critical for therapeutic efficacy von van Elsas, Marit J., Middelburg, Jim, Labrie, Camilla, Roelands, Jessica, Schaap, Gaby, Sluijter, Marjolein, Tonea, Ruxandra, Ovcinnikovs, Vitalijs, Lloyd, Katy, Schuurman, Janine, Riesenfeld, Samantha J., Gajewski, Thomas F., de Miranda, Noel F.C.C., van Hall, Thorbald, van der Burg, Sjoerd H.

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A Distinct Transcriptional Program in Human CAR T Cells Bearing the 4-1BB Signaling Domain Revealed by scRNA-Seq von Boroughs, Angela C., Larson, Rebecca C., Marjanovic, Nemanja D., Gosik, Kirk, Castano, Ana P., Porter, Caroline B.M., Lorrey, Selena J., Ashenberg, Orr, Jerby, Livnat, Hofree, Matan, Smith-Rosario, Gabriela, Morris, Robert, Gould, Joshua, Riley, Lauren S., Berger, Trisha R., Riesenfeld, Samantha J., Rozenblatt-Rosen, Orit, Choi, Bryan D., Regev, Aviv, Maus, Marcela V.

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Induction of a colitogenic phenotype in Th1-like cells depends on interleukin-23 receptor signaling von Pawlak, Mathias, DeTomaso, David, Schnell, Alexandra, Meyer Zu Horste, Gerd, Lee, Youjin, Nyman, Jackson, Dionne, Danielle, Regan, Brianna M L, Singh, Vasundhara, Delorey, Toni, Schramm, Markus A, Wang, Chao, Wallrapp, Antonia, Burkett, Patrick R, Riesenfeld, Samantha J, Anderson, Ana C, Regev, Aviv, Xavier, Ramnik J, Yosef, Nir, Kuchroo, Vijay K

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PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data von Sharpton, Thomas J, Riesenfeld, Samantha J, Kembel, Steven W, Ladau, Joshua, O'Dwyer, James P, Green, Jessica L, Eisen, Jonathan A, Pollard, Katherine S

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GATA4 controls regionalization of tissue immunity and commensal-driven immunopathology von Earley, Zachary M., Lisicka, Wioletta, Sifakis, Joseph J., Aguirre-Gamboa, Raúl, Kowalczyk, Anita, Barlow, Jacob T., Shaw, Dustin G., Discepolo, Valentina, Tan, Ineke L., Gona, Saideep, Ernest, Jordan D., Matzinger, Polly, Barreiro, Luis B., Morgun, Andrey, Bendelac, Albert, Ismagilov, Rustem F., Shulzhenko, Natalia, Riesenfeld, Samantha J., Jabri, Bana

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Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis von Riesenfeld, Samantha J, Pollard, Katherine S

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Quantum computing for oncology von Ramesh, Siddhi, Tomesh, Teague, Riesenfeld, Samantha J, Chong, Frederic T, Pearson, Alexander T

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SORTING AND SELECTION IN POSETS von DASKALAKIS, Constantinos, KARP, Richard M, MOSSEL, Elchanan, RIESENFELD, Samantha J, VERBIN, Elad

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Mouse fetal growth restriction through parental and fetal immune gene variation and intercellular communications cascade von Kaur, Gurman, Porter, Caroline B. M., Ashenberg, Orr, Lee, Jack, Riesenfeld, Samantha J., Hofree, Matan, Aggelakopoulou, Maria, Subramanian, Ayshwarya, Kuttikkatte, Subita Balaram, Attfield, Kathrine E., Desel, Christiane A. E., Davies, Jessica L., Evans, Hayley G., Avraham-Davidi, Inbal, Nguyen, Lan T., Dionne, Danielle A., Neumann, Anna E., Jensen, Lise Torp, Barber, Thomas R., Soilleux, Elizabeth, Carrington, Mary, McVean, Gil, Rozenblatt-Rosen, Orit, Regev, Aviv, Fugger, Lars

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